Diff of the two buildlogs: -- --- b1/build.log 2025-01-10 05:28:01.348224766 +0000 +++ b2/build.log 2025-01-10 05:43:09.386741153 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Feb 11 23:45:23 -12 2026 -I: pbuilder-time-stamp: 1770896723 +I: Current time: Fri Jan 10 19:28:04 +14 2025 +I: pbuilder-time-stamp: 1736486884 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/1388763/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3724210/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jan 10 05:28 /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/3724210/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3724210/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='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='abfdd5c77fb4404e9075b66d352bce26' - 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='1388763' - PS1='# ' - PS2='> ' + INVOCATION_ID=819f39eed14c4f53807b1da078306089 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3724210 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.IeLqSCSd/pbuilderrc_HRUQ --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.IeLqSCSd/b1 --logfile b1/build.log garli_2.1-9.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.IeLqSCSd/pbuilderrc_aiQZ --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.IeLqSCSd/b2 --logfile b2/build.log garli_2.1-9.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink01-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1388763/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3724210/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -266,7 +298,7 @@ Get: 153 http://deb.debian.org/debian trixie/main arm64 libopenmpi-dev arm64 5.0.6-3 [1088 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 mpi-default-dev arm64 1.18 [3372 B] Get: 155 http://deb.debian.org/debian trixie/main arm64 ncl-tools arm64 2.1.21+git20210811.b1213a7-6 [166 kB] -Fetched 117 MB in 1s (190 MB/s) +Fetched 117 MB in 1s (81.8 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.12-minimal:arm64. (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 ... 19969 files and directories currently installed.) @@ -777,8 +809,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Feb 12 11:45:53 UTC 2026. -Universal Time is now: Thu Feb 12 11:45:53 UTC 2026. +Local time is now: Fri Jan 10 05:29:23 UTC 2025. +Universal Time is now: Fri Jan 10 05:29:23 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -929,7 +961,11 @@ 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/3724210/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3724210/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 @@ -1031,8 +1067,8 @@ 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 @@ -1119,16 +1155,16 @@ mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o individual.o individual.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.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; + | ^~~ garlimain.cpp:434:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ 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, @@ -1195,36 +1231,21 @@ /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/aarch64-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 ()); - | ~~~~~~~~~~~~~~~~~ -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 -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, - from individual.cpp:28: + from adaptation.cpp:25: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/iomanip:42, - from individual.cpp:21: + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from adaptation.cpp:18: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1262,6 +1283,22 @@ /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/aarch64-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 ()); + | ~~~~~~~~~~~~~~~~~ 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{ | ^~~~~~~~~~~~~~~ @@ -1280,7 +1317,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from population.h:23: + from configreader.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1318,11 +1355,16 @@ /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{ | ^~~~~~~~~~~~~~~ @@ -1332,7 +1374,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from adaptation.cpp:18: + from population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1370,29 +1412,19 @@ /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: + 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 | ^~~~~~~~~~~~~~~ @@ -1436,8 +1468,7 @@ | ^ 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{ | ^~~~~~~~~~~~~~~ @@ -1447,7 +1478,7 @@ 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 | ^~~~~~~~~~~~~~~ @@ -1485,14 +1516,10 @@ /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{ | ^~~~~~~~~~~~~~~ @@ -1502,7 +1529,7 @@ 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 | ^~~~~~~~~~~~~~~ @@ -1540,7 +1567,6 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)': adaptation.cpp:271:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 271 | fread((char *) this, 1, scalarSize, in); @@ -1602,6 +1628,16 @@ 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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] @@ -1627,6 +1694,10 @@ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ +model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': +model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1667,41 +1738,6 @@ optimization.cpp:1099:87: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1099 | pair Tree::CalcDerivativesRateHet(TreeNode *nd1, TreeNode *nd2){ | ^ -model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': -model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3675:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3675 | fread(&o, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3677:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3677 | fread(&o, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3684:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3684 | fread((char*) &(b[i]), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3691:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3691 | fread((char*) &(rateMults[i]), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3692:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3692 | fread((char*) &(rateProbs[i]), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3699:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3699 | fread((char*) &a, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3705:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3705 | fread((char*) &p, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3710:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3710 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3713:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3713 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': -model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp In file included from tree.h:35, from individual.h:21, @@ -1756,6 +1792,22 @@ 170 | for(register int i=0;i' when C++17 is enabled changed to match C++14 in GCC 10.1 875 | tree0->CalcDerivativesRateHet(nd->anc, nd); @@ -1841,13 +1893,7 @@ 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/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1857,8 +1903,10 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -1895,7 +1943,13 @@ 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 datamatr.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1922,24 +1976,6 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp -In file included from /usr/include/stdio.h:970, - from /usr/include/c++/14/cstdio:42, - from /usr/include/c++/14/ext/string_conversions.h:45, - from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/aarch64-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/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, @@ -1964,38 +2000,6 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -garlimain.cpp: In function 'int SubGarliMain(int)': -garlimain.cpp:323:49: warning: '%d' directive writing between 2 and 10 bytes into a region of size 6 [-Wformat-overflow=] - 323 | else sprintf(temp, ".run%d", rank); - | ^~ -garlimain.cpp:323:44: note: directive argument in the range [10, 2147483647] - 323 | else sprintf(temp, ".run%d", rank); - | ^~~~~~~~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'int SubGarliMain(int)' at garlimain.cpp:323:16: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 15 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 ()); - | ~~~~~~~~~~~~~~~~~ -garlimain.cpp: In function 'int SubGarliMain(int)': -garlimain.cpp:322:59: warning: '%d' directive writing between 1 and 11 bytes into a region of size 5 [-Wformat-overflow=] - 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); - | ^~ -garlimain.cpp:322:53: note: directive argument in the range [-2147483648, 9] - 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); - | ^~~~~~~~~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'int SubGarliMain(int)' at garlimain.cpp:322:25: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 17 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 ()); - | ~~~~~~~~~~~~~~~~~ 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 -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp In file included from tree.h:35, from individual.h:21, @@ -2045,6 +2049,38 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +garlimain.cpp: In function 'int SubGarliMain(int)': +garlimain.cpp:323:49: warning: '%d' directive writing between 2 and 10 bytes into a region of size 6 [-Wformat-overflow=] + 323 | else sprintf(temp, ".run%d", rank); + | ^~ +garlimain.cpp:323:44: note: directive argument in the range [10, 2147483647] + 323 | else sprintf(temp, ".run%d", rank); + | ^~~~~~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'int SubGarliMain(int)' at garlimain.cpp:323:16: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 15 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 ()); + | ~~~~~~~~~~~~~~~~~ +garlimain.cpp: In function 'int SubGarliMain(int)': +garlimain.cpp:322:59: warning: '%d' directive writing between 1 and 11 bytes into a region of size 5 [-Wformat-overflow=] + 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); + | ^~ +garlimain.cpp:322:53: note: directive argument in the range [-2147483648, 9] + 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); + | ^~~~~~~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'int SubGarliMain(int)' at garlimain.cpp:322:25: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 17 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 ()); + | ~~~~~~~~~~~~~~~~~ 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 Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE optPrecision){ | ^ 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 -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp +In file included from /usr/include/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 population.cpp:25: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/aarch64-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/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/aarch64-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: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/aarch64-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/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] tree.cpp: In member function 'void Tree::ReadBinaryFormattedTree(FILE*)': tree.cpp:6808:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6808 | fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in); @@ -2126,9 +2198,8 @@ 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 translatetable.h:24, + from translatetable.cpp:19: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2148,22 +2219,6 @@ 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/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 population.cpp:25: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/aarch64-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/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' In file included from /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, @@ -2186,7 +2241,6 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); @@ -2213,24 +2267,6 @@ 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{ | ^~~~~~~~~~~~~~~ @@ -2570,7 +2606,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from configreader.cpp:21: + from adaptation.cpp:18: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2615,7 +2651,9 @@ | ^ In file included from tree.h:35, from individual.h:21, - from model.cpp:26: + from population.h:31, + from funcs.h:25, + from configreader.cpp:30: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2625,7 +2663,7 @@ 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 configreader.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2663,20 +2701,20 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, - from garlimain.cpp:40: + from funcs.h:25, + from individual.cpp:28: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from population.h:23: + from /usr/include/c++/14/iomanip:42, + from individual.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2716,17 +2754,34 @@ | ^~~~~~~ In file included from tree.h:35, from individual.h:21, + from model.cpp:26: +reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 58 | class DistEquals:public binary_function{ + | ^~~~~~~~~~~~~~~ +In file included from tree.h:35, + from individual.h:21, from population.h:31, - from funcs.h:25, - from individual.cpp:28: + from garlimain.cpp:40: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/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 model.cpp:17: +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct 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: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2736,6 +2791,18 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 65 | class DistEqualsWithinCutSubtree:public binary_function{ + | ^~~~~~~~~~~~~~~ +reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 72 | class NodeEquals:public binary_function{ + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2746,6 +2813,10 @@ reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ +reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': +reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) @@ -2757,52 +2828,14 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': -reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; - | ~~~~~~~^~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -In file included from tree.h:35, - from individual.h:21, - from population.h:31, - from funcs.h:25, - from funcs.cpp:30: -reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 58 | class DistEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/string:49, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from population.h:23: -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 65 | class DistEqualsWithinCutSubtree:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 72 | class NodeEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': -reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ -In file included from 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 std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; + | ~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) @@ -2821,19 +2854,14 @@ /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{ | ^~~~~~~~~~~~~~~ @@ -2843,7 +2871,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from adaptation.cpp:18: + from population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2885,18 +2913,15 @@ funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -3012,42 +3049,6 @@ optimization.cpp:1099:87: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1099 | pair Tree::CalcDerivativesRateHet(TreeNode *nd1, TreeNode *nd2){ | ^ -model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': -model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3675:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3675 | fread(&o, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3677:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3677 | fread(&o, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3684:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3684 | fread((char*) &(b[i]), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3691:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3691 | fread((char*) &(rateMults[i]), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3692:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3692 | fread((char*) &(rateProbs[i]), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3699:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3699 | fread((char*) &a, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3705:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3705 | fread((char*) &p, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3710:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3710 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3713:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3713 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': -model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -3100,50 +3101,55 @@ funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i' when C++17 is enabled changed to match C++14 in GCC 10.1 8463 | pair Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE optPrecision){ | ^ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp In file included from /usr/include/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 population.cpp:25: + 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/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3456,25 +3511,6 @@ from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, - from datamatr.h:23, - from sequencedata.h:27, - from sequencedata.cpp:21: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/aarch64-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/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/aarch64-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 translatetable.h:24, from translatetable.cpp:19: In function 'int sprintf(char*, const char*, ...)', @@ -6081,7 +6117,7 @@ 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 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6231,7 +6267,7 @@ pass 10: -6247.0222 (branch= 0.0000 alpha= 0.0000) Looking for minimum length branches... Final score = -6247.0222 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6374,7 +6410,7 @@ pass 11: -6434.5092 (branch= 0.0000) Looking for minimum length branches... Final score = -6434.5092 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6528,7 +6564,7 @@ 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 7 seconds +Time used = 0 hours, 0 minutes and 40 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6680,7 +6716,7 @@ 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 5 seconds +Time used = 0 hours, 0 minutes and 26 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6886,7 +6922,7 @@ pass 81: -3350.2337 (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 = -3350.2337 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7094,7 +7130,7 @@ pass 76: -3325.9822 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3325.9822 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7577,7 +7613,7 @@ pass 14: -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 2 seconds +Time used = 0 hours, 0 minutes and 11 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -7831,7 +7867,7 @@ pass 36: -13306.2061 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) Looking for minimum length branches... Final score = -13306.2061 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 10 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -9800,7 +9836,7 @@ pass 495: -208.3585 (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 2 seconds +Time used = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -10064,7 +10100,7 @@ pass 373: -208.1243 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... Final score = -208.1243 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -10360,7 +10396,7 @@ pass 503: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... Final score = -208.3583 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 5 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -10653,7 +10689,7 @@ pass 491: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.3583 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -13370,25 +13406,6 @@ Optimizing branchlengths... improved 0.317 lnL 900 -88.9507 0.010 879 1000 -88.8871 0.010 879 -1100 -88.8475 0.010 879 -1200 -88.8463 0.010 879 -1300 -88.8312 0.010 879 -1400 -88.8046 0.010 879 -1500 -88.8000 0.010 879 -1600 -88.7604 0.010 879 -1700 -88.7532 0.010 879 -1800 -88.7145 0.010 879 -1900 -88.6979 0.010 879 -2000 -88.6746 0.010 879 -2100 -88.6394 0.010 879 -2200 -88.6224 0.010 879 -2300 -88.6154 0.010 879 -2400 -88.6058 0.010 879 -2500 -88.5913 0.010 879 -2600 -88.5622 0.010 879 -2700 -88.5467 0.010 879 -2800 -88.5396 0.010 879 -2900 -88.5337 0.010 879 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13485,9 +13502,9 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 2967, seed 410219061, best lnL -88.527 +Bootstrap rep 1 (of 1) generation 1091, seed 1440454805, best lnL -88.850 gen current_lnL precision last_tree_imp -2967 -88.5266 0.010 879 +1091 -88.8497 0.010 879 MODEL REPORT - Parameter values are FINAL Model 1 @@ -13501,33 +13518,33 @@ 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 3.1074 + 0.9578 with an invariant (invariable) site category, proportion estimated - 0.2947 + 0.1315 Substitution rate categories under this model: rate proportion - 0.0000 0.2947 - 0.4567 0.2351 - 0.9014 0.2351 - 1.6419 0.2351 + 0.0000 0.1315 + 0.1794 0.2895 + 0.7011 0.2895 + 2.1195 0.2895 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 2 branches were collapsed. + 3 branches were collapsed. ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -88.5266 +Replicate 1 : -88.8497 Parameter estimates: alpha pinv -rep 1: 3.107 0.295 +rep 1: 0.958 0.131 Treelengths: TL -rep 1: 2.368 +rep 1: 2.344 Saving best tree to bootstrap file ch.a.G3.boot.tre @@ -13659,21 +13676,6 @@ 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 -110.5065 0.010 707 -1100 -110.4789 0.010 707 -1200 -110.4460 0.010 707 -1300 -110.4042 0.010 707 -1400 -110.3747 0.010 707 -1500 -110.3652 0.010 707 -1600 -110.2967 0.010 707 -1700 -110.2780 0.010 707 -1800 -110.2329 0.010 707 -1900 -110.2137 0.010 707 -2000 -110.1884 0.010 707 -2100 -110.1532 0.010 707 -2200 -110.1459 0.010 707 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13760,11 +13762,15 @@ STARTING RUN Restarting from checkpoint... - generation 2235, seed 1343948392, best lnL -110.145 + generation 764, seed 928557790, best lnL -110.591 gen current_lnL precision last_tree_imp -2235 -110.1447 0.010 707 +764 -110.5910 0.010 707 +800 -110.5642 0.010 707 +900 -110.5555 0.010 707 +1000 -110.5065 0.010 707 +NOTE: ****Specified generation limit (1000) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones @@ -13776,39 +13782,46 @@ 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 3.5916 + 1.3049 with an invariant (invariable) site category, proportion estimated - 0.1699 + 0.0988 Substitution rate categories under this model: rate proportion - 0.0000 0.1699 - 0.4304 0.2075 - 0.7598 0.2075 - 1.0842 0.2075 - 1.7256 0.2075 + 0.0000 0.0988 + 0.1936 0.2253 + 0.5525 0.2253 + 1.0366 0.2253 + 2.2174 0.2253 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - No branches were short enough to be collapsed. + 1 branches were collapsed. Saving site likelihoods to file ch.a.G4.sitelikes.log ... +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 : -110.1447 +Replicate 1 : -110.5065 Parameter estimates: alpha pinv -rep 1: 3.592 0.170 +rep 1: 1.305 0.099 Treelengths: TL -rep 1: 2.701 +rep 1: 2.534 Saving final tree from best search rep (#1) to ch.a.G4.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.G4.internalstates.log +WARNING: Internal states inferred on tree from prematurely terminated search + ####################################################### TREEFILES PASS Running checkpoint test ./check/a.conf @@ -13946,52 +13959,15 @@ 2300 -111.6817 0.010 563 2400 -111.6817 0.010 563 2500 -111.6817 0.010 563 -2600 -111.6816 0.010 563 -2700 -111.6816 0.010 563 -2800 -111.6816 0.010 563 -2900 -111.6815 0.010 563 -3000 -111.6815 0.010 563 -3100 -111.6815 0.010 563 -3200 -111.6815 0.010 563 -Reached termination condition! -last topological improvement at gen 563 -Improvement over last 500 gen = 0.00009 - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 20 (amino acid data) - Amino Acid Rate Matrix: Jones - Equilibrium State Frequencies: empirical (observed) values (+F) - (ACDEFGHIKLMNPQRSTVWY) - 0.0165 0.0083 0.0496 0.0909 0.0909 - 0.0083 0.0744 0.0083 0.0083 0.1074 - 0.1157 0.0248 0.1240 0.0331 0.0083 - 0.0826 0.0496 0.0579 0.0083 0.0331 - Rate Heterogeneity Model: - no rate heterogeneity - -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - No branches were short enough to be collapsed. - -Saving site likelihoods to file ch.a.sitelikes.log ... - -####################################################### - -Completed 1 replicate search(es) (of 1). -Results: -Replicate 1 : -111.6815 - -Parameter estimates: - Model contains no estimated parameters - -Treelengths: - TL -rep 1: 2.607 +NOTE: ****Specified time limit (5 seconds) reached... -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 +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<- ############################################################## @@ -14068,9 +14044,9 @@ STARTING RUN Restarting from checkpoint... - generation 3200, seed 1669543796, best lnL -111.681 + generation 2589, seed 268789828, best lnL -111.682 gen current_lnL precision last_tree_imp -3200 -111.6815 0.010 563 +2589 -111.6816 0.010 563 MODEL REPORT - Parameter values are FINAL Model 1 @@ -14086,7 +14062,7 @@ no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - No branches were short enough to be collapsed. + 1 branches were collapsed. Saving site likelihoods to file ch.a.sitelikes.log ... @@ -14094,14 +14070,14 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -111.6815 +Replicate 1 : -111.6816 Parameter estimates: Model contains no estimated parameters Treelengths: TL -rep 1: 2.607 +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 @@ -14230,24 +14206,6 @@ 0 -208.9856 0.500 0 10 -207.1401 0.500 10 20 -205.6892 0.500 18 -30 -205.6499 0.500 18 -40 -205.6371 0.500 18 -50 -205.6175 0.500 18 -60 -205.5990 0.500 53 -70 -205.5741 0.500 53 -80 -205.4022 0.500 76 -90 -205.3871 0.500 76 -100 -205.3829 0.500 76 -110 -205.3431 0.500 106 -120 -205.3431 0.500 106 -130 -205.2505 0.500 121 -140 -205.2440 0.500 121 -150 -205.1047 0.500 121 -160 -205.0609 0.500 121 -170 -204.9813 0.500 121 -180 -204.9247 0.500 172 -190 -204.8909 0.500 172 -200 -204.7980 0.500 172 NOTE: ****Specified time limit (10 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14334,15 +14292,24 @@ STARTING RUN Restarting from checkpoint... - generation 209, seed 524846382, best lnL -204.714 + generation 23, seed 1300521576, best lnL -205.650 gen current_lnL precision last_tree_imp -209 -204.7143 0.500 209 +23 -205.6499 0.500 18 +30 -205.6499 0.500 18 +40 -205.6371 0.500 18 +50 -205.6175 0.500 18 +60 -205.5990 0.500 53 +70 -205.5741 0.500 53 +80 -205.4022 0.500 76 +90 -205.3871 0.500 76 +100 -205.3829 0.500 76 +NOTE: ****Specified generation limit (100) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates - AC = 1.586, AG = 4.089, AT = 0.040, CG = 2.453, CT = 3.968, GT = 1.000 + AC = 1.586, AG = 3.999, AT = 0.040, CG = 2.453, CT = 3.968, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) @@ -14363,31 +14330,38 @@ 2 nonsynonymous rate categories, rate and proportion of each estimated (this is effectively the M3 model of PAML) dN/dS Proportion - 0.0473 0.5211 + 0.0490 0.5211 0.4995 0.4789 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file ch.c.M3x2.sitelikes.log ... +WARNING: Site likelihoods being output on prematurely terminated search ... + +NOTE: ***Search was terminated before full auto-termination condition was reached! +Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** + ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -204.7143 +Replicate 1 : -205.3829 Parameter estimates: w(0) p(0) w(1) p(1) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) -rep 1: 0.047 0.521 0.499 0.479 1.586 4.089 0.04 2.453 3.968 1 +rep 1: 0.049 0.521 0.499 0.479 1.586 3.999 0.04 2.453 3.968 1 Treelengths: TL -rep 1: 7.651 +rep 1: 7.371 Saving final tree from best search rep (#1) to ch.c.M3x2.best.tre Inferring internal state probabilities on best tree... saving to file ch.c.M3x2.internalstates.log +WARNING: Internal states inferred on tree from prematurely terminated search + ####################################################### TREEFILES PASS Running checkpoint test ./check/c.conf @@ -14517,23 +14491,6 @@ 20 -195.3342 0.500 0 30 -195.2778 0.500 0 40 -195.2556 0.500 0 -50 -195.2139 0.500 0 -60 -195.1631 0.500 0 -70 -195.0045 0.500 0 -80 -194.9480 0.500 0 -90 -194.9094 0.500 0 -100 -194.9094 0.500 0 -110 -194.8988 0.500 0 -120 -194.8988 0.500 0 -130 -194.8986 0.500 0 -140 -194.8502 0.500 0 -150 -194.7087 0.500 0 -160 -194.7087 0.500 0 -170 -194.5940 0.500 168 -180 -194.5930 0.500 168 -190 -194.5696 0.500 168 -200 -194.2416 0.500 196 -210 -194.2416 0.500 196 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14621,16 +14578,23 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 213, seed 1848149578, best lnL -194.222 +Bootstrap rep 1 (of 1) generation 40, seed 2068370778, best lnL -195.256 gen current_lnL precision last_tree_imp -213 -194.2220 0.500 196 +40 -195.2556 0.500 0 +50 -195.2139 0.500 0 +60 -195.1631 0.500 0 +70 -195.0045 0.500 0 +80 -194.9480 0.500 0 +90 -194.9094 0.500 0 +100 -194.9094 0.500 0 +NOTE: ****Specified generation limit (100) reached... -MODEL REPORT - Parameter values are FINAL +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) = 0.120505 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates - AC = 1.637, AG = 5.879, AT = 0.011, CG = 4.174, CT = 2.324, GT = 1.000 + AC = 1.637, AG = 5.679, AT = 0.011, CG = 4.174, CT = 2.324, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) @@ -14654,23 +14618,27 @@ No branches were short enough to be collapsed. +NOTE: ***Search was terminated before full auto-termination condition was reached! +Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** + + ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -194.2220 +Replicate 1 : -194.9094 Parameter estimates: w(0) p(0) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) -rep 1: 0.121 1.000 1.637 5.879 0.01146 4.174 2.324 1 +rep 1: 0.121 1.000 1.637 5.679 0.01146 4.174 2.324 1 Treelengths: TL -rep 1: 10.277 +rep 1: 9.255 Saving best tree to bootstrap file ch.c.boot.tre ->>>Completed Bootstrap rep 1<<< +WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/g.dnaBnoZ.conf @@ -14840,25 +14808,6 @@ 1700 -3352.2830 0.010 0 1800 -3352.2030 0.010 0 1900 -3351.8474 0.010 0 -2000 -3351.7685 0.010 0 -2100 -3351.6185 0.010 0 -2200 -3351.3743 0.010 0 -2300 -3351.3495 0.010 0 -2400 -3351.3419 0.010 0 -2500 -3351.2390 0.010 0 -2600 -3351.1730 0.010 0 -2700 -3351.1728 0.010 0 -2800 -3351.1190 0.010 0 -2900 -3351.1178 0.010 0 -3000 -3351.1136 0.010 0 -3100 -3351.1012 0.010 0 -3200 -3351.0892 0.010 0 -3300 -3351.0874 0.010 0 -3400 -3351.0857 0.010 0 -3500 -3351.0846 0.010 0 -3600 -3351.0820 0.010 0 -3700 -3351.0489 0.010 0 -3800 -3351.0367 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14962,79 +14911,67 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 3881, seed 521097619, best lnL -3350.983 +Search rep 1 (of 2) generation 1946, seed 893036513, best lnL -3351.773 gen current_lnL precision last_tree_imp -3881 -3350.9829 0.010 0 +1946 -3351.7734 0.010 0 +2000 -3351.7685 0.010 0 +2100 -3351.6185 0.010 0 +2200 -3351.3743 0.010 0 +2300 -3351.3495 0.010 0 +2400 -3351.3419 0.010 0 +2500 -3351.2390 0.010 0 +2600 -3351.1730 0.010 0 +2700 -3351.1728 0.010 0 +2800 -3351.1190 0.010 0 +2900 -3351.1178 0.010 0 +3000 -3351.1136 0.010 0 +3100 -3351.1012 0.010 0 +3200 -3351.0892 0.010 0 +3300 -3351.0874 0.010 0 +3400 -3351.0857 0.010 0 +3500 -3351.0846 0.010 0 +3600 -3351.0820 0.010 0 +3700 -3351.0489 0.010 0 +3800 -3351.0367 0.010 0 3900 -3350.9821 0.010 0 4000 -3350.9821 0.010 0 4100 -3350.9752 0.010 0 4200 -3350.9687 0.010 0 4300 -3350.9681 0.010 0 4400 -3350.9641 0.010 0 -4500 -3350.9641 0.010 0 -4600 -3350.9235 0.010 0 -4700 -3350.9232 0.010 0 -4800 -3350.9222 0.010 0 -4900 -3350.9222 0.010 0 -5000 -3350.9212 0.010 0 -5100 -3350.8984 0.010 0 -5200 -3350.8802 0.010 0 -5300 -3350.8789 0.010 0 -5400 -3350.8598 0.010 0 -5500 -3350.8007 0.010 0 -5600 -3350.7520 0.010 0 -5700 -3350.7435 0.010 0 -5800 -3350.6967 0.010 0 -5900 -3350.6924 0.010 0 -6000 -3350.6869 0.010 0 -6100 -3350.6726 0.010 0 -6200 -3350.6726 0.010 0 -6300 -3350.6692 0.010 0 -6400 -3350.6687 0.010 0 -6500 -3350.6687 0.010 0 -6600 -3350.6647 0.010 0 -6700 -3350.6647 0.010 0 -6800 -3350.6599 0.010 0 -6900 -3350.6258 0.010 0 -7000 -3350.6223 0.010 0 -7100 -3350.6215 0.010 0 -7200 -3350.6215 0.010 0 -7300 -3350.6209 0.010 0 -7400 -3350.5924 0.010 0 -7500 -3350.5907 0.010 0 -7600 -3350.5865 0.010 0 -7700 -3350.5853 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3350.5834 +Current score = -3350.9641 Performing final optimizations... -pass 1 : -3350.5621 (branch= 0.0000 alpha= 0.0000 pinv= 0.0212 eq freqs= 0.0001 rel rates= 0.0000 subset rates= 0.0000) -pass 2 : -3350.5218 (branch= 0.0051 alpha= 0.0163 pinv= 0.0153 eq freqs= 0.0025 rel rates= 0.0001 subset rates= 0.0010) -pass 3 : -3350.4840 (branch= 0.0049 alpha= 0.0136 pinv= 0.0140 eq freqs= 0.0013 rel rates= 0.0040 subset rates= 0.0000) -pass 4 : -3350.4541 (branch= 0.0014 alpha= 0.0138 pinv= 0.0125 eq freqs= 0.0000 rel rates= 0.0010 subset rates= 0.0011) -pass 5 : -3350.4291 (branch= 0.0022 alpha= 0.0110 pinv= 0.0114 eq freqs= 0.0003 rel rates= 0.0000 subset rates= 0.0000) -pass 6 : -3350.4052 (branch= 0.0008 alpha= 0.0120 pinv= 0.0101 eq freqs= 0.0000 rel rates= 0.0009 subset rates= 0.0000) -pass 7 : -3350.3835 (branch= 0.0008 alpha= 0.0100 pinv= 0.0091 eq freqs= 0.0000 rel rates= 0.0007 subset rates= 0.0010) -pass 8 : -3350.3653 (branch= 0.0011 alpha= 0.0087 pinv= 0.0082 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) -pass 9 : -3350.3494 (branch= 0.0002 alpha= 0.0079 pinv= 0.0073 eq freqs= 0.0000 rel rates= 0.0004 subset rates= 0.0000) -pass 10: -3350.3350 (branch= 0.0000 alpha= 0.0075 pinv= 0.0065 eq freqs= 0.0000 rel rates= 0.0004 subset rates= 0.0000) -pass 11: -3350.3222 (branch= 0.0000 alpha= 0.0067 pinv= 0.0058 eq freqs= 0.0000 rel rates= 0.0004 subset rates= 0.0000) -pass 12: -3350.3109 (branch= 0.0000 alpha= 0.0058 pinv= 0.0051 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) -pass 13: -3350.3009 (branch= 0.0000 alpha= 0.0052 pinv= 0.0046 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) -pass 14: -3350.2920 (branch= 0.0000 alpha= 0.0046 pinv= 0.0040 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) -pass 15: -3350.2841 (branch= 0.0000 alpha= 0.0041 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) -pass 16: -3350.2773 (branch= 0.0000 alpha= 0.0036 pinv= 0.0031 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) -pass 17: -3350.2712 (branch= 0.0000 alpha= 0.0031 pinv= 0.0027 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) -pass 18: -3350.2660 (branch= 0.0000 alpha= 0.0027 pinv= 0.0024 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) -pass 19: -3350.2614 (branch= 0.0000 alpha= 0.0024 pinv= 0.0021 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) -pass 20: -3350.2574 (branch= 0.0000 alpha= 0.0021 pinv= 0.0018 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 1 : -3350.9091 (branch= 0.0000 alpha= 0.0000 pinv= 0.0107 eq freqs= 0.0001 rel rates= 0.0442 subset rates= 0.0000) +pass 2 : -3350.8283 (branch= 0.0027 alpha= 0.0107 pinv= 0.0195 eq freqs= 0.0064 rel rates= 0.0398 subset rates= 0.0018) +pass 3 : -3350.7588 (branch= 0.0066 alpha= 0.0174 pinv= 0.0174 eq freqs= 0.0017 rel rates= 0.0263 subset rates= 0.0000) +pass 4 : -3350.6976 (branch= 0.0020 alpha= 0.0166 pinv= 0.0157 eq freqs= 0.0009 rel rates= 0.0240 subset rates= 0.0019) +pass 5 : -3350.6429 (branch= 0.0050 alpha= 0.0147 pinv= 0.0147 eq freqs= 0.0007 rel rates= 0.0197 subset rates= 0.0000) +pass 6 : -3350.5943 (branch= 0.0010 alpha= 0.0140 pinv= 0.0131 eq freqs= 0.0000 rel rates= 0.0188 subset rates= 0.0016) +pass 7 : -3350.5523 (branch= 0.0022 alpha= 0.0124 pinv= 0.0120 eq freqs= 0.0001 rel rates= 0.0152 subset rates= 0.0000) +pass 8 : -3350.5140 (branch= 0.0004 alpha= 0.0112 pinv= 0.0109 eq freqs= 0.0000 rel rates= 0.0144 subset rates= 0.0013) +pass 9 : -3350.4804 (branch= 0.0013 alpha= 0.0104 pinv= 0.0099 eq freqs= 0.0001 rel rates= 0.0120 subset rates= 0.0000) +pass 10: -3350.4505 (branch= 0.0002 alpha= 0.0093 pinv= 0.0096 eq freqs= 0.0000 rel rates= 0.0108 subset rates= 0.0000) +pass 11: -3350.4231 (branch= 0.0001 alpha= 0.0090 pinv= 0.0086 eq freqs= 0.0000 rel rates= 0.0097 subset rates= 0.0000) +pass 12: -3350.3995 (branch= 0.0001 alpha= 0.0081 pinv= 0.0072 eq freqs= 0.0000 rel rates= 0.0083 subset rates= 0.0000) +pass 13: -3350.3776 (branch= 0.0000 alpha= 0.0072 pinv= 0.0064 eq freqs= 0.0000 rel rates= 0.0072 subset rates= 0.0010) +pass 14: -3350.3593 (branch= 0.0006 alpha= 0.0061 pinv= 0.0058 eq freqs= 0.0000 rel rates= 0.0057 subset rates= 0.0000) +pass 15: -3350.3435 (branch= 0.0001 alpha= 0.0054 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0052 subset rates= 0.0000) +pass 16: -3350.3293 (branch= 0.0000 alpha= 0.0050 pinv= 0.0046 eq freqs= 0.0000 rel rates= 0.0046 subset rates= 0.0000) +pass 17: -3350.3166 (branch= 0.0000 alpha= 0.0045 pinv= 0.0040 eq freqs= 0.0000 rel rates= 0.0041 subset rates= 0.0000) +pass 18: -3350.3055 (branch= 0.0000 alpha= 0.0040 pinv= 0.0036 eq freqs= 0.0000 rel rates= 0.0035 subset rates= 0.0000) +pass 19: -3350.2958 (branch= 0.0000 alpha= 0.0035 pinv= 0.0031 eq freqs= 0.0000 rel rates= 0.0031 subset rates= 0.0000) +pass 20: -3350.2873 (branch= 0.0000 alpha= 0.0031 pinv= 0.0028 eq freqs= 0.0000 rel rates= 0.0026 subset rates= 0.0000) + optimization up to ... +pass 30: -3350.2449 (branch= 0.0000 alpha= 0.0156 pinv= 0.0140 eq freqs= 0.0000 rel rates= 0.0128 subset rates= 0.0000) optimization up to ... -pass 30: -3350.2379 (branch= 0.0000 alpha= 0.0101 pinv= 0.0090 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) +pass 40: -3350.2354 (branch= 0.0000 alpha= 0.0034 pinv= 0.0031 eq freqs= 0.0000 rel rates= 0.0030 subset rates= 0.0000) optimization up to ... -pass 40: -3350.2338 (branch= 0.0000 alpha= 0.0021 pinv= 0.0019 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 50: -3350.2335 (branch= 0.0000 alpha= 0.0006 pinv= 0.0006 eq freqs= 0.0000 rel rates= 0.0007 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2330 (branch= 0.0000 alpha= 0.0004 pinv= 0.0004 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +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) optimization up to ... -pass 54: -3350.2329 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 67: -3350.2330 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -3350.2330 Time used so far = 0 hours, 0 minutes and 12 seconds @@ -15043,21 +14980,21 @@ Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.136, AG = 10.494, AT = 2.712, CG = 0.001, CT = 22.118, GT = 1.000 + AC = 3.116, AG = 10.427, AT = 2.693, CG = 0.001, CT = 21.957, 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 - 0.5743 + 0.5766 with an invariant (invariable) site category, proportion estimated - 0.3646 + 0.3654 Substitution rate categories under this model: rate proportion - 0.0000 0.3646 - 0.0479 0.1588 - 0.2977 0.1588 - 0.8676 0.1588 - 2.7868 0.1588 + 0.0000 0.3654 + 0.0483 0.1587 + 0.2990 0.1587 + 0.8689 0.1587 + 2.7838 0.1587 Model 2 Number of states = 2 (binary data) @@ -15088,14 +15025,14 @@ 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: 3.136 10.49 2.712 0.001 22.12 1 0.333 0.222 0.157 0.288 0.574 0.365 +rep 1: 3.116 10.43 2.693 0.001 21.96 1 0.333 0.222 0.157 0.288 0.577 0.365 Partition model subset 2: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) -rep 1: 0.791 1.821 0.179 +rep 1: 0.790 1.821 0.179 Saving final tree from best search rep (#1) to ch.g.dnaBnoZ.best.tre ####################################################### @@ -15250,17 +15187,6 @@ Optimization precision reduced Optimizing parameters... improved 1.812 lnL Optimizing branchlengths... improved 0.023 lnL -700 -3321.3649 0.255 1 -800 -3321.0294 0.255 1 -900 -3321.0142 0.255 1 -1000 -3320.9667 0.255 1 -1100 -3320.8654 0.255 1 -Optimization precision reduced - Optimizing parameters... improved 0.575 lnL - Optimizing branchlengths... improved 0.059 lnL -1200 -3320.1519 0.010 1 -1300 -3320.0935 0.010 1 -1400 -3320.0786 0.010 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15361,75 +15287,75 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 1415, seed 175898382, best lnL -3320.034 +Search rep 1 (of 2) generation 665, seed 744658408, best lnL -3321.417 gen current_lnL precision last_tree_imp -1415 -3320.0341 0.010 1 -1500 -3320.0251 0.010 1 -1600 -3320.0162 0.010 1 -1700 -3320.0146 0.010 1 -1800 -3319.8207 0.010 1 -1900 -3319.6041 0.010 1 -2000 -3319.5586 0.010 1 -2100 -3319.5579 0.010 1 -2200 -3319.4756 0.010 1 -2300 -3319.3806 0.010 1 -2400 -3319.3433 0.010 1 +665 -3321.4166 0.255 1 +700 -3321.3649 0.255 1 +800 -3321.0294 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 0.575 lnL + Optimizing branchlengths... improved 0.059 lnL NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3319.3420 +Current score = -3320.1635 Performing final optimizations... -pass 1 : -3319.0823 (branch= 0.0088 alpha= 0.0000 pinv= 0.0150 eq freqs= 0.0116 rel rates= 0.1613 ins/del rates= 0.0631) -pass 2 : -3318.8938 (branch= 0.0313 alpha= 0.0087 pinv= 0.0159 eq freqs= 0.0000 rel rates= 0.1263 ins/del rates= 0.0063) -pass 3 : -3318.7347 (branch= 0.0299 alpha= 0.0112 pinv= 0.0147 eq freqs= 0.0017 rel rates= 0.0922 ins/del rates= 0.0094) -pass 4 : -3318.5982 (branch= 0.0186 alpha= 0.0109 pinv= 0.0140 eq freqs= 0.0010 rel rates= 0.0869 ins/del rates= 0.0050) -pass 5 : -3318.4890 (branch= 0.0118 alpha= 0.0108 pinv= 0.0133 eq freqs= 0.0006 rel rates= 0.0685 ins/del rates= 0.0043) -pass 6 : -3318.3957 (branch= 0.0081 alpha= 0.0102 pinv= 0.0124 eq freqs= 0.0005 rel rates= 0.0587 ins/del rates= 0.0033) -pass 7 : -3318.3160 (branch= 0.0051 alpha= 0.0097 pinv= 0.0116 eq freqs= 0.0001 rel rates= 0.0513 ins/del rates= 0.0019) -pass 8 : -3318.2470 (branch= 0.0036 alpha= 0.0097 pinv= 0.0106 eq freqs= 0.0002 rel rates= 0.0434 ins/del rates= 0.0015) -pass 9 : -3318.1876 (branch= 0.0023 alpha= 0.0090 pinv= 0.0098 eq freqs= 0.0001 rel rates= 0.0373 ins/del rates= 0.0010) -pass 10: -3318.1357 (branch= 0.0015 alpha= 0.0085 pinv= 0.0089 eq freqs= 0.0001 rel rates= 0.0322 ins/del rates= 0.0006) -pass 11: -3318.0907 (branch= 0.0010 alpha= 0.0077 pinv= 0.0081 eq freqs= 0.0000 rel rates= 0.0276 ins/del rates= 0.0005) -pass 12: -3318.0516 (branch= 0.0006 alpha= 0.0075 pinv= 0.0074 eq freqs= 0.0001 rel rates= 0.0233 ins/del rates= 0.0003) -pass 13: -3318.0177 (branch= 0.0004 alpha= 0.0067 pinv= 0.0067 eq freqs= 0.0000 rel rates= 0.0199 ins/del rates= 0.0002) -pass 14: -3317.9880 (branch= 0.0003 alpha= 0.0062 pinv= 0.0060 eq freqs= 0.0000 rel rates= 0.0171 ins/del rates= 0.0001) -pass 15: -3317.9621 (branch= 0.0002 alpha= 0.0056 pinv= 0.0054 eq freqs= 0.0000 rel rates= 0.0147 ins/del rates= 0.0001) -pass 16: -3317.9394 (branch= 0.0001 alpha= 0.0051 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0126 ins/del rates= 0.0000) -pass 17: -3317.9196 (branch= 0.0001 alpha= 0.0046 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0108 ins/del rates= 0.0000) -pass 18: -3317.9023 (branch= 0.0000 alpha= 0.0041 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0093 ins/del rates= 0.0000) -pass 19: -3317.8871 (branch= 0.0000 alpha= 0.0037 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0080 ins/del rates= 0.0000) -pass 20: -3317.8739 (branch= 0.0000 alpha= 0.0033 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0069 ins/del rates= 0.0000) +pass 1 : -3319.7831 (branch= 0.0376 alpha= 0.0099 pinv= 0.0161 eq freqs= 0.0000 rel rates= 0.2966 ins/del rates= 0.0202) +pass 2 : -3319.4609 (branch= 0.0458 alpha= 0.0055 pinv= 0.0162 eq freqs= 0.0000 rel rates= 0.2392 ins/del rates= 0.0154) +pass 3 : -3319.1875 (branch= 0.0353 alpha= 0.0088 pinv= 0.0153 eq freqs= 0.0028 rel rates= 0.2006 ins/del rates= 0.0106) +pass 4 : -3318.9772 (branch= 0.0197 alpha= 0.0114 pinv= 0.0145 eq freqs= 0.0000 rel rates= 0.1581 ins/del rates= 0.0065) +pass 5 : -3318.7949 (branch= 0.0156 alpha= 0.0101 pinv= 0.0139 eq freqs= 0.0030 rel rates= 0.1341 ins/del rates= 0.0055) +pass 6 : -3318.6473 (branch= 0.0089 alpha= 0.0110 pinv= 0.0129 eq freqs= 0.0005 rel rates= 0.1104 ins/del rates= 0.0039) +pass 7 : -3318.5220 (branch= 0.0064 alpha= 0.0099 pinv= 0.0121 eq freqs= 0.0006 rel rates= 0.0938 ins/del rates= 0.0026) +pass 8 : -3318.4152 (branch= 0.0044 alpha= 0.0093 pinv= 0.0113 eq freqs= 0.0002 rel rates= 0.0797 ins/del rates= 0.0019) +pass 9 : -3318.3258 (branch= 0.0029 alpha= 0.0093 pinv= 0.0103 eq freqs= 0.0002 rel rates= 0.0654 ins/del rates= 0.0013) +pass 10: -3318.2500 (branch= 0.0019 alpha= 0.0088 pinv= 0.0095 eq freqs= 0.0002 rel rates= 0.0545 ins/del rates= 0.0008) +pass 11: -3318.1857 (branch= 0.0013 alpha= 0.0083 pinv= 0.0087 eq freqs= 0.0001 rel rates= 0.0454 ins/del rates= 0.0005) +pass 12: -3318.1309 (branch= 0.0008 alpha= 0.0077 pinv= 0.0079 eq freqs= 0.0001 rel rates= 0.0379 ins/del rates= 0.0004) +pass 13: -3318.0841 (branch= 0.0005 alpha= 0.0072 pinv= 0.0071 eq freqs= 0.0001 rel rates= 0.0317 ins/del rates= 0.0002) +pass 14: -3318.0444 (branch= 0.0003 alpha= 0.0067 pinv= 0.0065 eq freqs= 0.0001 rel rates= 0.0260 ins/del rates= 0.0001) +pass 15: -3318.0102 (branch= 0.0002 alpha= 0.0061 pinv= 0.0058 eq freqs= 0.0001 rel rates= 0.0220 ins/del rates= 0.0001) +pass 16: -3317.9806 (branch= 0.0001 alpha= 0.0055 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0187 ins/del rates= 0.0000) +pass 17: -3317.9548 (branch= 0.0001 alpha= 0.0050 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0159 ins/del rates= 0.0000) +pass 18: -3317.9326 (branch= 0.0001 alpha= 0.0044 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0136 ins/del rates= 0.0000) +pass 19: -3317.9132 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0116 ins/del rates= 0.0000) +pass 20: -3317.8964 (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: -3317.8074 (branch= 0.0000 alpha= 0.0172 pinv= 0.0158 eq freqs= 0.0001 rel rates= 0.0334 ins/del rates= 0.0000) +pass 30: -3317.8127 (branch= 0.0001 alpha= 0.0188 pinv= 0.0173 eq freqs= 0.0001 rel rates= 0.0474 ins/del rates= 0.0000) optimization up to ... -pass 40: -3317.7916 (branch= 0.0001 alpha= 0.0041 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0078 ins/del rates= 0.0000) +pass 40: -3317.7928 (branch= 0.0001 alpha= 0.0046 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0109 ins/del rates= 0.0000) optimization up to ... -pass 50: -3317.7880 (branch= 0.0000 alpha= 0.0009 pinv= 0.0008 eq freqs= 0.0000 rel rates= 0.0019 ins/del rates= 0.0000) +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) optimization up to ... -pass 60: -3317.7873 (branch= 0.0000 alpha= 0.0002 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0004 ins/del rates= 0.0000) +pass 60: -3317.7873 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0006 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) + 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) Looking for minimum length branches... Final score = -3317.7871 -Time used so far = 0 hours, 0 minutes and 12 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 = 3.065, AG = 10.266, AT = 2.657, CG = 0.001, CT = 21.543, GT = 1.000 + AC = 3.063, AG = 10.256, AT = 2.654, CG = 0.001, CT = 21.522, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3328 0.2223 0.1567 0.2882 + (ACGT) 0.3328 0.2223 0.1566 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.5742 + 0.5746 with an invariant (invariable) site category, proportion estimated - 0.3610 + 0.3612 Substitution rate categories under this model: rate proportion - 0.0000 0.3610 - 0.0478 0.1597 - 0.2976 0.1597 - 0.8676 0.1597 - 2.7869 0.1597 + 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) @@ -15461,7 +15387,7 @@ 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: 3.065 10.27 2.657 0.001 21.54 1 0.333 0.222 0.157 0.288 0.574 0.361 +rep 1: 3.063 10.26 2.654 0.001 21.52 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del @@ -15624,70 +15550,15 @@ 7400 -210.2807 0.010 1104 7600 -210.2625 0.010 1104 7800 -210.1872 0.010 1104 -8000 -210.1732 0.010 1104 -8200 -210.1282 0.010 1104 -8400 -210.1102 0.010 1104 -8600 -210.0895 0.010 1104 -8800 -210.0543 0.010 1104 -9000 -210.0430 0.010 1104 -9200 -209.9789 0.010 1104 -9400 -209.9602 0.010 1104 -9600 -209.9462 0.010 1104 -9800 -209.9220 0.010 1104 -10000 -209.8835 0.010 1104 - Optimizing parameters... improved 0.525 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 = 5.313, AG = 9.304, AT = 0.233, CG = 9.751, CT = 15.559, GT = 1.000 - Equilibrium State Frequencies: estimated - (ACGT) 0.2351 0.3311 0.2101 0.2237 - Rate Heterogeneity Model: - 3 discrete gamma distributed rate categories, alpha param estimated - 4.2032 - with an invariant (invariable) site category, proportion estimated - 0.2928 - Substitution rate categories under this model: - rate proportion - 0.0000 0.2928 - 0.5214 0.2357 - 0.9267 0.2357 - 1.5520 0.2357 - -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - No branches were short enough to be collapsed. - -Saving site likelihoods to file ch.n.G3.sitelikes.log ... -WARNING: Site likelihoods being output on prematurely terminated search ... - -NOTE: ***Search was terminated before full auto-termination condition was reached! -Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** - - -####################################################### - -Completed 1 replicate search(es) (of 1). -Results: -Replicate 1 : -209.3587 - -Parameter estimates: - r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 5.313 9.304 0.2334 9.751 15.56 1 0.235 0.331 0.210 0.224 4.203 0.293 - -Treelengths: - TL -rep 1: 2.312 - -Saving final tree from best search rep (#1) to ch.n.G3.best.tre -Inferring internal state probabilities on best tree... saving to file ch.n.G3.internalstates.log +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<- ############################################################## @@ -15758,28 +15629,38 @@ STARTING RUN Restarting from checkpoint... - generation 10001, seed 447301326, best lnL -209.359 + generation 7932, seed 1075956117, best lnL -210.177 gen current_lnL precision last_tree_imp -10001 -209.3587 0.010 1104 +7932 -210.1766 0.010 1104 +8000 -210.1732 0.010 1104 +8100 -210.1384 0.010 1104 +8200 -210.1282 0.010 1104 +8300 -210.1126 0.010 1104 +8400 -210.1102 0.010 1104 +8500 -210.1086 0.010 1104 +8600 -210.0895 0.010 1104 +Reached termination condition! +last topological improvement at gen 1104 +Improvement over last 500 gen = 0.04897 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 5.313, AG = 9.304, AT = 0.233, CG = 9.751, CT = 15.559, GT = 1.000 + AC = 3.919, AG = 6.881, AT = 0.186, CG = 6.998, CT = 11.153, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2351 0.3311 0.2101 0.2237 + (ACGT) 0.2363 0.3327 0.2105 0.2206 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 4.2032 + 1.8479 with an invariant (invariable) site category, proportion estimated - 0.2928 + 0.1921 Substitution rate categories under this model: rate proportion - 0.0000 0.2928 - 0.5214 0.2357 - 0.9267 0.2357 - 1.5520 0.2357 + 0.0000 0.1921 + 0.3353 0.2693 + 0.8372 0.2693 + 1.8275 0.2693 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. @@ -15790,15 +15671,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -209.3587 +Replicate 1 : -210.0895 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 5.313 9.304 0.2334 9.751 15.56 1 0.235 0.331 0.210 0.224 4.203 0.293 +rep 1: 3.919 6.881 0.186 6.998 11.15 1 0.236 0.333 0.210 0.221 1.848 0.192 Treelengths: TL -rep 1: 2.312 +rep 1: 2.357 Saving final tree from best search rep (#1) to ch.n.G3.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.G3.internalstates.log @@ -15947,77 +15828,15 @@ 5400 -165.5971 0.010 843 5600 -165.4763 0.010 843 5800 -165.3720 0.010 843 -6000 -165.3450 0.010 843 -6200 -165.2641 0.010 843 -6400 -165.1347 0.010 843 -6600 -165.0583 0.010 843 -6800 -165.0556 0.010 843 -7000 -164.9209 0.010 843 -7200 -164.8000 0.010 843 -7400 -164.7201 0.010 7384 -7600 -164.6618 0.010 7384 -7800 -164.5210 0.010 7384 -8000 -164.4382 0.010 7384 -8200 -164.2990 0.010 7384 -8400 -164.1760 0.010 7384 -8600 -164.1243 0.010 7384 -8800 -163.9562 0.010 7384 -9000 -163.8540 0.010 7384 -9200 -163.8477 0.010 7384 -9400 -163.7482 0.010 7384 -9600 -163.6369 0.010 7384 -9800 -163.6000 0.010 7384 -10000 -163.5760 0.010 7384 - Optimizing parameters... improved 1.387 lnL - Optimizing branchlengths... improved 0.022 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 = 8.582, AT = 1.923, CG = 3.484, CT = 33.018, GT = 1.000 - Equilibrium State Frequencies: estimated - (ACGT) 0.1298 0.4236 0.2357 0.2109 - Rate Heterogeneity Model: - 4 discrete gamma distributed rate categories, alpha param estimated - 36.9465 - with an invariant (invariable) site category, proportion estimated - 0.3606 - Substitution rate categories under this model: - rate proportion - 0.0000 0.3606 - 0.7993 0.1599 - 0.9391 0.1599 - 1.0454 0.1599 - 1.2161 0.1599 - -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 3 branches were collapsed. - - -NOTE: ***Search was terminated before full auto-termination condition was reached! -Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** - - -####################################################### - -Completed 1 replicate search(es) (of 1). -Results: -Replicate 1 : -162.1666 - -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: 0.6228 8.582 1.923 3.484 33.02 1 0.130 0.424 0.236 0.211 36.946 0.361 - -Treelengths: - TL -rep 1: 3.165 +NOTE: ****Specified time limit (5 seconds) reached... -Saving best tree to bootstrap file ch.n.G4.boot.tre +NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY +TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE +FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF +(set restart = 1 in the config file). IF YOU WANT TO USE THE +PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY +ADD "end;" TO THE TREE FILES. -WARNING: Tree from prematurely terminated search saved to bootstrap file -####################################################### Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## @@ -16089,11 +15908,55 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 10001, seed 172398639, best lnL -162.167 +Bootstrap rep 1 (of 1) generation 5912, seed 1099354606, best lnL -165.346 gen current_lnL precision last_tree_imp -10001 -162.1666 0.010 7384 +5912 -165.3456 0.010 843 +6000 -165.3450 0.010 843 +6100 -165.2860 0.010 843 +6200 -165.2641 0.010 843 +6300 -165.1569 0.010 843 +6400 -165.1347 0.010 843 +6500 -165.1040 0.010 843 +6600 -165.0583 0.010 843 +6700 -165.0567 0.010 843 +6800 -165.0556 0.010 843 +6900 -164.9354 0.010 843 +7000 -164.9209 0.010 843 +7100 -164.8349 0.010 843 +7200 -164.8000 0.010 843 +7300 -164.7628 0.010 843 +7400 -164.7201 0.010 7384 +7500 -164.6621 0.010 7384 +7600 -164.6618 0.010 7384 +7700 -164.5341 0.010 7384 +7800 -164.5210 0.010 7384 +7900 -164.4746 0.010 7384 +8000 -164.4382 0.010 7384 +8100 -164.3292 0.010 7384 +8200 -164.2990 0.010 7384 +8300 -164.1854 0.010 7384 +8400 -164.1760 0.010 7384 +8500 -164.1672 0.010 7384 +8600 -164.1243 0.010 7384 +8700 -163.9938 0.010 7384 +8800 -163.9562 0.010 7384 +8900 -163.9225 0.010 7384 +9000 -163.8540 0.010 7384 +9100 -163.8506 0.010 7384 +9200 -163.8477 0.010 7384 +9300 -163.7793 0.010 7384 +9400 -163.7482 0.010 7384 +9500 -163.7088 0.010 7384 +9600 -163.6369 0.010 7384 +9700 -163.6119 0.010 7384 +9800 -163.6000 0.010 7384 +9900 -163.5963 0.010 7384 +10000 -163.5760 0.010 7384 + Optimizing parameters... improved 1.387 lnL + Optimizing branchlengths... improved 0.022 lnL +NOTE: ****Specified generation limit (10000) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates @@ -16117,6 +15980,10 @@ 3 branches were collapsed. +NOTE: ***Search was terminated before full auto-termination condition was reached! +Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** + + ####################################################### Completed 1 replicate search(es) (of 1). @@ -16133,7 +16000,7 @@ Saving best tree to bootstrap file ch.n.G4.boot.tre ->>>Completed Bootstrap rep 1<<< +WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/n.conf @@ -17008,16 +16875,6 @@ Optimizing parameters... improved 0.015 lnL Optimizing branchlengths... improved 0.000 lnL 1600 -13370.4816 0.206 0 -1700 -13370.4688 0.206 0 -1800 -13370.4569 0.206 0 -1900 -13370.4339 0.206 0 -2000 -13370.4174 0.206 0 -Optimization precision reduced - Optimizing parameters... improved 0.006 lnL - Optimizing branchlengths... improved 0.000 lnL -2100 -13370.4112 0.108 0 -2200 -13370.3996 0.108 0 -2300 -13370.3996 0.108 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17140,16 +16997,24 @@ Subset 3: Random seed for bootstrap reweighting: 486988955 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 2358, seed 592356425, best lnL -13370.396 +Bootstrap rep 1 (of 1) generation 1657, seed 225363076, best lnL -13370.478 gen current_lnL precision last_tree_imp -2358 -13370.3962 0.108 0 +1657 -13370.4777 0.206 0 +1700 -13370.4688 0.206 0 +1800 -13370.4569 0.206 0 +1900 -13370.4339 0.206 0 +2000 -13370.4174 0.206 0 +Optimization precision reduced + Optimizing parameters... improved 0.006 lnL + Optimizing branchlengths... improved 0.000 lnL +NOTE: ****Specified generation limit (2000) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) - AC = 1.663, AG = 2.639, AT = 1.246, CG = 1.246, CT = 4.221, GT = 1.000 + AC = 1.663, AG = 2.558, AT = 1.235, CG = 1.235, CT = 4.221, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3082 0.1810 0.3087 0.2020 Rate Heterogeneity Model: @@ -17168,22 +17033,22 @@ User specified matrix type: ( 0 1 2 1 0 3 ) AC = 2.621, AG = 4.245, AT = 0.820, CG = 4.245, CT = 2.621, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2821 0.1749 0.1597 0.3834 + (ACGT) 0.2814 0.1768 0.1593 0.3825 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.2449 + 0.2457 Substitution rate categories under this model: rate proportion 0.0019 0.2500 - 0.0630 0.2500 - 0.4906 0.2500 - 3.4445 0.2500 + 0.0636 0.2500 + 0.4923 0.2500 + 3.4422 0.2500 Model 3 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) - AC = 1.000, AG = 5.311, AT = 4.309, CG = 0.629, CT = 5.311, GT = 1.000 + AC = 1.000, AG = 5.311, AT = 4.291, CG = 0.629, CT = 5.311, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1554 0.3464 0.2763 0.2219 Rate Heterogeneity Model: @@ -17205,25 +17070,29 @@ No branches were short enough to be collapsed. +NOTE: ***Search was terminated before full auto-termination condition was reached! +Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** + + ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13370.3962 +Replicate 1 : -13370.4112 Parameter estimates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 1.663 2.639 1.246 1.246 4.221 1 0.308 0.181 0.309 0.202 0.366 +rep 1: 1.663 2.558 1.235 1.235 4.221 1 0.308 0.181 0.309 0.202 0.366 Partition model subset 2: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 2.621 4.245 0.8204 4.245 2.621 1 0.282 0.175 0.160 0.383 0.245 +rep 1: 2.621 4.245 0.8204 4.245 2.621 1 0.281 0.177 0.159 0.382 0.246 Partition model subset 3: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 1 5.311 4.309 0.6292 5.311 1 0.155 0.346 0.276 0.222 4.126 0.049 +rep 1: 1 5.311 4.291 0.6292 5.311 1 0.155 0.346 0.276 0.222 4.126 0.049 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) @@ -17231,7 +17100,7 @@ Saving best tree to bootstrap file ch.p.3diff.boot.tre ->>>Completed Bootstrap rep 1<<< +WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mk.ssr.conf @@ -17450,7 +17319,7 @@ pass 16: -467.6788 (branch= 0.0000 subset rates= 0.0011) Looking for minimum length branches... Final score = -467.6787 -Time used so far = 0 hours, 0 minutes and 1 seconds +Time used so far = 0 hours, 0 minutes and 5 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17530,6 +17399,134 @@ 300 -467.7962 0.010 0 400 -467.7838 0.010 0 500 -467.7798 0.010 0 +NOTE: ****Specified time limit (5 seconds) reached... + +NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY +TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE +FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF +(set restart = 1 in the config file). IF YOU WANT TO USE THE +PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY +ADD "end;" TO THE TREE FILES. + +Running GARLI Version 2.1. () +->Single processor version for 64-bit OS<- +############################################################## + This is GARLI 2.1: maximum likelihood phylogenetic inference + using nucleotide, amino acid, codon and morphology-like data, + as well as partitioned models. + General program usage is extensively documented here: + http://www.nescent.org/wg/garli/ + See this page for details on partitioned model usage: + http://www.nescent.org/wg_garli/Using_partitioned_models + and this page for details on Mkv mophology model usage: + http://www.nescent.org/wg_garli/Mkv_morphology_model + PLEASE LET ME KNOW OF ANY PROBLEMS AT: + garli.support@gmail.com +############################################################## +Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0 +Using NCL version 2.1.17 + +####################################################### +Reading config file ./restart/p.mk.ssr.conf +################################################### +READING OF DATA +Attempting to read data file in Nexus format (using NCL): + data/L2001.30x52.nex ... +Reading CHARACTERS block... +Warning: + Skipping command: OPTIONS +at line 23, column (approximately) 9 (file position 611) +storing implied block: TAXA +storing read block: CHARACTERS + found standard data... successful +Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS + successful + +################################################### +PARTITIONING OF DATA AND MODELS +GARLI data subset 1 + CHARACTERS block #1 ("Untitled CHARACTERS Block 1") + Data read as Standard k-state data, + modeled as Standard k-state data +NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. +Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 + + Subset of data with 2 states: + chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 + Summary of data: + 30 sequences. + 0 constant characters. + 39 parsimony-informative characters. + 0 uninformative variable characters. + 39 total characters. + 39 unique patterns in compressed data matrix. +NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. +Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 + + Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: + char 90 + Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: + char 90 + Subset of data with 3 states: + chars 54 61 62 64 71 72 83 90-102 \ 6 + Summary of data: + 30 sequences. + 0 constant characters. + 10 parsimony-informative characters. + 0 uninformative variable characters. + 10 total characters. + 10 unique patterns in compressed data matrix. +NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. +Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 + + Subset of data with 4 states: + chars 52 59 73 + Summary of data: + 30 sequences. + 0 constant characters. + 0 parsimony-informative characters. + 3 uninformative variable characters. + 3 total characters. + 3 unique patterns in compressed data matrix. +NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. +Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 + +NOTE: No characters found with 5 observed states. +NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. +Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 + +NOTE: No characters found with 6 observed states. + +################################################### +NOTE: Unlike many programs, the amount of system memory that Garli will +use can be controlled by the user. +(This comes from the availablememory setting in the configuration file. +Availablememory should NOT be set to more than the actual amount of +physical memory that your computer has installed) + +For this dataset: + Mem level availablememory setting + great >= 1 MB + good approx 0 MB to 1 MB + low approx 0 MB to 1 MB + very low approx 0 MB to 1 MB +the minimum required availablememory is 1 MB + +You specified that Garli should use at most 512.0 MB of memory. + +Garli will actually use approx. 0.5 MB of memory +**Your memory level is: great (you don't need to change anything)** + +####################################################### +Loading starting model and/or tree from file data/L.start +Reading TREES block...storing read block: TREES + successful +STARTING RUN + +Restarting from checkpoint... +Search rep 2 (of 5) generation 550, seed 1908230784, best lnL -467.778 +gen current_lnL precision last_tree_imp +550 -467.7775 0.010 0 600 -467.7754 0.010 0 700 -467.7606 0.010 0 800 -467.7583 0.010 0 @@ -17578,7 +17575,7 @@ pass 17: -467.6782 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6782 -Time used so far = 0 hours, 0 minutes and 2 seconds +Time used so far = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17720,7 +17717,7 @@ pass 15: -467.6783 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6783 -Time used so far = 0 hours, 0 minutes and 4 seconds +Time used so far = 0 hours, 0 minutes and 11 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17801,189 +17798,29 @@ 400 -467.7763 0.010 0 500 -467.7632 0.010 0 600 -467.7576 0.010 0 -700 -467.7510 0.010 0 -800 -467.7434 0.010 0 -900 -467.7350 0.010 0 -1000 -467.7339 0.010 0 -1100 -467.7315 0.010 0 -1200 -467.7296 0.010 0 -1300 -467.7277 0.010 0 -1400 -467.7252 0.010 0 -1500 -467.7239 0.010 0 -1600 -467.7228 0.010 0 -1700 -467.7195 0.010 0 -1800 -467.7177 0.010 0 -1900 -467.7171 0.010 0 -2000 -467.7150 0.010 0 -2100 -467.7139 0.010 0 -2200 -467.7117 0.010 0 -2300 -467.7101 0.010 0 -2400 -467.7097 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... - -NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY -TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE -FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF -(set restart = 1 in the config file). IF YOU WANT TO USE THE -PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY -ADD "end;" TO THE TREE FILES. - -Running GARLI Version 2.1. () -->Single processor version for 64-bit OS<- -############################################################## - This is GARLI 2.1: maximum likelihood phylogenetic inference - using nucleotide, amino acid, codon and morphology-like data, - as well as partitioned models. - General program usage is extensively documented here: - http://www.nescent.org/wg/garli/ - See this page for details on partitioned model usage: - http://www.nescent.org/wg_garli/Using_partitioned_models - and this page for details on Mkv mophology model usage: - http://www.nescent.org/wg_garli/Mkv_morphology_model - PLEASE LET ME KNOW OF ANY PROBLEMS AT: - garli.support@gmail.com -############################################################## -Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0 -Using NCL version 2.1.17 - -####################################################### -Reading config file ./restart/p.mk.ssr.conf -################################################### -READING OF DATA -Attempting to read data file in Nexus format (using NCL): - data/L2001.30x52.nex ... -Reading CHARACTERS block... -Warning: - Skipping command: OPTIONS -at line 23, column (approximately) 9 (file position 611) -storing implied block: TAXA -storing read block: CHARACTERS - found standard data... successful -Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS - successful - -################################################### -PARTITIONING OF DATA AND MODELS -GARLI data subset 1 - CHARACTERS block #1 ("Untitled CHARACTERS Block 1") - Data read as Standard k-state data, - modeled as Standard k-state data -NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. -Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 - - Subset of data with 2 states: - chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 - Summary of data: - 30 sequences. - 0 constant characters. - 39 parsimony-informative characters. - 0 uninformative variable characters. - 39 total characters. - 39 unique patterns in compressed data matrix. -NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. -Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 - - Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: - char 90 - Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: - char 90 - Subset of data with 3 states: - chars 54 61 62 64 71 72 83 90-102 \ 6 - Summary of data: - 30 sequences. - 0 constant characters. - 10 parsimony-informative characters. - 0 uninformative variable characters. - 10 total characters. - 10 unique patterns in compressed data matrix. -NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. -Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 - - Subset of data with 4 states: - chars 52 59 73 - Summary of data: - 30 sequences. - 0 constant characters. - 0 parsimony-informative characters. - 3 uninformative variable characters. - 3 total characters. - 3 unique patterns in compressed data matrix. -NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. -Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 - -NOTE: No characters found with 5 observed states. -NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. -Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 - -NOTE: No characters found with 6 observed states. - -################################################### -NOTE: Unlike many programs, the amount of system memory that Garli will -use can be controlled by the user. -(This comes from the availablememory setting in the configuration file. -Availablememory should NOT be set to more than the actual amount of -physical memory that your computer has installed) - -For this dataset: - Mem level availablememory setting - great >= 1 MB - good approx 0 MB to 1 MB - low approx 0 MB to 1 MB - very low approx 0 MB to 1 MB -the minimum required availablememory is 1 MB - -You specified that Garli should use at most 512.0 MB of memory. - -Garli will actually use approx. 0.5 MB of memory -**Your memory level is: great (you don't need to change anything)** - -####################################################### -Loading starting model and/or tree from file data/L.start -Reading TREES block...storing read block: TREES - successful -STARTING RUN - -Restarting from checkpoint... -Search rep 4 (of 5) generation 2499, seed 1737888404, best lnL -467.709 -gen current_lnL precision last_tree_imp -2499 -467.7091 0.010 0 -2500 -467.7091 0.010 0 -2600 -467.7082 0.010 0 -2700 -467.7078 0.010 0 -2800 -467.7078 0.010 0 -2900 -467.7074 0.010 0 -3000 -467.7070 0.010 0 -3100 -467.7067 0.010 0 -3200 -467.7066 0.010 0 -3300 -467.7066 0.010 0 -3400 -467.7066 0.010 0 -Reached termination condition! -last topological improvement at gen 0 -Improvement over last 500 gen = 0.00074 -Current score = -467.7066 +Current score = -467.7546 Performing final optimizations... -pass 1 : -467.7066 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -467.6910 (branch= 0.0152 subset rates= 0.0004) -pass 3 : -467.6850 (branch= 0.0047 subset rates= 0.0013) -pass 4 : -467.6842 (branch= 0.0008 subset rates= 0.0000) -pass 5 : -467.6829 (branch= 0.0014 subset rates= 0.0000) -pass 6 : -467.6822 (branch= 0.0007 subset rates= 0.0000) -pass 7 : -467.6814 (branch= 0.0008 subset rates= 0.0000) -pass 8 : -467.6804 (branch= 0.0010 subset rates= 0.0000) -pass 9 : -467.6800 (branch= 0.0004 subset rates= 0.0000) -pass 10: -467.6798 (branch= 0.0002 subset rates= 0.0000) -pass 11: -467.6797 (branch= 0.0001 subset rates= 0.0000) -pass 12: -467.6797 (branch= 0.0001 subset rates= 0.0000) -pass 13: -467.6791 (branch= 0.0000 subset rates= 0.0006) -pass 14: -467.6784 (branch= 0.0005 subset rates= 0.0001) -pass 15: -467.6784 (branch= 0.0000 subset rates= 0.0000) -pass 16: -467.6784 (branch= 0.0000 subset rates= 0.0000) -pass 17: -467.6784 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -467.7490 (branch= 0.0056 subset rates= 0.0001) +pass 2 : -467.7178 (branch= 0.0312 subset rates= 0.0000) +pass 3 : -467.7063 (branch= 0.0114 subset rates= 0.0000) +pass 4 : -467.6936 (branch= 0.0116 subset rates= 0.0011) +pass 5 : -467.6882 (branch= 0.0054 subset rates= 0.0000) +pass 6 : -467.6855 (branch= 0.0027 subset rates= 0.0000) +pass 7 : -467.6841 (branch= 0.0014 subset rates= 0.0000) +pass 8 : -467.6809 (branch= 0.0004 subset rates= 0.0027) +pass 9 : -467.6795 (branch= 0.0014 subset rates= 0.0000) +pass 10: -467.6790 (branch= 0.0005 subset rates= 0.0000) +pass 11: -467.6789 (branch= 0.0002 subset rates= 0.0000) +pass 12: -467.6788 (branch= 0.0001 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 6 seconds +Final score = -467.6788 +Time used so far = 0 hours, 0 minutes and 12 seconds -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 2 (standard data) Character change matrix: @@ -18009,151 +17846,19 @@ no rate heterogeneity Subset rate multipliers: - 0.79 1.47 2.18 + 0.79 1.48 2.16 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. ->>>Completed Search rep 4 (of 5)<<< - ->>>Search rep 5 (of 5)<<< -Obtained starting tree 1 from Nexus -MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) -Model 1 - Number of states = 2 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity +>>>Terminated Search rep 4 (of 5)<<< -Model 3 - Number of states = 4 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 1.00 1.00 1.00 -Starting with seed=1967985483 - -Initial ln Likelihood: -587.3865 -optimizing: starting branch lengths, subset rates... -pass 1:+ 109.204 (branch= 103.65 scale= 0.82 subset rates= 4.74) -pass 2:+ 9.632 (branch= 8.64 scale= 0.02 subset rates= 0.97) -pass 3:+ 0.698 (branch= 0.53 scale= 0.00 subset rates= 0.17) -pass 4:+ 0.015 (branch= 0.01 scale= 0.00 subset rates= 0.00) -pass 5:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -467.8378 -gen current_lnL precision last_tree_imp -0 -467.8378 0.010 0 -100 -467.8022 0.010 0 -200 -467.7991 0.010 0 -300 -467.7923 0.010 0 -400 -467.7864 0.010 0 -500 -467.7746 0.010 0 -600 -467.7698 0.010 0 -700 -467.7652 0.010 0 -800 -467.7626 0.010 0 -900 -467.7592 0.010 0 -1000 -467.7433 0.010 0 -1100 -467.7340 0.010 0 -1200 -467.7319 0.010 0 -1300 -467.7289 0.010 0 -1400 -467.7281 0.010 0 -1500 -467.7247 0.010 0 -1600 -467.7214 0.010 0 -1700 -467.7210 0.010 0 -1800 -467.7171 0.010 0 -1900 -467.7155 0.010 0 -2000 -467.7149 0.010 0 -2100 -467.7138 0.010 0 -2200 -467.7116 0.010 0 -2300 -467.7112 0.010 0 -2400 -467.7106 0.010 0 -2500 -467.7093 0.010 0 -2600 -467.7087 0.010 0 -2700 -467.7064 0.010 0 -2800 -467.7061 0.010 0 -2900 -467.7061 0.010 0 -3000 -467.7050 0.010 0 -3100 -467.7049 0.010 0 -3200 -467.7048 0.010 0 -3300 -467.7045 0.010 0 -3400 -467.7038 0.010 0 -3500 -467.7033 0.010 0 -3600 -467.7030 0.010 0 -3700 -467.7029 0.010 0 -3800 -467.7028 0.010 0 -3900 -467.7026 0.010 0 -4000 -467.7024 0.010 0 -Reached termination condition! -last topological improvement at gen 0 -Improvement over last 500 gen = 0.00087 -Current score = -467.7024 -Performing final optimizations... -pass 1 : -467.7024 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -467.6856 (branch= 0.0146 subset rates= 0.0022) -pass 3 : -467.6856 (branch= 0.0000 subset rates= 0.0000) -pass 4 : -467.6846 (branch= 0.0010 subset rates= 0.0000) -pass 5 : -467.6843 (branch= 0.0003 subset rates= 0.0000) -pass 6 : -467.6824 (branch= 0.0019 subset rates= 0.0000) -pass 7 : -467.6807 (branch= 0.0012 subset rates= 0.0005) -pass 8 : -467.6793 (branch= 0.0013 subset rates= 0.0000) -pass 9 : -467.6789 (branch= 0.0005 subset rates= 0.0000) -pass 10: -467.6786 (branch= 0.0002 subset rates= 0.0001) -pass 11: -467.6784 (branch= 0.0002 subset rates= 0.0000) -pass 12: -467.6784 (branch= 0.0001 subset rates= 0.0000) -pass 13: -467.6783 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6783 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -467.6783 -Time used = 0 hours, 0 minutes and 8 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 0.79 1.47 2.18 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. +NOTE: ***Search was terminated before full auto-termination condition was reached! +Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ->>>Completed Search rep 5 (of 5)<<< ####################################################### -Completed 5 replicate search(es) (of 5). +Completed 4 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. @@ -18161,8 +17866,7 @@ Replicate 1 : -467.6787 Replicate 2 : -467.6782 (best) (same topology as 1) Replicate 3 : -467.6783 (same topology as 1) -Replicate 4 : -467.6784 (same topology as 1) -Replicate 5 : -467.6783 (same topology as 1) +Replicate 4 : -467.6788 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -18180,10 +17884,7 @@ rep 1: 3.839 0.788 1.477 2.167 rep 2: 3.845 0.786 1.478 2.195 rep 3: 3.843 0.786 1.480 2.179 -rep 4: 3.841 0.788 1.475 2.178 -rep 5: 3.841 0.787 1.475 2.182 - -Saving final trees from all search reps to ch.p.mk.ssr.best.all.tre +rep 4: 3.840 0.788 1.480 2.163 Saving final tree from best search rep (#2) to ch.p.mk.ssr.best.tre ####################################################### @@ -18406,7 +18107,7 @@ pass 18: -477.4316 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.4316 -Time used so far = 0 hours, 0 minutes and 1 seconds +Time used so far = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18494,183 +18195,6 @@ 900 -477.6956 0.010 102 1000 -477.6943 0.010 102 1100 -477.6894 0.010 102 -1200 -477.6880 0.010 102 -1300 -477.6826 0.010 102 -1400 -477.6813 0.010 102 -1500 -477.6800 0.010 102 -1600 -477.6784 0.010 102 -1700 -477.6774 0.010 102 -1800 -477.6759 0.010 102 -1900 -477.6746 0.010 102 -2000 -477.6742 0.010 102 -2100 -477.6737 0.010 102 -2200 -477.6736 0.010 102 -2300 -477.6735 0.010 102 -2400 -477.6730 0.010 102 -2500 -477.6728 0.010 102 -2600 -477.6718 0.010 102 -2700 -477.6708 0.010 102 -2800 -477.6700 0.010 102 -2900 -477.6696 0.010 102 -3000 -477.6692 0.010 102 -3100 -477.3606 0.010 3081 -3200 -477.3479 0.010 3081 -3300 -477.3079 0.010 3204 -3400 -477.2956 0.010 3204 -3500 -477.2896 0.010 3204 -3600 -477.2877 0.010 3204 -3700 -477.2853 0.010 3204 -3800 -477.2850 0.010 3204 -3900 -477.2791 0.010 3204 -4000 -477.2789 0.010 3204 -4100 -477.2787 0.010 3204 -4200 -477.2785 0.010 3204 -4300 -477.2780 0.010 3204 -4400 -477.2765 0.010 3204 -4500 -477.2761 0.010 3204 -4600 -477.2757 0.010 3204 -4700 -477.2752 0.010 3204 -4800 -477.2750 0.010 3204 -4900 -477.2746 0.010 3204 -5000 -477.2741 0.010 3204 - Optimizing parameters... improved 0.032 lnL - Optimizing branchlengths... improved 0.000 lnL -5100 -477.2414 0.010 3204 -5200 -477.2404 0.010 3204 -5300 -477.2404 0.010 3204 -5400 -477.2394 0.010 3204 -5500 -477.2393 0.010 3204 -5600 -477.2382 0.010 3204 -5700 -477.2353 0.010 3204 -5800 -477.2347 0.010 3204 -5900 -477.2346 0.010 3204 -6000 -477.2345 0.010 3204 -6100 -477.2339 0.010 3204 -6200 -477.2338 0.010 3204 -6300 -477.2335 0.010 3204 -6400 -477.2331 0.010 3204 -6500 -477.2322 0.010 3204 -6600 -477.2321 0.010 3204 -6700 -477.2318 0.010 3204 -6800 -477.2317 0.010 3204 -6900 -477.2314 0.010 3204 -7000 -477.2311 0.010 3204 -7100 -477.2311 0.010 3204 -Reached termination condition! -last topological improvement at gen 3204 -Improvement over last 500 gen = 0.00097 -Current score = -477.2311 -Performing final optimizations... -pass 1 : -477.2311 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -477.2252 (branch= 0.0058 subset rates= 0.0000) -pass 3 : -477.2165 (branch= 0.0087 subset rates= 0.0000) -pass 4 : -477.2146 (branch= 0.0019 subset rates= 0.0000) -pass 5 : -477.2146 (branch= 0.0000 subset rates= 0.0000) -pass 6 : -477.2140 (branch= 0.0006 subset rates= 0.0000) -pass 7 : -477.2127 (branch= 0.0013 subset rates= 0.0000) -pass 8 : -477.2123 (branch= 0.0004 subset rates= 0.0000) -pass 9 : -477.2121 (branch= 0.0002 subset rates= 0.0000) -pass 10: -477.2121 (branch= 0.0000 subset rates= 0.0000) -pass 11: -477.2120 (branch= 0.0000 subset rates= 0.0000) -pass 12: -477.2120 (branch= 0.0000 subset rates= 0.0000) -pass 13: -477.2120 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -477.2120 -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 2 (of 5)<<< - ->>>Search rep 3 (of 5)<<< -Obtained starting tree 1 from Nexus -MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 1.00 1.00 1.00 -Starting with seed=1080847507 - -Initial ln Likelihood: -664.0673 -optimizing: starting branch lengths, subset rates... -pass 1:+ 161.772 (branch= 148.02 scale= 3.68 subset rates= 10.07) -pass 2:+ 19.334 (branch= 15.28 scale= 0.00 subset rates= 4.06) -pass 3:+ 4.166 (branch= 2.92 scale= 0.04 subset rates= 1.21) -pass 4:+ 0.777 (branch= 0.52 scale= 0.00 subset rates= 0.26) -pass 5:+ 0.105 (branch= 0.10 scale= 0.00 subset rates= 0.00) -pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -477.9144 -gen current_lnL precision last_tree_imp -0 -477.9144 0.010 0 -100 -477.8474 0.010 38 -200 -477.7709 0.010 188 -300 -477.7604 0.010 188 -400 -477.7468 0.010 188 -500 -477.7408 0.010 188 -600 -477.7022 0.010 520 -700 -477.6898 0.010 520 -800 -477.6823 0.010 520 -900 -477.6795 0.010 520 -1000 -477.6777 0.010 520 -1100 -477.3824 0.010 1037 -1200 -477.3598 0.010 1037 -1300 -477.3536 0.010 1037 -1400 -477.3511 0.010 1037 -1500 -477.3003 0.010 1443 -1600 -477.2712 0.010 1502 -1700 -477.2687 0.010 1502 -1800 -477.2676 0.010 1502 -1900 -477.2646 0.010 1502 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -18796,236 +18320,91 @@ STARTING RUN Restarting from checkpoint... -Search rep 3 (of 5) generation 1900, seed 1384392929, best lnL -477.265 +Search rep 2 (of 5) generation 1108, seed 957308108, best lnL -477.689 gen current_lnL precision last_tree_imp -1900 -477.2646 0.010 1502 -2000 -477.2617 0.010 1502 -2100 -477.2612 0.010 1502 -2200 -477.2604 0.010 1502 -2300 -477.2603 0.010 1502 -2400 -477.2602 0.010 1502 -2500 -477.2593 0.010 1502 -2600 -477.2570 0.010 1502 -2700 -477.2567 0.010 1502 -2800 -477.2566 0.010 1502 -2900 -477.2547 0.010 1502 -3000 -477.2523 0.010 1502 -3100 -477.2522 0.010 1502 -3200 -477.2512 0.010 1502 -3300 -477.2512 0.010 1502 -3400 -477.2508 0.010 1502 -3500 -477.2506 0.010 1502 -3600 -477.2505 0.010 1502 -3700 -477.2498 0.010 1502 -3800 -477.2495 0.010 1502 -3900 -477.2494 0.010 1502 -4000 -477.2491 0.010 1502 -4100 -477.2490 0.010 1502 -4200 -477.2486 0.010 1502 -4300 -477.2482 0.010 1502 -4400 -477.2475 0.010 1502 -4500 -477.2459 0.010 1502 -4600 -477.2457 0.010 1502 -4700 -477.2452 0.010 1502 -4800 -477.2452 0.010 1502 -4900 -477.2451 0.010 1502 -5000 -477.2444 0.010 1502 - Optimizing parameters... improved 0.000 lnL +1108 -477.6893 0.010 102 +1200 -477.6880 0.010 102 +1300 -477.6826 0.010 102 +1400 -477.6813 0.010 102 +1500 -477.6800 0.010 102 +1600 -477.6784 0.010 102 +1700 -477.6774 0.010 102 +1800 -477.6759 0.010 102 +1900 -477.6746 0.010 102 +2000 -477.6742 0.010 102 +2100 -477.6737 0.010 102 +2200 -477.6736 0.010 102 +2300 -477.6735 0.010 102 +2400 -477.6730 0.010 102 +2500 -477.6728 0.010 102 +2600 -477.6718 0.010 102 +2700 -477.6708 0.010 102 +2800 -477.6700 0.010 102 +2900 -477.6696 0.010 102 +3000 -477.6692 0.010 102 +3100 -477.3606 0.010 3081 +3200 -477.3479 0.010 3081 +3300 -477.3079 0.010 3204 +3400 -477.2956 0.010 3204 +3500 -477.2896 0.010 3204 +3600 -477.2877 0.010 3204 +3700 -477.2853 0.010 3204 +3800 -477.2850 0.010 3204 +3900 -477.2791 0.010 3204 +4000 -477.2789 0.010 3204 +4100 -477.2787 0.010 3204 +4200 -477.2785 0.010 3204 +4300 -477.2780 0.010 3204 +4400 -477.2765 0.010 3204 +4500 -477.2761 0.010 3204 +4600 -477.2757 0.010 3204 +4700 -477.2752 0.010 3204 +4800 -477.2750 0.010 3204 +4900 -477.2746 0.010 3204 +5000 -477.2741 0.010 3204 + Optimizing parameters... improved 0.032 lnL Optimizing branchlengths... improved 0.000 lnL -5100 -477.2437 0.010 1502 -5200 -477.2432 0.010 1502 -5300 -477.2414 0.010 1502 -5400 -477.2414 0.010 1502 -5500 -477.2413 0.010 1502 -5600 -477.2413 0.010 1502 -5700 -477.2408 0.010 1502 -5800 -477.2401 0.010 1502 -5900 -477.2398 0.010 1502 -6000 -477.2397 0.010 1502 -6100 -477.2396 0.010 1502 -6200 -477.2395 0.010 1502 -6300 -477.2394 0.010 1502 +5100 -477.2414 0.010 3204 +5200 -477.2404 0.010 3204 +5300 -477.2404 0.010 3204 +5400 -477.2394 0.010 3204 +5500 -477.2393 0.010 3204 +5600 -477.2382 0.010 3204 +5700 -477.2353 0.010 3204 +5800 -477.2347 0.010 3204 +5900 -477.2346 0.010 3204 +6000 -477.2345 0.010 3204 +6100 -477.2339 0.010 3204 +6200 -477.2338 0.010 3204 +6300 -477.2335 0.010 3204 +6400 -477.2331 0.010 3204 +6500 -477.2322 0.010 3204 +6600 -477.2321 0.010 3204 +6700 -477.2318 0.010 3204 +6800 -477.2317 0.010 3204 +6900 -477.2314 0.010 3204 +7000 -477.2311 0.010 3204 +7100 -477.2311 0.010 3204 Reached termination condition! -last topological improvement at gen 1502 -Improvement over last 500 gen = 0.00076 -Current score = -477.2394 +last topological improvement at gen 3204 +Improvement over last 500 gen = 0.00097 +Current score = -477.2311 Performing final optimizations... -pass 1 : -477.2329 (branch= 0.0000 subset rates= 0.0065) -pass 2 : -477.2269 (branch= 0.0060 subset rates= 0.0000) -pass 3 : -477.2189 (branch= 0.0080 subset rates= 0.0000) -pass 4 : -477.2164 (branch= 0.0019 subset rates= 0.0006) -pass 5 : -477.2145 (branch= 0.0004 subset rates= 0.0014) -pass 6 : -477.2139 (branch= 0.0006 subset rates= 0.0000) -pass 7 : -477.2131 (branch= 0.0009 subset rates= 0.0000) -pass 8 : -477.2123 (branch= 0.0007 subset rates= 0.0000) +pass 1 : -477.2311 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -477.2252 (branch= 0.0058 subset rates= 0.0000) +pass 3 : -477.2165 (branch= 0.0087 subset rates= 0.0000) +pass 4 : -477.2146 (branch= 0.0019 subset rates= 0.0000) +pass 5 : -477.2146 (branch= 0.0000 subset rates= 0.0000) +pass 6 : -477.2140 (branch= 0.0006 subset rates= 0.0000) +pass 7 : -477.2127 (branch= 0.0013 subset rates= 0.0000) +pass 8 : -477.2123 (branch= 0.0004 subset rates= 0.0000) pass 9 : -477.2121 (branch= 0.0002 subset rates= 0.0000) -pass 10: -477.2120 (branch= 0.0001 subset rates= 0.0000) +pass 10: -477.2121 (branch= 0.0000 subset rates= 0.0000) pass 11: -477.2120 (branch= 0.0000 subset rates= 0.0000) -pass 12: -477.2119 (branch= 0.0000 subset rates= 0.0000) -pass 13: -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 8 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate 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 2.61 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. - ->>>Completed Search rep 3 (of 5)<<< - ->>>Search rep 4 (of 5)<<< -Obtained starting tree 1 from Nexus -MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 1.00 1.00 1.00 -Starting with seed=400322308 - -Initial ln Likelihood: -654.1007 -optimizing: starting branch lengths, subset rates... -pass 1:+ 156.419 (branch= 145.69 scale= 0.69 subset rates= 10.04) -pass 2:+ 13.874 (branch= 9.83 scale= 0.02 subset rates= 4.03) -pass 3:+ 3.407 (branch= 2.09 scale= 0.00 subset rates= 1.32) -pass 4:+ 1.440 (branch= 1.12 scale= 0.00 subset rates= 0.32) -pass 5:+ 0.938 (branch= 0.91 scale= 0.00 subset rates= 0.03) -pass 6:+ 0.186 (branch= 0.17 scale= 0.01 subset rates= 0.00) -pass 7:+ 0.010 (branch= 0.01 scale= 0.00 subset rates= 0.00) -lnL after optimization: -477.8267 -gen current_lnL precision last_tree_imp -0 -477.8267 0.010 0 -100 -477.7290 0.010 85 -200 -477.7137 0.010 85 -300 -477.5306 0.010 252 -400 -477.5199 0.010 252 -500 -477.5148 0.010 252 -600 -477.5109 0.010 252 -700 -477.5029 0.010 252 -800 -477.4995 0.010 252 -900 -477.4992 0.010 252 -1000 -477.4974 0.010 252 -1100 -477.4952 0.010 252 -1200 -477.4909 0.010 252 -1300 -477.4896 0.010 252 -1400 -477.4869 0.010 252 -1500 -477.4868 0.010 252 -1600 -477.4844 0.010 252 -1700 -477.4840 0.010 252 -1800 -477.4826 0.010 252 -1900 -477.4817 0.010 252 -2000 -477.4817 0.010 252 -2100 -477.4807 0.010 252 -2200 -477.4799 0.010 252 -2300 -477.4773 0.010 252 -2400 -477.4759 0.010 252 -2500 -477.4758 0.010 252 -2600 -477.4753 0.010 252 -2700 -477.4735 0.010 252 -2800 -477.4725 0.010 252 -2900 -477.4719 0.010 252 -3000 -477.4715 0.010 252 -3100 -477.4703 0.010 252 -3200 -477.4694 0.010 252 -3300 -477.4689 0.010 252 -3400 -477.4677 0.010 252 -3500 -477.4673 0.010 252 -3600 -477.4671 0.010 252 -3700 -477.4669 0.010 252 -3800 -477.4666 0.010 252 -3900 -477.4661 0.010 252 -4000 -477.4655 0.010 252 -4100 -477.4653 0.010 252 -4200 -477.4652 0.010 252 -4300 -477.4649 0.010 252 -4400 -477.4633 0.010 252 -4500 -477.4632 0.010 252 -4600 -477.4629 0.010 252 -4700 -477.4618 0.010 252 -4800 -477.4612 0.010 252 -4900 -477.4611 0.010 252 -5000 -477.4609 0.010 252 - Optimizing parameters... improved 0.000 lnL - Optimizing branchlengths... improved 0.000 lnL -5100 -477.4606 0.010 252 -5200 -477.4604 0.010 252 -5300 -477.4602 0.010 252 -5400 -477.4598 0.010 252 -5500 -477.4595 0.010 252 -5600 -477.4594 0.010 252 -5700 -477.4592 0.010 252 -5800 -477.4592 0.010 252 -Reached termination condition! -last topological improvement at gen 252 -Improvement over last 500 gen = 0.00098 -Current score = -477.4592 -Performing final optimizations... -pass 1 : -477.4573 (branch= 0.0000 subset rates= 0.0019) -pass 2 : -477.4520 (branch= 0.0052 subset rates= 0.0000) -pass 3 : -477.4385 (branch= 0.0113 subset rates= 0.0021) -pass 4 : -477.4368 (branch= 0.0018 subset rates= 0.0000) -pass 5 : -477.4353 (branch= 0.0015 subset rates= 0.0000) -pass 6 : -477.4342 (branch= 0.0011 subset rates= 0.0000) -pass 7 : -477.4327 (branch= 0.0007 subset rates= 0.0008) -pass 8 : -477.4322 (branch= 0.0005 subset rates= 0.0000) -pass 9 : -477.4319 (branch= 0.0002 subset rates= 0.0000) -pass 10: -477.4318 (branch= 0.0001 subset rates= 0.0000) -pass 11: -477.4317 (branch= 0.0001 subset rates= 0.0000) -pass 12: -477.4317 (branch= 0.0000 subset rates= 0.0000) -pass 13: -477.4316 (branch= 0.0000 subset rates= 0.0000) -pass 14: -477.4316 (branch= 0.0000 subset rates= 0.0000) -pass 15: -477.4316 (branch= 0.0000 subset rates= 0.0000) -pass 16: -477.4316 (branch= 0.0000 subset rates= 0.0000) -pass 17: -477.4316 (branch= 0.0000 subset rates= 0.0000) +pass 12: -477.2120 (branch= 0.0000 subset rates= 0.0000) +pass 13: -477.2120 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.4315 +Final score = -477.2120 Time used so far = 0 hours, 0 minutes and 11 seconds MODEL REPORT - Parameter values are FINAL @@ -19054,13 +18433,13 @@ no rate heterogeneity Subset rate multipliers: - 0.63 1.91 2.74 + 0.64 1.91 2.62 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. + 8 branches were collapsed. ->>>Completed Search rep 4 (of 5)<<< +>>>Completed Search rep 2 (of 5)<<< ->>>Search rep 5 (of 5)<<< +>>>Search rep 3 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 @@ -19089,45 +18468,52 @@ Subset rate multipliers: 1.00 1.00 1.00 -Starting with seed=328833807 +Starting with seed=1080847507 -Initial ln Likelihood: -660.1326 +Initial ln Likelihood: -664.0673 optimizing: starting branch lengths, subset rates... -pass 1:+ 159.381 (branch= 147.15 scale= 2.32 subset rates= 9.91) -pass 2:+ 16.729 (branch= 12.80 scale= 0.00 subset rates= 3.93) -pass 3:+ 3.088 (branch= 1.77 scale= 0.02 subset rates= 1.30) -pass 4:+ 0.890 (branch= 0.55 scale= 0.00 subset rates= 0.34) -pass 5:+ 1.052 (branch= 1.02 scale= 0.00 subset rates= 0.03) -pass 6:+ 0.985 (branch= 0.98 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.201 (branch= 0.20 scale= 0.00 subset rates= 0.00) -pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -477.8081 +pass 1:+ 161.772 (branch= 148.02 scale= 3.68 subset rates= 10.07) +pass 2:+ 19.334 (branch= 15.28 scale= 0.00 subset rates= 4.06) +pass 3:+ 4.166 (branch= 2.92 scale= 0.04 subset rates= 1.21) +pass 4:+ 0.777 (branch= 0.52 scale= 0.00 subset rates= 0.26) +pass 5:+ 0.105 (branch= 0.10 scale= 0.00 subset rates= 0.00) +pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -477.9144 gen current_lnL precision last_tree_imp -0 -477.8081 0.010 0 +0 -477.9144 0.010 0 +100 -477.8474 0.010 38 +200 -477.7709 0.010 188 +300 -477.7604 0.010 188 +400 -477.7468 0.010 188 +500 -477.7408 0.010 188 +600 -477.7022 0.010 520 +700 -477.6898 0.010 520 +800 -477.6823 0.010 520 +900 -477.6795 0.010 520 +1000 -477.6777 0.010 520 +1100 -477.3824 0.010 1037 +1200 -477.3598 0.010 1037 +1300 -477.3536 0.010 1037 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -477.8005 +Current score = -477.3511 Performing final optimizations... -pass 1 : -477.7727 (branch= 0.0278 subset rates= 0.0000) -pass 2 : -477.7167 (branch= 0.0560 subset rates= 0.0000) -pass 3 : -477.7045 (branch= 0.0122 subset rates= 0.0001) -pass 4 : -477.6944 (branch= 0.0101 subset rates= 0.0000) -pass 5 : -477.6900 (branch= 0.0044 subset rates= 0.0000) -pass 6 : -477.6877 (branch= 0.0023 subset rates= 0.0000) -pass 7 : -477.6861 (branch= 0.0016 subset rates= 0.0000) -pass 8 : -477.6857 (branch= 0.0003 subset rates= 0.0000) -pass 9 : -477.6853 (branch= 0.0004 subset rates= 0.0000) -pass 10: -477.6851 (branch= 0.0002 subset rates= 0.0000) -pass 11: -477.6850 (branch= 0.0001 subset rates= 0.0000) -pass 12: -477.6850 (branch= 0.0001 subset rates= 0.0000) -pass 13: -477.6849 (branch= 0.0000 subset rates= 0.0000) -pass 14: -477.6849 (branch= 0.0000 subset rates= 0.0000) -pass 15: -477.6849 (branch= 0.0000 subset rates= 0.0000) -pass 16: -477.6849 (branch= 0.0000 subset rates= 0.0000) -pass 17: -477.6848 (branch= 0.0000 subset rates= 0.0000) -pass 18: -477.6848 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -477.2802 (branch= 0.0627 subset rates= 0.0083) +pass 2 : -477.2534 (branch= 0.0268 subset rates= 0.0000) +pass 3 : -477.2314 (branch= 0.0216 subset rates= 0.0004) +pass 4 : -477.2248 (branch= 0.0066 subset rates= 0.0000) +pass 5 : -477.2170 (branch= 0.0074 subset rates= 0.0005) +pass 6 : -477.2143 (branch= 0.0027 subset rates= 0.0000) +pass 7 : -477.2129 (branch= 0.0014 subset rates= 0.0000) +pass 8 : -477.2123 (branch= 0.0006 subset rates= 0.0000) +pass 9 : -477.2122 (branch= 0.0001 subset rates= 0.0000) +pass 10: -477.2121 (branch= 0.0001 subset rates= 0.0000) +pass 11: -477.2120 (branch= 0.0001 subset rates= 0.0001) +pass 12: -477.2120 (branch= 0.0000 subset rates= 0.0000) +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 = -477.6848 -Time used = 0 hours, 0 minutes and 12 seconds +Final score = -477.2119 +Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 @@ -19155,11 +18541,11 @@ no rate heterogeneity Subset rate multipliers: - 0.63 1.91 2.81 + 0.64 1.91 2.61 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 9 branches were collapsed. + 8 branches were collapsed. ->>>Terminated Search rep 5 (of 5)<<< +>>>Terminated Search rep 3 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -19167,16 +18553,14 @@ ####################################################### -Completed 5 replicate search(es) (of 5). +Completed 3 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -477.4316 Replicate 2 : -477.2120 -Replicate 3 : -477.2119 (best) (same topology as 2) -Replicate 4 : -477.4315 (same topology as 1) -Replicate 5 : -477.6848 (TERMINATED PREMATURELY) +Replicate 3 : -477.2119 (best) (same topology as 2) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -19193,9 +18577,7 @@ TL R(1) R(2) R(3) rep 1: 4.928 0.632 1.916 2.734 rep 2: 4.672 0.642 1.910 2.621 -rep 3: 4.671 0.643 1.910 2.613 -rep 4: 4.929 0.632 1.913 2.743 -rep 5: 4.919 0.629 1.905 2.811 +rep 3: 4.671 0.642 1.910 2.614 Saving final tree from best search rep (#3) to ch.p.mkO.ssr.best.tre ####################################################### @@ -19422,7 +18804,7 @@ pass 13: -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 1 seconds +Time used so far = 0 hours, 0 minutes and 3 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -19508,6 +18890,137 @@ 3600 -425.5873 0.010 688 3700 -425.5869 0.010 688 3800 -425.5861 0.010 688 +NOTE: ****Specified time limit (5 seconds) reached... + +NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY +TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE +FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF +(set restart = 1 in the config file). IF YOU WANT TO USE THE +PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY +ADD "end;" TO THE TREE FILES. + +Running GARLI Version 2.1. () +->Single processor version for 64-bit OS<- +############################################################## + This is GARLI 2.1: maximum likelihood phylogenetic inference + using nucleotide, amino acid, codon and morphology-like data, + as well as partitioned models. + General program usage is extensively documented here: + http://www.nescent.org/wg/garli/ + See this page for details on partitioned model usage: + http://www.nescent.org/wg_garli/Using_partitioned_models + and this page for details on Mkv mophology model usage: + http://www.nescent.org/wg_garli/Mkv_morphology_model + PLEASE LET ME KNOW OF ANY PROBLEMS AT: + garli.support@gmail.com +############################################################## +Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0 +Using NCL version 2.1.17 + +####################################################### +Reading config file ./restart/p.mkv.ssr.conf +################################################### +READING OF DATA +Attempting to read data file in Nexus format (using NCL): + data/L2001.30x52.nex ... +Reading CHARACTERS block... +Warning: + Skipping command: OPTIONS +at line 23, column (approximately) 9 (file position 611) +storing implied block: TAXA +storing read block: CHARACTERS + found standard data... successful +Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS + successful + +################################################### +PARTITIONING OF DATA AND MODELS +GARLI data subset 1 + CHARACTERS block #1 ("Untitled CHARACTERS Block 1") + Data read as Standard k-state data, variable only, + modeled as Standard k-state data, variable only +NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. +Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 + + Subset of data with 2 states: + chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 + Summary of data: + 30 sequences. + 0 constant characters. + 39 parsimony-informative characters. + 0 uninformative variable characters. + 39 total characters. + 39 unique patterns in compressed data matrix. +NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. +Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 + + Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: + char 90 + Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: + char 90 + Subset of data with 3 states: + chars 54 61 62 64 71 72 83 90-102 \ 6 + Summary of data: + 30 sequences. + 0 constant characters. + 10 parsimony-informative characters. + 0 uninformative variable characters. + 10 total characters. + 10 unique patterns in compressed data matrix. +NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. +Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 + + Subset of data with 4 states: + chars 52 59 73 + Summary of data: + 30 sequences. + 0 constant characters. + 0 parsimony-informative characters. + 3 uninformative variable characters. + 3 total characters. + 3 unique patterns in compressed data matrix. +NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. +Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 + +NOTE: No characters found with 5 observed states. +NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. +Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 + +NOTE: No characters found with 6 observed states. + +################################################### +NOTE: Unlike many programs, the amount of system memory that Garli will +use can be controlled by the user. +(This comes from the availablememory setting in the configuration file. +Availablememory should NOT be set to more than the actual amount of +physical memory that your computer has installed) + +For this dataset: + Mem level availablememory setting + great >= 1 MB + good approx 0 MB to 1 MB + low approx 0 MB to 1 MB + very low approx 0 MB to 1 MB +the minimum required availablememory is 1 MB + +You specified that Garli should use at most 512.0 MB of memory. + +Garli will actually use approx. 0.6 MB of memory +**Your memory level is: great (you don't need to change anything)** + +####################################################### +Loading starting model and/or tree from file data/L.start +Reading TREES block...storing read block: TREES + successful +STARTING RUN + Subset 1: Random seed for bootstrap reweighting: 42 + Subset 2: Random seed for bootstrap reweighting: 1339106791 + Subset 3: Random seed for bootstrap reweighting: 974568031 + +Restarting from checkpoint... +Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 3834, seed 289721326, best lnL -425.586 +gen current_lnL precision last_tree_imp +3834 -425.5861 0.010 688 3900 -425.5859 0.010 688 4000 -425.5858 0.010 688 4100 -425.5857 0.010 688 @@ -19542,7 +19055,7 @@ pass 13: -425.5487 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.5487 -Time used so far = 0 hours, 0 minutes and 4 seconds +Time used so far = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -19652,7 +19165,7 @@ pass 13: -425.3200 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.3200 -Time used so far = 0 hours, 0 minutes and 5 seconds +Time used so far = 0 hours, 0 minutes and 11 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -19702,205 +19215,29 @@ gen current_lnL precision last_tree_imp 0 -439.2316 0.010 0 100 -433.6971 0.010 75 -NOTE: ****Specified time limit (5 seconds) reached... - -NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY -TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE -FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF -(set restart = 1 in the config file). IF YOU WANT TO USE THE -PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY -ADD "end;" TO THE TREE FILES. - -Running GARLI Version 2.1. () -->Single processor version for 64-bit OS<- -############################################################## - This is GARLI 2.1: maximum likelihood phylogenetic inference - using nucleotide, amino acid, codon and morphology-like data, - as well as partitioned models. - General program usage is extensively documented here: - http://www.nescent.org/wg/garli/ - See this page for details on partitioned model usage: - http://www.nescent.org/wg_garli/Using_partitioned_models - and this page for details on Mkv mophology model usage: - http://www.nescent.org/wg_garli/Mkv_morphology_model - PLEASE LET ME KNOW OF ANY PROBLEMS AT: - garli.support@gmail.com -############################################################## -Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0 -Using NCL version 2.1.17 - -####################################################### -Reading config file ./restart/p.mkv.ssr.conf -################################################### -READING OF DATA -Attempting to read data file in Nexus format (using NCL): - data/L2001.30x52.nex ... -Reading CHARACTERS block... -Warning: - Skipping command: OPTIONS -at line 23, column (approximately) 9 (file position 611) -storing implied block: TAXA -storing read block: CHARACTERS - found standard data... successful -Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS - successful - -################################################### -PARTITIONING OF DATA AND MODELS -GARLI data subset 1 - CHARACTERS block #1 ("Untitled CHARACTERS Block 1") - Data read as Standard k-state data, variable only, - modeled as Standard k-state data, variable only -NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. -Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 - - Subset of data with 2 states: - chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 - Summary of data: - 30 sequences. - 0 constant characters. - 39 parsimony-informative characters. - 0 uninformative variable characters. - 39 total characters. - 39 unique patterns in compressed data matrix. -NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. -Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 - - Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: - char 90 - Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: - char 90 - Subset of data with 3 states: - chars 54 61 62 64 71 72 83 90-102 \ 6 - Summary of data: - 30 sequences. - 0 constant characters. - 10 parsimony-informative characters. - 0 uninformative variable characters. - 10 total characters. - 10 unique patterns in compressed data matrix. -NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. -Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 - - Subset of data with 4 states: - chars 52 59 73 - Summary of data: - 30 sequences. - 0 constant characters. - 0 parsimony-informative characters. - 3 uninformative variable characters. - 3 total characters. - 3 unique patterns in compressed data matrix. -NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. -Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 - -NOTE: No characters found with 5 observed states. -NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. -Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 - -NOTE: No characters found with 6 observed states. - -################################################### -NOTE: Unlike many programs, the amount of system memory that Garli will -use can be controlled by the user. -(This comes from the availablememory setting in the configuration file. -Availablememory should NOT be set to more than the actual amount of -physical memory that your computer has installed) - -For this dataset: - Mem level availablememory setting - great >= 1 MB - good approx 0 MB to 1 MB - low approx 0 MB to 1 MB - very low approx 0 MB to 1 MB -the minimum required availablememory is 1 MB - -You specified that Garli should use at most 512.0 MB of memory. - -Garli will actually use approx. 0.6 MB of memory -**Your memory level is: great (you don't need to change anything)** - -####################################################### -Loading starting model and/or tree from file data/L.start -Reading TREES block...storing read block: TREES - successful -STARTING RUN - Subset 1: Random seed for bootstrap reweighting: 42 - Subset 2: Random seed for bootstrap reweighting: 1339106791 - Subset 3: Random seed for bootstrap reweighting: 974568031 - -Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 4 (of 5) generation 100, seed 1285025734, best lnL -433.697 -gen current_lnL precision last_tree_imp -100 -433.6971 0.010 75 200 -432.2075 0.010 188 300 -429.7506 0.010 212 -400 -427.9705 0.010 391 -500 -427.8319 0.010 409 -600 -425.6450 0.010 594 -700 -425.6393 0.010 594 -800 -425.6316 0.010 594 -900 -425.6267 0.010 594 -1000 -425.6213 0.010 594 -1100 -425.6180 0.010 594 -1200 -425.6150 0.010 594 -1300 -425.6135 0.010 594 -1400 -425.6117 0.010 594 -1500 -425.6100 0.010 594 -1600 -425.6084 0.010 594 -1700 -425.6069 0.010 594 -1800 -425.6062 0.010 594 -1900 -425.6059 0.010 594 -2000 -425.6052 0.010 594 -2100 -425.6037 0.010 594 -2200 -425.6024 0.010 594 -2300 -425.6018 0.010 594 -2400 -425.6018 0.010 594 -2500 -425.6013 0.010 594 -2600 -425.6001 0.010 594 -2700 -425.4320 0.010 2689 -2800 -425.4168 0.010 2689 -2900 -425.4131 0.010 2689 -3000 -425.4102 0.010 2689 -3100 -425.4087 0.010 2689 -3200 -425.4073 0.010 2689 -3300 -425.4065 0.010 2689 -3400 -425.4060 0.010 2689 -3500 -425.4059 0.010 2689 -3600 -425.4051 0.010 2689 -3700 -425.4050 0.010 2689 -3800 -425.4044 0.010 2689 -3900 -425.4042 0.010 2689 -4000 -425.4037 0.010 2689 -4100 -425.4031 0.010 2689 -4200 -425.4031 0.010 2689 -4300 -425.4029 0.010 2689 -4400 -425.4029 0.010 2689 -4500 -425.4027 0.010 2689 -Reached termination condition! -last topological improvement at gen 2689 -Improvement over last 500 gen = 0.00095 -Current score = -425.4027 +NOTE: ****Specified time limit (5 seconds) reached... +Current score = -429.7506 Performing final optimizations... -pass 1 : -425.3565 (branch= 0.0000 subset rates= 0.0462) -pass 2 : -425.3282 (branch= 0.0241 subset rates= 0.0042) -pass 3 : -425.3241 (branch= 0.0034 subset rates= 0.0007) -pass 4 : -425.3221 (branch= 0.0021 subset rates= 0.0000) -pass 5 : -425.3215 (branch= 0.0006 subset rates= 0.0000) -pass 6 : -425.3215 (branch= 0.0000 subset rates= 0.0000) -pass 7 : -425.3213 (branch= 0.0001 subset rates= 0.0000) -pass 8 : -425.3207 (branch= 0.0006 subset rates= 0.0000) -pass 9 : -425.3203 (branch= 0.0004 subset rates= 0.0000) -pass 10: -425.3202 (branch= 0.0001 subset rates= 0.0000) -pass 11: -425.3202 (branch= 0.0000 subset rates= 0.0000) -pass 12: -425.3202 (branch= 0.0000 subset rates= 0.0000) -pass 13: -425.3202 (branch= 0.0000 subset rates= 0.0000) -pass 14: -425.3202 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -429.1426 (branch= 0.0435 subset rates= 0.5644) +pass 2 : -428.9978 (branch= 0.1432 subset rates= 0.0017) +pass 3 : -428.9349 (branch= 0.0629 subset rates= 0.0000) +pass 4 : -428.9120 (branch= 0.0219 subset rates= 0.0010) +pass 5 : -428.9054 (branch= 0.0066 subset rates= 0.0000) +pass 6 : -428.9029 (branch= 0.0025 subset rates= 0.0000) +pass 7 : -428.9020 (branch= 0.0009 subset rates= 0.0000) +pass 8 : -428.9019 (branch= 0.0002 subset rates= 0.0000) +pass 9 : -428.9017 (branch= 0.0002 subset rates= 0.0000) +pass 10: -428.9016 (branch= 0.0001 subset rates= 0.0000) +pass 11: -428.9016 (branch= 0.0000 subset rates= 0.0000) +pass 12: -428.9016 (branch= 0.0000 subset rates= 0.0000) +pass 13: -428.9016 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -425.3202 -Time used so far = 0 hours, 0 minutes and 8 seconds +Final score = -428.9016 +Time used so far = 0 hours, 0 minutes and 12 seconds -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 2 (standard data) Character change matrix: @@ -19926,122 +19263,19 @@ no rate heterogeneity Subset rate multipliers: - 0.87 1.54 1.15 + 0.88 1.49 1.09 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 9 branches were collapsed. - ->>>Completed Bootstrap rep 1 (of 1) Search rep 4 (of 5)<<< - ->>>Bootstrap rep 1 (of 1) Search rep 5 (of 5)<<< -Obtained starting tree 1 from Nexus -Starting with seed=1829735943 - -Initial ln Likelihood: -577.6348 -optimizing: starting branch lengths, subset rates... -pass 1:+ 126.243 (branch= 125.45 scale= 0.66 subset rates= 0.13) -pass 2:+ 10.674 (branch= 10.61 scale= 0.00 subset rates= 0.06) -pass 3:+ 1.219 (branch= 1.20 scale= 0.00 subset rates= 0.02) -pass 4:+ 0.036 (branch= 0.04 scale= 0.00 subset rates= 0.00) -pass 5:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -439.4628 -gen current_lnL precision last_tree_imp -0 -439.4628 0.010 0 -100 -434.5867 0.010 95 -200 -428.9362 0.010 159 -300 -427.3221 0.010 246 -400 -426.3903 0.010 361 -500 -425.7484 0.010 480 -600 -425.6942 0.010 504 -700 -425.6413 0.010 643 -800 -425.6318 0.010 643 -900 -425.6262 0.010 643 -1000 -425.6152 0.010 643 -1100 -425.6071 0.010 643 -1200 -425.6045 0.010 643 -1300 -425.6027 0.010 643 -1400 -425.5977 0.010 643 -1500 -425.5957 0.010 643 -1600 -425.5949 0.010 643 -1700 -425.5923 0.010 643 -1800 -425.5913 0.010 643 -1900 -425.5877 0.010 643 -2000 -425.5869 0.010 643 -2100 -425.5868 0.010 643 -2200 -425.5863 0.010 643 -2300 -425.5857 0.010 643 -2400 -425.5855 0.010 643 -2500 -425.5849 0.010 643 -2600 -425.5837 0.010 643 -2700 -425.5834 0.010 643 -2800 -425.5830 0.010 643 -2900 -425.5826 0.010 643 -3000 -425.5824 0.010 643 -3100 -425.5823 0.010 643 -3200 -425.5816 0.010 643 -3300 -425.5813 0.010 643 -3400 -425.5807 0.010 643 -3500 -425.5806 0.010 643 -3600 -425.5806 0.010 643 -3700 -425.5799 0.010 643 -3800 -425.5799 0.010 643 -3900 -425.5798 0.010 643 -Reached termination condition! -last topological improvement at gen 643 -Improvement over last 500 gen = 0.00096 -Current score = -425.5798 -Performing final optimizations... -pass 1 : -425.5783 (branch= 0.0000 subset rates= 0.0015) -pass 2 : -425.5555 (branch= 0.0222 subset rates= 0.0005) -pass 3 : -425.5540 (branch= 0.0015 subset rates= 0.0000) -pass 4 : -425.5519 (branch= 0.0021 subset rates= 0.0000) -pass 5 : -425.5507 (branch= 0.0012 subset rates= 0.0000) -pass 6 : -425.5503 (branch= 0.0004 subset rates= 0.0000) -pass 7 : -425.5499 (branch= 0.0004 subset rates= 0.0000) -pass 8 : -425.5490 (branch= 0.0004 subset rates= 0.0005) -pass 9 : -425.5488 (branch= 0.0001 subset rates= 0.0000) -pass 10: -425.5487 (branch= 0.0001 subset rates= 0.0000) -pass 11: -425.5486 (branch= 0.0001 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) -Looking for minimum length branches... -Final score = -425.5486 -Time used = 0 hours, 0 minutes and 10 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (standard data) - Character change matrix: - One rate (symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity + 10 branches were collapsed. -Model 2 - Number of states = 3 (standard data) - Character change matrix: - One rate (symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity +>>>Terminated Bootstrap rep 1 (of 1) Search rep 4 (of 5)<<< -Model 3 - Number of states = 4 (standard data) - Character change matrix: - One rate (symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 0.87 1.53 1.12 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 9 branches were collapsed. +NOTE: ***Search was terminated before full auto-termination condition was reached! +Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ->>>Completed Bootstrap rep 1 (of 1) Search rep 5 (of 5)<<< ####################################################### -Completed 5 replicate search(es) (of 5). +Completed 4 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. @@ -20049,8 +19283,7 @@ Replicate 1 : -425.5486 Replicate 2 : -425.5487 (same topology as 1) Replicate 3 : -425.3200 (best) -Replicate 4 : -425.3202 (same topology as 3) -Replicate 5 : -425.5486 (same topology as 1) +Replicate 4 : -428.9016 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -20068,12 +19301,10 @@ rep 1: 3.038 0.869 1.527 1.123 rep 2: 3.034 0.867 1.533 1.126 rep 3: 2.977 0.864 1.542 1.148 -rep 4: 2.980 0.865 1.535 1.148 -rep 5: 3.038 0.868 1.529 1.120 +rep 4: 3.193 0.881 1.485 1.085 Saving tree from best search rep (#3) to bootstrap file ch.p.mkv.ssr.boot.tre ->>>Completed Bootstrap rep 1<<< ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkvO.ssr.conf @@ -20293,7 +19524,7 @@ pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -473.9508 -Time used so far = 0 hours, 0 minutes and 2 seconds +Time used so far = 0 hours, 0 minutes and 5 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -20376,263 +19607,6 @@ 400 -474.5533 0.010 345 500 -474.2022 0.010 476 600 -474.1845 0.010 476 -700 -474.1655 0.010 476 -800 -474.0667 0.010 780 -900 -474.0382 0.010 814 -1000 -474.0329 0.010 814 -1100 -474.0260 0.010 814 -1200 -474.0207 0.010 814 -1300 -474.0175 0.010 814 -1400 -474.0120 0.010 814 -1500 -474.0098 0.010 814 -1600 -474.0089 0.010 814 -1700 -474.0056 0.010 814 -1800 -474.0046 0.010 814 -1900 -474.0042 0.010 814 -2000 -474.0037 0.010 814 -2100 -474.0026 0.010 814 -2200 -474.0018 0.010 814 -2300 -474.0013 0.010 814 -2400 -474.0002 0.010 814 -2500 -473.9996 0.010 814 -2600 -473.9993 0.010 814 -2700 -473.9993 0.010 814 -2800 -473.9991 0.010 814 -2900 -473.9989 0.010 814 -3000 -473.9989 0.010 814 -Reached termination condition! -last topological improvement at gen 814 -Improvement over last 500 gen = 0.00071 -Current score = -473.9989 -Performing final optimizations... -pass 1 : -473.9858 (branch= 0.0079 subset rates= 0.0052) -pass 2 : -473.9634 (branch= 0.0160 subset rates= 0.0064) -pass 3 : -473.9573 (branch= 0.0048 subset rates= 0.0013) -pass 4 : -473.9546 (branch= 0.0026 subset rates= 0.0000) -pass 5 : -473.9540 (branch= 0.0007 subset rates= 0.0000) -pass 6 : -473.9522 (branch= 0.0015 subset rates= 0.0002) -pass 7 : -473.9516 (branch= 0.0006 subset rates= 0.0000) -pass 8 : -473.9511 (branch= 0.0005 subset rates= 0.0000) -pass 9 : -473.9509 (branch= 0.0001 subset rates= 0.0000) -pass 10: -473.9509 (branch= 0.0001 subset rates= 0.0000) -pass 11: -473.9508 (branch= 0.0000 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) -Looking for minimum length branches... -Final score = -473.9508 -Time used so far = 0 hours, 0 minutes and 4 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 0.59 2.07 2.81 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. - ->>>Completed Search rep 2 (of 5)<<< - ->>>Search rep 3 (of 5)<<< -Obtained starting tree 1 from Nexus -MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 1.00 1.00 1.00 -Starting with seed=286368817 - -Initial ln Likelihood: -652.0823 -optimizing: starting branch lengths, subset rates... -pass 1:+ 160.614 (branch= 149.48 scale= 0.59 subset rates= 10.55) -pass 2:+ 10.707 (branch= 5.57 scale= 0.00 subset rates= 5.13) -pass 3:+ 4.869 (branch= 2.96 scale= 0.01 subset rates= 1.89) -pass 4:+ 0.896 (branch= 0.26 scale= 0.00 subset rates= 0.64) -pass 5:+ 0.115 (branch= 0.06 scale= 0.01 subset rates= 0.04) -pass 6:+ 0.020 (branch= 0.02 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.021 (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: -474.8398 -gen current_lnL precision last_tree_imp -0 -474.8398 0.010 0 -100 -474.7989 0.010 0 -200 -474.7681 0.010 0 -300 -474.6839 0.010 284 -400 -474.6659 0.010 284 -500 -474.6475 0.010 404 -600 -474.0464 0.010 593 -700 -474.0349 0.010 593 -800 -474.0230 0.010 593 -900 -474.0209 0.010 593 -1000 -474.0130 0.010 593 -1100 -474.0064 0.010 593 -1200 -474.0053 0.010 593 -1300 -474.0035 0.010 593 -1400 -473.9981 0.010 593 -1500 -473.9951 0.010 593 -1600 -473.9932 0.010 593 -1700 -473.9920 0.010 593 -1800 -473.9911 0.010 593 -1900 -473.9904 0.010 593 -2000 -473.9903 0.010 593 -2100 -473.9901 0.010 593 -2200 -473.9891 0.010 593 -2300 -473.9850 0.010 593 -2400 -473.9843 0.010 593 -2500 -473.9843 0.010 593 -2600 -473.9840 0.010 593 -2700 -473.9838 0.010 593 -2800 -473.9838 0.010 593 -2900 -473.9835 0.010 593 -Reached termination condition! -last topological improvement at gen 593 -Improvement over last 500 gen = 0.00081 -Current score = -473.9835 -Performing final optimizations... -pass 1 : -473.9820 (branch= 0.0000 subset rates= 0.0015) -pass 2 : -473.9648 (branch= 0.0172 subset rates= 0.0000) -pass 3 : -473.9599 (branch= 0.0038 subset rates= 0.0010) -pass 4 : -473.9559 (branch= 0.0015 subset rates= 0.0025) -pass 5 : -473.9533 (branch= 0.0026 subset rates= 0.0000) -pass 6 : -473.9522 (branch= 0.0012 subset rates= 0.0000) -pass 7 : -473.9513 (branch= 0.0009 subset rates= 0.0000) -pass 8 : -473.9509 (branch= 0.0004 subset rates= 0.0000) -pass 9 : -473.9509 (branch= 0.0001 subset rates= 0.0000) -pass 10: -473.9508 (branch= 0.0001 subset rates= 0.0000) -pass 11: -473.9508 (branch= 0.0000 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: -473.9507 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -473.9507 -Time used so far = 0 hours, 0 minutes and 5 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 0.59 2.07 2.81 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. - ->>>Completed Search rep 3 (of 5)<<< - ->>>Search rep 4 (of 5)<<< -Obtained starting tree 1 from Nexus -MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 1.00 1.00 1.00 -Starting with seed=274781070 - -Initial ln Likelihood: -666.9404 -optimizing: starting branch lengths, subset rates... -pass 1:+ 166.009 (branch= 155.23 scale= 0.87 subset rates= 9.91) -pass 2:+ 16.814 (branch= 12.53 scale= 0.00 subset rates= 4.29) -pass 3:+ 7.072 (branch= 5.49 scale= 0.00 subset rates= 1.58) -pass 4:+ 1.900 (branch= 1.29 scale= 0.01 subset rates= 0.59) -pass 5:+ 0.210 (branch= 0.19 scale= 0.00 subset rates= 0.02) -pass 6:+ 0.043 (branch= 0.03 scale= 0.01 subset rates= 0.00) -pass 7:+ 0.018 (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: -474.8745 -gen current_lnL precision last_tree_imp -0 -474.8745 0.010 0 -100 -474.8391 0.010 0 -200 -474.7434 0.010 147 -300 -474.0572 0.010 266 -400 -474.0437 0.010 266 -500 -474.0285 0.010 266 -600 -474.0173 0.010 266 -700 -474.0063 0.010 266 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -20758,59 +19732,54 @@ STARTING RUN Restarting from checkpoint... -Search rep 4 (of 5) generation 790, seed 813837298, best lnL -474.005 +Search rep 2 (of 5) generation 602, seed 147732682, best lnL -474.184 gen current_lnL precision last_tree_imp -790 -474.0054 0.010 266 -800 -474.0054 0.010 266 -900 -473.9993 0.010 266 -1000 -473.9988 0.010 266 -1100 -473.9969 0.010 266 -1200 -473.9909 0.010 266 -1300 -473.9881 0.010 266 -1400 -473.9872 0.010 266 -1500 -473.9862 0.010 266 -1600 -473.9856 0.010 266 -1700 -473.9840 0.010 266 -1800 -473.9822 0.010 266 -1900 -473.9820 0.010 266 -2000 -473.9817 0.010 266 -2100 -473.9798 0.010 266 -2200 -473.9789 0.010 266 -2300 -473.9787 0.010 266 -2400 -473.9780 0.010 266 -2500 -473.9778 0.010 266 -2600 -473.9775 0.010 266 -2700 -473.9772 0.010 266 -2800 -473.9769 0.010 266 -2900 -473.9764 0.010 266 -3000 -473.9762 0.010 266 -3100 -473.9755 0.010 266 -3200 -473.9752 0.010 266 -3300 -473.9752 0.010 266 -3400 -473.9749 0.010 266 -3500 -473.9749 0.010 266 -3600 -473.9748 0.010 266 +602 -474.1845 0.010 476 +700 -474.1655 0.010 476 +800 -474.0667 0.010 780 +900 -474.0382 0.010 814 +1000 -474.0329 0.010 814 +1100 -474.0260 0.010 814 +1200 -474.0207 0.010 814 +1300 -474.0175 0.010 814 +1400 -474.0120 0.010 814 +1500 -474.0098 0.010 814 +1600 -474.0089 0.010 814 +1700 -474.0056 0.010 814 +1800 -474.0046 0.010 814 +1900 -474.0042 0.010 814 +2000 -474.0037 0.010 814 +2100 -474.0026 0.010 814 +2200 -474.0018 0.010 814 +2300 -474.0013 0.010 814 +2400 -474.0002 0.010 814 +2500 -473.9996 0.010 814 +2600 -473.9993 0.010 814 +2700 -473.9993 0.010 814 +2800 -473.9991 0.010 814 +2900 -473.9989 0.010 814 +3000 -473.9989 0.010 814 Reached termination condition! -last topological improvement at gen 266 -Improvement over last 500 gen = 0.00077 -Current score = -473.9748 +last topological improvement at gen 814 +Improvement over last 500 gen = 0.00071 +Current score = -473.9989 Performing final optimizations... -pass 1 : -473.9721 (branch= 0.0000 subset rates= 0.0026) -pass 2 : -473.9598 (branch= 0.0092 subset rates= 0.0031) -pass 3 : -473.9553 (branch= 0.0045 subset rates= 0.0000) -pass 4 : -473.9538 (branch= 0.0014 subset rates= 0.0000) -pass 5 : -473.9514 (branch= 0.0008 subset rates= 0.0016) -pass 6 : -473.9503 (branch= 0.0011 subset rates= 0.0000) -pass 7 : -473.9494 (branch= 0.0009 subset rates= 0.0000) -pass 8 : -473.9486 (branch= 0.0008 subset rates= 0.0000) -pass 9 : -473.9484 (branch= 0.0002 subset rates= 0.0000) -pass 10: -473.9484 (branch= 0.0000 subset rates= 0.0000) -pass 11: -473.9483 (branch= 0.0001 subset rates= 0.0000) -pass 12: -473.9483 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9483 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -473.9858 (branch= 0.0079 subset rates= 0.0052) +pass 2 : -473.9634 (branch= 0.0160 subset rates= 0.0064) +pass 3 : -473.9573 (branch= 0.0048 subset rates= 0.0013) +pass 4 : -473.9546 (branch= 0.0026 subset rates= 0.0000) +pass 5 : -473.9540 (branch= 0.0007 subset rates= 0.0000) +pass 6 : -473.9522 (branch= 0.0015 subset rates= 0.0002) +pass 7 : -473.9516 (branch= 0.0006 subset rates= 0.0000) +pass 8 : -473.9511 (branch= 0.0005 subset rates= 0.0000) +pass 9 : -473.9509 (branch= 0.0001 subset rates= 0.0000) +pass 10: -473.9509 (branch= 0.0001 subset rates= 0.0000) +pass 11: -473.9508 (branch= 0.0000 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) Looking for minimum length branches... -Final score = -473.9483 -Time used so far = 0 hours, 0 minutes and 7 seconds +Final score = -473.9508 +Time used so far = 0 hours, 0 minutes and 8 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -20840,11 +19809,11 @@ Subset rate multipliers: 0.59 2.07 2.81 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. + 8 branches were collapsed. ->>>Completed Search rep 4 (of 5)<<< +>>>Completed Search rep 2 (of 5)<<< ->>>Search rep 5 (of 5)<<< +>>>Search rep 3 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 @@ -20873,83 +19842,64 @@ Subset rate multipliers: 1.00 1.00 1.00 -Starting with seed=1552091353 +Starting with seed=286368817 -Initial ln Likelihood: -640.2108 +Initial ln Likelihood: -652.0823 optimizing: starting branch lengths, subset rates... -pass 1:+ 143.282 (branch= 132.71 scale= 0.78 subset rates= 9.79) -pass 2:+ 14.819 (branch= 10.30 scale= 0.00 subset rates= 4.52) -pass 3:+ 5.712 (branch= 4.15 scale= 0.00 subset rates= 1.57) -pass 4:+ 1.307 (branch= 0.70 scale= 0.02 subset rates= 0.59) -pass 5:+ 0.205 (branch= 0.18 scale= 0.00 subset rates= 0.03) -pass 6:+ 0.047 (branch= 0.05 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8383 +pass 1:+ 160.614 (branch= 149.48 scale= 0.59 subset rates= 10.55) +pass 2:+ 10.707 (branch= 5.57 scale= 0.00 subset rates= 5.13) +pass 3:+ 4.869 (branch= 2.96 scale= 0.01 subset rates= 1.89) +pass 4:+ 0.896 (branch= 0.26 scale= 0.00 subset rates= 0.64) +pass 5:+ 0.115 (branch= 0.06 scale= 0.01 subset rates= 0.04) +pass 6:+ 0.020 (branch= 0.02 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.021 (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: -474.8398 gen current_lnL precision last_tree_imp -0 -474.8383 0.010 0 -100 -474.7519 0.010 5 -200 -474.7172 0.010 184 -300 -474.2068 0.010 275 -400 -474.1952 0.010 275 -500 -474.0201 0.010 424 -600 -474.0106 0.010 424 -700 -474.0076 0.010 424 -800 -474.0052 0.010 424 -900 -474.0030 0.010 424 -1000 -474.0024 0.010 424 -1100 -473.9996 0.010 424 -1200 -473.9991 0.010 424 -1300 -473.9971 0.010 424 -1400 -473.9955 0.010 424 -1500 -473.9947 0.010 424 -1600 -473.9946 0.010 424 -1700 -473.9939 0.010 424 -1800 -473.9929 0.010 424 -1900 -473.9923 0.010 424 -2000 -473.9911 0.010 424 -2100 -473.9904 0.010 424 -2200 -473.9901 0.010 424 -2300 -473.9893 0.010 424 -2400 -473.9887 0.010 424 -2500 -473.9880 0.010 424 -2600 -473.9861 0.010 424 -2700 -473.9846 0.010 424 -2800 -473.9845 0.010 424 -2900 -473.9841 0.010 424 -3000 -473.9835 0.010 424 -3100 -473.9830 0.010 424 -3200 -473.9825 0.010 424 -3300 -473.9823 0.010 424 -3400 -473.9820 0.010 424 -3500 -473.9818 0.010 424 -3600 -473.9812 0.010 424 -3700 -473.9810 0.010 424 -3800 -473.9810 0.010 424 -3900 -473.9806 0.010 424 -4000 -473.9806 0.010 424 -4100 -473.9802 0.010 424 -Reached termination condition! -last topological improvement at gen 424 -Improvement over last 500 gen = 0.00100 -Current score = -473.9802 +0 -474.8398 0.010 0 +100 -474.7989 0.010 0 +200 -474.7681 0.010 0 +300 -474.6839 0.010 284 +400 -474.6659 0.010 284 +500 -474.6475 0.010 404 +600 -474.0464 0.010 593 +700 -474.0349 0.010 593 +800 -474.0230 0.010 593 +900 -474.0209 0.010 593 +1000 -474.0130 0.010 593 +1100 -474.0064 0.010 593 +1200 -474.0053 0.010 593 +1300 -474.0035 0.010 593 +1400 -473.9981 0.010 593 +1500 -473.9951 0.010 593 +1600 -473.9932 0.010 593 +1700 -473.9920 0.010 593 +1800 -473.9911 0.010 593 +1900 -473.9904 0.010 593 +2000 -473.9903 0.010 593 +2100 -473.9901 0.010 593 +2200 -473.9891 0.010 593 +NOTE: ****Specified time limit (5 seconds) reached... +Current score = -473.9886 Performing final optimizations... -pass 1 : -473.9756 (branch= 0.0000 subset rates= 0.0047) -pass 2 : -473.9579 (branch= 0.0177 subset rates= 0.0000) -pass 3 : -473.9554 (branch= 0.0025 subset rates= 0.0000) -pass 4 : -473.9538 (branch= 0.0016 subset rates= 0.0000) -pass 5 : -473.9531 (branch= 0.0008 subset rates= 0.0000) -pass 6 : -473.9524 (branch= 0.0007 subset rates= 0.0000) -pass 7 : -473.9517 (branch= 0.0007 subset rates= 0.0000) -pass 8 : -473.9515 (branch= 0.0002 subset rates= 0.0000) -pass 9 : -473.9511 (branch= 0.0003 subset rates= 0.0000) -pass 10: -473.9511 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -473.9871 (branch= 0.0000 subset rates= 0.0015) +pass 2 : -473.9630 (branch= 0.0216 subset rates= 0.0026) +pass 3 : -473.9578 (branch= 0.0051 subset rates= 0.0000) +pass 4 : -473.9559 (branch= 0.0019 subset rates= 0.0000) +pass 5 : -473.9536 (branch= 0.0023 subset rates= 0.0000) +pass 6 : -473.9526 (branch= 0.0010 subset rates= 0.0000) +pass 7 : -473.9517 (branch= 0.0009 subset rates= 0.0000) +pass 8 : -473.9514 (branch= 0.0002 subset rates= 0.0000) +pass 9 : -473.9513 (branch= 0.0002 subset rates= 0.0000) +pass 10: -473.9512 (branch= 0.0001 subset rates= 0.0000) pass 11: -473.9511 (branch= 0.0000 subset rates= 0.0000) -pass 12: -473.9511 (branch= 0.0000 subset rates= 0.0000) +pass 12: -473.9510 (branch= 0.0001 subset rates= 0.0001) +pass 13: -473.9510 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -473.9511 -Time used = 0 hours, 0 minutes and 9 seconds +Final score = -473.9510 +Time used so far = 0 hours, 0 minutes and 12 seconds -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 2 (ordered standard data) Character change matrix: @@ -20975,24 +19925,26 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.07 2.80 + 0.59 2.06 2.81 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. ->>>Completed Search rep 5 (of 5)<<< +>>>Terminated Search rep 3 (of 5)<<< + +NOTE: ***Search was terminated before full auto-termination condition was reached! +Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** + ####################################################### -Completed 5 replicate search(es) (of 5). +Completed 3 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -473.9508 -Replicate 2 : -473.9508 (same topology as 1) -Replicate 3 : -473.9507 (same topology as 1) -Replicate 4 : -473.9483 (best) -Replicate 5 : -473.9511 (same topology as 1) +Replicate 2 : -473.9508 (best) (same topology as 1) +Replicate 3 : -473.9510 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -21009,13 +19961,9 @@ TL R(1) R(2) R(3) rep 1: 4.349 0.589 2.064 2.800 rep 2: 4.350 0.587 2.069 2.805 -rep 3: 4.350 0.588 2.067 2.805 -rep 4: 4.349 0.587 2.066 2.811 -rep 5: 4.351 0.587 2.073 2.798 - -Saving final trees from all search reps to ch.p.mkvO.ssr.best.all.tre +rep 3: 4.347 0.589 2.060 2.806 -Saving final tree from best search rep (#4) to ch.p.mkvO.ssr.best.tre +Saving final tree from best search rep (#2) to ch.p.mkvO.ssr.best.tre ####################################################### TREEFILES PASS ALL TESTS COMPLETED SUCCESSFULLY @@ -21089,10 +20037,10 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'garli' in '../garli_2.1-9_arm64.deb'. -dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-9_arm64.deb'. dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-9_arm64.deb'. -dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-9_arm64.deb'. dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-9_all.deb'. +dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-9_arm64.deb'. +dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-9_arm64.deb'. dpkg-genbuildinfo --build=binary -O../garli_2.1-9_arm64.buildinfo dpkg-genchanges --build=binary -O../garli_2.1-9_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -21100,12 +20048,14 @@ 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/3724210/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3724210/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/1388763 and its subdirectories -I: Current time: Wed Feb 11 23:50:59 -12 2026 -I: pbuilder-time-stamp: 1770897059 +I: removing directory /srv/workspace/pbuilder/3724210 and its subdirectories +I: Current time: Fri Jan 10 19:43:08 +14 2025 +I: pbuilder-time-stamp: 1736487788