Diff of the two buildlogs: -- --- b1/build.log 2025-02-15 14:41:13.975892760 +0000 +++ b2/build.log 2025-02-15 14:46:48.016724456 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Feb 15 02:37:29 -12 2025 -I: pbuilder-time-stamp: 1739630249 +I: Current time: Sat Mar 21 11:04:17 +14 2026 +I: pbuilder-time-stamp: 1774040657 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -22,51 +22,83 @@ 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/482919/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3445071/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Mar 20 21:04 /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/3445071/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3445071/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='f4fac899090a4e5da6de06321d8a6c90' - 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='482919' - PS1='# ' - PS2='> ' + INVOCATION_ID=eb10bb0309ba4984a19904a36a56c15b + 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=3445071 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.MTHZwnpF/pbuilderrc_ESUp --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.MTHZwnpF/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.MTHZwnpF/pbuilderrc_qOpc --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.MTHZwnpF/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 infom01-amd64 6.1.0-31-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/482919/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3445071/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -217,7 +249,7 @@ Get: 105 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 5.0.6-4 [1088 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.18 [3372 B] Get: 107 http://deb.debian.org/debian unstable/main amd64 ncl-tools amd64 2.1.21+git20210811.b1213a7-6 [190 kB] -Fetched 109 MB in 4s (26.4 MB/s) +Fetched 109 MB in 1s (82.9 MB/s) Preconfiguring packages ... Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19808 files and directories currently installed.) @@ -669,7 +701,11 @@ 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/3445071/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3445071/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 @@ -774,8 +810,8 @@ checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... 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 @@ -894,22 +930,6 @@ | ~~~~~~~~~~~~~~~~~ /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=] -configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': -configoptions.cpp:337:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] - 337 | sprintf(modName, "model%d", modelNum); - | ^~ -configoptions.cpp:337:34: note: directive argument in the range [0, 2147483647] - 337 | sprintf(modName, "model%d", modelNum); - | ^~~~~~~~~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)' at configoptions.cpp:337:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ In file included from bipartition.cpp:20: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ @@ -954,7 +974,6 @@ /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 optimization.o optimization.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -1007,11 +1026,30 @@ /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{ | ^~~~~~~~~~~~~~~ @@ -1062,17 +1100,16 @@ In file included from tree.h:35, from individual.h:21, from population.h:31, - from garlimain.cpp:40: + from funcs.h:25, + from individual.cpp:28: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/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 | ^~~~~~~~~~~~~~~ @@ -1103,6 +1140,7 @@ /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 optimization.o optimization.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; @@ -1110,6 +1148,15 @@ /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; @@ -1166,22 +1209,11 @@ /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{ | ^~~~~~~~~~~~~~~ @@ -1191,7 +1223,7 @@ 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 | ^~~~~~~~~~~~~~~ @@ -1229,19 +1261,34 @@ /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 model.cpp:17: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1279,15 +1326,8 @@ /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] @@ -1442,6 +1443,41 @@ 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 mpitrick.cpp:21: +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 65 | class DistEqualsWithinCutSubtree:public binary_function{ + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 72 | class NodeEquals:public binary_function{ + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': +reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_function.h:1435: +/usr/include/c++/14/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': +reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': +reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; + | ~~~~~~~^~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;idlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from tree.h:35, - from individual.h:21, - from population.h:31, - from funcs.h:25, - from mpitrick.cpp:27: -reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 58 | class DistEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/string:49, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from mpitrick.cpp:21: -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 65 | class DistEqualsWithinCutSubtree:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 72 | class NodeEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': -reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_function.h:1435: -/usr/include/c++/14/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': -reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': -reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; - | ~~~~~~~^~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/iomanip:42, - from individual.cpp:21: + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from configreader.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2334,12 +2372,6 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from 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{ - | ^~~~~~~~~~~~~~~ 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; @@ -2347,13 +2379,25 @@ /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/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 | ^~~~~~~~~~~~~~~ @@ -2439,13 +2483,13 @@ reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2466,7 +2508,7 @@ 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 | ^~~~~~~~~~~~~~~ @@ -2504,10 +2546,6 @@ /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 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 | ^~~~~~~~~~~~~~~ @@ -2612,10 +2652,13 @@ /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; @@ -2772,11 +2773,46 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': +model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3675:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3675 | fread(&o, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3677:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3677 | fread(&o, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3684:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3684 | fread((char*) &(b[i]), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3691:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3691 | fread((char*) &(rateMults[i]), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3692:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3692 | fread((char*) &(rateProbs[i]), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3699:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3699 | fread((char*) &a, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3705:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3705 | fread((char*) &p, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3710:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3710 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3713:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3713 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from optimization.cpp:21: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i>>Completed Bootstrap rep 1<<< -####################################################### Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## @@ -13241,9 +13226,9 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 3100, seed 1872184071, best lnL -88.525 +Bootstrap rep 1 (of 1) generation 1974, seed 752378600, best lnL -88.683 gen current_lnL precision last_tree_imp -3100 -88.5249 0.010 879 +1974 -88.6834 0.010 879 MODEL REPORT - Parameter values are FINAL Model 1 @@ -13257,15 +13242,15 @@ 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 3.1527 + 1.6318 with an invariant (invariable) site category, proportion estimated - 0.2947 + 0.1912 Substitution rate categories under this model: rate proportion - 0.0000 0.2947 - 0.4599 0.2351 - 0.9028 0.2351 - 1.6373 0.2351 + 0.0000 0.1912 + 0.3051 0.2696 + 0.8168 0.2696 + 1.8780 0.2696 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 2 branches were collapsed. @@ -13275,15 +13260,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -88.5249 +Replicate 1 : -88.6834 Parameter estimates: alpha pinv -rep 1: 3.153 0.295 +rep 1: 1.632 0.191 Treelengths: TL -rep 1: 2.365 +rep 1: 2.363 Saving best tree to bootstrap file ch.a.G3.boot.tre @@ -13420,19 +13405,6 @@ 1000 -110.5066 0.010 707 1100 -110.4789 0.010 707 1200 -110.4461 0.010 707 -1300 -110.4042 0.010 707 -1400 -110.3747 0.010 707 -1500 -110.3652 0.010 707 -1600 -110.2968 0.010 707 -1700 -110.2780 0.010 707 -1800 -110.2330 0.010 707 -1900 -110.2137 0.010 707 -2000 -110.1885 0.010 707 -2100 -110.1532 0.010 707 -2200 -110.1459 0.010 707 -2300 -110.1348 0.010 707 -2400 -110.1188 0.010 707 -2500 -110.0921 0.010 707 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13519,9 +13491,9 @@ STARTING RUN Restarting from checkpoint... - generation 2524, seed 920182691, best lnL -110.091 + generation 1234, seed 1926818987, best lnL -110.446 gen current_lnL precision last_tree_imp -2524 -110.0914 0.010 707 +1234 -110.4458 0.010 707 MODEL REPORT - Parameter values are FINAL Model 1 @@ -13535,19 +13507,19 @@ 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.5128 + 1.4529 with an invariant (invariable) site category, proportion estimated - 0.2028 + 0.0913 Substitution rate categories under this model: rate proportion - 0.0000 0.2028 - 0.4805 0.1993 - 0.7913 0.1993 - 1.0840 0.1993 - 1.6442 0.1993 + 0.0000 0.0913 + 0.2180 0.2272 + 0.5805 0.2272 + 1.0475 0.2272 + 2.1540 0.2272 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 ... @@ -13555,15 +13527,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -110.0914 +Replicate 1 : -110.4458 Parameter estimates: alpha pinv -rep 1: 4.513 0.203 +rep 1: 1.453 0.091 Treelengths: TL -rep 1: 2.663 +rep 1: 2.615 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 @@ -14007,17 +13979,6 @@ 180 -204.9247 0.500 172 190 -204.8909 0.500 172 200 -204.7980 0.500 172 -210 -204.7143 0.500 209 -220 -204.6664 0.500 209 -230 -204.3372 0.500 228 -240 -204.3152 0.500 228 -250 -203.9441 0.500 245 -260 -203.9053 0.500 245 -270 -203.8090 0.500 245 -280 -203.8090 0.500 245 -290 -203.7595 0.500 245 -300 -203.7386 0.500 245 -310 -203.7108 0.500 245 NOTE: ****Specified time limit (10 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14104,15 +14065,15 @@ STARTING RUN Restarting from checkpoint... - generation 314, seed 1405230162, best lnL -203.677 + generation 208, seed 896699740, best lnL -204.798 gen current_lnL precision last_tree_imp -314 -203.6773 0.500 245 +208 -204.7979 0.500 172 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates - AC = 1.668, AG = 4.221, AT = 0.041, CG = 2.532, CT = 4.060, GT = 1.000 + AC = 1.586, AG = 4.089, 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) @@ -14145,15 +14106,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -203.6773 +Replicate 1 : -204.7979 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 1.668 4.221 0.04129 2.532 4.06 1 +rep 1: 0.047 0.521 0.499 0.479 1.586 4.089 0.04 2.453 3.968 1 Treelengths: TL -rep 1: 8.076 +rep 1: 7.899 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 @@ -14300,23 +14261,6 @@ 150 -194.7085 0.500 0 160 -194.7085 0.500 0 170 -194.5936 0.500 168 -180 -194.5926 0.500 168 -190 -194.5693 0.500 168 -200 -194.2413 0.500 196 -210 -194.2413 0.500 196 -220 -194.2043 0.500 196 -230 -194.1525 0.500 196 -240 -194.0255 0.500 234 -250 -194.0104 0.500 234 -260 -193.9860 0.500 234 -270 -193.8167 0.500 234 -280 -193.8167 0.500 234 -290 -193.7620 0.500 234 -300 -193.7592 0.500 234 -310 -193.7487 0.500 234 -320 -193.6856 0.500 234 -330 -193.3200 0.500 324 -340 -193.2196 0.500 324 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14404,16 +14348,16 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 345, seed 1463033373, best lnL -193.219 +Bootstrap rep 1 (of 1) generation 174, seed 14196197, best lnL -194.593 gen current_lnL precision last_tree_imp -345 -193.2193 0.500 324 +174 -194.5930 0.500 168 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 61 (codon data, standard code) One estimated dN/dS ratio (aka omega) = 0.120507 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates - AC = 1.745, AG = 6.152, AT = 0.012, CG = 4.367, CT = 2.255, GT = 1.000 + AC = 1.637, AG = 5.804, 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) @@ -14441,15 +14385,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -193.2193 +Replicate 1 : -194.5930 Parameter estimates: w(0) p(0) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) -rep 1: 0.121 1.000 1.745 6.152 0.01199 4.367 2.255 1 +rep 1: 0.121 1.000 1.637 5.804 0.01146 4.174 2.324 1 Treelengths: TL -rep 1: 8.209 +rep 1: 10.151 Saving best tree to bootstrap file ch.c.boot.tre @@ -14643,27 +14587,6 @@ 3700 -3350.9418 0.010 0 3800 -3350.9275 0.010 0 3900 -3350.8675 0.010 0 -4000 -3350.8675 0.010 0 -4100 -3350.8578 0.010 0 -4200 -3350.8523 0.010 0 -4300 -3350.8521 0.010 0 -4400 -3350.8480 0.010 0 -4500 -3350.8480 0.010 0 -4600 -3350.8168 0.010 0 -4700 -3350.8148 0.010 0 -4800 -3350.8148 0.010 0 -4900 -3350.8148 0.010 0 -5000 -3350.8140 0.010 0 -5100 -3350.7921 0.010 0 -5200 -3350.7743 0.010 0 -5300 -3350.7724 0.010 0 -5400 -3350.7562 0.010 0 -5500 -3350.7006 0.010 0 -5600 -3350.6580 0.010 0 -5700 -3350.6554 0.010 0 -5800 -3350.6195 0.010 0 -5900 -3350.6124 0.010 0 -6000 -3350.6088 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14767,9 +14690,30 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 6069, seed 381556359, best lnL -3350.600 +Search rep 1 (of 2) generation 3972, seed 849816746, best lnL -3350.867 gen current_lnL precision last_tree_imp -6069 -3350.5997 0.010 0 +3972 -3350.8675 0.010 0 +4000 -3350.8675 0.010 0 +4100 -3350.8578 0.010 0 +4200 -3350.8523 0.010 0 +4300 -3350.8521 0.010 0 +4400 -3350.8480 0.010 0 +4500 -3350.8480 0.010 0 +4600 -3350.8168 0.010 0 +4700 -3350.8148 0.010 0 +4800 -3350.8148 0.010 0 +4900 -3350.8148 0.010 0 +5000 -3350.8140 0.010 0 +5100 -3350.7921 0.010 0 +5200 -3350.7743 0.010 0 +5300 -3350.7724 0.010 0 +5400 -3350.7562 0.010 0 +5500 -3350.7006 0.010 0 +5600 -3350.6580 0.010 0 +5700 -3350.6554 0.010 0 +5800 -3350.6195 0.010 0 +5900 -3350.6124 0.010 0 +6000 -3350.6088 0.010 0 6100 -3350.5997 0.010 0 6200 -3350.5989 0.010 0 6300 -3350.5944 0.010 0 @@ -14782,238 +14726,60 @@ 7000 -3350.5549 0.010 0 7100 -3350.5524 0.010 0 7200 -3350.5463 0.010 0 -7300 -3350.5463 0.010 0 -7400 -3350.5431 0.010 0 -7500 -3350.5408 0.010 0 -7600 -3350.5321 0.010 0 -7700 -3350.5313 0.010 0 -7800 -3350.5313 0.010 0 -7900 -3350.5313 0.010 0 -8000 -3350.5125 0.010 0 -8100 -3350.5125 0.010 0 -8200 -3350.5124 0.010 0 -8300 -3350.5091 0.010 0 -8400 -3350.5003 0.010 0 -8500 -3350.4986 0.010 0 -8600 -3350.4798 0.010 0 -8700 -3350.4787 0.010 0 -8800 -3350.4784 0.010 0 -8900 -3350.4761 0.010 0 -9000 -3350.4758 0.010 0 -9100 -3350.4501 0.010 0 -9200 -3350.4501 0.010 0 -9300 -3350.4501 0.010 0 -9400 -3350.4495 0.010 0 -9500 -3350.4492 0.010 0 -9600 -3350.4482 0.010 0 -9700 -3350.4481 0.010 0 -9800 -3350.4481 0.010 0 -9900 -3350.4481 0.010 0 -10000 -3350.4473 0.010 0 - Optimizing parameters... improved 0.000 lnL - Optimizing branchlengths... improved 0.000 lnL -10100 -3350.4468 0.010 0 -10200 -3350.4465 0.010 0 -10300 -3350.4462 0.010 0 -10400 -3350.4462 0.010 0 -10500 -3350.4461 0.010 0 -10600 -3350.4455 0.010 0 -10700 -3350.4455 0.010 0 -10800 -3350.4455 0.010 0 -10900 -3350.4454 0.010 0 -11000 -3350.4453 0.010 0 -11100 -3350.4453 0.010 0 -Reached termination condition! -last topological improvement at gen 0 -Improvement over last 500 gen = 0.00025 -Current score = -3350.4453 -Performing final optimizations... -pass 1 : -3350.4342 (branch= 0.0000 alpha= 0.0000 pinv= 0.0110 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 2 : -3350.4116 (branch= 0.0000 alpha= 0.0121 pinv= 0.0104 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 3 : -3350.3874 (branch= 0.0000 alpha= 0.0108 pinv= 0.0093 eq freqs= 0.0000 rel rates= 0.0040 subset rates= 0.0000) -pass 4 : -3350.3700 (branch= 0.0007 alpha= 0.0081 pinv= 0.0085 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 5 : -3350.3533 (branch= 0.0009 alpha= 0.0083 pinv= 0.0075 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 6 : -3350.3374 (branch= 0.0012 alpha= 0.0079 pinv= 0.0067 eq freqs= 0.0002 rel rates= 0.0000 subset rates= 0.0000) -pass 7 : -3350.3242 (branch= 0.0005 alpha= 0.0066 pinv= 0.0060 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 8 : -3350.3128 (branch= 0.0001 alpha= 0.0060 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 9 : -3350.3027 (branch= 0.0001 alpha= 0.0051 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) -pass 10: -3350.2927 (branch= 0.0000 alpha= 0.0048 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0010) -pass 11: -3350.2845 (branch= 0.0009 alpha= 0.0036 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 12: -3350.2778 (branch= 0.0001 alpha= 0.0033 pinv= 0.0032 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 13: -3350.2718 (branch= 0.0000 alpha= 0.0031 pinv= 0.0028 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 14: -3350.2665 (branch= 0.0000 alpha= 0.0028 pinv= 0.0025 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 15: -3350.2619 (branch= 0.0000 alpha= 0.0025 pinv= 0.0022 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 16: -3350.2578 (branch= 0.0000 alpha= 0.0021 pinv= 0.0019 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 17: -3350.2543 (branch= 0.0000 alpha= 0.0019 pinv= 0.0016 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 18: -3350.2513 (branch= 0.0000 alpha= 0.0016 pinv= 0.0014 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 19: -3350.2487 (branch= 0.0000 alpha= 0.0014 pinv= 0.0012 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) -pass 20: -3350.2463 (branch= 0.0000 alpha= 0.0012 pinv= 0.0011 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) - optimization up to ... -pass 30: -3350.2355 (branch= 0.0000 alpha= 0.0056 pinv= 0.0051 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) - optimization up to ... -pass 40: -3350.2334 (branch= 0.0000 alpha= 0.0011 pinv= 0.0010 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) - optimization up to ... -pass 50: -3350.2330 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 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 11 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 4 (nucleotide data) - Nucleotide Relative Rate Matrix: 6 rates - AC = 3.149, AG = 10.535, AT = 2.724, CG = 0.001, CT = 22.212, 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 - 0.5740 - with an invariant (invariable) site category, proportion estimated - 0.3645 - Substitution rate categories under this model: - rate proportion - 0.0000 0.3645 - 0.0478 0.1589 - 0.2975 0.1589 - 0.8675 0.1589 - 2.7872 0.1589 - -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: - 1.82 0.18 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - No branches were short enough to be collapsed. - ->>>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 -1100 -3353.1654 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3352.9151 +Current score = -3350.5463 Performing final optimizations... -pass 1 : -3352.4113 (branch= 0.0000 alpha= 0.0052 pinv= 0.0190 eq freqs= 0.0214 rel rates= 0.3992 subset rates= 0.0591) -pass 2 : -3352.0275 (branch= 0.0574 alpha= 0.0135 pinv= 0.0173 eq freqs= 0.0142 rel rates= 0.2654 subset rates= 0.0160) -pass 3 : -3351.7304 (branch= 0.0306 alpha= 0.0100 pinv= 0.0167 eq freqs= 0.0031 rel rates= 0.2264 subset rates= 0.0103) -pass 4 : -3351.4978 (branch= 0.0203 alpha= 0.0109 pinv= 0.0159 eq freqs= 0.0009 rel rates= 0.1789 subset rates= 0.0057) -pass 5 : -3351.3075 (branch= 0.0124 alpha= 0.0110 pinv= 0.0150 eq freqs= 0.0005 rel rates= 0.1471 subset rates= 0.0043) -pass 6 : -3351.1471 (branch= 0.0075 alpha= 0.0103 pinv= 0.0141 eq freqs= 0.0006 rel rates= 0.1257 subset rates= 0.0023) -pass 7 : -3351.0096 (branch= 0.0055 alpha= 0.0111 pinv= 0.0130 eq freqs= 0.0006 rel rates= 0.1052 subset rates= 0.0021) -pass 8 : -3350.8959 (branch= 0.0044 alpha= 0.0105 pinv= 0.0120 eq freqs= 0.0003 rel rates= 0.0856 subset rates= 0.0010) -pass 9 : -3350.8002 (branch= 0.0027 alpha= 0.0097 pinv= 0.0109 eq freqs= 0.0002 rel rates= 0.0722 subset rates= 0.0000) -pass 10: -3350.7148 (branch= 0.0006 alpha= 0.0098 pinv= 0.0105 eq freqs= 0.0002 rel rates= 0.0628 subset rates= 0.0014) -pass 11: -3350.6459 (branch= 0.0009 alpha= 0.0092 pinv= 0.0095 eq freqs= 0.0002 rel rates= 0.0490 subset rates= 0.0000) -pass 12: -3350.5875 (branch= 0.0003 alpha= 0.0083 pinv= 0.0081 eq freqs= 0.0001 rel rates= 0.0416 subset rates= 0.0000) -pass 13: -3350.5364 (branch= 0.0001 alpha= 0.0079 pinv= 0.0073 eq freqs= 0.0001 rel rates= 0.0347 subset rates= 0.0011) -pass 14: -3350.4952 (branch= 0.0005 alpha= 0.0070 pinv= 0.0066 eq freqs= 0.0001 rel rates= 0.0270 subset rates= 0.0000) -pass 15: -3350.4597 (branch= 0.0001 alpha= 0.0061 pinv= 0.0059 eq freqs= 0.0000 rel rates= 0.0233 subset rates= 0.0000) -pass 16: -3350.4288 (branch= 0.0000 alpha= 0.0057 pinv= 0.0052 eq freqs= 0.0001 rel rates= 0.0199 subset rates= 0.0000) -pass 17: -3350.4021 (branch= 0.0000 alpha= 0.0051 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0169 subset rates= 0.0000) -pass 18: -3350.3789 (branch= 0.0000 alpha= 0.0046 pinv= 0.0041 eq freqs= 0.0000 rel rates= 0.0143 subset rates= 0.0000) -pass 19: -3350.3590 (branch= 0.0000 alpha= 0.0041 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0122 subset rates= 0.0000) -pass 20: -3350.3418 (branch= 0.0000 alpha= 0.0036 pinv= 0.0032 eq freqs= 0.0000 rel rates= 0.0104 subset rates= 0.0000) - optimization up to ... -pass 30: -3350.2581 (branch= 0.0000 alpha= 0.0182 pinv= 0.0166 eq freqs= 0.0001 rel rates= 0.0488 subset rates= 0.0000) - optimization up to ... -pass 40: -3350.2389 (branch= 0.0000 alpha= 0.0040 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0113 subset rates= 0.0000) +pass 1 : -3350.5200 (branch= 0.0000 alpha= 0.0111 pinv= 0.0150 eq freqs= 0.0001 rel rates= 0.0000 subset rates= 0.0000) +pass 2 : -3350.4886 (branch= 0.0000 alpha= 0.0156 pinv= 0.0131 eq freqs= 0.0026 rel rates= 0.0000 subset rates= 0.0000) +pass 3 : -3350.4544 (branch= 0.0021 alpha= 0.0138 pinv= 0.0116 eq freqs= 0.0000 rel rates= 0.0068 subset rates= 0.0000) +pass 4 : -3350.4280 (branch= 0.0009 alpha= 0.0141 pinv= 0.0106 eq freqs= 0.0000 rel rates= 0.0008 subset rates= 0.0000) +pass 5 : -3350.4058 (branch= 0.0028 alpha= 0.0096 pinv= 0.0098 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 6 : -3350.3851 (branch= 0.0007 alpha= 0.0100 pinv= 0.0087 eq freqs= 0.0000 rel rates= 0.0012 subset rates= 0.0000) +pass 7 : -3350.3659 (branch= 0.0004 alpha= 0.0084 pinv= 0.0078 eq freqs= 0.0002 rel rates= 0.0014 subset rates= 0.0010) +pass 8 : -3350.3498 (branch= 0.0010 alpha= 0.0072 pinv= 0.0071 eq freqs= 0.0001 rel rates= 0.0007 subset rates= 0.0000) +pass 9 : -3350.3357 (branch= 0.0002 alpha= 0.0066 pinv= 0.0063 eq freqs= 0.0001 rel rates= 0.0009 subset rates= 0.0000) +pass 10: -3350.3229 (branch= 0.0000 alpha= 0.0063 pinv= 0.0056 eq freqs= 0.0000 rel rates= 0.0008 subset rates= 0.0000) +pass 11: -3350.3114 (branch= 0.0001 alpha= 0.0057 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0007 subset rates= 0.0000) +pass 12: -3350.3013 (branch= 0.0000 alpha= 0.0050 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0006 subset rates= 0.0000) +pass 13: -3350.2924 (branch= 0.0000 alpha= 0.0045 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0006 subset rates= 0.0000) +pass 14: -3350.2845 (branch= 0.0000 alpha= 0.0039 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0005 subset rates= 0.0000) +pass 15: -3350.2776 (branch= 0.0000 alpha= 0.0035 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0004 subset rates= 0.0000) +pass 16: -3350.2715 (branch= 0.0000 alpha= 0.0030 pinv= 0.0027 eq freqs= 0.0000 rel rates= 0.0004 subset rates= 0.0000) +pass 17: -3350.2662 (branch= 0.0000 alpha= 0.0027 pinv= 0.0023 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) +pass 18: -3350.2616 (branch= 0.0000 alpha= 0.0023 pinv= 0.0020 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) +pass 19: -3350.2576 (branch= 0.0000 alpha= 0.0020 pinv= 0.0018 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 20: -3350.2541 (branch= 0.0000 alpha= 0.0017 pinv= 0.0015 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2346 (branch= 0.0000 alpha= 0.0008 pinv= 0.0007 eq freqs= 0.0000 rel rates= 0.0028 subset rates= 0.0000) +pass 30: -3350.2372 (branch= 0.0000 alpha= 0.0084 pinv= 0.0076 eq freqs= 0.0000 rel rates= 0.0008 subset rates= 0.0000) optimization up to ... -pass 60: -3350.2336 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0007 subset rates= 0.0000) +pass 40: -3350.2337 (branch= 0.0000 alpha= 0.0018 pinv= 0.0016 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) optimization up to ... -pass 70: -3350.2334 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 50: -3350.2331 (branch= 0.0000 alpha= 0.0003 pinv= 0.0003 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) optimization up to ... -pass 72: -3350.2334 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 52: -3350.2330 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -3350.2334 -Time used = 0 hours, 0 minutes and 12 seconds +Final score = -3350.2331 +Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.109, AG = 10.393, AT = 2.683, CG = 0.001, CT = 21.851, GT = 1.000 + AC = 3.126, AG = 10.457, AT = 2.702, CG = 0.001, CT = 22.022, 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 - 0.5789 + 0.5749 with an invariant (invariable) site category, proportion estimated - 0.3661 + 0.3646 Substitution rate categories under this model: rate proportion - 0.0000 0.3661 - 0.0488 0.1585 - 0.3003 0.1585 - 0.8702 0.1585 - 2.7807 0.1585 + 0.0000 0.3646 + 0.0480 0.1588 + 0.2980 0.1588 + 0.8679 0.1588 + 2.7861 0.1588 Model 2 Number of states = 2 (binary data) @@ -15028,7 +14794,7 @@ NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. ->>>Terminated Search rep 2 (of 2)<<< +>>>Terminated Search rep 1 (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!*** @@ -15036,28 +14802,22 @@ ####################################################### -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. +Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3350.2330 (best) -Replicate 2 : -3350.2334 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 1 : -3350.2331 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.149 10.54 2.724 0.001 22.21 1 0.333 0.222 0.157 0.288 0.574 0.365 -rep 2: 3.109 10.39 2.683 0.001 21.85 1 0.333 0.222 0.157 0.288 0.579 0.366 +rep 1: 3.126 10.46 2.702 0.001 22.02 1 0.333 0.222 0.157 0.288 0.575 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 2: 0.788 1.820 0.180 +rep 1: 0.790 1.821 0.179 Saving final tree from best search rep (#1) to ch.g.dnaBnoZ.best.tre ####################################################### @@ -15225,11 +14985,6 @@ 1400 -3320.0695 0.010 1 1500 -3320.0226 0.010 1 1600 -3320.0183 0.010 1 -1700 -3320.0152 0.010 1 -1800 -3319.8191 0.010 1 -1900 -3319.6008 0.010 1 -2000 -3319.5579 0.010 1 -2100 -3319.5506 0.010 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15330,9 +15085,14 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 2165, seed 115933236, best lnL -3319.467 +Search rep 1 (of 2) generation 1647, seed 934540049, best lnL -3320.017 gen current_lnL precision last_tree_imp -2165 -3319.4670 0.010 1 +1647 -3320.0174 0.010 1 +1700 -3320.0152 0.010 1 +1800 -3319.8191 0.010 1 +1900 -3319.6008 0.010 1 +2000 -3319.5579 0.010 1 +2100 -3319.5506 0.010 1 2200 -3319.4670 0.010 1 2300 -3319.3661 0.010 1 2400 -3319.3307 0.010 1 @@ -15341,71 +15101,64 @@ 2700 -3319.1207 0.010 1 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 -3700 -3318.6811 0.010 1 -3800 -3318.6807 0.010 1 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3318.6807 +Current score = -3319.0228 Performing final optimizations... -pass 1 : -3318.5984 (branch= 0.0003 alpha= 0.0000 pinv= 0.0180 eq freqs= 0.0001 rel rates= 0.0327 ins/del rates= 0.0313) -pass 2 : -3318.4800 (branch= 0.0502 alpha= 0.0060 pinv= 0.0138 eq freqs= 0.0000 rel rates= 0.0374 ins/del rates= 0.0110) -pass 3 : -3318.3730 (branch= 0.0363 alpha= 0.0093 pinv= 0.0127 eq freqs= 0.0021 rel rates= 0.0338 ins/del rates= 0.0128) -pass 4 : -3318.2916 (branch= 0.0230 alpha= 0.0084 pinv= 0.0123 eq freqs= 0.0000 rel rates= 0.0290 ins/del rates= 0.0088) -pass 5 : -3318.2237 (branch= 0.0145 alpha= 0.0081 pinv= 0.0115 eq freqs= 0.0005 rel rates= 0.0274 ins/del rates= 0.0059) -pass 6 : -3318.1684 (branch= 0.0087 alpha= 0.0081 pinv= 0.0106 eq freqs= 0.0000 rel rates= 0.0242 ins/del rates= 0.0037) -pass 7 : -3318.1207 (branch= 0.0059 alpha= 0.0079 pinv= 0.0098 eq freqs= 0.0002 rel rates= 0.0215 ins/del rates= 0.0024) -pass 8 : -3318.0795 (branch= 0.0036 alpha= 0.0076 pinv= 0.0089 eq freqs= 0.0000 rel rates= 0.0195 ins/del rates= 0.0015) -pass 9 : -3318.0434 (branch= 0.0024 alpha= 0.0073 pinv= 0.0081 eq freqs= 0.0000 rel rates= 0.0173 ins/del rates= 0.0010) -pass 10: -3318.0119 (branch= 0.0015 alpha= 0.0068 pinv= 0.0073 eq freqs= 0.0000 rel rates= 0.0152 ins/del rates= 0.0007) -pass 11: -3317.9840 (branch= 0.0010 alpha= 0.0063 pinv= 0.0066 eq freqs= 0.0000 rel rates= 0.0135 ins/del rates= 0.0004) -pass 12: -3317.9596 (branch= 0.0006 alpha= 0.0059 pinv= 0.0060 eq freqs= 0.0000 rel rates= 0.0118 ins/del rates= 0.0003) -pass 13: -3317.9379 (branch= 0.0004 alpha= 0.0054 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0104 ins/del rates= 0.0002) -pass 14: -3317.9189 (branch= 0.0002 alpha= 0.0049 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0091 ins/del rates= 0.0001) -pass 15: -3317.9021 (branch= 0.0001 alpha= 0.0044 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0078 ins/del rates= 0.0001) -pass 16: -3317.8874 (branch= 0.0001 alpha= 0.0040 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0068 ins/del rates= 0.0000) -pass 17: -3317.8744 (branch= 0.0000 alpha= 0.0036 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0060 ins/del rates= 0.0000) -pass 18: -3317.8631 (branch= 0.0000 alpha= 0.0032 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0051 ins/del rates= 0.0000) -pass 19: -3317.8530 (branch= 0.0000 alpha= 0.0028 pinv= 0.0026 eq freqs= 0.0000 rel rates= 0.0045 ins/del rates= 0.0000) -pass 20: -3317.8443 (branch= 0.0000 alpha= 0.0025 pinv= 0.0023 eq freqs= 0.0000 rel rates= 0.0039 ins/del rates= 0.0000) - optimization up to ... -pass 30: -3317.8003 (branch= 0.0000 alpha= 0.0129 pinv= 0.0119 eq freqs= 0.0000 rel rates= 0.0191 ins/del rates= 0.0000) +pass 1 : -3318.8373 (branch= 0.0065 alpha= 0.0000 pinv= 0.0184 eq freqs= 0.0066 rel rates= 0.1041 ins/del rates= 0.0500) +pass 2 : -3318.6959 (branch= 0.0286 alpha= 0.0062 pinv= 0.0149 eq freqs= 0.0000 rel rates= 0.0852 ins/del rates= 0.0064) +pass 3 : -3318.5645 (branch= 0.0311 alpha= 0.0121 pinv= 0.0135 eq freqs= 0.0000 rel rates= 0.0656 ins/del rates= 0.0091) +pass 4 : -3318.4573 (branch= 0.0208 alpha= 0.0094 pinv= 0.0132 eq freqs= 0.0000 rel rates= 0.0572 ins/del rates= 0.0066) +pass 5 : -3318.3666 (branch= 0.0137 alpha= 0.0095 pinv= 0.0124 eq freqs= 0.0013 rel rates= 0.0484 ins/del rates= 0.0054) +pass 6 : -3318.2908 (branch= 0.0086 alpha= 0.0090 pinv= 0.0116 eq freqs= 0.0004 rel rates= 0.0425 ins/del rates= 0.0037) +pass 7 : -3318.2267 (branch= 0.0058 alpha= 0.0088 pinv= 0.0107 eq freqs= 0.0000 rel rates= 0.0365 ins/del rates= 0.0023) +pass 8 : -3318.1709 (branch= 0.0038 alpha= 0.0087 pinv= 0.0099 eq freqs= 0.0001 rel rates= 0.0317 ins/del rates= 0.0016) +pass 9 : -3318.1224 (branch= 0.0024 alpha= 0.0081 pinv= 0.0090 eq freqs= 0.0001 rel rates= 0.0277 ins/del rates= 0.0011) +pass 10: -3318.0802 (branch= 0.0016 alpha= 0.0077 pinv= 0.0082 eq freqs= 0.0001 rel rates= 0.0240 ins/del rates= 0.0007) +pass 11: -3318.0433 (branch= 0.0010 alpha= 0.0072 pinv= 0.0075 eq freqs= 0.0000 rel rates= 0.0208 ins/del rates= 0.0004) +pass 12: -3318.0109 (branch= 0.0007 alpha= 0.0066 pinv= 0.0067 eq freqs= 0.0000 rel rates= 0.0180 ins/del rates= 0.0003) +pass 13: -3317.9825 (branch= 0.0004 alpha= 0.0061 pinv= 0.0061 eq freqs= 0.0000 rel rates= 0.0156 ins/del rates= 0.0002) +pass 14: -3317.9575 (branch= 0.0003 alpha= 0.0056 pinv= 0.0055 eq freqs= 0.0000 rel rates= 0.0135 ins/del rates= 0.0001) +pass 15: -3317.9357 (branch= 0.0002 alpha= 0.0050 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0116 ins/del rates= 0.0001) +pass 16: -3317.9166 (branch= 0.0001 alpha= 0.0046 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0101 ins/del rates= 0.0000) +pass 17: -3317.8997 (branch= 0.0001 alpha= 0.0041 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0087 ins/del rates= 0.0000) +pass 18: -3317.8850 (branch= 0.0000 alpha= 0.0037 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0075 ins/del rates= 0.0000) +pass 19: -3317.8722 (branch= 0.0000 alpha= 0.0033 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0065 ins/del rates= 0.0000) +pass 20: -3317.8609 (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: -3317.8043 (branch= 0.0000 alpha= 0.0152 pinv= 0.0140 eq freqs= 0.0001 rel rates= 0.0273 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) optimization up to ... -pass 40: -3317.7899 (branch= 0.0001 alpha= 0.0030 pinv= 0.0028 eq freqs= 0.0000 rel rates= 0.0045 ins/del rates= 0.0000) +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) optimization up to ... -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) +pass 60: -3317.7872 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0003 ins/del rates= 0.0000) optimization up to ... -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) +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 67: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) +pass 71: -3317.7870 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... -Final score = -3317.7871 +Final score = -3317.7870 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.067, AG = 10.271, AT = 2.659, CG = 0.001, CT = 21.553, GT = 1.000 + AC = 3.068, AG = 10.273, AT = 2.658, CG = 0.001, CT = 21.556, 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 - 0.5744 + 0.5747 with an invariant (invariable) site category, proportion estimated - 0.3611 + 0.3612 Substitution rate categories under this model: rate proportion - 0.0000 0.3611 + 0.0000 0.3612 0.0479 0.1597 - 0.2977 0.1597 - 0.8677 0.1597 - 2.7868 0.1597 + 0.2979 0.1597 + 0.8678 0.1597 + 2.7863 0.1597 Model 2 Number of states = 2 (0/1 coding of gaps) @@ -15431,13 +15184,13 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3317.7871 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3317.7870 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.067 10.27 2.659 0.001 21.55 1 0.333 0.222 0.157 0.288 0.574 0.361 +rep 1: 3.068 10.27 2.658 0.001 21.56 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del @@ -15447,7 +15200,7 @@ Treelengths: TL -rep 1: 1.418 +rep 1: 1.419 Saving final tree from best search rep (#1) to ch.g.dnaMix.best.tre ####################################################### @@ -17001,16 +16754,6 @@ Optimizing branchlengths... improved 0.000 lnL 2600 -13370.3703 0.010 0 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 -3600 -13370.3463 0.010 0 -3700 -13370.3463 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17133,18 +16876,18 @@ Subset 3: Random seed for bootstrap reweighting: 486988955 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 3729, seed 846294598, best lnL -13370.346 +Bootstrap rep 1 (of 1) generation 2749, seed 1597823594, best lnL -13370.369 gen current_lnL precision last_tree_imp -3729 -13370.3459 0.010 0 +2749 -13370.3692 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 = 1.727, AG = 2.686, AT = 1.284, CG = 1.284, CT = 4.404, GT = 1.000 + AC = 1.719, AG = 2.662, AT = 1.270, CG = 1.270, CT = 4.304, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3076 0.1804 0.3103 0.2017 + (ACGT) 0.3084 0.1807 0.3089 0.2021 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.3662 @@ -17159,9 +16902,9 @@ Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) - AC = 2.623, AG = 4.225, AT = 0.813, CG = 4.225, CT = 2.623, GT = 1.000 + AC = 2.632, AG = 4.243, AT = 0.813, CG = 4.243, CT = 2.632, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2818 0.1757 0.1595 0.3830 + (ACGT) 0.2819 0.1752 0.1596 0.3832 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.2452 @@ -17176,21 +16919,21 @@ Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) - AC = 1.000, AG = 5.303, AT = 4.268, CG = 0.630, CT = 5.303, GT = 1.000 + AC = 1.000, AG = 5.303, AT = 4.268, CG = 0.629, CT = 5.303, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1555 0.3463 0.2762 0.2219 + (ACGT) 0.1555 0.3463 0.2763 0.2219 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.1990 + 4.1267 with an invariant (invariable) site category, proportion estimated - 0.0493 + 0.0487 Substitution rate categories under this model: rate proportion - 0.0000 0.0493 - 0.4650 0.2377 - 0.7818 0.2377 - 1.0843 0.2377 - 1.6689 0.2377 + 0.0000 0.0487 + 0.4612 0.2378 + 0.7795 0.2378 + 1.0844 0.2378 + 1.6750 0.2378 Subset rate multipliers: 0.53 0.29 2.18 @@ -17202,25 +16945,25 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13370.3459 +Replicate 1 : -13370.3692 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: 1.727 2.686 1.284 1.284 4.404 1 0.308 0.180 0.310 0.202 0.366 +rep 1: 1.719 2.662 1.27 1.27 4.304 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: 2.623 4.225 0.813 4.225 2.623 1 0.282 0.176 0.160 0.383 0.245 +rep 1: 2.632 4.243 0.813 4.243 2.632 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 -rep 1: 1 5.303 4.268 0.6297 5.303 1 0.155 0.346 0.276 0.222 4.199 0.049 +rep 1: 1 5.303 4.268 0.6292 5.303 1 0.155 0.346 0.276 0.222 4.127 0.049 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 1.763 0.531 0.287 2.183 +rep 1: 1.762 0.530 0.287 2.183 Saving best tree to bootstrap file ch.p.3diff.boot.tre @@ -17584,7 +17327,7 @@ 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 2 seconds +Time used so far = 0 hours, 0 minutes and 3 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17694,6 +17437,134 @@ 3200 -467.7140 0.010 0 3300 -467.7139 0.010 0 3400 -467.7136 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 3 (of 5) generation 3499, seed 484860369, best lnL -467.714 +gen current_lnL precision last_tree_imp +3499 -467.7136 0.010 0 3500 -467.7136 0.010 0 3600 -467.7132 0.010 0 3700 -467.7130 0.010 0 @@ -17736,7 +17607,7 @@ 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 3 seconds +Time used so far = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17881,7 +17752,7 @@ 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 5 seconds +Time used so far = 0 hours, 0 minutes and 8 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17974,134 +17845,6 @@ 1500 -467.7218 0.010 0 1600 -467.7207 0.010 0 1700 -467.7200 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 1702, seed 1855484280, best lnL -467.720 -gen current_lnL precision last_tree_imp -1702 -467.7200 0.010 0 1800 -467.7184 0.010 0 1900 -467.7125 0.010 0 2000 -467.7120 0.010 0 @@ -18144,7 +17887,7 @@ 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 6 seconds +Time used = 0 hours, 0 minutes and 11 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18568,7 +18311,7 @@ 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 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18663,6 +18406,134 @@ 1700 -477.4788 0.010 223 1800 -477.4783 0.010 223 1900 -477.4780 0.010 223 +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.mkO.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 ordered k-state data, + modeled as Standard ordered 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 3 (of 5) generation 1956, seed 924494456, best lnL -477.477 +gen current_lnL precision last_tree_imp +1956 -477.4771 0.010 223 2000 -477.4771 0.010 223 2100 -477.4766 0.010 223 2200 -477.4761 0.010 223 @@ -18722,7 +18593,7 @@ 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 4 seconds +Time used so far = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18844,134 +18715,6 @@ 4200 -477.4633 0.010 417 4300 -477.4619 0.010 417 4400 -477.4614 0.010 417 -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.mkO.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 ordered k-state data, - modeled as Standard ordered 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 4469, seed 1519578352, best lnL -477.461 -gen current_lnL precision last_tree_imp -4469 -477.4613 0.010 417 4500 -477.4613 0.010 417 4600 -477.4613 0.010 417 4700 -477.4611 0.010 417 @@ -19016,7 +18759,7 @@ 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 6 seconds +Time used so far = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -19125,43 +18868,27 @@ 3100 -477.2842 0.010 2379 3200 -477.2833 0.010 2379 3300 -477.2805 0.010 2379 -3400 -477.2804 0.010 2379 -3500 -477.2790 0.010 2379 -3600 -477.2786 0.010 2379 -3700 -477.2775 0.010 2379 -3800 -477.2774 0.010 2379 -3900 -477.2748 0.010 2379 -4000 -477.2746 0.010 2379 -4100 -477.2744 0.010 2379 -4200 -477.2738 0.010 2379 -4300 -477.2735 0.010 2379 -4400 -477.2735 0.010 2379 -4500 -477.2732 0.010 2379 -4600 -477.2732 0.010 2379 -4700 -477.2732 0.010 2379 -Reached termination condition! -last topological improvement at gen 2379 -Improvement over last 500 gen = 0.00062 -Current score = -477.2732 +NOTE: ****Specified time limit (5 seconds) reached... +Current score = -477.2804 Performing final optimizations... -pass 1 : -477.2407 (branch= 0.0198 subset rates= 0.0127) -pass 2 : -477.2245 (branch= 0.0119 subset rates= 0.0043) -pass 3 : -477.2106 (branch= 0.0127 subset rates= 0.0013) -pass 4 : -477.2092 (branch= 0.0014 subset rates= 0.0000) -pass 5 : -477.2084 (branch= 0.0008 subset rates= 0.0000) -pass 6 : -477.2064 (branch= 0.0020 subset rates= 0.0000) -pass 7 : -477.2057 (branch= 0.0007 subset rates= 0.0000) -pass 8 : -477.2052 (branch= 0.0005 subset rates= 0.0000) -pass 9 : -477.2050 (branch= 0.0002 subset rates= 0.0000) -pass 10: -477.2049 (branch= 0.0001 subset rates= 0.0000) -pass 11: -477.2044 (branch= 0.0000 subset rates= 0.0005) -pass 12: -477.2044 (branch= 0.0000 subset rates= 0.0000) -pass 13: -477.2044 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -477.2472 (branch= 0.0214 subset rates= 0.0118) +pass 2 : -477.2293 (branch= 0.0126 subset rates= 0.0052) +pass 3 : -477.2135 (branch= 0.0150 subset rates= 0.0007) +pass 4 : -477.2129 (branch= 0.0006 subset rates= 0.0000) +pass 5 : -477.2099 (branch= 0.0030 subset rates= 0.0000) +pass 6 : -477.2081 (branch= 0.0012 subset rates= 0.0006) +pass 7 : -477.2050 (branch= 0.0022 subset rates= 0.0009) +pass 8 : -477.2046 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -477.2045 (branch= 0.0002 subset rates= 0.0000) +pass 10: -477.2044 (branch= 0.0001 subset rates= 0.0000) +pass 11: -477.2044 (branch= 0.0000 subset rates= 0.0000) +pass 12: -477.2043 (branch= 0.0000 subset rates= 0.0000) +pass 13: -477.2043 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.2044 -Time used = 0 hours, 0 minutes and 7 seconds +Final score = -477.2043 +Time used = 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: @@ -19187,11 +18914,15 @@ no rate heterogeneity Subset rate multipliers: - 0.64 1.94 2.62 + 0.64 1.93 2.63 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. ->>>Completed Search rep 5 (of 5)<<< +>>>Terminated Search rep 5 (of 5)<<< + +NOTE: ***Search was terminated before full auto-termination condition was reached! +Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** + ####################################################### @@ -19204,7 +18935,7 @@ Replicate 2 : -477.2121 (same topology as 1) Replicate 3 : -477.4316 Replicate 4 : -477.4316 (same topology as 3) -Replicate 5 : -477.2044 (best) +Replicate 5 : -477.2043 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -19223,9 +18954,7 @@ rep 2: 4.668 0.644 1.904 2.619 rep 3: 4.930 0.631 1.914 2.747 rep 4: 4.929 0.631 1.918 2.733 -rep 5: 4.694 0.635 1.936 2.620 - -Saving final trees from all search reps to ch.p.mkO.ssr.best.all.tre +rep 5: 4.695 0.635 1.934 2.627 Saving final tree from best search rep (#5) to ch.p.mkO.ssr.best.tre ####################################################### @@ -19451,7 +19180,7 @@ pass 12: -425.5486 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.5486 -Time used so far = 0 hours, 0 minutes and 2 seconds +Time used so far = 0 hours, 0 minutes and 1 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -19564,7 +19293,7 @@ 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 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -19644,6 +19373,137 @@ 3000 -425.3584 0.010 803 3100 -425.3582 0.010 803 3200 -425.3573 0.010 803 +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 3 (of 5) generation 3297, seed 332587988, best lnL -425.357 +gen current_lnL precision last_tree_imp +3297 -425.3570 0.010 803 3300 -425.3569 0.010 803 3400 -425.3569 0.010 803 3500 -425.3566 0.010 803 @@ -19676,7 +19536,7 @@ 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 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -19787,7 +19647,7 @@ 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 5 seconds +Time used so far = 0 hours, 0 minutes and 8 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -19855,137 +19715,6 @@ 1700 -425.3782 0.010 444 1800 -425.3769 0.010 444 1900 -425.3760 0.010 444 -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 5 (of 5) generation 1900, seed 49853522, best lnL -425.376 -gen current_lnL precision last_tree_imp -1900 -425.3760 0.010 444 2000 -425.3756 0.010 444 2100 -425.3741 0.010 444 2200 -425.3735 0.010 444 @@ -20023,7 +19752,7 @@ 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 6 seconds +Time used = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -20313,7 +20042,7 @@ 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 1 seconds +Time used so far = 0 hours, 0 minutes and 2 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -20442,7 +20171,7 @@ 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 2 seconds +Time used so far = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -20541,6 +20270,134 @@ 2000 -474.4747 0.010 535 2100 -474.4733 0.010 535 2200 -474.4720 0.010 535 +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.mkvO.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 ordered k-state data, variable only, + modeled as Standard ordered 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 + +Restarting from checkpoint... +Search rep 3 (of 5) generation 2299, seed 1102504294, best lnL -474.471 +gen current_lnL precision last_tree_imp +2299 -474.4709 0.010 535 2300 -474.4709 0.010 535 2400 -474.4703 0.010 535 2500 -474.4697 0.010 535 @@ -20581,7 +20438,7 @@ 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 4 seconds +Time used so far = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -20704,7 +20561,7 @@ 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 5 seconds +Time used so far = 0 hours, 0 minutes and 8 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -20809,134 +20666,6 @@ 2600 -473.9863 0.010 437 2700 -473.9844 0.010 437 2800 -473.9842 0.010 437 -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.mkvO.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 ordered k-state data, variable only, - modeled as Standard ordered 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 - -Restarting from checkpoint... -Search rep 5 (of 5) generation 2823, seed 134915077, best lnL -473.984 -gen current_lnL precision last_tree_imp -2823 -473.9842 0.010 437 2900 -473.9841 0.010 437 3000 -473.9841 0.010 437 3100 -473.9835 0.010 437 @@ -20973,7 +20702,7 @@ 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 6 seconds +Time used = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -21106,9 +20835,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'garli' in '../garli_2.1-9_amd64.deb'. -dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-9_amd64.deb'. dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-9_amd64.deb'. +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-genbuildinfo --build=binary -O../garli_2.1-9_amd64.buildinfo @@ -21118,12 +20847,14 @@ 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/3445071/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3445071/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/482919 and its subdirectories -I: Current time: Sat Feb 15 02:41:12 -12 2025 -I: pbuilder-time-stamp: 1739630472 +I: removing directory /srv/workspace/pbuilder/3445071 and its subdirectories +I: Current time: Sat Mar 21 11:09:47 +14 2026 +I: pbuilder-time-stamp: 1774040987