Diff of the two buildlogs: -- --- b1/build.log 2024-12-21 11:31:06.875731421 +0000 +++ b2/build.log 2024-12-21 11:36:55.723770446 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Jan 23 05:48:45 -12 2026 -I: pbuilder-time-stamp: 1769190525 +I: Current time: Sun Dec 22 01:31:09 +14 2024 +I: pbuilder-time-stamp: 1734780669 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -26,51 +26,83 @@ 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/768998/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1743073/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 21 11:31 /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/1743073/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1743073/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='29b6f59989714d878037c9a3c9a1e30c' - 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='768998' - PS1='# ' - PS2='> ' + INVOCATION_ID=8a44858ad3d34759a9109fd8e30f3cb1 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1743073 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.z0eIE6Jx/pbuilderrc_OCLc --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.z0eIE6Jx/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' + 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.z0eIE6Jx/pbuilderrc_HsEk --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.z0eIE6Jx/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' I: uname -a - Linux infom02-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/768998/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1743073/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -269,7 +301,7 @@ Get: 153 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 5.0.6-3 [1088 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.17 [3148 B] Get: 155 http://deb.debian.org/debian unstable/main amd64 ncl-tools amd64 2.1.21+git20210811.b1213a7-6 [190 kB] -Fetched 126 MB in 2s (63.2 MB/s) +Fetched 126 MB in 1s (88.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19967 files and directories currently installed.) @@ -780,8 +812,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Jan 23 17:49:57 UTC 2026. -Universal Time is now: Fri Jan 23 17:49:57 UTC 2026. +Local time is now: Sat Dec 21 11:32:09 UTC 2024. +Universal Time is now: Sat Dec 21 11:32:09 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -933,7 +965,11 @@ 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/1743073/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1743073/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 @@ -1035,8 +1071,8 @@ 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 @@ -1123,16 +1159,16 @@ 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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, @@ -1219,7 +1255,8 @@ In file included from tree.h:35, from individual.h:21, from population.h:31, - from garlimain.cpp:40: + 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{ | ^~~~~~~~~~~~~~~ @@ -1229,7 +1266,7 @@ 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 | ^~~~~~~~~~~~~~~ @@ -1271,7 +1308,7 @@ from individual.h:21, from population.h:31, from funcs.h:25, - from funcs.cpp:30: + from adaptation.cpp:25: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -1281,7 +1318,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from population.h:23: + from adaptation.cpp:18: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1319,24 +1356,20 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from garlimain.cpp:46: -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/iomanip:42, - from individual.cpp:21: + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1367,10 +1400,6 @@ /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 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; @@ -1378,11 +1407,19 @@ /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{ | ^~~~~~~~~~~~~~~ @@ -1392,7 +1429,7 @@ 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 | ^~~~~~~~~~~~~~~ @@ -1427,22 +1464,27 @@ 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; | ~~~~~~~^~~~~~~~~~~~~~~~~~ +In file included from garlimain.cpp:46: +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from model.cpp:17: + 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 | ^~~~~~~~~~~~~~~ @@ -1486,9 +1528,7 @@ | ^ In file included from tree.h:35, from individual.h:21, - from population.h:31, - from funcs.h:25, - from configreader.cpp:30: + from model.cpp:26: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -1498,7 +1538,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from configreader.cpp:21: + from model.cpp:17: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1514,10 +1554,6 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); @@ -1533,7 +1569,6 @@ /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 -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; @@ -1549,7 +1584,7 @@ datamatr.cpp:1390:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1390 | fscanf(inf, "%d %d", &num_taxa, &num_chars); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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); @@ -1611,6 +1646,13 @@ adaptation.cpp:305:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 305 | fread((char *) anyModelnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)': +configreader.cpp:602:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 602 | fread(&ch, sizeof(char), 1, file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +configreader.cpp:605:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(&ch, sizeof(char), 1, file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); @@ -1646,13 +1688,6 @@ model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)': -configreader.cpp:602:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 602 | fread(&ch, sizeof(char), 1, file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -configreader.cpp:605:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(&ch, sizeof(char), 1, file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from tree.h:35, from optimization.cpp:19: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -1703,6 +1738,7 @@ funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;idlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h: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: +population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': +population.cpp:3066:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] + 3066 | sprintf(oStr, "R(%d)", d + 1); + | ^~ +population.cpp:3066:47: note: directive argument in the range [1, 2147483647] + 3066 | sprintf(oStr, "R(%d)", d + 1); + | ^~~~~~~ In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -2223,22 +2275,6 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': -population.cpp:3066:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] - 3066 | sprintf(oStr, "R(%d)", d + 1); - | ^~ -population.cpp:3066:47: note: directive argument in the range [1, 2147483647] - 3066 | sprintf(oStr, "R(%d)", d + 1); - | ^~~~~~~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -2303,6 +2339,7 @@ make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/garli-2.1/tests' make[4]: Entering directory '/build/reproducible-path/garli-2.1' +make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/reproducible-path/garli-2.1' make[3]: Leaving directory '/build/reproducible-path/garli-2.1' make[2]: Leaving directory '/build/reproducible-path/garli-2.1' @@ -2370,8 +2407,8 @@ 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 @@ -2548,11 +2585,11 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, - from garlimain.cpp:40: + from funcs.h:25, + from adaptation.cpp:25: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2562,7 +2599,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from population.h:23: + from adaptation.cpp:18: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2600,7 +2637,6 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from garlimain.cpp:46: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; + | ~~~~~~~^~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from model.cpp:17: + 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 | ^~~~~~~~~~~~~~~ @@ -2678,13 +2726,6 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': -reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; - | ~~~~~~~^~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); @@ -2707,19 +2748,25 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/iomanip:42, - from individual.cpp:21: + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2760,8 +2807,7 @@ In file included from tree.h:35, from individual.h:21, from population.h:31, - from funcs.h:25, - from adaptation.cpp:25: + from garlimain.cpp:40: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2771,7 +2817,7 @@ 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 | ^~~~~~~~~~~~~~~ @@ -2813,19 +2859,14 @@ 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{ | ^~~~~~~~~~~~~~~ @@ -2835,7 +2876,7 @@ 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 | ^~~~~~~~~~~~~~~ @@ -2873,16 +2914,7 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -3031,7 +3068,6 @@ /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 -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp In file included from optimization.cpp:21: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -3089,6 +3125,7 @@ funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i>>Completed Search rep 1 (of 2)<<< + +>>>Search rep 2 (of 2)<<< +Obtained starting tree 1 from Nexus +MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) +Model 1 + Number of states = 4 (nucleotide data) + Nucleotide Relative Rate Matrix: 6 rates + AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 + Equilibrium State Frequencies: estimated + (ACGT) 0.3220 0.2180 0.1602 0.2999 + Rate Heterogeneity Model: + 4 discrete gamma distributed rate categories, alpha param estimated + 0.5000 + with an invariant (invariable) site category, proportion estimated + 0.1629 + Substitution rate categories under this model: + rate proportion + 0.0000 0.1629 + 0.0334 0.2093 + 0.2519 0.2093 + 0.8203 0.2093 + 2.8944 0.2093 + +Model 2 + Number of states = 2 (binary data) + Character change matrix: + Binary, no all-zero columns (2-state symmetric one rate model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 1.00 1.00 +Starting with seed=324912533 + +Initial ln Likelihood: -3809.7967 +optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates... +pass 1:+ 333.583 (branch= 249.59 scale= 0.00 alpha= 13.92 freqs= 3.34 rel rates= 7.80 pinv= 0.01 subset rates= 58.92) +pass 2:+ 52.967 (branch= 8.19 scale= 0.00 alpha= 0.01 freqs= 0.69 rel rates= 0.01 pinv= 0.00 subset rates= 44.05) +pass 3:+ 30.628 (branch= 0.62 scale= 0.00 alpha= 2.05 freqs= 0.04 rel rates= 0.67 pinv= 0.00 subset rates= 27.24) +pass 4:+ 22.076 (branch= 8.01 scale= 2.17 alpha= 2.52 freqs= 0.05 rel rates= 0.68 pinv= 0.01 subset rates= 8.64) +pass 5:+ 9.556 (branch= 4.13 scale= 2.16 alpha= 0.72 freqs= 0.06 rel rates= 1.07 pinv= 0.00 subset rates= 1.42) +pass 6:+ 2.556 (branch= 0.60 scale= 1.88 alpha= 0.00 freqs= 0.06 rel rates= 0.00 pinv= 0.00 subset rates= 0.00) +pass 7:+ 0.066 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.06 rel rates= 0.00 pinv= 0.00 subset rates= 0.00) +lnL after optimization: -3358.3643 +gen current_lnL precision last_tree_imp +0 -3358.3643 0.500 0 +100 -3357.8111 0.500 0 +200 -3357.6450 0.500 0 +300 -3357.2610 0.500 0 +400 -3357.0686 0.500 0 +500 -3356.5064 0.500 0 +Optimization precision reduced + Optimizing parameters... improved 0.883 lnL + Optimizing branchlengths... improved 0.000 lnL +600 -3355.0889 0.255 0 +700 -3354.6659 0.255 0 +800 -3354.4474 0.255 0 +900 -3354.4277 0.255 0 +1000 -3354.1592 0.255 0 +Optimization precision reduced + Optimizing parameters... improved 0.780 lnL + Optimizing branchlengths... improved 0.155 lnL +NOTE: ****Specified time limit (5 seconds) reached... +Current score = -3353.1873 +Performing final optimizations... +pass 1 : -3352.5964 (branch= 0.0325 alpha= 0.0000 pinv= 0.0406 eq freqs= 0.0213 rel rates= 0.4383 subset rates= 0.0582) +pass 2 : -3352.1806 (branch= 0.0506 alpha= 0.0120 pinv= 0.0167 eq freqs= 0.0124 rel rates= 0.3129 subset rates= 0.0112) +pass 3 : -3351.8525 (branch= 0.0348 alpha= 0.0108 pinv= 0.0160 eq freqs= 0.0031 rel rates= 0.2544 subset rates= 0.0090) +pass 4 : -3351.5937 (branch= 0.0210 alpha= 0.0104 pinv= 0.0152 eq freqs= 0.0011 rel rates= 0.2049 subset rates= 0.0062) +pass 5 : -3351.3799 (branch= 0.0170 alpha= 0.0098 pinv= 0.0144 eq freqs= 0.0010 rel rates= 0.1673 subset rates= 0.0042) +pass 6 : -3351.1985 (branch= 0.0077 alpha= 0.0100 pinv= 0.0134 eq freqs= 0.0006 rel rates= 0.1466 subset rates= 0.0031) +pass 7 : -3351.0497 (branch= 0.0055 alpha= 0.0103 pinv= 0.0124 eq freqs= 0.0003 rel rates= 0.1176 subset rates= 0.0026) +pass 8 : -3350.9244 (branch= 0.0047 alpha= 0.0097 pinv= 0.0114 eq freqs= 0.0003 rel rates= 0.0976 subset rates= 0.0015) +pass 9 : -3350.8207 (branch= 0.0028 alpha= 0.0095 pinv= 0.0104 eq freqs= 0.0003 rel rates= 0.0808 subset rates= 0.0000) +pass 10: -3350.7299 (branch= 0.0006 alpha= 0.0094 pinv= 0.0101 eq freqs= 0.0002 rel rates= 0.0688 subset rates= 0.0017) +pass 11: -3350.6581 (branch= 0.0012 alpha= 0.0087 pinv= 0.0085 eq freqs= 0.0002 rel rates= 0.0531 subset rates= 0.0000) +pass 12: -3350.5960 (branch= 0.0003 alpha= 0.0079 pinv= 0.0077 eq freqs= 0.0001 rel rates= 0.0450 subset rates= 0.0011) +pass 13: -3350.5448 (branch= 0.0008 alpha= 0.0071 pinv= 0.0070 eq freqs= 0.0001 rel rates= 0.0362 subset rates= 0.0000) +pass 14: -3350.5010 (branch= 0.0002 alpha= 0.0064 pinv= 0.0063 eq freqs= 0.0001 rel rates= 0.0308 subset rates= 0.0000) +pass 15: -3350.4637 (branch= 0.0000 alpha= 0.0061 pinv= 0.0056 eq freqs= 0.0001 rel rates= 0.0255 subset rates= 0.0000) +pass 16: -3350.4318 (branch= 0.0000 alpha= 0.0056 pinv= 0.0050 eq freqs= 0.0001 rel rates= 0.0213 subset rates= 0.0000) +pass 17: -3350.4043 (branch= 0.0000 alpha= 0.0049 pinv= 0.0044 eq freqs= 0.0001 rel rates= 0.0181 subset rates= 0.0000) +pass 18: -3350.3808 (branch= 0.0000 alpha= 0.0044 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0152 subset rates= 0.0000) +pass 19: -3350.3605 (branch= 0.0000 alpha= 0.0038 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0129 subset rates= 0.0000) +pass 20: -3350.3431 (branch= 0.0000 alpha= 0.0034 pinv= 0.0031 eq freqs= 0.0000 rel rates= 0.0110 subset rates= 0.0000) + optimization up to ... +pass 30: -3350.2585 (branch= 0.0000 alpha= 0.0172 pinv= 0.0157 eq freqs= 0.0001 rel rates= 0.0516 subset rates= 0.0000) + optimization up to ... +pass 40: -3350.2393 (branch= 0.0000 alpha= 0.0038 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0119 subset rates= 0.0000) + optimization up to ... +pass 50: -3350.2349 (branch= 0.0000 alpha= 0.0007 pinv= 0.0007 eq freqs= 0.0000 rel rates= 0.0030 subset rates= 0.0000) + optimization up to ... +pass 60: -3350.2339 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0008 subset rates= 0.0000) + optimization up to ... +pass 70: -3350.2336 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) + optimization up to ... +pass 72: -3350.2336 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -3350.2336 +Time used = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.149, AG = 10.532, AT = 2.723, CG = 0.001, CT = 22.192, GT = 1.000 + AC = 3.107, AG = 10.388, AT = 2.683, CG = 0.001, CT = 21.829, 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 - 0.5744 + 0.5793 with an invariant (invariable) site category, proportion estimated - 0.3646 + 0.3662 Substitution rate categories under this model: rate proportion - 0.0000 0.3646 - 0.0479 0.1588 - 0.2977 0.1588 - 0.8677 0.1588 - 2.7867 0.1588 + 0.0000 0.3662 + 0.0489 0.1584 + 0.3006 0.1584 + 0.8704 0.1584 + 2.7802 0.1584 Model 2 Number of states = 2 (binary data) @@ -15115,7 +15317,7 @@ NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. ->>>Terminated Search rep 1 (of 2)<<< +>>>Terminated Search rep 2 (of 2)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -15123,22 +15325,28 @@ ####################################################### -Completed 1 replicate search(es) (of 2). +Completed 2 replicate search(es) (of 2). + +NOTE: Unless the following output indicates that search replicates found the + same topology, you should assume that they found different topologies. Results: -Replicate 1 : -3350.2330 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3350.2330 (best) +Replicate 2 : -3350.2336 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.149 10.53 2.723 0.001 22.19 1 0.333 0.222 0.157 0.288 0.574 0.365 +rep 1: 3.149 10.54 2.724 0.001 22.21 1 0.333 0.222 0.157 0.288 0.574 0.365 +rep 2: 3.107 10.39 2.683 0.001 21.83 1 0.333 0.222 0.157 0.288 0.579 0.366 Partition model subset 2: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) -rep 1: 0.790 1.821 0.179 +rep 1: 0.791 1.821 0.179 +rep 2: 0.787 1.820 0.180 Saving final tree from best search rep (#1) to ch.g.dnaBnoZ.best.tre ####################################################### @@ -15308,6 +15516,7 @@ 1600 -3320.0183 0.010 1 1700 -3320.0152 0.010 1 1800 -3319.8191 0.010 1 +1900 -3319.6008 0.010 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15408,10 +15617,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 1816, seed 1561543006, best lnL -3319.817 +Search rep 1 (of 2) generation 1977, seed 1556869602, best lnL -3319.558 gen current_lnL precision last_tree_imp -1816 -3319.8173 0.010 1 -1900 -3319.6008 0.010 1 +1977 -3319.5579 0.010 1 2000 -3319.5579 0.010 1 2100 -3319.5506 0.010 1 2200 -3319.4670 0.010 1 @@ -15423,62 +15631,68 @@ 2800 -3319.0998 0.010 1 2900 -3319.0298 0.010 1 3000 -3319.0197 0.010 1 +3100 -3319.0161 0.010 1 +3200 -3319.0102 0.010 1 +3300 -3318.9726 0.010 1 +3400 -3318.9435 0.010 1 +3500 -3318.8796 0.010 1 +3600 -3318.8786 0.010 1 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3319.0161 +Current score = -3318.6825 Performing final optimizations... -pass 1 : -3318.8411 (branch= 0.0055 alpha= 0.0000 pinv= 0.0170 eq freqs= 0.0001 rel rates= 0.1020 ins/del rates= 0.0503) -pass 2 : -3318.7028 (branch= 0.0289 alpha= 0.0065 pinv= 0.0150 eq freqs= 0.0000 rel rates= 0.0814 ins/del rates= 0.0065) -pass 3 : -3318.5668 (branch= 0.0300 alpha= 0.0109 pinv= 0.0138 eq freqs= 0.0045 rel rates= 0.0683 ins/del rates= 0.0085) -pass 4 : -3318.4565 (branch= 0.0237 alpha= 0.0107 pinv= 0.0130 eq freqs= 0.0008 rel rates= 0.0553 ins/del rates= 0.0068) -pass 5 : -3318.3686 (branch= 0.0134 alpha= 0.0088 pinv= 0.0125 eq freqs= 0.0004 rel rates= 0.0475 ins/del rates= 0.0053) -pass 6 : -3318.2926 (branch= 0.0089 alpha= 0.0092 pinv= 0.0116 eq freqs= 0.0000 rel rates= 0.0425 ins/del rates= 0.0038) -pass 7 : -3318.2279 (branch= 0.0056 alpha= 0.0087 pinv= 0.0108 eq freqs= 0.0002 rel rates= 0.0370 ins/del rates= 0.0024) -pass 8 : -3318.1720 (branch= 0.0039 alpha= 0.0086 pinv= 0.0099 eq freqs= 0.0000 rel rates= 0.0319 ins/del rates= 0.0016) -pass 9 : -3318.1233 (branch= 0.0024 alpha= 0.0082 pinv= 0.0091 eq freqs= 0.0001 rel rates= 0.0279 ins/del rates= 0.0011) -pass 10: -3318.0810 (branch= 0.0016 alpha= 0.0077 pinv= 0.0082 eq freqs= 0.0000 rel rates= 0.0240 ins/del rates= 0.0007) -pass 11: -3318.0440 (branch= 0.0010 alpha= 0.0072 pinv= 0.0075 eq freqs= 0.0000 rel rates= 0.0209 ins/del rates= 0.0004) -pass 12: -3318.0115 (branch= 0.0007 alpha= 0.0066 pinv= 0.0067 eq freqs= 0.0000 rel rates= 0.0181 ins/del rates= 0.0003) -pass 13: -3317.9830 (branch= 0.0004 alpha= 0.0061 pinv= 0.0061 eq freqs= 0.0000 rel rates= 0.0157 ins/del rates= 0.0002) -pass 14: -3317.9580 (branch= 0.0003 alpha= 0.0056 pinv= 0.0055 eq freqs= 0.0000 rel rates= 0.0136 ins/del rates= 0.0001) -pass 15: -3317.9361 (branch= 0.0002 alpha= 0.0051 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0117 ins/del rates= 0.0001) -pass 16: -3317.9169 (branch= 0.0001 alpha= 0.0046 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0101 ins/del rates= 0.0000) -pass 17: -3317.9000 (branch= 0.0001 alpha= 0.0041 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0088 ins/del rates= 0.0000) -pass 18: -3317.8853 (branch= 0.0000 alpha= 0.0037 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0076 ins/del rates= 0.0000) -pass 19: -3317.8725 (branch= 0.0000 alpha= 0.0033 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0065 ins/del rates= 0.0000) -pass 20: -3317.8611 (branch= 0.0000 alpha= 0.0029 pinv= 0.0027 eq freqs= 0.0000 rel rates= 0.0057 ins/del rates= 0.0000) - optimization up to ... -pass 30: -3317.8044 (branch= 0.0000 alpha= 0.0152 pinv= 0.0139 eq freqs= 0.0001 rel rates= 0.0275 ins/del rates= 0.0000) +pass 1 : -3318.6178 (branch= 0.0002 alpha= 0.0000 pinv= 0.0153 eq freqs= 0.0001 rel rates= 0.0295 ins/del rates= 0.0196) +pass 2 : -3318.4941 (branch= 0.0525 alpha= 0.0047 pinv= 0.0140 eq freqs= 0.0000 rel rates= 0.0366 ins/del rates= 0.0158) +pass 3 : -3318.3806 (branch= 0.0414 alpha= 0.0097 pinv= 0.0128 eq freqs= 0.0022 rel rates= 0.0336 ins/del rates= 0.0138) +pass 4 : -3318.2978 (branch= 0.0234 alpha= 0.0085 pinv= 0.0123 eq freqs= 0.0000 rel rates= 0.0292 ins/del rates= 0.0093) +pass 5 : -3318.2288 (branch= 0.0150 alpha= 0.0080 pinv= 0.0115 eq freqs= 0.0005 rel rates= 0.0277 ins/del rates= 0.0062) +pass 6 : -3318.1726 (branch= 0.0093 alpha= 0.0080 pinv= 0.0107 eq freqs= 0.0000 rel rates= 0.0244 ins/del rates= 0.0038) +pass 7 : -3318.1243 (branch= 0.0061 alpha= 0.0080 pinv= 0.0098 eq freqs= 0.0002 rel rates= 0.0217 ins/del rates= 0.0025) +pass 8 : -3318.0827 (branch= 0.0038 alpha= 0.0076 pinv= 0.0090 eq freqs= 0.0000 rel rates= 0.0195 ins/del rates= 0.0017) +pass 9 : -3318.0463 (branch= 0.0024 alpha= 0.0072 pinv= 0.0082 eq freqs= 0.0000 rel rates= 0.0174 ins/del rates= 0.0010) +pass 10: -3318.0144 (branch= 0.0015 alpha= 0.0069 pinv= 0.0074 eq freqs= 0.0000 rel rates= 0.0154 ins/del rates= 0.0007) +pass 11: -3317.9863 (branch= 0.0010 alpha= 0.0064 pinv= 0.0067 eq freqs= 0.0000 rel rates= 0.0136 ins/del rates= 0.0004) +pass 12: -3317.9615 (branch= 0.0006 alpha= 0.0059 pinv= 0.0060 eq freqs= 0.0000 rel rates= 0.0119 ins/del rates= 0.0003) +pass 13: -3317.9397 (branch= 0.0004 alpha= 0.0054 pinv= 0.0054 eq freqs= 0.0000 rel rates= 0.0105 ins/del rates= 0.0002) +pass 14: -3317.9205 (branch= 0.0002 alpha= 0.0049 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0091 ins/del rates= 0.0001) +pass 15: -3317.9035 (branch= 0.0001 alpha= 0.0044 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0080 ins/del rates= 0.0001) +pass 16: -3317.8885 (branch= 0.0001 alpha= 0.0040 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0070 ins/del rates= 0.0000) +pass 17: -3317.8754 (branch= 0.0000 alpha= 0.0036 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0061 ins/del rates= 0.0000) +pass 18: -3317.8640 (branch= 0.0000 alpha= 0.0032 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0052 ins/del rates= 0.0000) +pass 19: -3317.8538 (branch= 0.0000 alpha= 0.0029 pinv= 0.0026 eq freqs= 0.0000 rel rates= 0.0046 ins/del rates= 0.0000) +pass 20: -3317.8450 (branch= 0.0000 alpha= 0.0026 pinv= 0.0023 eq freqs= 0.0000 rel rates= 0.0039 ins/del rates= 0.0000) + optimization up to ... +pass 30: -3317.8005 (branch= 0.0000 alpha= 0.0130 pinv= 0.0120 eq freqs= 0.0001 rel rates= 0.0194 ins/del rates= 0.0000) optimization up to ... -pass 40: -3317.7909 (branch= 0.0001 alpha= 0.0036 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0064 ins/del rates= 0.0000) +pass 40: -3317.7900 (branch= 0.0001 alpha= 0.0031 pinv= 0.0028 eq freqs= 0.0000 rel rates= 0.0046 ins/del rates= 0.0000) optimization up to ... -pass 50: -3317.7878 (branch= 0.0000 alpha= 0.0008 pinv= 0.0007 eq freqs= 0.0000 rel rates= 0.0015 ins/del rates= 0.0000) +pass 50: -3317.7876 (branch= 0.0000 alpha= 0.0006 pinv= 0.0006 eq freqs= 0.0000 rel rates= 0.0011 ins/del rates= 0.0000) optimization up to ... -pass 60: -3317.7872 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0004 ins/del rates= 0.0000) +pass 60: -3317.7872 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0002 ins/del rates= 0.0000) optimization up to ... -pass 69: -3317.7870 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) +pass 66: -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 = -3317.7870 +Final score = -3317.7871 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.067, AG = 10.271, AT = 2.658, CG = 0.001, CT = 21.562, GT = 1.000 + AC = 3.067, AG = 10.268, AT = 2.657, CG = 0.001, CT = 21.548, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3328 0.2223 0.1567 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.5747 + 0.5744 with an invariant (invariable) site category, proportion estimated - 0.3613 + 0.3611 Substitution rate categories under this model: rate proportion - 0.0000 0.3613 + 0.0000 0.3611 0.0479 0.1597 - 0.2979 0.1597 - 0.8679 0.1597 - 2.7863 0.1597 + 0.2977 0.1597 + 0.8677 0.1597 + 2.7867 0.1597 Model 2 Number of states = 2 (0/1 coding of gaps) @@ -15504,13 +15718,13 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3317.7870 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3317.7871 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.067 10.27 2.658 0.001 21.56 1 0.333 0.222 0.157 0.288 0.575 0.361 +rep 1: 3.067 10.27 2.657 0.001 21.55 1 0.333 0.222 0.157 0.288 0.574 0.361 Partition model subset 2: ins del @@ -17076,6 +17290,12 @@ 2700 -13370.3695 0.010 0 2800 -13370.3692 0.010 0 2900 -13370.3688 0.010 0 +3000 -13370.3644 0.010 0 +3100 -13370.3583 0.010 0 +3200 -13370.3526 0.010 0 +3300 -13370.3479 0.010 0 +3400 -13370.3478 0.010 0 +3500 -13370.3466 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17198,18 +17418,18 @@ Subset 3: Random seed for bootstrap reweighting: 486988955 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 2979, seed 996087433, best lnL -13370.364 +Bootstrap rep 1 (of 1) generation 3502, seed 1590362200, best lnL -13370.347 gen current_lnL precision last_tree_imp -2979 -13370.3644 0.010 0 +3502 -13370.3466 0.010 0 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) - AC = 1.719, AG = 2.662, AT = 1.270, CG = 1.270, CT = 4.304, GT = 1.000 + AC = 1.727, AG = 2.686, AT = 1.284, CG = 1.284, CT = 4.404, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3084 0.1807 0.3089 0.2021 + (ACGT) 0.3076 0.1804 0.3103 0.2017 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.3662 @@ -17224,7 +17444,7 @@ Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) - AC = 2.631, AG = 4.225, AT = 0.813, CG = 4.225, CT = 2.631, GT = 1.000 + AC = 2.623, AG = 4.225, AT = 0.813, CG = 4.225, CT = 2.623, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2819 0.1752 0.1596 0.3832 Rate Heterogeneity Model: @@ -17248,14 +17468,14 @@ 4 discrete gamma distributed rate categories, alpha param estimated 4.1990 with an invariant (invariable) site category, proportion estimated - 0.0487 + 0.0493 Substitution rate categories under this model: rate proportion - 0.0000 0.0487 - 0.4650 0.2378 - 0.7818 0.2378 - 1.0843 0.2378 - 1.6689 0.2378 + 0.0000 0.0493 + 0.4650 0.2377 + 0.7818 0.2377 + 1.0843 0.2377 + 1.6689 0.2377 Subset rate multipliers: 0.53 0.29 2.18 @@ -17267,17 +17487,17 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13370.3644 +Replicate 1 : -13370.3466 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: 1.719 2.662 1.27 1.27 4.304 1 0.308 0.181 0.309 0.202 0.366 +rep 1: 1.727 2.686 1.284 1.284 4.404 1 0.308 0.180 0.310 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: 2.631 4.225 0.813 4.225 2.631 1 0.282 0.175 0.160 0.383 0.245 +rep 1: 2.623 4.225 0.813 4.225 2.623 1 0.282 0.175 0.160 0.383 0.245 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 @@ -17285,7 +17505,7 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 1.762 0.530 0.287 2.183 +rep 1: 1.767 0.531 0.287 2.183 Saving best tree to bootstrap file ch.p.3diff.boot.tre @@ -17649,7 +17869,7 @@ pass 14: -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 3 seconds +Time used so far = 0 hours, 0 minutes and 2 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17801,7 +18021,7 @@ pass 15: -467.6782 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6782 -Time used so far = 0 hours, 0 minutes and 5 seconds +Time used so far = 0 hours, 0 minutes and 3 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17882,134 +18102,6 @@ 300 -467.7875 0.010 143 400 -467.7813 0.010 143 500 -467.7699 0.010 143 -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 585, seed 913213310, best lnL -467.758 -gen current_lnL precision last_tree_imp -585 -467.7580 0.010 143 600 -467.7578 0.010 143 700 -467.7446 0.010 143 800 -467.7412 0.010 143 @@ -18074,7 +18166,7 @@ pass 15: -467.6786 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6786 -Time used so far = 0 hours, 0 minutes and 7 seconds +Time used so far = 0 hours, 0 minutes and 5 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18180,6 +18272,134 @@ 2800 -467.7049 0.010 0 2900 -467.7048 0.010 0 3000 -467.7041 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 5 (of 5) generation 3051, seed 1368715803, best lnL -467.704 +gen current_lnL precision last_tree_imp +3051 -467.7041 0.010 0 3100 -467.7041 0.010 0 3200 -467.7038 0.010 0 3300 -467.7032 0.010 0 @@ -18209,7 +18429,7 @@ pass 14: -467.6785 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6785 -Time used = 0 hours, 0 minutes and 9 seconds +Time used = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18633,7 +18853,7 @@ pass 13: -477.2121 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.2121 -Time used so far = 0 hours, 0 minutes and 3 seconds +Time used so far = 0 hours, 0 minutes and 2 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18869,6 +19089,29 @@ 200 -477.7377 0.010 42 300 -477.7206 0.010 42 400 -477.5657 0.010 324 +500 -477.5326 0.010 417 +600 -477.5291 0.010 417 +700 -477.5243 0.010 417 +800 -477.5166 0.010 417 +900 -477.5080 0.010 417 +1000 -477.5038 0.010 417 +1100 -477.5010 0.010 417 +1200 -477.4982 0.010 417 +1300 -477.4970 0.010 417 +1400 -477.4967 0.010 417 +1500 -477.4935 0.010 417 +1600 -477.4915 0.010 417 +1700 -477.4905 0.010 417 +1800 -477.4881 0.010 417 +1900 -477.4874 0.010 417 +2000 -477.4867 0.010 417 +2100 -477.4867 0.010 417 +2200 -477.4851 0.010 417 +2300 -477.4837 0.010 417 +2400 -477.4824 0.010 417 +2500 -477.4820 0.010 417 +2600 -477.4796 0.010 417 +2700 -477.4792 0.010 417 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -18994,32 +19237,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 4 (of 5) generation 460, seed 423881230, best lnL -477.534 +Search rep 4 (of 5) generation 2785, seed 145278016, best lnL -477.477 gen current_lnL precision last_tree_imp -460 -477.5343 0.010 417 -500 -477.5326 0.010 417 -600 -477.5291 0.010 417 -700 -477.5243 0.010 417 -800 -477.5166 0.010 417 -900 -477.5080 0.010 417 -1000 -477.5038 0.010 417 -1100 -477.5010 0.010 417 -1200 -477.4982 0.010 417 -1300 -477.4970 0.010 417 -1400 -477.4967 0.010 417 -1500 -477.4935 0.010 417 -1600 -477.4915 0.010 417 -1700 -477.4905 0.010 417 -1800 -477.4881 0.010 417 -1900 -477.4874 0.010 417 -2000 -477.4867 0.010 417 -2100 -477.4867 0.010 417 -2200 -477.4851 0.010 417 -2300 -477.4837 0.010 417 -2400 -477.4824 0.010 417 -2500 -477.4820 0.010 417 -2600 -477.4796 0.010 417 -2700 -477.4792 0.010 417 +2785 -477.4770 0.010 417 2800 -477.4766 0.010 417 2900 -477.4759 0.010 417 3000 -477.4746 0.010 417 @@ -19081,7 +19301,7 @@ pass 15: -477.4316 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.4316 -Time used so far = 0 hours, 0 minutes and 9 seconds +Time used so far = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -19224,7 +19444,7 @@ pass 13: -477.2044 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.2044 -Time used = 0 hours, 0 minutes and 11 seconds +Time used = 0 hours, 0 minutes and 8 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -19629,7 +19849,7 @@ pass 13: -425.5492 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.5492 -Time used so far = 0 hours, 0 minutes and 3 seconds +Time used so far = 0 hours, 0 minutes and 2 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -19741,7 +19961,7 @@ pass 13: -425.3205 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.3205 -Time used so far = 0 hours, 0 minutes and 4 seconds +Time used so far = 0 hours, 0 minutes and 3 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -19821,137 +20041,6 @@ 2800 -425.3506 0.010 2010 2900 -425.3506 0.010 2010 3000 -425.3501 0.010 2010 -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 3036, seed 73693347, best lnL -425.350 -gen current_lnL precision last_tree_imp -3036 -425.3501 0.010 2010 3100 -425.3496 0.010 2010 3200 -425.3490 0.010 2010 3300 -425.3485 0.010 2010 @@ -19983,7 +20072,7 @@ pass 14: -425.3200 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.3200 -Time used so far = 0 hours, 0 minutes and 6 seconds +Time used so far = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -20088,7 +20177,7 @@ pass 13: -425.3214 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.3214 -Time used = 0 hours, 0 minutes and 7 seconds +Time used = 0 hours, 0 minutes and 5 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -20158,6 +20247,128 @@ >>>Completed Bootstrap rep 1<<< ####################################################### +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... +The checkpoint loaded indicates that this run already completed. +To start a new run set restart to 0 and change the output +file prefix (ofprefix). TREEFILES PASS Running checkpoint test ./check/p.mkvO.ssr.conf Running checkpoint test ./check/p.mkvO.ssr.conf @@ -20378,7 +20589,7 @@ pass 14: -473.9508 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -473.9508 -Time used so far = 0 hours, 0 minutes and 3 seconds +Time used so far = 0 hours, 0 minutes and 2 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -20507,7 +20718,7 @@ pass 14: -473.9508 (branch= 0.0000 subset rates= 0.0001) Looking for minimum length branches... Final score = -473.9508 -Time used so far = 0 hours, 0 minutes and 5 seconds +Time used so far = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -20603,6 +20814,22 @@ 1700 -474.4907 0.010 535 1800 -474.4796 0.010 535 1900 -474.4760 0.010 535 +2000 -474.4747 0.010 535 +2100 -474.4733 0.010 535 +2200 -474.4720 0.010 535 +2300 -474.4709 0.010 535 +2400 -474.4703 0.010 535 +2500 -474.4697 0.010 535 +2600 -474.4676 0.010 535 +2700 -474.4670 0.010 535 +2800 -474.4665 0.010 535 +2900 -474.4661 0.010 535 +3000 -474.4649 0.010 535 +3100 -474.4642 0.010 535 +3200 -474.4636 0.010 535 +3300 -474.4636 0.010 535 +3400 -474.4619 0.010 535 +3500 -474.4614 0.010 535 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -20728,25 +20955,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 3 (of 5) generation 1915, seed 1337167676, best lnL -474.476 +Search rep 3 (of 5) generation 3545, seed 74927160, best lnL -474.461 gen current_lnL precision last_tree_imp -1915 -474.4758 0.010 535 -2000 -474.4747 0.010 535 -2100 -474.4733 0.010 535 -2200 -474.4720 0.010 535 -2300 -474.4709 0.010 535 -2400 -474.4703 0.010 535 -2500 -474.4697 0.010 535 -2600 -474.4676 0.010 535 -2700 -474.4670 0.010 535 -2800 -474.4665 0.010 535 -2900 -474.4661 0.010 535 -3000 -474.4649 0.010 535 -3100 -474.4642 0.010 535 -3200 -474.4636 0.010 535 -3300 -474.4636 0.010 535 -3400 -474.4619 0.010 535 -3500 -474.4614 0.010 535 +3545 -474.4614 0.010 535 3600 -474.4611 0.010 535 3700 -474.4608 0.010 535 3800 -474.4608 0.010 535 @@ -20774,7 +20985,7 @@ pass 15: -474.4281 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -474.4281 -Time used so far = 0 hours, 0 minutes and 7 seconds +Time used so far = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -20897,7 +21108,7 @@ pass 14: -473.9508 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -473.9508 -Time used so far = 0 hours, 0 minutes and 8 seconds +Time used so far = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -21038,7 +21249,7 @@ pass 14: -473.9482 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -473.9482 -Time used = 0 hours, 0 minutes and 10 seconds +Time used = 0 hours, 0 minutes and 8 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -21172,10 +21383,10 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-9_amd64.deb'. -dpkg-deb: building package 'garli' in '../garli_2.1-9_amd64.deb'. -dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-9_amd64.deb'. dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-9_all.deb'. dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-9_amd64.deb'. +dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-9_amd64.deb'. +dpkg-deb: building package 'garli' in '../garli_2.1-9_amd64.deb'. dpkg-genbuildinfo --build=binary -O../garli_2.1-9_amd64.buildinfo dpkg-genchanges --build=binary -O../garli_2.1-9_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -21183,12 +21394,14 @@ 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/1743073/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1743073/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/768998 and its subdirectories -I: Current time: Fri Jan 23 05:54:06 -12 2026 -I: pbuilder-time-stamp: 1769190846 +I: removing directory /srv/workspace/pbuilder/1743073 and its subdirectories +I: Current time: Sun Dec 22 01:36:54 +14 2024 +I: pbuilder-time-stamp: 1734781014