Diff of the two buildlogs: -- --- b1/build.log 2024-12-20 23:38:15.941592127 +0000 +++ b2/build.log 2024-12-20 23:43:39.498851002 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Dec 20 11:29:21 -12 2024 -I: pbuilder-time-stamp: 1734737361 +I: Current time: Fri Jan 23 20:01:18 +14 2026 +I: pbuilder-time-stamp: 1769148078 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -27,54 +27,86 @@ dpkg-source: info: unpacking garli_2.1-9.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/34980/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4345/tmp/hooks/D01_modify_environment starting +debug: Running on ionos6-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jan 23 06:01 /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/4345/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4345/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='35af8123dc9649f0b942a98b5036d8dc' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='34980' - PS1='# ' - PS2='> ' + INVOCATION_ID=0c23c627d60049c797be7ffb5df2a584 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=4345 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.L6wO1cWn/pbuilderrc_L3KR --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.L6wO1cWn/b1 --logfile b1/build.log garli_2.1-9.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.L6wO1cWn/pbuilderrc_0Cf3 --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.L6wO1cWn/b2 --logfile b2/build.log garli_2.1-9.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos12-i386 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/34980/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/4345/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -169,7 +201,7 @@ Get: 49 http://deb.debian.org/debian unstable/main i386 libncl-dev i386 2.1.21+git20210811.b1213a7-6 [642 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 mpi-default-dev i386 1.17 [3144 B] Get: 51 http://deb.debian.org/debian unstable/main i386 ncl-tools i386 2.1.21+git20210811.b1213a7-6 [199 kB] -Fetched 42.1 MB in 1s (35.0 MB/s) +Fetched 42.1 MB in 1s (71.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19953 files and directories currently installed.) @@ -395,7 +427,11 @@ 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/4345/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/4345/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 @@ -497,8 +533,8 @@ checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking for gcc... gcc @@ -567,7 +603,7 @@ config.status: creating config.h config.status: executing depfiles commands dh_auto_build - make -j11 + make -j21 make[2]: Entering directory '/build/reproducible-path/garli-2.1' make all-recursive make[3]: Entering directory '/build/reproducible-path/garli-2.1' @@ -584,16 +620,26 @@ mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlireader.o garlireader.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o individual.o individual.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp +linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)': +linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1322 | register int nsq = n * n; + | ^~~ garlimain.cpp:434:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ garlimain.cpp:434:76: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ -linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)': -linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1322 | register int nsq = n * n; - | ^~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -616,24 +662,6 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -In file included from tree.h:35, - from individual.h:21, - from population.h:31, - from funcs.h:25, - from funcs.cpp:30: -reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 58 | class DistEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/string:49, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from population.h:23: -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ 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{ @@ -650,18 +678,6 @@ /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:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -680,6 +696,62 @@ reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': +reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; + | ~~~~~~~^~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': +configoptions.cpp:337:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] + 337 | sprintf(modName, "model%d", modelNum); + | ^~ +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/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +In file included from tree.h:35, + from individual.h:21, + from population.h:31, + from funcs.h:25, + from funcs.cpp:30: +reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 58 | class DistEquals:public binary_function{ + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/string:49, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from population.h:23: +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 65 | class DistEqualsWithinCutSubtree:public binary_function{ + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 72 | class NodeEquals:public binary_function{ + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); @@ -695,20 +767,10 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -/usr/include/c++/14/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ -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) - | ^~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ @@ -720,7 +782,7 @@ from individual.h:21, from population.h:31, from funcs.h:25, - from adaptation.cpp:25: + from configreader.cpp:30: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -730,7 +792,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from adaptation.cpp:18: + from configreader.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -772,26 +834,11 @@ funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -801,7 +848,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from population.h:23: + from adaptation.cpp:18: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -839,25 +886,20 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from garlimain.cpp:46: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/string:49, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/iomanip:42, - from individual.cpp:21: +In file included from /usr/include/c++/14/bits/refwrap.h:39, + from /usr/include/c++/14/vector:68, + from population.cpp:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -895,77 +937,15 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +In file included from population.cpp:49: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -975,7 +955,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from configreader.cpp:21: + from population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -999,6 +979,72 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +In file included from tree.h:35, + from individual.h:21, + from population.h:31, + from funcs.h:25, + from individual.cpp:28: +reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 58 | class DistEquals:public binary_function{ + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/string:49, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/iomanip:42, + from individual.cpp:21: +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h: In member function 'listIt ReconList::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:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 65 | class DistEqualsWithinCutSubtree:public binary_function{ + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 72 | class NodeEquals:public binary_function{ + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from tree.h:35, + from optimization.cpp:19: +reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 58 | class DistEquals:public binary_function{ + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/bits/refwrap.h:39, + from /usr/include/c++/14/vector:68, + from tree.h:24: +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': +reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_function.h:1435: +/usr/include/c++/14/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 65 | class DistEqualsWithinCutSubtree:public binary_function{ + | ^~~~~~~~~~~~~~~ +/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::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)); @@ -1013,22 +1059,35 @@ /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 = 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) + | ^~~~~~~ +reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': +reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; + | ~~~~~~~^~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from model.cpp:26: @@ -1079,14 +1138,35 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/bits/refwrap.h:39, - from /usr/include/c++/14/vector:68, - from tree.h:24: +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 | ^~~~~~~~~~~~~~~ @@ -1117,28 +1197,17 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': -reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; - | ~~~~~~~^~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -In file included from optimization.cpp:21: -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, - from population.cpp:23: + from tree.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1154,6 +1223,13 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': +reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; + | ~~~~~~~^~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); @@ -1176,27 +1252,86 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from population.cpp:49: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;idlen, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6845:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6845 | fread(&dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6849:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6849 | fread(&dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6855:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6855 | fread(&dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6858:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6858 | fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6862:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6862 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6865:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6865 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6868:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6868 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6872:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6872 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6878:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6878 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6881 | fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, - from configreader.cpp:18: + from /usr/include/c++/14/cstdio:42, + from /usr/include/c++/14/ext/string_conversions.h:45, + from /usr/include/c++/14/bits/basic_string.h:4154, + from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1313,7 +1478,9 @@ from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54: + from /usr/include/c++/14/string:54, + from translatetable.h:24, + from translatetable.cpp:19: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1329,13 +1496,7 @@ from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from datamatr.cpp:20: + from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1351,7 +1512,15 @@ from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54: + from /usr/include/c++/14/string:54, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from model.h:25, + from clamanager.h:25, + from condlike.cpp:22: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1364,9 +1533,7 @@ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, - from /usr/include/c++/14/cstdio:42, - from /usr/include/ncl/ncl.h:27, - from garlireader.cpp:41: + from configreader.cpp:18: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1378,10 +1545,6 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -1405,44 +1568,55 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -garlimain.cpp: In function 'int SubGarliMain(int)': -garlimain.cpp:323:49: warning: '%d' directive writing between 2 and 10 bytes into a region of size 6 [-Wformat-overflow=] - 323 | else sprintf(temp, ".run%d", rank); - | ^~ -garlimain.cpp:323:44: note: directive argument in the range [10, 2147483647] - 323 | else sprintf(temp, ".run%d", rank); - | ^~~~~~~~ +In file included from /usr/include/stdio.h:970, + from /usr/include/c++/14/cstdio:42, + from /usr/include/c++/14/ext/string_conversions.h:45, + from /usr/include/c++/14/bits/basic_string.h:4154, + from /usr/include/c++/14/string:54, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from datamatr.cpp:20: In function 'int sprintf(char*, const char*, ...)', - inlined from 'int SubGarliMain(int)' at garlimain.cpp:323:16: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 15 bytes into a destination of size 10 + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -garlimain.cpp: In function 'int SubGarliMain(int)': -garlimain.cpp:322:59: warning: '%d' directive writing between 1 and 11 bytes into a region of size 5 [-Wformat-overflow=] - 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); - | ^~ -garlimain.cpp:322:53: note: directive argument in the range [-2147483648, 9] - 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); - | ^~~~~~~~~ +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +In file included from /usr/include/stdio.h:970, + from /usr/include/c++/14/cstdio:42, + from /usr/include/c++/14/ext/string_conversions.h:45, + from /usr/include/c++/14/bits/basic_string.h:4154, + from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', - inlined from 'int SubGarliMain(int)' at garlimain.cpp:322:25: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 17 bytes into a destination of size 10 + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54: + from /usr/include/c++/14/string:54, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from treenode.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1454,65 +1628,11 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp -In file included from tree.h:35, - from individual.h:21, - from population.h:31, - from funcs.h:25, - from tree.cpp:33: -reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 58 | class DistEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/bits/refwrap.h:39, - from /usr/include/c++/14/vector:68, - from tree.cpp:21: -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 65 | class DistEqualsWithinCutSubtree:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 72 | class NodeEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': -reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_function.h:1435: -/usr/include/c++/14/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': -reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': -reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; - | ~~~~~~~^~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;idlen, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6845:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6845 | fread(&dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6849:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6849 | fread(&dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6855:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6855 | fread(&dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6858:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6858 | fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6862:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6862 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6865:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6865 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6868:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6868 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6872:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6872 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6878:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6878 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6881 | fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, - from /usr/include/c++/14/cstdio:42, - from /usr/include/c++/14/ext/string_conversions.h:45, - from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54, - from translatetable.h:24, - from translatetable.cpp:19: + from /usr/lib/i386-linux-gnu/mpich/include/mpicxx.h:41, + from /usr/lib/i386-linux-gnu/mpich/include/mpi.h:977, + from mpitrick.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1610,62 +1659,6 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -In file included from 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 adaptation.cpp:18: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2036,33 +2068,11 @@ /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) - | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, - from adaptation.cpp:25: + from funcs.cpp:30: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2072,7 +2082,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from adaptation.cpp:18: + from population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2103,46 +2113,6 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': -reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; - | ~~~~~~~^~~~~~~~~~~~~~~~~~ -/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 population.h:23: -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 65 | class DistEqualsWithinCutSubtree:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 72 | class NodeEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); @@ -2158,11 +2128,24 @@ /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) + | ^~~~~~~ +reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': +reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; + | ~~~~~~~^~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, - from funcs.h:25, - from funcs.cpp:30: + from garlimain.cpp:40: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2188,13 +2171,6 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': -reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; - | ~~~~~~~^~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); @@ -2221,21 +2197,41 @@ 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 configreader.cpp:21: +In file included from /usr/include/c++/14/bits/refwrap.h:39, + from /usr/include/c++/14/vector:68, + from population.cpp:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2273,26 +2269,11 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from garlimain.cpp:46: -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/bits/refwrap.h:39, - from /usr/include/c++/14/vector:68, - from tree.h:24: +In file included from /usr/include/c++/14/string:49, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from configreader.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2408,14 +2389,107 @@ | ^~~~~~~ In file included from tree.h:35, from individual.h:21, + from model.cpp:26: +reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 58 | class DistEquals:public binary_function{ + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/string:49, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from model.cpp:17: +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 65 | class DistEqualsWithinCutSubtree:public binary_function{ + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 72 | class NodeEquals:public binary_function{ + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': +reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_function.h:1435: +/usr/include/c++/14/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': +reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; + | ~~~~~~~^~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +In file included from tree.h:35, + from individual.h:21, from population.h:31, - from population.cpp:45: + from funcs.h:25, + from tree.cpp:33: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, - from population.cpp:23: + from tree.cpp:21: +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 65 | class DistEqualsWithinCutSubtree:public binary_function{ + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 72 | class NodeEquals:public binary_function{ + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': +reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_function.h:1435: +/usr/include/c++/14/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': +reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +In file included from tree.h:35, + from optimization.cpp:19: +reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 58 | class DistEquals:public binary_function{ + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/bits/refwrap.h:39, + from /usr/include/c++/14/vector:68, + from tree.h:24: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2443,6 +2517,13 @@ 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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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) + | ^~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ @@ -2453,19 +2534,28 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from model.cpp:17: + from /usr/include/c++/14/iomanip:42, + from individual.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2481,11 +2571,6 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -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 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)); @@ -2508,11 +2593,41 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from population.cpp:49: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;idlen, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6845:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6845 | fread(&dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6849:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6849 | fread(&dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6855:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6855 | fread(&dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6858:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6858 | fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6862:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6862 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6865:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6865 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6868:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6868 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6872:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6872 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6878:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6878 | fread((char*) &dum, sizeof(dum), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 6881 | fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from model.h:25, - from clamanager.h:25, - from condlike.cpp:22: + from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2629,9 +2783,7 @@ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, - from /usr/include/c++/14/cstdio:42, - from /usr/include/ncl/ncl.h:27, - from garlireader.cpp:41: + from configreader.cpp:18: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2647,7 +2799,13 @@ from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54: + from /usr/include/c++/14/string:54, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from treenode.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2660,7 +2818,12 @@ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, - from configreader.cpp:18: + from /usr/include/c++/14/cstdio:42, + from /usr/include/c++/14/ext/string_conversions.h:45, + from /usr/include/c++/14/bits/basic_string.h:4154, + from /usr/include/c++/14/string:54, + from translatetable.h:24, + from translatetable.cpp:19: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2676,7 +2839,15 @@ from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54: + from /usr/include/c++/14/string:54, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from model.h:25, + from clamanager.h:25, + from condlike.cpp:22: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2693,12 +2864,7 @@ from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from datamatr.cpp:20: + from population.cpp:25: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2710,21 +2876,10 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, - from /usr/include/c++/14/ext/string_conversions.h:45, - from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from rng.h:36, - from tree.h:30: + from /usr/include/ncl/ncl.h:27, + from garlireader.cpp:41: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2736,8 +2891,6 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -2754,13 +2907,18 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, - from population.cpp:25: + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from rng.h:36, + from tree.h:30: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2772,133 +2930,14 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp -In file included from tree.h:35, - from individual.h:21, - from population.h:31, - from funcs.h:25, - from tree.cpp:33: -reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 58 | class DistEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/bits/refwrap.h:39, - from /usr/include/c++/14/vector:68, - from tree.cpp:21: -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 65 | class DistEqualsWithinCutSubtree:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 72 | class NodeEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': -reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_function.h:1435: -/usr/include/c++/14/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': -reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': -reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; - | ~~~~~~~^~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;idlen, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6845:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6845 | fread(&dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6849:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6849 | fread(&dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6855:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6855 | fread(&dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6858:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6858 | fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6862:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6862 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6865:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6865 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6868:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6868 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6872:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6872 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6878:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6878 | fread((char*) &dum, sizeof(dum), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 6881 | fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, - from translatetable.h:24, - from translatetable.cpp:19: + from datamatr.h:23, + from sequencedata.h:27, + from tree.cpp:31: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2910,22 +2949,6 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': -population.cpp:3066:50: warning: '%d' directive writing between 1 and 9 bytes into a region of size 8 [-Wformat-overflow=] - 3066 | sprintf(oStr, "R(%d)", d + 1); - | ^~ -population.cpp:3066:47: note: directive argument in the range [1, 536870911] - 3066 | sprintf(oStr, "R(%d)", d + 1); - | ^~~~~~~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: -/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 13 bytes into a destination of size 10 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -2949,13 +2972,7 @@ from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from treenode.cpp:21: + from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2972,9 +2989,12 @@ from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, - from datamatr.h:23, - from sequencedata.h:27, - from tree.cpp:31: + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from datamatr.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2986,6 +3006,22 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': +population.cpp:3066:50: warning: '%d' directive writing between 1 and 9 bytes into a region of size 8 [-Wformat-overflow=] + 3066 | sprintf(oStr, "R(%d)", d + 1); + | ^~ +population.cpp:3066:47: note: directive argument in the range [1, 536870911] + 3066 | sprintf(oStr, "R(%d)", d + 1); + | ^~~~~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: +/usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 13 bytes into a destination of size 10 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-z,relro -Wl,-z,now -L/usr/lib -o Garli adaptation.o bipartition.o condlike.o configoptions.o configreader.o datamatr.o funcs.o garlimain.o garlireader.o individual.o linalg.o model.o optimization.o population.o rng.o sequencedata.o set.o translatetable.o tree.o treenode.o mpitrick.o -lncl -lncl make[3]: Leaving directory '/build/reproducible-path/garli-2.1/src' Making all in tests @@ -3002,7 +3038,7 @@ # get (mostly!) reproducible test results and avoid failures as described in bug #907905 find tests -name "*.conf" -exec sed -i~ 's/randseed *= *-1/randseed = 1\nbootstrapseed = 42/' \{\} \; dh_auto_test - make -j11 check "TESTSUITEFLAGS=-j11 --verbose" VERBOSE=1 + make -j21 check "TESTSUITEFLAGS=-j21 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/garli-2.1' Making check in src make[3]: Entering directory '/build/reproducible-path/garli-2.1/src' @@ -5522,7 +5558,7 @@ pass 13: -6242.8580 (branch= 0.0000 alpha= 0.0000) Looking for minimum length branches... Final score = -6242.8580 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5672,7 +5708,7 @@ pass 10: -6247.0222 (branch= 0.0000 alpha= 0.0000) Looking for minimum length branches... Final score = -6247.0222 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5969,7 +6005,7 @@ pass 10: -12956.1235 (branch= 0.0000 omega= 0.0000) Looking for minimum length branches... Final score = -12956.1235 -Time used = 0 hours, 0 minutes and 25 seconds +Time used = 0 hours, 0 minutes and 13 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6121,7 +6157,7 @@ pass 10: -13269.2298 (branch= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13269.2298 -Time used = 0 hours, 0 minutes and 18 seconds +Time used = 0 hours, 0 minutes and 9 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6306,11 +6342,11 @@ pass 13: -3350.7072 (branch= 0.0019 alpha= 0.0093 pinv= 0.0106 eq freqs= 0.0002 rel rates= 0.0577 subset rates= 0.0000) pass 14: -3350.6389 (branch= 0.0005 alpha= 0.0090 pinv= 0.0090 eq freqs= 0.0001 rel rates= 0.0486 subset rates= 0.0012) pass 15: -3350.5822 (branch= 0.0009 alpha= 0.0082 pinv= 0.0081 eq freqs= 0.0001 rel rates= 0.0392 subset rates= 0.0000) -pass 16: -3350.5338 (branch= 0.0003 alpha= 0.0075 pinv= 0.0073 eq freqs= 0.0001 rel rates= 0.0333 subset rates= 0.0000) -pass 17: -3350.4923 (branch= 0.0001 alpha= 0.0072 pinv= 0.0066 eq freqs= 0.0001 rel rates= 0.0275 subset rates= 0.0000) +pass 16: -3350.5337 (branch= 0.0003 alpha= 0.0075 pinv= 0.0073 eq freqs= 0.0001 rel rates= 0.0333 subset rates= 0.0000) +pass 17: -3350.4923 (branch= 0.0001 alpha= 0.0072 pinv= 0.0066 eq freqs= 0.0001 rel rates= 0.0274 subset rates= 0.0000) pass 18: -3350.4567 (branch= 0.0000 alpha= 0.0066 pinv= 0.0059 eq freqs= 0.0001 rel rates= 0.0231 subset rates= 0.0000) -pass 19: -3350.4262 (branch= 0.0000 alpha= 0.0058 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0193 subset rates= 0.0000) -pass 20: -3350.3998 (branch= 0.0000 alpha= 0.0052 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0165 subset rates= 0.0000) +pass 19: -3350.4262 (branch= 0.0000 alpha= 0.0059 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0193 subset rates= 0.0000) +pass 20: -3350.3998 (branch= 0.0000 alpha= 0.0052 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0164 subset rates= 0.0000) optimization up to ... pass 30: -3350.2717 (branch= 0.0000 alpha= 0.0276 pinv= 0.0250 eq freqs= 0.0002 rel rates= 0.0754 subset rates= 0.0000) optimization up to ... @@ -6320,12 +6356,14 @@ optimization up to ... pass 60: -3350.2340 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0011 subset rates= 0.0000) optimization up to ... -pass 70: -3350.2337 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 70: -3350.2338 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) optimization up to ... -pass 77: -3350.2336 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 80: -3350.2336 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) + optimization up to ... +pass 82: -3350.2336 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -3350.2336 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6338,7 +6376,7 @@ Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.11 10.4 2.687 0.001 21.85 1 0.333 0.222 0.157 0.288 0.579 0.366 +rep 1: 3.114 10.41 2.689 0.001 21.88 1 0.333 0.222 0.157 0.288 0.580 0.366 Partition model subset 2: Model contains no estimated parameters @@ -6351,9 +6389,9 @@ Writing optimized trees and models to scr.g.dnaBnoZ.best.all.tre ***********TEST************** -***Score is 3350.23362 +***Score is 3350.23358 ***Expected is 3350.2345 -***SCORE DIFFERENCE IS -.00088 +***SCORE DIFFERENCE IS -.00092 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/g.dnaBnoZ.conf *** Running scoring test ./scoring/g.dnaMix.conf @@ -6533,7 +6571,7 @@ pass 75: -3325.9822 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3325.9822 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6850,7 +6888,7 @@ pass 10: -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13931.0232 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7017,7 +7055,7 @@ pass 15: -14498.8854 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -14498.8854 -Time used = 0 hours, 0 minutes and 12 seconds +Time used = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -7271,7 +7309,7 @@ pass 35: -13306.2061 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) Looking for minimum length branches... Final score = -13306.2061 -Time used = 0 hours, 0 minutes and 8 seconds +Time used = 0 hours, 0 minutes and 4 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -9123,53 +9161,53 @@ 3000 -210.5163 0.010 1215 Reached termination condition! last topological improvement at gen 1215 -Improvement over last 500 gen = 0.03351 -Current score = -210.5119 +Improvement over last 500 gen = 0.03350 +Current score = -210.5120 Performing final optimizations... -pass 1 : -210.1432 (branch= 0.0000 alpha= 0.0976 pinv= 0.2252 eq freqs= 0.0000 rel rates= 0.0459) -pass 2 : -209.5398 (branch= 0.0000 alpha= 0.3289 pinv= 0.2490 eq freqs= 0.0028 rel rates= 0.0227) -pass 3 : -209.3300 (branch= 0.0346 alpha= 0.1445 pinv= 0.0169 eq freqs= 0.0069 rel rates= 0.0069) -pass 4 : -209.2583 (branch= 0.0471 alpha= 0.0154 pinv= 0.0019 eq freqs= 0.0011 rel rates= 0.0061) -pass 5 : -209.2211 (branch= 0.0234 alpha= 0.0069 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0069) -pass 6 : -209.1987 (branch= 0.0105 alpha= 0.0024 pinv= 0.0009 eq freqs= 0.0002 rel rates= 0.0084) -pass 7 : -209.1782 (branch= 0.0070 alpha= 0.0024 pinv= 0.0003 eq freqs= 0.0003 rel rates= 0.0104) -pass 8 : -209.1601 (branch= 0.0044 alpha= 0.0012 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0117) -pass 9 : -209.1461 (branch= 0.0023 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0111) -pass 10: -209.1349 (branch= 0.0009 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0099) -pass 11: -209.1252 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0089) -pass 12: -209.1165 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0082) -pass 13: -209.1087 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0075) -pass 14: -209.1016 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0069) -pass 15: -209.0948 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0065) -pass 16: -209.0886 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0061) -pass 17: -209.0827 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) -pass 18: -209.0772 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0054) -pass 19: -209.0719 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0052) -pass 20: -209.0671 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) - optimization up to ... -pass 30: -208.9998 (branch= 0.0075 alpha= 0.0000 pinv= 0.0003 eq freqs= 0.0012 rel rates= 0.0583) - optimization up to ... -pass 40: -208.8391 (branch= 0.0297 alpha= 0.0000 pinv= 0.0015 eq freqs= 0.0076 rel rates= 0.1218) - optimization up to ... -pass 50: -208.6974 (branch= 0.0133 alpha= 0.0000 pinv= 0.0014 eq freqs= 0.0057 rel rates= 0.1212) - optimization up to ... -pass 60: -208.6231 (branch= 0.0012 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0007 rel rates= 0.0722) - optimization up to ... -pass 70: -208.5738 (branch= 0.0003 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0488) +pass 1 : -210.1425 (branch= 0.0000 alpha= 0.0977 pinv= 0.2257 eq freqs= 0.0000 rel rates= 0.0461) +pass 2 : -209.5279 (branch= 0.0000 alpha= 0.3286 pinv= 0.2607 eq freqs= 0.0029 rel rates= 0.0224) +pass 3 : -209.3296 (branch= 0.0362 alpha= 0.1346 pinv= 0.0139 eq freqs= 0.0068 rel rates= 0.0067) +pass 4 : -209.2592 (branch= 0.0438 alpha= 0.0174 pinv= 0.0020 eq freqs= 0.0011 rel rates= 0.0061) +pass 5 : -209.2221 (branch= 0.0231 alpha= 0.0072 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0069) +pass 6 : -209.1992 (branch= 0.0107 alpha= 0.0026 pinv= 0.0009 eq freqs= 0.0002 rel rates= 0.0084) +pass 7 : -209.1783 (branch= 0.0076 alpha= 0.0022 pinv= 0.0003 eq freqs= 0.0003 rel rates= 0.0105) +pass 8 : -209.1601 (branch= 0.0045 alpha= 0.0012 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0118) +pass 9 : -209.1460 (branch= 0.0023 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0111) +pass 10: -209.1347 (branch= 0.0009 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0099) +pass 11: -209.1251 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0088) +pass 12: -209.1164 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0082) +pass 13: -209.1085 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0075) +pass 14: -209.1014 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0069) +pass 15: -209.0947 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0065) +pass 16: -209.0885 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0061) +pass 17: -209.0826 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) +pass 18: -209.0771 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0054) +pass 19: -209.0718 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0052) +pass 20: -209.0670 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) + optimization up to ... +pass 30: -208.9995 (branch= 0.0076 alpha= 0.0000 pinv= 0.0003 eq freqs= 0.0012 rel rates= 0.0584) + optimization up to ... +pass 40: -208.8390 (branch= 0.0297 alpha= 0.0000 pinv= 0.0015 eq freqs= 0.0076 rel rates= 0.1217) + optimization up to ... +pass 50: -208.6976 (branch= 0.0132 alpha= 0.0000 pinv= 0.0014 eq freqs= 0.0057 rel rates= 0.1211) + optimization up to ... +pass 60: -208.6234 (branch= 0.0012 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0007 rel rates= 0.0722) + optimization up to ... +pass 70: -208.5739 (branch= 0.0003 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0489) optimization up to ... -pass 80: -208.5378 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0356) +pass 80: -208.5380 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0356) optimization up to ... -pass 90: -208.5107 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0269) +pass 90: -208.5108 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0270) optimization up to ... -pass 100: -208.4896 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0210) +pass 100: -208.4896 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0211) optimization up to ... -pass 110: -208.4726 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0169) +pass 110: -208.4727 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0168) optimization up to ... pass 120: -208.4588 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0137) optimization up to ... -pass 130: -208.4472 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0115) +pass 130: -208.4473 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0115) optimization up to ... -pass 140: -208.4375 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0096) +pass 140: -208.4376 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0097) optimization up to ... pass 150: -208.4292 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0083) optimization up to ... @@ -9185,27 +9223,27 @@ optimization up to ... pass 210: -208.3981 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0037) optimization up to ... -pass 220: -208.3947 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) +pass 220: -208.3947 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0033) optimization up to ... -pass 230: -208.3916 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0031) +pass 230: -208.3917 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0030) optimization up to ... pass 240: -208.3889 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0028) optimization up to ... -pass 250: -208.3863 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0025) +pass 250: -208.3864 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0025) optimization up to ... -pass 260: -208.3840 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0023) +pass 260: -208.3841 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0023) optimization up to ... -pass 270: -208.3819 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) +pass 270: -208.3820 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) optimization up to ... -pass 280: -208.3800 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) +pass 280: -208.3800 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... -pass 290: -208.3781 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) +pass 290: -208.3782 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) optimization up to ... pass 300: -208.3765 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... -pass 310: -208.3749 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) +pass 310: -208.3750 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... -pass 320: -208.3734 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) +pass 320: -208.3735 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 330: -208.3721 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... @@ -9221,38 +9259,40 @@ optimization up to ... pass 390: -208.3655 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... -pass 400: -208.3646 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) +pass 400: -208.3647 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 410: -208.3638 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 420: -208.3630 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... -pass 430: -208.3623 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) +pass 430: -208.3623 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 440: -208.3615 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 450: -208.3609 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 460: -208.3602 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 460: -208.3602 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 470: -208.3596 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... -pass 480: -208.3593 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) +pass 480: -208.3592 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0004) optimization up to ... -pass 490: -208.3590 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) +pass 490: -208.3589 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... -pass 500: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) +pass 500: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... -pass 509: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) +pass 510: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) + optimization up to ... +pass 512: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... -Final score = -208.3584 -Time used = 0 hours, 0 minutes and 6 seconds +Final score = -208.3583 +Time used = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 122.311, AG = 188.753, AT = 6.967, CG = 204.934, CT = 194.972, GT = 1.000 + AC = 123.075, AG = 189.929, AT = 7.010, CG = 206.213, CT = 196.176, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2225 0.2906 0.2035 0.2835 Rate Heterogeneity Model: @@ -9276,11 +9316,11 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -208.3584 +Replicate 1 : -208.3583 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 122.3 188.8 6.967 204.9 195 1 0.223 0.291 0.203 0.283 999.900 0.278 +rep 1: 123.1 189.9 7.01 206.2 196.2 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL @@ -9417,43 +9457,43 @@ Current score = -211.2855 Performing final optimizations... pass 1 : -208.9741 (branch= 0.0000 alpha= 0.7616 pinv= 1.4574 eq freqs= 0.0064 rel rates= 0.0860) -pass 2 : -208.5660 (branch= 0.0406 alpha= 0.3181 pinv= 0.0098 eq freqs= 0.0118 rel rates= 0.0278) -pass 3 : -208.5065 (branch= 0.0302 alpha= 0.0021 pinv= 0.0000 eq freqs= 0.0017 rel rates= 0.0254) -pass 4 : -208.4811 (branch= 0.0032 alpha= 0.0000 pinv= 0.0017 eq freqs= 0.0000 rel rates= 0.0206) -pass 5 : -208.4602 (branch= 0.0023 alpha= 0.0007 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0175) -pass 6 : -208.4415 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0178) -pass 7 : -208.4245 (branch= 0.0009 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0158) -pass 8 : -208.4098 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0145) -pass 9 : -208.3958 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0136) -pass 10: -208.3830 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0126) -pass 11: -208.3715 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0114) -pass 12: -208.3611 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0104) -pass 13: -208.3514 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0096) -pass 14: -208.3425 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0089) -pass 15: -208.3343 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0082) -pass 16: -208.3268 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0075) -pass 17: -208.3195 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0073) -pass 18: -208.3129 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) -pass 19: -208.3065 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0063) -pass 20: -208.3007 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) +pass 2 : -208.5667 (branch= 0.0405 alpha= 0.3178 pinv= 0.0097 eq freqs= 0.0118 rel rates= 0.0276) +pass 3 : -208.5070 (branch= 0.0301 alpha= 0.0023 pinv= 0.0000 eq freqs= 0.0017 rel rates= 0.0256) +pass 4 : -208.4820 (branch= 0.0032 alpha= 0.0000 pinv= 0.0016 eq freqs= 0.0000 rel rates= 0.0202) +pass 5 : -208.4605 (branch= 0.0022 alpha= 0.0010 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0177) +pass 6 : -208.4419 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0177) +pass 7 : -208.4248 (branch= 0.0009 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0160) +pass 8 : -208.4101 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0143) +pass 9 : -208.3962 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0137) +pass 10: -208.3835 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0125) +pass 11: -208.3722 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0113) +pass 12: -208.3615 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0106) +pass 13: -208.3518 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0097) +pass 14: -208.3429 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0089) +pass 15: -208.3346 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0082) +pass 16: -208.3271 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0075) +pass 17: -208.3198 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0073) +pass 18: -208.3132 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) +pass 19: -208.3068 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0063) +pass 20: -208.3009 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) optimization up to ... -pass 30: -208.2567 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0439) +pass 30: -208.2568 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0440) optimization up to ... -pass 40: -208.2293 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0273) +pass 40: -208.2294 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0273) optimization up to ... -pass 50: -208.2105 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0187) +pass 50: -208.2105 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0189) optimization up to ... -pass 60: -208.1969 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0136) +pass 60: -208.1968 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0137) optimization up to ... pass 70: -208.1864 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0104) optimization up to ... pass 80: -208.1782 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0082) optimization up to ... -pass 90: -208.1715 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) +pass 90: -208.1716 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) optimization up to ... pass 100: -208.1661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0055) optimization up to ... -pass 110: -208.1614 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) +pass 110: -208.1615 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) optimization up to ... pass 120: -208.1575 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0039) optimization up to ... @@ -9463,7 +9503,7 @@ optimization up to ... pass 150: -208.1485 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) optimization up to ... -pass 160: -208.1461 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0023) +pass 160: -208.1461 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... pass 170: -208.1440 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) optimization up to ... @@ -9499,7 +9539,7 @@ optimization up to ... pass 330: -208.1265 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... -pass 340: -208.1259 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 340: -208.1260 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 350: -208.1254 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... @@ -9507,16 +9547,16 @@ optimization up to ... pass 370: -208.1244 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) optimization up to ... -pass 373: -208.1243 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) +pass 372: -208.1243 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.1243 -Time used = 0 hours, 0 minutes and 7 seconds +Time used = 0 hours, 0 minutes and 5 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 22.244, AG = 32.321, AT = 0.001, CG = 36.409, CT = 80.319, GT = 1.000 + AC = 22.239, AG = 32.314, AT = 0.001, CG = 36.402, CT = 80.320, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2210 0.3445 0.2161 0.2184 Rate Heterogeneity Model: @@ -9544,7 +9584,7 @@ Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 22.24 32.32 0.001 36.41 80.32 1 0.221 0.344 0.216 0.218 999.900 0.338 +rep 1: 22.24 32.31 0.001 36.4 80.32 1 0.221 0.344 0.216 0.218 999.900 0.338 Treelengths: TL @@ -9672,148 +9712,158 @@ Optimization precision reduced Optimizing parameters... improved 1.908 lnL Optimizing branchlengths... improved 0.702 lnL -2000 -210.9689 0.010 1502 +2000 -210.9688 0.010 1502 2500 -210.8711 0.010 1502 -3000 -210.7511 0.010 2883 -3500 -210.7006 0.010 2883 -4000 -210.6776 0.010 2883 -4500 -210.6528 0.010 2883 -5000 -210.5910 0.010 4692 -5500 -210.5256 0.010 4692 -6000 -210.4351 0.010 4692 -6500 -210.4174 0.010 4692 +3000 -210.7510 0.010 2883 +3500 -210.7005 0.010 2883 +4000 -210.6775 0.010 2883 +4500 -210.6526 0.010 2883 +5000 -210.5940 0.010 4692 +5500 -210.5367 0.010 5207 +6000 -210.4081 0.010 5812 +6500 -210.3701 0.010 5812 +7000 -210.3450 0.010 5812 +7500 -210.3290 0.010 5812 +8000 -210.1893 0.010 7789 +8500 -210.0964 0.010 7789 +9000 -210.0080 0.010 7789 +9500 -209.9339 0.010 7789 +10000 -209.8869 0.010 9713 + Optimizing parameters... improved 0.477 lnL + Optimizing branchlengths... improved 0.000 lnL +10500 -209.3800 0.010 9713 +11000 -209.3651 0.010 9713 +11500 -209.3535 0.010 9713 Reached termination condition! -last topological improvement at gen 4692 -Improvement over last 500 gen = 0.02291 -Current score = -210.4049 +last topological improvement at gen 9713 +Improvement over last 500 gen = 0.01208 +Current score = -209.3469 Performing final optimizations... -pass 1 : -209.9406 (branch= 0.0001 alpha= 0.0823 pinv= 0.2856 eq freqs= 0.0000 rel rates= 0.0962) -pass 2 : -209.3924 (branch= 0.0062 alpha= 0.3452 pinv= 0.1692 eq freqs= 0.0000 rel rates= 0.0276) -pass 3 : -209.2775 (branch= 0.0331 alpha= 0.0616 pinv= 0.0125 eq freqs= 0.0043 rel rates= 0.0032) -pass 4 : -209.2277 (branch= 0.0299 alpha= 0.0092 pinv= 0.0000 eq freqs= 0.0031 rel rates= 0.0077) -pass 5 : -209.1812 (branch= 0.0279 alpha= 0.0113 pinv= 0.0007 eq freqs= 0.0008 rel rates= 0.0058) -pass 6 : -209.1484 (branch= 0.0164 alpha= 0.0062 pinv= 0.0006 eq freqs= 0.0007 rel rates= 0.0089) -pass 7 : -209.1265 (branch= 0.0077 alpha= 0.0037 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0100) -pass 8 : -209.1126 (branch= 0.0038 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0092) -pass 9 : -209.1029 (branch= 0.0012 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0080) -pass 10: -209.0949 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0071) -pass 11: -209.0879 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0064) -pass 12: -209.0819 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0057) -pass 13: -209.0762 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0054) -pass 14: -209.0710 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0049) -pass 15: -209.0658 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) -pass 16: -209.0606 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0048) -pass 17: -209.0550 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) -pass 18: -209.0489 (branch= 0.0007 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0053) -pass 19: -209.0423 (branch= 0.0010 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0055) -pass 20: -209.0349 (branch= 0.0013 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0060) - optimization up to ... -pass 30: -208.9078 (branch= 0.0251 alpha= 0.0000 pinv= 0.0009 eq freqs= 0.0049 rel rates= 0.0960) +pass 1 : -209.2605 (branch= 0.0000 alpha= 0.0678 pinv= 0.0119 eq freqs= 0.0000 rel rates= 0.0066) +pass 2 : -209.2247 (branch= 0.0171 alpha= 0.0188 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) +pass 3 : -209.1584 (branch= 0.0447 alpha= 0.0139 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0029) +pass 4 : -209.1042 (branch= 0.0278 alpha= 0.0139 pinv= 0.0006 eq freqs= 0.0040 rel rates= 0.0079) +pass 5 : -209.0705 (branch= 0.0171 alpha= 0.0065 pinv= 0.0000 eq freqs= 0.0014 rel rates= 0.0088) +pass 6 : -209.0535 (branch= 0.0083 alpha= 0.0003 pinv= 0.0000 eq freqs= 0.0012 rel rates= 0.0071) +pass 7 : -209.0438 (branch= 0.0023 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0012 rel rates= 0.0062) +pass 8 : -209.0357 (branch= 0.0020 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0056) +pass 9 : -209.0274 (branch= 0.0020 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0059) +pass 10: -209.0185 (branch= 0.0023 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0062) +pass 11: -209.0085 (branch= 0.0028 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0068) +pass 12: -208.9981 (branch= 0.0025 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0004 rel rates= 0.0075) +pass 13: -208.9862 (branch= 0.0029 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0005 rel rates= 0.0084) +pass 14: -208.9729 (branch= 0.0033 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0006 rel rates= 0.0093) +pass 15: -208.9583 (branch= 0.0036 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0007 rel rates= 0.0102) +pass 16: -208.9425 (branch= 0.0038 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0008 rel rates= 0.0111) +pass 17: -208.9255 (branch= 0.0039 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0009 rel rates= 0.0120) +pass 18: -208.9075 (branch= 0.0038 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0010 rel rates= 0.0130) +pass 19: -208.8892 (branch= 0.0037 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0010 rel rates= 0.0135) +pass 20: -208.8700 (branch= 0.0036 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0010 rel rates= 0.0143) optimization up to ... -pass 40: -208.7374 (branch= 0.0228 alpha= 0.0000 pinv= 0.0019 eq freqs= 0.0081 rel rates= 0.1377) +pass 30: -208.7099 (branch= 0.0200 alpha= 0.0000 pinv= 0.0018 eq freqs= 0.0077 rel rates= 0.1306) optimization up to ... -pass 50: -208.6461 (branch= 0.0028 alpha= 0.0000 pinv= 0.0004 eq freqs= 0.0016 rel rates= 0.0865) +pass 40: -208.6301 (branch= 0.0017 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0010 rel rates= 0.0768) optimization up to ... -pass 60: -208.5898 (branch= 0.0004 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0556) +pass 50: -208.5785 (branch= 0.0003 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0510) optimization up to ... -pass 70: -208.5497 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0397) +pass 60: -208.5414 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0367) optimization up to ... -pass 80: -208.5198 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0297) +pass 70: -208.5134 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0278) optimization up to ... -pass 90: -208.4966 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0230) +pass 80: -208.4917 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0215) optimization up to ... -pass 100: -208.4783 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0182) +pass 90: -208.4743 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0173) optimization up to ... -pass 110: -208.4635 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0147) +pass 100: -208.4602 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0140) optimization up to ... -pass 120: -208.4511 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0123) +pass 110: -208.4485 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0117) optimization up to ... -pass 130: -208.4408 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0102) +pass 120: -208.4386 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0098) optimization up to ... -pass 140: -208.4321 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0087) +pass 130: -208.4301 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0084) optimization up to ... -pass 150: -208.4246 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0074) +pass 140: -208.4229 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0071) optimization up to ... -pass 160: -208.4181 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0065) +pass 150: -208.4167 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0062) optimization up to ... -pass 170: -208.4125 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0056) +pass 160: -208.4112 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0054) optimization up to ... -pass 180: -208.4076 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) +pass 170: -208.4065 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) optimization up to ... -pass 190: -208.4033 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0043) +pass 180: -208.4022 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0042) optimization up to ... -pass 200: -208.3994 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0039) +pass 190: -208.3984 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0038) optimization up to ... -pass 210: -208.3959 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) +pass 200: -208.3950 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) optimization up to ... -pass 220: -208.3928 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0031) +pass 210: -208.3919 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0031) optimization up to ... -pass 230: -208.3898 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) +pass 220: -208.3892 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0028) optimization up to ... -pass 240: -208.3872 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) +pass 230: -208.3866 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) optimization up to ... -pass 250: -208.3848 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) +pass 240: -208.3843 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0023) optimization up to ... -pass 260: -208.3826 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) +pass 250: -208.3821 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) optimization up to ... -pass 270: -208.3806 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) +pass 260: -208.3801 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... -pass 280: -208.3788 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) +pass 270: -208.3783 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) optimization up to ... -pass 290: -208.3771 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) +pass 280: -208.3766 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... -pass 300: -208.3754 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) +pass 290: -208.3751 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... -pass 310: -208.3740 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) +pass 300: -208.3736 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... -pass 320: -208.3726 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) +pass 310: -208.3722 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... -pass 330: -208.3713 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) +pass 320: -208.3710 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... -pass 340: -208.3700 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) +pass 330: -208.3698 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... -pass 350: -208.3689 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) +pass 340: -208.3686 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... -pass 360: -208.3678 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) +pass 350: -208.3676 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... -pass 370: -208.3668 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) +pass 360: -208.3666 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... -pass 380: -208.3659 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) +pass 370: -208.3656 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... -pass 390: -208.3650 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) +pass 380: -208.3647 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... -pass 400: -208.3641 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) +pass 390: -208.3639 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... -pass 410: -208.3633 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) +pass 400: -208.3631 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... -pass 420: -208.3625 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) +pass 410: -208.3623 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... -pass 430: -208.3618 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 420: -208.3616 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 440: -208.3611 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 430: -208.3609 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 450: -208.3604 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 440: -208.3603 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... -pass 460: -208.3598 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 450: -208.3596 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... -pass 470: -208.3592 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 460: -208.3592 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) optimization up to ... -pass 480: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) +pass 470: -208.3589 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... -pass 490: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) +pass 480: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... -pass 491: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) +pass 490: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... -Final score = -208.3584 -Time used = 0 hours, 0 minutes and 8 seconds +Final score = -208.3583 +Time used = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 122.675, AG = 189.304, AT = 6.999, CG = 205.533, CT = 195.564, GT = 1.000 + AC = 122.734, AG = 189.877, AT = 7.006, CG = 205.815, CT = 195.714, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2225 0.2906 0.2035 0.2835 + (ACGT) 0.2225 0.2906 0.2034 0.2835 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 999.9000 @@ -9840,11 +9890,11 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -208.3584 +Replicate 1 : -208.3583 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 122.7 189.3 6.999 205.5 195.6 1 0.223 0.291 0.203 0.283 999.900 0.278 +rep 1: 122.7 189.9 7.006 205.8 195.7 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL @@ -9971,73 +10021,73 @@ Optimization precision reduced Optimizing parameters... improved 1.494 lnL Optimizing branchlengths... improved 0.350 lnL -1500 -210.9424 0.010 1230 +1500 -210.9425 0.010 1230 2000 -210.7769 0.010 1230 2500 -210.6534 0.010 1230 3000 -210.6127 0.010 1230 Reached termination condition! last topological improvement at gen 1230 -Improvement over last 500 gen = 0.03865 +Improvement over last 500 gen = 0.03867 Current score = -210.5968 Performing final optimizations... -pass 1 : -210.1948 (branch= 0.0000 alpha= 0.1301 pinv= 0.2110 eq freqs= 0.0000 rel rates= 0.0609) -pass 2 : -209.5704 (branch= 0.0039 alpha= 0.3419 pinv= 0.2425 eq freqs= 0.0034 rel rates= 0.0327) -pass 3 : -209.3335 (branch= 0.0544 alpha= 0.1398 pinv= 0.0224 eq freqs= 0.0092 rel rates= 0.0111) -pass 4 : -209.2507 (branch= 0.0578 alpha= 0.0172 pinv= 0.0013 eq freqs= 0.0022 rel rates= 0.0042) -pass 5 : -209.2005 (branch= 0.0351 alpha= 0.0090 pinv= 0.0011 eq freqs= 0.0004 rel rates= 0.0046) -pass 6 : -209.1719 (branch= 0.0156 alpha= 0.0050 pinv= 0.0004 eq freqs= 0.0005 rel rates= 0.0072) -pass 7 : -209.1457 (branch= 0.0098 alpha= 0.0033 pinv= 0.0002 eq freqs= 0.0013 rel rates= 0.0115) -pass 8 : -209.1242 (branch= 0.0072 alpha= 0.0015 pinv= 0.0000 eq freqs= 0.0011 rel rates= 0.0117) -pass 9 : -209.1104 (branch= 0.0030 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0009 rel rates= 0.0098) -pass 10: -209.1003 (branch= 0.0011 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0084) -pass 11: -209.0921 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0074) -pass 12: -209.0851 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0065) -pass 13: -209.0788 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0059) -pass 14: -209.0733 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0054) -pass 15: -209.0680 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0051) -pass 16: -209.0632 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) -pass 17: -209.0583 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) -pass 18: -209.0534 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) -pass 19: -209.0481 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) -pass 20: -209.0424 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0052) - optimization up to ... -pass 30: -208.9333 (branch= 0.0198 alpha= 0.0000 pinv= 0.0007 eq freqs= 0.0039 rel rates= 0.0847) - optimization up to ... -pass 40: -208.7577 (branch= 0.0266 alpha= 0.0000 pinv= 0.0020 eq freqs= 0.0087 rel rates= 0.1383) - optimization up to ... -pass 50: -208.6571 (branch= 0.0041 alpha= 0.0000 pinv= 0.0006 eq freqs= 0.0023 rel rates= 0.0936) - optimization up to ... -pass 60: -208.5973 (branch= 0.0005 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0589) +pass 1 : -210.1949 (branch= 0.0000 alpha= 0.1301 pinv= 0.2109 eq freqs= 0.0000 rel rates= 0.0609) +pass 2 : -209.5752 (branch= 0.0039 alpha= 0.3416 pinv= 0.2382 eq freqs= 0.0034 rel rates= 0.0327) +pass 3 : -209.3362 (branch= 0.0533 alpha= 0.1441 pinv= 0.0218 eq freqs= 0.0090 rel rates= 0.0108) +pass 4 : -209.2540 (branch= 0.0528 alpha= 0.0215 pinv= 0.0016 eq freqs= 0.0022 rel rates= 0.0041) +pass 5 : -209.2037 (branch= 0.0351 alpha= 0.0090 pinv= 0.0010 eq freqs= 0.0004 rel rates= 0.0048) +pass 6 : -209.1737 (branch= 0.0170 alpha= 0.0052 pinv= 0.0003 eq freqs= 0.0005 rel rates= 0.0070) +pass 7 : -209.1473 (branch= 0.0104 alpha= 0.0033 pinv= 0.0002 eq freqs= 0.0012 rel rates= 0.0111) +pass 8 : -209.1252 (branch= 0.0071 alpha= 0.0022 pinv= 0.0000 eq freqs= 0.0011 rel rates= 0.0118) +pass 9 : -209.1109 (branch= 0.0034 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0009 rel rates= 0.0099) +pass 10: -209.1007 (branch= 0.0012 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0084) +pass 11: -209.0923 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0074) +pass 12: -209.0852 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0066) +pass 13: -209.0790 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0060) +pass 14: -209.0734 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0054) +pass 15: -209.0681 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0051) +pass 16: -209.0633 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) +pass 17: -209.0584 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) +pass 18: -209.0535 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) +pass 19: -209.0482 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) +pass 20: -209.0425 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0052) + optimization up to ... +pass 30: -208.9336 (branch= 0.0198 alpha= 0.0000 pinv= 0.0007 eq freqs= 0.0039 rel rates= 0.0846) + optimization up to ... +pass 40: -208.7570 (branch= 0.0268 alpha= 0.0000 pinv= 0.0020 eq freqs= 0.0088 rel rates= 0.1390) + optimization up to ... +pass 50: -208.6569 (branch= 0.0042 alpha= 0.0000 pinv= 0.0006 eq freqs= 0.0023 rel rates= 0.0931) + optimization up to ... +pass 60: -208.5971 (branch= 0.0005 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0588) optimization up to ... -pass 70: -208.5553 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0416) +pass 70: -208.5550 (branch= 0.0002 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0417) optimization up to ... -pass 80: -208.5239 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0311) +pass 80: -208.5239 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0309) optimization up to ... -pass 90: -208.4999 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0238) +pass 90: -208.4998 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0239) optimization up to ... -pass 100: -208.4809 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0189) +pass 100: -208.4809 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0188) optimization up to ... pass 110: -208.4656 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0152) optimization up to ... pass 120: -208.4529 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0126) optimization up to ... -pass 130: -208.4423 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0105) +pass 130: -208.4424 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0105) optimization up to ... -pass 140: -208.4334 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0089) +pass 140: -208.4333 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0090) optimization up to ... -pass 150: -208.4257 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0076) +pass 150: -208.4256 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0076) optimization up to ... -pass 160: -208.4191 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) +pass 160: -208.4191 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0065) optimization up to ... pass 170: -208.4134 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0057) optimization up to ... -pass 180: -208.4083 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) +pass 180: -208.4084 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) optimization up to ... pass 190: -208.4039 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0044) optimization up to ... -pass 200: -208.3999 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) +pass 200: -208.4000 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0039) optimization up to ... -pass 210: -208.3963 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0036) +pass 210: -208.3964 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0035) optimization up to ... pass 220: -208.3932 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... @@ -10051,7 +10101,7 @@ optimization up to ... pass 270: -208.3809 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... -pass 280: -208.3790 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) +pass 280: -208.3791 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 290: -208.3773 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... @@ -10091,22 +10141,20 @@ optimization up to ... pass 470: -208.3593 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... -pass 480: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 480: -208.3588 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) optimization up to ... -pass 490: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) - optimization up to ... -pass 492: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) +pass 490: -208.3585 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... -Final score = -208.3584 -Time used = 0 hours, 0 minutes and 7 seconds +Final score = -208.3585 +Time used = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 122.522, AG = 189.082, AT = 6.990, CG = 205.290, CT = 195.326, GT = 1.000 + AC = 121.995, AG = 188.263, AT = 6.960, CG = 204.402, CT = 194.488, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2225 0.2906 0.2035 0.2835 + (ACGT) 0.2225 0.2905 0.2035 0.2835 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 999.9000 @@ -10133,11 +10181,11 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -208.3584 +Replicate 1 : -208.3585 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 122.5 189.1 6.99 205.3 195.3 1 0.223 0.291 0.203 0.283 999.900 0.278 +rep 1: 122 188.3 6.96 204.4 194.5 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL @@ -12809,6 +12857,13 @@ 500 -90.3850 0.500 215 600 -90.2906 0.500 215 700 -90.2169 0.500 215 +800 -90.1648 0.500 215 +Optimization precision reduced + Optimizing parameters... improved 0.159 lnL + Optimizing branchlengths... improved 0.317 lnL +900 -88.9507 0.010 879 +1000 -88.8871 0.010 879 +1100 -88.8475 0.010 879 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12905,18 +12960,11 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 742, seed 2077777172, best lnL -90.186 +Bootstrap rep 1 (of 1) generation 1155, seed 391600625, best lnL -88.847 gen current_lnL precision last_tree_imp -742 -90.1864 0.500 215 -800 -90.1648 0.500 215 -Optimization precision reduced - Optimizing parameters... improved 0.159 lnL - Optimizing branchlengths... improved 0.317 lnL -900 -88.9507 0.010 879 -1000 -88.8871 0.010 879 -NOTE: ****Specified generation limit (1000) reached... +1155 -88.8465 0.010 879 -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones @@ -12928,41 +12976,37 @@ 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 0.9045 + 0.9578 with an invariant (invariable) site category, proportion estimated - 0.1355 + 0.1315 Substitution rate categories under this model: rate proportion - 0.0000 0.1355 - 0.1669 0.2882 - 0.6855 0.2882 - 2.1476 0.2882 + 0.0000 0.1315 + 0.1794 0.2895 + 0.7011 0.2895 + 2.1195 0.2895 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. -NOTE: ***Search was terminated before full auto-termination condition was reached! -Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** - - ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -88.8871 +Replicate 1 : -88.8465 Parameter estimates: alpha pinv -rep 1: 0.904 0.136 +rep 1: 0.958 0.132 Treelengths: TL -rep 1: 2.441 +rep 1: 2.331 Saving best tree to bootstrap file ch.a.G3.boot.tre -WARNING: Tree from prematurely terminated search saved to bootstrap file +>>>Completed Bootstrap rep 1<<< ####################################################### TREEFILES PASS Running checkpoint test ./check/a.G4.conf @@ -13085,6 +13129,12 @@ 300 -112.3224 0.500 84 400 -112.1061 0.500 84 500 -111.8129 0.500 84 +600 -111.7788 0.500 84 +Optimization precision reduced + Optimizing parameters... improved 0.386 lnL + Optimizing branchlengths... improved 0.390 lnL +700 -110.8142 0.010 615 +800 -110.5642 0.010 707 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13171,15 +13221,9 @@ STARTING RUN Restarting from checkpoint... - generation 554, seed 2134268789, best lnL -111.786 + generation 883, seed 1342804714, best lnL -110.555 gen current_lnL precision last_tree_imp -554 -111.7863 0.500 84 -600 -111.7788 0.500 84 -Optimization precision reduced - Optimizing parameters... improved 0.386 lnL - Optimizing branchlengths... improved 0.390 lnL -700 -110.8142 0.010 615 -800 -110.5642 0.010 707 +883 -110.5555 0.010 707 900 -110.5555 0.010 707 1000 -110.5065 0.010 707 NOTE: ****Specified generation limit (1000) reached... @@ -13367,6 +13411,17 @@ 1700 -111.6818 0.010 563 1800 -111.6818 0.010 563 1900 -111.6818 0.010 563 +2000 -111.6817 0.010 563 +2100 -111.6817 0.010 563 +2200 -111.6817 0.010 563 +2300 -111.6817 0.010 563 +2400 -111.6817 0.010 563 +2500 -111.6817 0.010 563 +2600 -111.6816 0.010 563 +2700 -111.6816 0.010 563 +2800 -111.6816 0.010 563 +2900 -111.6815 0.010 563 +3000 -111.6815 0.010 563 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13452,9 +13507,9 @@ STARTING RUN Restarting from checkpoint... - generation 1965, seed 702611603, best lnL -111.682 + generation 3064, seed 1298060065, best lnL -111.682 gen current_lnL precision last_tree_imp -1965 -111.6817 0.010 563 +3064 -111.6815 0.010 563 MODEL REPORT - Parameter values are FINAL Model 1 @@ -13470,7 +13525,7 @@ no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 1 branches were collapsed. + No branches were short enough to be collapsed. Saving site likelihoods to file ch.a.sitelikes.log ... @@ -13478,14 +13533,14 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -111.6817 +Replicate 1 : -111.6815 Parameter estimates: Model contains no estimated parameters Treelengths: TL -rep 1: 2.605 +rep 1: 2.607 Saving final tree from best search rep (#1) to ch.a.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.internalstates.log @@ -13618,6 +13673,11 @@ 40 -205.6371 0.500 18 50 -205.6175 0.500 18 60 -205.5990 0.500 53 +70 -205.5741 0.500 53 +80 -205.4022 0.500 76 +90 -205.3871 0.500 76 +100 -205.3829 0.500 76 +110 -205.3431 0.500 106 NOTE: ****Specified time limit (10 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13704,16 +13764,11 @@ STARTING RUN Restarting from checkpoint... - generation 60, seed 1308822963, best lnL -205.599 + generation 116, seed 1919088460, best lnL -205.343 gen current_lnL precision last_tree_imp -60 -205.5990 0.500 53 -70 -205.5741 0.500 53 -80 -205.4022 0.500 76 -90 -205.3871 0.500 76 -100 -205.3829 0.500 76 -NOTE: ****Specified generation limit (100) reached... +116 -205.3431 0.500 106 -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates @@ -13745,17 +13800,12 @@ No branches were short enough to be collapsed. Saving site likelihoods to file ch.c.M3x2.sitelikes.log ... -WARNING: Site likelihoods being output on prematurely terminated search ... - -NOTE: ***Search was terminated before full auto-termination condition was reached! -Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** - ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -205.3829 +Replicate 1 : -205.3431 Parameter estimates: w(0) p(0) w(1) p(1) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) @@ -13763,13 +13813,11 @@ Treelengths: TL -rep 1: 7.371 +rep 1: 7.779 Saving final tree from best search rep (#1) to ch.c.M3x2.best.tre Inferring internal state probabilities on best tree... saving to file ch.c.M3x2.internalstates.log -WARNING: Internal states inferred on tree from prematurely terminated search - ####################################################### TREEFILES PASS Running checkpoint test ./check/c.conf @@ -13900,6 +13948,11 @@ 30 -195.2776 0.500 0 40 -195.2555 0.500 0 50 -195.2137 0.500 0 +60 -195.1629 0.500 0 +70 -195.0043 0.500 0 +80 -194.9478 0.500 0 +90 -194.9092 0.500 0 +100 -194.9092 0.500 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13987,17 +14040,11 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 52, seed 754137322, best lnL -195.214 +Bootstrap rep 1 (of 1) generation 102, seed 1947138151, best lnL -194.909 gen current_lnL precision last_tree_imp -52 -195.2137 0.500 0 -60 -195.1629 0.500 0 -70 -195.0043 0.500 0 -80 -194.9478 0.500 0 -90 -194.9092 0.500 0 -100 -194.9092 0.500 0 -NOTE: ****Specified generation limit (100) reached... +102 -194.9092 0.500 0 -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 61 (codon data, standard code) One estimated dN/dS ratio (aka omega) = 0.120505 @@ -14026,10 +14073,6 @@ No branches were short enough to be collapsed. -NOTE: ***Search was terminated before full auto-termination condition was reached! -Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** - - ####################################################### Completed 1 replicate search(es) (of 1). @@ -14046,7 +14089,7 @@ Saving best tree to bootstrap file ch.c.boot.tre -WARNING: Tree from prematurely terminated search saved to bootstrap file +>>>Completed Bootstrap rep 1<<< ####################################################### TREEFILES PASS Running checkpoint test ./check/g.dnaBnoZ.conf @@ -14211,6 +14254,16 @@ 1200 -3352.6779 0.010 0 1300 -3352.5564 0.010 0 1400 -3352.3174 0.010 0 +1500 -3352.2778 0.010 0 +1600 -3352.1759 0.010 0 +1700 -3352.1636 0.010 0 +1800 -3352.0841 0.010 0 +1900 -3351.7369 0.010 0 +2000 -3351.6702 0.010 0 +2100 -3351.4829 0.010 0 +2200 -3351.2993 0.010 0 +2300 -3351.2513 0.010 0 +2400 -3351.2155 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14314,78 +14367,87 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 1408, seed 1138782053, best lnL -3352.317 +Search rep 1 (of 2) generation 2446, seed 658475098, best lnL -3351.203 gen current_lnL precision last_tree_imp -1408 -3352.3174 0.010 0 -1500 -3352.2778 0.010 0 -1600 -3352.1759 0.010 0 -1700 -3352.1636 0.010 0 -1800 -3352.0841 0.010 0 -1900 -3351.7369 0.010 0 -2000 -3351.6702 0.010 0 -2100 -3351.4829 0.010 0 -2200 -3351.2993 0.010 0 -2300 -3351.2513 0.010 0 -2400 -3351.2155 0.010 0 +2446 -3351.2027 0.010 0 2500 -3351.1237 0.010 0 +2600 -3351.0612 0.010 0 +2700 -3351.0610 0.010 0 +2800 -3351.0554 0.010 0 +2900 -3351.0122 0.010 0 +3000 -3351.0122 0.010 0 +3100 -3350.9995 0.010 0 +3200 -3350.9822 0.010 0 +3300 -3350.9797 0.010 0 +3400 -3350.9771 0.010 0 +3500 -3350.9769 0.010 0 +3600 -3350.9764 0.010 0 +3700 -3350.9432 0.010 0 +3800 -3350.9290 0.010 0 +3900 -3350.8687 0.010 0 +4000 -3350.8687 0.010 0 +4100 -3350.8589 0.010 0 +4200 -3350.8534 0.010 0 +4300 -3350.8532 0.010 0 +4400 -3350.8506 0.010 0 +4500 -3350.8506 0.010 0 +4600 -3350.8163 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3351.1237 +Current score = -3350.8150 Performing final optimizations... -pass 1 : -3351.0219 (branch= 0.0000 alpha= 0.0000 pinv= 0.0230 eq freqs= 0.0150 rel rates= 0.0606 subset rates= 0.0032) -pass 2 : -3350.9202 (branch= 0.0031 alpha= 0.0104 pinv= 0.0174 eq freqs= 0.0000 rel rates= 0.0709 subset rates= 0.0000) -pass 3 : -3350.8301 (branch= 0.0090 alpha= 0.0165 pinv= 0.0154 eq freqs= 0.0014 rel rates= 0.0458 subset rates= 0.0020) -pass 4 : -3350.7577 (branch= 0.0058 alpha= 0.0131 pinv= 0.0145 eq freqs= 0.0000 rel rates= 0.0378 subset rates= 0.0012) -pass 5 : -3350.6916 (branch= 0.0065 alpha= 0.0131 pinv= 0.0135 eq freqs= 0.0000 rel rates= 0.0317 subset rates= 0.0013) -pass 6 : -3350.6372 (branch= 0.0025 alpha= 0.0112 pinv= 0.0124 eq freqs= 0.0002 rel rates= 0.0281 subset rates= 0.0000) -pass 7 : -3350.5870 (branch= 0.0006 alpha= 0.0116 pinv= 0.0112 eq freqs= 0.0000 rel rates= 0.0257 subset rates= 0.0011) -pass 8 : -3350.5427 (branch= 0.0019 alpha= 0.0106 pinv= 0.0102 eq freqs= 0.0003 rel rates= 0.0213 subset rates= 0.0000) -pass 9 : -3350.5047 (branch= 0.0004 alpha= 0.0096 pinv= 0.0093 eq freqs= 0.0001 rel rates= 0.0187 subset rates= 0.0000) -pass 10: -3350.4688 (branch= 0.0001 alpha= 0.0091 pinv= 0.0089 eq freqs= 0.0000 rel rates= 0.0165 subset rates= 0.0012) -pass 11: -3350.4392 (branch= 0.0007 alpha= 0.0080 pinv= 0.0075 eq freqs= 0.0000 rel rates= 0.0133 subset rates= 0.0000) -pass 12: -3350.4134 (branch= 0.0001 alpha= 0.0071 pinv= 0.0068 eq freqs= 0.0000 rel rates= 0.0119 subset rates= 0.0000) -pass 13: -3350.3903 (branch= 0.0000 alpha= 0.0067 pinv= 0.0060 eq freqs= 0.0000 rel rates= 0.0104 subset rates= 0.0000) -pass 14: -3350.3699 (branch= 0.0000 alpha= 0.0060 pinv= 0.0054 eq freqs= 0.0000 rel rates= 0.0090 subset rates= 0.0000) -pass 15: -3350.3520 (branch= 0.0000 alpha= 0.0054 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0077 subset rates= 0.0000) -pass 16: -3350.3363 (branch= 0.0000 alpha= 0.0048 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0067 subset rates= 0.0000) -pass 17: -3350.3226 (branch= 0.0000 alpha= 0.0042 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0057 subset rates= 0.0000) -pass 18: -3350.3107 (branch= 0.0000 alpha= 0.0037 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0049 subset rates= 0.0000) -pass 19: -3350.3003 (branch= 0.0000 alpha= 0.0033 pinv= 0.0029 eq freqs= 0.0000 rel rates= 0.0042 subset rates= 0.0000) -pass 20: -3350.2912 (branch= 0.0000 alpha= 0.0029 pinv= 0.0026 eq freqs= 0.0000 rel rates= 0.0036 subset rates= 0.0000) - optimization up to ... -pass 30: -3350.2462 (branch= 0.0000 alpha= 0.0144 pinv= 0.0130 eq freqs= 0.0001 rel rates= 0.0175 subset rates= 0.0000) - optimization up to ... -pass 40: -3350.2361 (branch= 0.0000 alpha= 0.0031 pinv= 0.0029 eq freqs= 0.0000 rel rates= 0.0041 subset rates= 0.0000) +pass 1 : -3350.7667 (branch= 0.0000 alpha= 0.0000 pinv= 0.0231 eq freqs= 0.0001 rel rates= 0.0252 subset rates= 0.0000) +pass 2 : -3350.7202 (branch= 0.0033 alpha= 0.0101 pinv= 0.0167 eq freqs= 0.0000 rel rates= 0.0152 subset rates= 0.0010) +pass 3 : -3350.6643 (branch= 0.0087 alpha= 0.0173 pinv= 0.0146 eq freqs= 0.0000 rel rates= 0.0153 subset rates= 0.0000) +pass 4 : -3350.6136 (branch= 0.0040 alpha= 0.0124 pinv= 0.0138 eq freqs= 0.0014 rel rates= 0.0163 subset rates= 0.0028) +pass 5 : -3350.5659 (branch= 0.0068 alpha= 0.0122 pinv= 0.0128 eq freqs= 0.0004 rel rates= 0.0141 subset rates= 0.0014) +pass 6 : -3350.5283 (branch= 0.0024 alpha= 0.0106 pinv= 0.0116 eq freqs= 0.0000 rel rates= 0.0129 subset rates= 0.0000) +pass 7 : -3350.4925 (branch= 0.0008 alpha= 0.0111 pinv= 0.0104 eq freqs= 0.0000 rel rates= 0.0121 subset rates= 0.0015) +pass 8 : -3350.4617 (branch= 0.0018 alpha= 0.0096 pinv= 0.0095 eq freqs= 0.0000 rel rates= 0.0097 subset rates= 0.0000) +pass 9 : -3350.4338 (branch= 0.0002 alpha= 0.0087 pinv= 0.0086 eq freqs= 0.0000 rel rates= 0.0094 subset rates= 0.0011) +pass 10: -3350.4092 (branch= 0.0010 alpha= 0.0081 pinv= 0.0077 eq freqs= 0.0000 rel rates= 0.0077 subset rates= 0.0000) +pass 11: -3350.3878 (branch= 0.0001 alpha= 0.0072 pinv= 0.0069 eq freqs= 0.0000 rel rates= 0.0071 subset rates= 0.0000) +pass 12: -3350.3684 (branch= 0.0000 alpha= 0.0068 pinv= 0.0062 eq freqs= 0.0000 rel rates= 0.0064 subset rates= 0.0000) +pass 13: -3350.3512 (branch= 0.0000 alpha= 0.0062 pinv= 0.0055 eq freqs= 0.0000 rel rates= 0.0055 subset rates= 0.0000) +pass 14: -3350.3359 (branch= 0.0000 alpha= 0.0055 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0048 subset rates= 0.0000) +pass 15: -3350.3225 (branch= 0.0000 alpha= 0.0049 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0041 subset rates= 0.0000) +pass 16: -3350.3107 (branch= 0.0000 alpha= 0.0043 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0036 subset rates= 0.0000) +pass 17: -3350.3004 (branch= 0.0000 alpha= 0.0038 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0031 subset rates= 0.0000) +pass 18: -3350.2914 (branch= 0.0000 alpha= 0.0034 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0027 subset rates= 0.0000) +pass 19: -3350.2835 (branch= 0.0000 alpha= 0.0030 pinv= 0.0026 eq freqs= 0.0000 rel rates= 0.0023 subset rates= 0.0000) +pass 20: -3350.2766 (branch= 0.0000 alpha= 0.0026 pinv= 0.0023 eq freqs= 0.0000 rel rates= 0.0020 subset rates= 0.0000) + optimization up to ... +pass 30: -3350.2425 (branch= 0.0000 alpha= 0.0128 pinv= 0.0116 eq freqs= 0.0000 rel rates= 0.0096 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2339 (branch= 0.0000 alpha= 0.0006 pinv= 0.0005 eq freqs= 0.0000 rel rates= 0.0011 subset rates= 0.0000) +pass 40: -3350.2350 (branch= 0.0000 alpha= 0.0027 pinv= 0.0025 eq freqs= 0.0000 rel rates= 0.0023 subset rates= 0.0000) optimization up to ... -pass 60: -3350.2335 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 50: -3350.2335 (branch= 0.0000 alpha= 0.0005 pinv= 0.0005 eq freqs= 0.0000 rel rates= 0.0005 subset rates= 0.0000) optimization up to ... -pass 70: -3350.2334 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 60: -3350.2332 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) optimization up to ... -pass 71: -3350.2334 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 62: -3350.2332 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -3350.2334 -Time used so far = 0 hours, 0 minutes and 13 seconds +Final score = -3350.2332 +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 = 3.116, AG = 10.417, AT = 2.691, CG = 0.001, CT = 21.902, GT = 1.000 + AC = 3.111, AG = 10.405, AT = 2.687, CG = 0.001, CT = 21.893, 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 + 0.5770 with an invariant (invariable) site category, proportion estimated - 0.3662 + 0.3655 Substitution rate categories under this model: rate proportion - 0.0000 0.3662 - 0.0488 0.1584 - 0.3003 0.1584 - 0.8702 0.1584 - 2.7807 0.1584 + 0.0000 0.3655 + 0.0484 0.1586 + 0.2993 0.1586 + 0.8691 0.1586 + 2.7832 0.1586 Model 2 Number of states = 2 (binary data) @@ -14410,20 +14472,20 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3350.2334 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3350.2332 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.116 10.42 2.691 0.001 21.9 1 0.333 0.222 0.157 0.288 0.579 0.366 +rep 1: 3.111 10.41 2.687 0.001 21.89 1 0.333 0.222 0.157 0.288 0.577 0.365 Partition model subset 2: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) -rep 1: 0.788 1.820 0.180 +rep 1: 0.789 1.820 0.180 Saving final tree from best search rep (#1) to ch.g.dnaBnoZ.best.tre ####################################################### @@ -14573,6 +14635,13 @@ 200 -3324.7543 0.500 1 300 -3324.3007 0.500 1 400 -3323.9848 0.500 1 +500 -3323.6818 0.500 1 +600 -3323.3459 0.500 1 +Optimization precision reduced + Optimizing parameters... improved 1.812 lnL + Optimizing branchlengths... improved 0.023 lnL +700 -3321.3649 0.255 1 +800 -3321.0294 0.255 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14673,75 +14742,77 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 493, seed 1330261031, best lnL -3323.682 +Search rep 1 (of 2) generation 873, seed 866366283, best lnL -3321.014 gen current_lnL precision last_tree_imp -493 -3323.6818 0.500 1 -500 -3323.6818 0.500 1 -600 -3323.3459 0.500 1 -Optimization precision reduced - Optimizing parameters... improved 1.812 lnL - Optimizing branchlengths... improved 0.023 lnL -700 -3321.3649 0.255 1 -800 -3321.0294 0.255 1 +873 -3321.0142 0.255 1 900 -3321.0142 0.255 1 +1000 -3320.9667 0.255 1 +1100 -3320.8654 0.255 1 +Optimization precision reduced + Optimizing parameters... improved 0.576 lnL + Optimizing branchlengths... improved 0.057 lnL +1200 -3320.1587 0.010 1 +1300 -3320.0989 0.010 1 +1400 -3320.0706 0.010 1 +1500 -3320.0213 0.010 1 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3320.9684 +Current score = -3320.0123 Performing final optimizations... -pass 1 : -3320.2910 (branch= 0.0812 alpha= 0.0000 pinv= 0.0165 eq freqs= 0.0053 rel rates= 0.5492 ins/del rates= 0.0252) -pass 2 : -3319.8331 (branch= 0.0649 alpha= 0.0065 pinv= 0.0163 eq freqs= 0.0000 rel rates= 0.3496 ins/del rates= 0.0205) -pass 3 : -3319.4759 (branch= 0.0441 alpha= 0.0079 pinv= 0.0160 eq freqs= 0.0070 rel rates= 0.2671 ins/del rates= 0.0151) -pass 4 : -3319.2077 (branch= 0.0229 alpha= 0.0107 pinv= 0.0153 eq freqs= 0.0013 rel rates= 0.2089 ins/del rates= 0.0091) -pass 5 : -3318.9892 (branch= 0.0167 alpha= 0.0109 pinv= 0.0147 eq freqs= 0.0012 rel rates= 0.1686 ins/del rates= 0.0065) -pass 6 : -3318.8024 (branch= 0.0125 alpha= 0.0097 pinv= 0.0138 eq freqs= 0.0011 rel rates= 0.1443 ins/del rates= 0.0054) -pass 7 : -3318.6458 (branch= 0.0078 alpha= 0.0103 pinv= 0.0129 eq freqs= 0.0004 rel rates= 0.1220 ins/del rates= 0.0033) -pass 8 : -3318.5189 (branch= 0.0049 alpha= 0.0104 pinv= 0.0121 eq freqs= 0.0002 rel rates= 0.0973 ins/del rates= 0.0021) -pass 9 : -3318.4112 (branch= 0.0035 alpha= 0.0097 pinv= 0.0112 eq freqs= 0.0002 rel rates= 0.0816 ins/del rates= 0.0015) -pass 10: -3318.3194 (branch= 0.0023 alpha= 0.0095 pinv= 0.0109 eq freqs= 0.0002 rel rates= 0.0678 ins/del rates= 0.0010) -pass 11: -3318.2442 (branch= 0.0015 alpha= 0.0089 pinv= 0.0094 eq freqs= 0.0002 rel rates= 0.0545 ins/del rates= 0.0007) -pass 12: -3318.1805 (branch= 0.0010 alpha= 0.0083 pinv= 0.0086 eq freqs= 0.0001 rel rates= 0.0453 ins/del rates= 0.0004) -pass 13: -3318.1262 (branch= 0.0007 alpha= 0.0078 pinv= 0.0078 eq freqs= 0.0001 rel rates= 0.0376 ins/del rates= 0.0003) -pass 14: -3318.0799 (branch= 0.0004 alpha= 0.0072 pinv= 0.0071 eq freqs= 0.0001 rel rates= 0.0314 ins/del rates= 0.0002) -pass 15: -3318.0407 (branch= 0.0003 alpha= 0.0067 pinv= 0.0064 eq freqs= 0.0001 rel rates= 0.0257 ins/del rates= 0.0001) -pass 16: -3318.0068 (branch= 0.0002 alpha= 0.0060 pinv= 0.0057 eq freqs= 0.0001 rel rates= 0.0218 ins/del rates= 0.0001) -pass 17: -3317.9776 (branch= 0.0001 alpha= 0.0054 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0184 ins/del rates= 0.0000) -pass 18: -3317.9523 (branch= 0.0001 alpha= 0.0049 pinv= 0.0046 eq freqs= 0.0000 rel rates= 0.0157 ins/del rates= 0.0000) -pass 19: -3317.9303 (branch= 0.0000 alpha= 0.0044 pinv= 0.0041 eq freqs= 0.0000 rel rates= 0.0134 ins/del rates= 0.0000) -pass 20: -3317.9112 (branch= 0.0000 alpha= 0.0039 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0114 ins/del rates= 0.0000) - optimization up to ... -pass 30: -3317.8162 (branch= 0.0001 alpha= 0.0212 pinv= 0.0195 eq freqs= 0.0001 rel rates= 0.0541 ins/del rates= 0.0000) - optimization up to ... -pass 40: -3317.7937 (branch= 0.0001 alpha= 0.0052 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0124 ins/del rates= 0.0000) +pass 1 : -3319.5850 (branch= 0.0156 alpha= 0.0000 pinv= 0.0136 eq freqs= 0.0000 rel rates= 0.3437 ins/del rates= 0.0543) +pass 2 : -3319.2796 (branch= 0.0317 alpha= 0.0164 pinv= 0.0158 eq freqs= 0.0097 rel rates= 0.2223 ins/del rates= 0.0095) +pass 3 : -3319.0488 (branch= 0.0289 alpha= 0.0140 pinv= 0.0153 eq freqs= 0.0000 rel rates= 0.1665 ins/del rates= 0.0061) +pass 4 : -3318.8659 (branch= 0.0166 alpha= 0.0108 pinv= 0.0148 eq freqs= 0.0022 rel rates= 0.1332 ins/del rates= 0.0054) +pass 5 : -3318.7048 (branch= 0.0129 alpha= 0.0113 pinv= 0.0140 eq freqs= 0.0011 rel rates= 0.1173 ins/del rates= 0.0045) +pass 6 : -3318.5751 (branch= 0.0079 alpha= 0.0112 pinv= 0.0131 eq freqs= 0.0005 rel rates= 0.0936 ins/del rates= 0.0033) +pass 7 : -3318.4652 (branch= 0.0052 alpha= 0.0104 pinv= 0.0123 eq freqs= 0.0006 rel rates= 0.0793 ins/del rates= 0.0022) +pass 8 : -3318.3708 (branch= 0.0034 alpha= 0.0103 pinv= 0.0113 eq freqs= 0.0002 rel rates= 0.0677 ins/del rates= 0.0015) +pass 9 : -3318.2900 (branch= 0.0027 alpha= 0.0092 pinv= 0.0105 eq freqs= 0.0001 rel rates= 0.0572 ins/del rates= 0.0011) +pass 10: -3318.2209 (branch= 0.0017 alpha= 0.0090 pinv= 0.0096 eq freqs= 0.0001 rel rates= 0.0480 ins/del rates= 0.0008) +pass 11: -3318.1619 (branch= 0.0011 alpha= 0.0085 pinv= 0.0087 eq freqs= 0.0001 rel rates= 0.0401 ins/del rates= 0.0005) +pass 12: -3318.1113 (branch= 0.0007 alpha= 0.0079 pinv= 0.0079 eq freqs= 0.0001 rel rates= 0.0336 ins/del rates= 0.0003) +pass 13: -3318.0684 (branch= 0.0004 alpha= 0.0074 pinv= 0.0072 eq freqs= 0.0001 rel rates= 0.0275 ins/del rates= 0.0002) +pass 14: -3318.0315 (branch= 0.0003 alpha= 0.0068 pinv= 0.0065 eq freqs= 0.0001 rel rates= 0.0232 ins/del rates= 0.0001) +pass 15: -3317.9994 (branch= 0.0002 alpha= 0.0061 pinv= 0.0059 eq freqs= 0.0000 rel rates= 0.0198 ins/del rates= 0.0001) +pass 16: -3317.9715 (branch= 0.0001 alpha= 0.0055 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0169 ins/del rates= 0.0000) +pass 17: -3317.9472 (branch= 0.0001 alpha= 0.0050 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0145 ins/del rates= 0.0000) +pass 18: -3317.9261 (branch= 0.0000 alpha= 0.0045 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0123 ins/del rates= 0.0000) +pass 19: -3317.9077 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0106 ins/del rates= 0.0000) +pass 20: -3317.8917 (branch= 0.0000 alpha= 0.0036 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0090 ins/del rates= 0.0000) + optimization up to ... +pass 30: -3317.8117 (branch= 0.0001 alpha= 0.0190 pinv= 0.0175 eq freqs= 0.0001 rel rates= 0.0434 ins/del rates= 0.0000) + optimization up to ... +pass 40: -3317.7926 (branch= 0.0001 alpha= 0.0047 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0100 ins/del rates= 0.0000) optimization up to ... -pass 50: -3317.7885 (branch= 0.0000 alpha= 0.0011 pinv= 0.0010 eq freqs= 0.0000 rel rates= 0.0030 ins/del rates= 0.0000) +pass 50: -3317.7882 (branch= 0.0001 alpha= 0.0010 pinv= 0.0009 eq freqs= 0.0000 rel rates= 0.0024 ins/del rates= 0.0000) optimization up to ... -pass 60: -3317.7873 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0007 ins/del rates= 0.0000) +pass 60: -3317.7873 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0005 ins/del rates= 0.0000) optimization up to ... -pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 ins/del rates= 0.0000) +pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) optimization up to ... -pass 73: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) +pass 73: -3317.7870 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... -Final score = -3317.7871 -Time used so far = 0 hours, 0 minutes and 13 seconds +Final score = -3317.7870 +Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.066, AG = 10.264, AT = 2.655, CG = 0.001, CT = 21.539, GT = 1.000 + AC = 3.068, AG = 10.268, AT = 2.657, CG = 0.001, CT = 21.552, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3328 0.2223 0.1567 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.5749 + 0.5750 with an invariant (invariable) site category, proportion estimated - 0.3614 + 0.3613 Substitution rate categories under this model: rate proportion - 0.0000 0.3614 + 0.0000 0.3613 0.0480 0.1597 - 0.2980 0.1597 + 0.2981 0.1597 0.8680 0.1597 - 2.7860 0.1597 + 2.7859 0.1597 Model 2 Number of states = 2 (0/1 coding of gaps) @@ -14767,13 +14838,13 @@ 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: 3.066 10.26 2.655 0.001 21.54 1 0.333 0.222 0.157 0.288 0.575 0.361 +rep 1: 3.068 10.27 2.657 0.001 21.55 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del @@ -14783,7 +14854,7 @@ Treelengths: TL -rep 1: 1.419 +rep 1: 1.418 Saving final tree from best search rep (#1) to ch.g.dnaMix.best.tre ####################################################### @@ -14922,6 +14993,18 @@ 4600 -210.6258 0.010 1104 4800 -210.5949 0.010 1104 5000 -210.5740 0.010 1104 +5200 -210.5694 0.010 1104 +5400 -210.5461 0.010 1104 +5600 -210.5152 0.010 1104 +5800 -210.4823 0.010 1104 +6000 -210.4633 0.010 1104 +6200 -210.4596 0.010 1104 +6400 -210.4468 0.010 1104 +6600 -210.4214 0.010 1104 +6800 -210.3965 0.010 1104 +7000 -210.3383 0.010 1104 +7200 -210.3217 0.010 1104 +7400 -210.2807 0.010 1104 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15001,35 +15084,45 @@ STARTING RUN Restarting from checkpoint... - generation 5151, seed 390961462, best lnL -210.570 + generation 7539, seed 1889724579, best lnL -210.263 gen current_lnL precision last_tree_imp -5151 -210.5697 0.010 1104 -5200 -210.5694 0.010 1104 +7539 -210.2625 0.010 1104 +7600 -210.2625 0.010 1104 +7700 -210.2313 0.010 1104 +7800 -210.1873 0.010 1104 +7900 -210.1766 0.010 1104 +8000 -210.1732 0.010 1104 +8100 -210.1384 0.010 1104 +8200 -210.1282 0.010 1104 +8300 -210.1126 0.010 1104 +8400 -210.1102 0.010 1104 +8500 -210.1087 0.010 1104 +8600 -210.0895 0.010 1104 Reached termination condition! last topological improvement at gen 1104 -Improvement over last 500 gen = 0.04047 +Improvement over last 500 gen = 0.04891 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 2.798, AG = 5.231, AT = 0.196, CG = 4.937, CT = 7.821, GT = 1.000 + AC = 3.918, AG = 6.882, AT = 0.186, CG = 6.998, CT = 11.153, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2331 0.3366 0.2107 0.2196 + (ACGT) 0.2363 0.3327 0.2105 0.2206 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 1.2338 + 1.8479 with an invariant (invariable) site category, proportion estimated - 0.1337 + 0.1921 Substitution rate categories under this model: rate proportion - 0.0000 0.1337 - 0.2378 0.2888 - 0.7622 0.2888 - 1.9999 0.2888 + 0.0000 0.1921 + 0.3353 0.2693 + 0.8372 0.2693 + 1.8275 0.2693 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 1 branches were collapsed. + No branches were short enough to be collapsed. Saving site likelihoods to file ch.n.G3.sitelikes.log ... @@ -15037,15 +15130,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -210.5694 +Replicate 1 : -210.0895 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 2.798 5.231 0.1964 4.937 7.821 1 0.233 0.337 0.211 0.220 1.234 0.134 +rep 1: 3.918 6.882 0.186 6.998 11.15 1 0.236 0.333 0.210 0.221 1.848 0.192 Treelengths: TL -rep 1: 2.254 +rep 1: 2.358 Saving final tree from best search rep (#1) to ch.n.G3.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.G3.internalstates.log @@ -15168,36 +15261,28 @@ 800 -169.9099 0.500 296 Optimization precision reduced Optimizing parameters... improved 2.192 lnL - Optimizing branchlengths... improved 0.321 lnL -1000 -167.2062 0.010 843 -1200 -167.1470 0.010 843 -1400 -167.0481 0.010 843 -1600 -166.9636 0.010 843 -1800 -166.8217 0.010 843 -2000 -166.6783 0.010 843 -2200 -166.5883 0.010 843 -2400 -166.4575 0.010 843 -2600 -166.3858 0.010 843 -2800 -166.3653 0.010 843 -3000 -166.3065 0.010 843 -3200 -166.2781 0.010 843 -3400 -166.2093 0.010 843 -3600 -166.0613 0.010 843 -3800 -165.9516 0.010 843 -4000 -165.8994 0.010 843 -4200 -165.8521 0.010 843 -4400 -165.7753 0.010 843 -4600 -165.6384 0.010 843 -4800 -165.6163 0.010 843 -5000 -165.5786 0.010 843 -5200 -165.5685 0.010 843 -5400 -165.5324 0.010 843 -5600 -165.3816 0.010 843 -5800 -165.2859 0.010 843 -6000 -165.2075 0.010 843 -6200 -165.1217 0.010 843 -6400 -164.9323 0.010 843 -6600 -164.7902 0.010 843 + Optimizing branchlengths... improved 0.320 lnL +1000 -167.2074 0.010 843 +1200 -167.1480 0.010 843 +1400 -167.0491 0.010 843 +1600 -166.9644 0.010 843 +1800 -166.8226 0.010 843 +2000 -166.6791 0.010 843 +2200 -166.5890 0.010 843 +2400 -166.4580 0.010 843 +2600 -166.3863 0.010 843 +2800 -166.3659 0.010 843 +3000 -166.3073 0.010 843 +3200 -166.2790 0.010 843 +3400 -166.2102 0.010 843 +3600 -166.0622 0.010 843 +3800 -165.9523 0.010 843 +4000 -165.9343 0.010 843 +4200 -165.8879 0.010 843 +4400 -165.8803 0.010 843 +4600 -165.7812 0.010 843 +4800 -165.7686 0.010 843 +5000 -165.6811 0.010 843 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15278,65 +15363,81 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 6705, seed 1902263460, best lnL -164.789 +Bootstrap rep 1 (of 1) generation 5102, seed 1047974991, best lnL -165.664 gen current_lnL precision last_tree_imp -6705 -164.7888 0.010 843 -6800 -164.7536 0.010 843 -6900 -164.5302 0.010 843 -7000 -164.5192 0.010 843 -7100 -164.4099 0.010 843 -7200 -164.2828 0.010 843 -7300 -164.2325 0.010 843 -7400 -164.1755 0.010 843 -7500 -164.1233 0.010 843 -7600 -164.0834 0.010 843 -7700 -163.9602 0.010 843 -7800 -163.9585 0.010 843 -7900 -163.9336 0.010 843 -8000 -163.8260 0.010 843 -8100 -163.7648 0.010 843 -8200 -163.7640 0.010 843 -8300 -163.6798 0.010 843 -8400 -163.6065 0.010 843 -8500 -163.6037 0.010 843 -8600 -163.5241 0.010 843 -8700 -163.4093 0.010 843 -8800 -163.3973 0.010 843 -8900 -163.3756 0.010 843 -9000 -163.3331 0.010 843 -9100 -163.3254 0.010 843 -9200 -163.3200 0.010 843 -9300 -163.2929 0.010 843 -9400 -163.2860 0.010 843 -9500 -163.2701 0.010 843 -9600 -163.2585 0.010 843 -9700 -163.2185 0.010 843 -9800 -163.2174 0.010 843 -9900 -163.2161 0.010 843 -10000 -163.2061 0.010 843 - Optimizing parameters... improved 1.203 lnL - Optimizing branchlengths... improved 0.010 lnL +5102 -165.6637 0.010 843 +5200 -165.6633 0.010 843 +5300 -165.6255 0.010 843 +5400 -165.5975 0.010 843 +5500 -165.5247 0.010 843 +5600 -165.4766 0.010 843 +5700 -165.4319 0.010 843 +5800 -165.3724 0.010 843 +5900 -165.3462 0.010 843 +6000 -165.3454 0.010 843 +6100 -165.2863 0.010 843 +6200 -165.2645 0.010 843 +6300 -165.1572 0.010 843 +6400 -165.1352 0.010 843 +6500 -165.1044 0.010 843 +6600 -165.0587 0.010 843 +6700 -165.0571 0.010 843 +6800 -165.0560 0.010 843 +6900 -164.9358 0.010 843 +7000 -164.9213 0.010 843 +7100 -164.8353 0.010 843 +7200 -164.8005 0.010 843 +7300 -164.7633 0.010 843 +7400 -164.7206 0.010 7384 +7500 -164.6626 0.010 7384 +7600 -164.6623 0.010 7384 +7700 -164.5345 0.010 7384 +7800 -164.5214 0.010 7384 +7900 -164.4750 0.010 7384 +8000 -164.4386 0.010 7384 +8100 -164.3297 0.010 7384 +8200 -164.2994 0.010 7384 +8300 -164.1857 0.010 7384 +8400 -164.1764 0.010 7384 +8500 -164.1676 0.010 7384 +8600 -164.1247 0.010 7384 +8700 -163.9942 0.010 7384 +8800 -163.9566 0.010 7384 +8900 -163.9228 0.010 7384 +9000 -163.8544 0.010 7384 +9100 -163.8510 0.010 7384 +9200 -163.8481 0.010 7384 +9300 -163.7797 0.010 7384 +9400 -163.7486 0.010 7384 +9500 -163.7091 0.010 7384 +9600 -163.6371 0.010 7384 +9700 -163.6121 0.010 7384 +9800 -163.6002 0.010 7384 +9900 -163.5966 0.010 7384 +10000 -163.5762 0.010 7384 + Optimizing parameters... improved 1.517 lnL + Optimizing branchlengths... improved 0.024 lnL NOTE: ****Specified generation limit (10000) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 0.840, AG = 12.212, AT = 2.930, CG = 4.820, CT = 55.192, GT = 1.000 + AC = 0.623, AG = 8.556, AT = 1.923, CG = 3.484, CT = 32.886, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1330 0.4224 0.2438 0.2008 + (ACGT) 0.1298 0.4236 0.2357 0.2109 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 39.2376 + 526.3244 with an invariant (invariable) site category, proportion estimated - 0.3493 + 0.3606 Substitution rate categories under this model: rate proportion - 0.0000 0.3493 - 0.8050 0.1627 - 0.9411 0.1627 - 1.0443 0.1627 - 1.2095 0.1627 + 0.0000 0.3606 + 0.9452 0.1599 + 0.9853 0.1599 + 1.0136 0.1599 + 1.0559 0.1599 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 3 branches were collapsed. @@ -15350,15 +15451,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -161.9932 +Replicate 1 : -162.0354 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 0.8397 12.21 2.93 4.82 55.19 1 0.133 0.422 0.244 0.201 39.238 0.349 +rep 1: 0.6227 8.556 1.923 3.484 32.89 1 0.130 0.424 0.236 0.211 526.324 0.361 Treelengths: TL -rep 1: 3.542 +rep 1: 3.168 Saving best tree to bootstrap file ch.n.G4.boot.tre @@ -15505,15 +15606,58 @@ 8000 -212.6638 0.010 3769 8200 -212.6580 0.010 3769 8400 -212.6570 0.010 3769 -NOTE: ****Specified time limit (5 seconds) reached... +8600 -212.6363 0.010 3769 +8800 -212.5814 0.010 3769 +9000 -212.5438 0.010 3769 +9200 -212.5311 0.010 3769 +9400 -212.5139 0.010 3769 +9600 -212.5123 0.010 3769 +9800 -212.5095 0.010 3769 +10000 -212.5014 0.010 3769 + Optimizing parameters... improved 0.000 lnL + Optimizing branchlengths... improved 0.000 lnL +NOTE: ****Specified generation limit (10000) reached... -NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY -TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE -FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF -(set restart = 1 in the config file). IF YOU WANT TO USE THE -PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY -ADD "end;" TO THE TREE FILES. +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +Model 1 + Number of states = 4 (nucleotide data) + Nucleotide Relative Rate Matrix: 6 rates + AC = 7.821, AG = 15.066, AT = 0.614, CG = 15.029, CT = 9.551, GT = 1.000 + Equilibrium State Frequencies: estimated + (ACGT) 0.2189 0.2871 0.1831 0.3108 + Rate Heterogeneity Model: + no rate heterogeneity +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 1 branches were collapsed. + +Saving site likelihoods to file ch.n.sitelikes.log ... +WARNING: Site likelihoods being output on prematurely terminated search ... + +NOTE: ***Search was terminated before full auto-termination condition was reached! +Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** + + +####################################################### + +Completed 1 replicate search(es) (of 1). +Results: +Replicate 1 : -212.5014 + +Parameter estimates: + r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) +rep 1: 7.821 15.07 0.6138 15.03 9.551 1 0.219 0.287 0.183 0.311 + +Treelengths: + TL +rep 1: 1.722 + +Saving final tree from best search rep (#1) to ch.n.best.tre +Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log + +WARNING: Internal states inferred on tree from prematurely terminated search + +####################################################### Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## @@ -15584,21 +15728,17 @@ STARTING RUN Restarting from checkpoint... - generation 8468, seed 643910720, best lnL -212.650 + generation 10001, seed 1459438551, best lnL -212.501 gen current_lnL precision last_tree_imp -8468 -212.6501 0.010 3769 -8500 -212.6501 0.010 3769 -Reached termination condition! -last topological improvement at gen 3769 -Improvement over last 500 gen = 0.01375 +10001 -212.5014 0.010 3769 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 5.648, AG = 10.889, AT = 0.436, CG = 10.683, CT = 7.058, GT = 1.000 + AC = 7.821, AG = 15.066, AT = 0.614, CG = 15.029, CT = 9.551, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2206 0.2885 0.1829 0.3080 + (ACGT) 0.2189 0.2871 0.1831 0.3108 Rate Heterogeneity Model: no rate heterogeneity @@ -15611,15 +15751,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -212.6501 +Replicate 1 : -212.5014 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) -rep 1: 5.648 10.89 0.4364 10.68 7.058 1 0.221 0.288 0.183 0.308 +rep 1: 7.821 15.07 0.6138 15.03 9.551 1 0.219 0.287 0.183 0.311 Treelengths: TL -rep 1: 1.727 +rep 1: 1.722 Saving final tree from best search rep (#1) to ch.n.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log @@ -15749,43 +15889,108 @@ Optimization precision reduced Optimizing parameters... improved 1.908 lnL Optimizing branchlengths... improved 0.702 lnL -1600 -211.2008 0.010 1502 -1800 -211.0870 0.010 1502 -2000 -210.9689 0.010 1502 +1600 -211.2006 0.010 1502 +1800 -211.0868 0.010 1502 +2000 -210.9688 0.010 1502 2200 -210.8961 0.010 1502 2400 -210.8906 0.010 1502 -2600 -210.8174 0.010 1502 -2800 -210.7848 0.010 1502 -3000 -210.7511 0.010 2883 -3200 -210.7244 0.010 2883 -3400 -210.7007 0.010 2883 -3600 -210.6994 0.010 2883 -3800 -210.6779 0.010 2883 -4000 -210.6776 0.010 2883 -4200 -210.6762 0.010 2883 -4400 -210.6528 0.010 2883 -4600 -210.6398 0.010 2883 -4800 -210.5994 0.010 4692 -5000 -210.5910 0.010 4692 -5200 -210.5711 0.010 4692 -5400 -210.5437 0.010 4692 -5600 -210.5248 0.010 4692 -5800 -210.4688 0.010 4692 -6000 -210.4351 0.010 4692 -6200 -210.4278 0.010 4692 -6400 -210.4185 0.010 4692 -6600 -210.4167 0.010 4692 -6800 -210.3984 0.010 4692 -7000 -210.3950 0.010 4692 -NOTE: ****Specified time limit (5 seconds) reached... +2600 -210.8172 0.010 1502 +2800 -210.7846 0.010 1502 +3000 -210.7510 0.010 2883 +3200 -210.7242 0.010 2883 +3400 -210.7005 0.010 2883 +3600 -210.6992 0.010 2883 +3800 -210.6778 0.010 2883 +4000 -210.6775 0.010 2883 +4200 -210.6761 0.010 2883 +4400 -210.6526 0.010 2883 +4600 -210.6396 0.010 2883 +4800 -210.6026 0.010 4692 +5000 -210.5940 0.010 4692 +5200 -210.5720 0.010 4692 +5400 -210.5439 0.010 5207 +5600 -210.5367 0.010 5207 +5800 -210.4677 0.010 5207 +6000 -210.4081 0.010 5812 +6200 -210.4005 0.010 5812 +6400 -210.3714 0.010 5812 +6600 -210.3661 0.010 5812 +6800 -210.3533 0.010 5812 +7000 -210.3450 0.010 5812 +7200 -210.3444 0.010 5812 +7400 -210.3290 0.010 5812 +7600 -210.3233 0.010 5812 +7800 -210.2350 0.010 7789 +8000 -210.1893 0.010 7789 +8200 -210.1873 0.010 7789 +8400 -210.1348 0.010 7789 +8600 -210.0952 0.010 7789 +8800 -210.0512 0.010 7789 +9000 -210.0080 0.010 7789 +9200 -209.9885 0.010 7789 +9400 -209.9480 0.010 7789 +9600 -209.9338 0.010 7789 +9800 -209.8897 0.010 9713 +10000 -209.8869 0.010 9713 + Optimizing parameters... improved 0.477 lnL + Optimizing branchlengths... improved 0.000 lnL +NOTE: ****Specified generation limit (10000) reached... -NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY -TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE -FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF -(set restart = 1 in the config file). IF YOU WANT TO USE THE -PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY -ADD "end;" TO THE TREE FILES. +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +Model 1 + Number of states = 4 (nucleotide data) + Nucleotide Relative Rate Matrix: 6 rates + AC = 2.658, AG = 4.802, AT = 0.044, CG = 4.939, CT = 9.263, GT = 1.000 + Equilibrium State Frequencies: estimated + (ACGT) 0.2412 0.3354 0.2106 0.2128 + Rate Heterogeneity Model: + 4 discrete gamma distributed rate categories, alpha param estimated + 4.4382 + with an invariant (invariable) site category, proportion estimated + 0.3025 + Substitution rate categories under this model: + rate proportion + 0.0000 0.3025 + 0.4769 0.1744 + 0.7891 0.1744 + 1.0841 0.1744 + 1.6498 0.1744 + +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + No branches were short enough to be collapsed. + + +NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with + a positive constraint, it is possible for a constrained branch itself to be collapsed. + If you care, be careful to check whether this has happened or turn off branch collapsing. + +Saving site likelihoods to file ch.n.const.sitelikes.log ... +WARNING: Site likelihoods being output on prematurely terminated search ... +NOTE: ***Search was terminated before full auto-termination condition was reached! +Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** + + +####################################################### + +Completed 1 replicate search(es) (of 1). +Results: +Replicate 1 : -209.4100 + +Parameter estimates: + r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv +rep 1: 2.658 4.802 0.04398 4.939 9.263 1 0.241 0.335 0.211 0.213 4.438 0.302 + +Treelengths: + TL +rep 1: 2.411 + +Saving final tree from best search rep (#1) to ch.n.const.best.tre +Inferring internal state probabilities on best tree... saving to file ch.n.const.internalstates.log + +WARNING: Internal states inferred on tree from prematurely terminated search + +####################################################### Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## @@ -15864,36 +16069,32 @@ STARTING RUN Restarting from checkpoint... - generation 7130, seed 1622107173, best lnL -210.395 + generation 10001, seed 1730967105, best lnL -209.410 gen current_lnL precision last_tree_imp -7130 -210.3950 0.010 4692 -7200 -210.3950 0.010 4692 -Reached termination condition! -last topological improvement at gen 4692 -Improvement over last 500 gen = 0.00995 +10001 -209.4100 0.010 9713 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 2.134, AG = 4.038, AT = 0.190, CG = 3.824, CT = 6.948, GT = 1.000 + AC = 2.658, AG = 4.802, AT = 0.044, CG = 4.939, CT = 9.263, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2403 0.3352 0.2122 0.2124 + (ACGT) 0.2412 0.3354 0.2106 0.2128 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 1.4069 + 4.4382 with an invariant (invariable) site category, proportion estimated - 0.1702 + 0.3025 Substitution rate categories under this model: rate proportion - 0.0000 0.1702 - 0.2106 0.2075 - 0.5723 0.2075 - 1.0445 0.2075 - 2.1727 0.2075 + 0.0000 0.3025 + 0.4769 0.1744 + 0.7891 0.1744 + 1.0841 0.1744 + 1.6498 0.1744 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 1 branches were collapsed. + No branches were short enough to be collapsed. NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with @@ -15906,15 +16107,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -210.3950 +Replicate 1 : -209.4100 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 2.134 4.038 0.1902 3.824 6.948 1 0.240 0.335 0.212 0.212 1.407 0.170 +rep 1: 2.658 4.802 0.04398 4.939 9.263 1 0.241 0.335 0.211 0.213 4.438 0.302 Treelengths: TL -rep 1: 2.398 +rep 1: 2.411 Saving final tree from best search rep (#1) to ch.n.const.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.const.internalstates.log @@ -16124,6 +16325,20 @@ 700 -13371.0754 0.402 0 800 -13370.9489 0.402 0 900 -13370.7802 0.402 0 +1000 -13370.6791 0.402 0 +Optimization precision reduced + Optimizing parameters... improved 0.037 lnL + Optimizing branchlengths... improved 0.000 lnL +1100 -13370.5869 0.304 0 +1200 -13370.5240 0.304 0 +1300 -13370.5103 0.304 0 +1400 -13370.5063 0.304 0 +1500 -13370.4967 0.304 0 +Optimization precision reduced + Optimizing parameters... improved 0.015 lnL + Optimizing branchlengths... improved 0.000 lnL +1600 -13370.4816 0.206 0 +1700 -13370.4688 0.206 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16246,77 +16461,77 @@ Subset 3: Random seed for bootstrap reweighting: 486988955 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 904, seed 1520195435, best lnL -13370.780 +Bootstrap rep 1 (of 1) generation 1788, seed 930691638, best lnL -13370.459 gen current_lnL precision last_tree_imp -904 -13370.7802 0.402 0 -1000 -13370.6791 0.402 0 +1788 -13370.4595 0.206 0 +1800 -13370.4569 0.206 0 +1900 -13370.4339 0.206 0 +2000 -13370.4174 0.206 0 Optimization precision reduced - Optimizing parameters... improved 0.037 lnL + Optimizing parameters... improved 0.006 lnL Optimizing branchlengths... improved 0.000 lnL -1100 -13370.5869 0.304 0 -NOTE: ****Specified time limit (1 seconds) reached... +NOTE: ****Specified generation limit (2000) reached... -MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) - AC = 1.598, AG = 2.495, AT = 1.210, CG = 1.210, CT = 4.135, GT = 1.000 + AC = 1.663, AG = 2.558, AT = 1.235, CG = 1.235, CT = 4.221, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3116 0.1804 0.3067 0.2014 + (ACGT) 0.3082 0.1810 0.3087 0.2020 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.3640 + 0.3662 Substitution rate categories under this model: rate proportion - 0.0119 0.2500 - 0.1544 0.2500 - 0.6892 0.2500 - 3.1446 0.2500 + 0.0122 0.2500 + 0.1561 0.2500 + 0.6919 0.2500 + 3.1398 0.2500 Model 2 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) - AC = 2.627, AG = 4.239, AT = 0.821, CG = 4.239, CT = 2.627, GT = 1.000 + AC = 2.621, AG = 4.245, AT = 0.820, CG = 4.245, CT = 2.621, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2812 0.1772 0.1597 0.3819 + (ACGT) 0.2814 0.1768 0.1593 0.3825 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.2460 + 0.2457 Substitution rate categories under this model: rate proportion 0.0019 0.2500 - 0.0638 0.2500 - 0.4929 0.2500 - 3.4413 0.2500 + 0.0636 0.2500 + 0.4923 0.2500 + 3.4422 0.2500 Model 3 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) - AC = 1.000, AG = 5.347, AT = 4.290, CG = 0.632, CT = 5.347, GT = 1.000 + AC = 1.000, AG = 5.311, AT = 4.291, CG = 0.629, CT = 5.311, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1555 0.3460 0.2769 0.2216 + (ACGT) 0.1554 0.3464 0.2763 0.2219 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.1101 + 4.1264 with an invariant (invariable) site category, proportion estimated - 0.0486 + 0.0487 Substitution rate categories under this model: rate proportion - 0.0000 0.0486 - 0.4603 0.2379 - 0.7789 0.2379 - 1.0844 0.2379 - 1.6764 0.2379 + 0.0000 0.0487 + 0.4612 0.2378 + 0.7795 0.2378 + 1.0844 0.2378 + 1.6750 0.2378 Subset rate multipliers: 0.53 0.29 2.18 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. ->>>Terminated Bootstrap rep 1 (of 1) <<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -16326,25 +16541,25 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13370.5240 (TERMINATED PREMATURELY) +Replicate 1 : -13370.4112 Parameter estimates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 1.598 2.495 1.21 1.21 4.135 1 0.312 0.180 0.307 0.201 0.364 +rep 1: 1.663 2.558 1.235 1.235 4.221 1 0.308 0.181 0.309 0.202 0.366 Partition model subset 2: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 2.627 4.239 0.8212 4.239 2.627 1 0.281 0.177 0.160 0.382 0.246 +rep 1: 2.621 4.245 0.8204 4.245 2.621 1 0.281 0.177 0.159 0.382 0.246 Partition model subset 3: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 1 5.347 4.29 0.6325 5.347 1 0.156 0.346 0.277 0.222 4.110 0.049 +rep 1: 1 5.311 4.291 0.6292 5.311 1 0.155 0.346 0.276 0.222 4.126 0.049 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 1.772 0.530 0.287 2.183 +rep 1: 1.762 0.530 0.287 2.183 Saving best tree to bootstrap file ch.p.3diff.boot.tre @@ -16559,14 +16774,13 @@ pass 8 : -467.6798 (branch= 0.0003 subset rates= 0.0013) pass 9 : -467.6793 (branch= 0.0006 subset rates= 0.0000) pass 10: -467.6791 (branch= 0.0002 subset rates= 0.0000) -pass 11: -467.6786 (branch= 0.0001 subset rates= 0.0004) -pass 12: -467.6783 (branch= 0.0003 subset rates= 0.0000) -pass 13: -467.6782 (branch= 0.0001 subset rates= 0.0000) -pass 14: -467.6782 (branch= 0.0000 subset rates= 0.0000) -pass 15: -467.6782 (branch= 0.0000 subset rates= 0.0000) +pass 11: -467.6790 (branch= 0.0001 subset rates= 0.0000) +pass 12: -467.6790 (branch= 0.0000 subset rates= 0.0000) +pass 13: -467.6790 (branch= 0.0000 subset rates= 0.0000) +pass 14: -467.6789 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -467.6782 -Time used so far = 0 hours, 0 minutes and 5 seconds +Final score = -467.6789 +Time used so far = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -16594,7 +16808,7 @@ no rate heterogeneity Subset rate multipliers: - 0.79 1.48 2.18 + 0.79 1.48 2.16 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. @@ -16641,6 +16855,18 @@ lnL after optimization: -467.8445 gen current_lnL precision last_tree_imp 0 -467.8445 0.010 0 +100 -467.8198 0.010 0 +200 -467.8068 0.010 0 +300 -467.7949 0.010 0 +400 -467.7826 0.010 0 +500 -467.7787 0.010 0 +600 -467.7743 0.010 0 +700 -467.7597 0.010 0 +800 -467.7573 0.010 0 +900 -467.7534 0.010 0 +1000 -467.7459 0.010 0 +1100 -467.7436 0.010 0 +1200 -467.7413 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16766,21 +16992,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 55, seed 1941991272, best lnL -467.826 +Search rep 2 (of 5) generation 1225, seed 1758295693, best lnL -467.741 gen current_lnL precision last_tree_imp -55 -467.8263 0.010 0 -100 -467.8198 0.010 0 -200 -467.8068 0.010 0 -300 -467.7949 0.010 0 -400 -467.7826 0.010 0 -500 -467.7787 0.010 0 -600 -467.7743 0.010 0 -700 -467.7597 0.010 0 -800 -467.7573 0.010 0 -900 -467.7534 0.010 0 -1000 -467.7459 0.010 0 -1100 -467.7436 0.010 0 -1200 -467.7413 0.010 0 +1225 -467.7412 0.010 0 1300 -467.7398 0.010 0 1400 -467.7386 0.010 0 1500 -467.7376 0.010 0 @@ -16821,7 +17035,7 @@ 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 10 seconds +Time used so far = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -16904,26 +17118,54 @@ 500 -467.7598 0.010 75 600 -467.7543 0.010 75 700 -467.7490 0.010 75 +800 -467.7446 0.010 75 +900 -467.7384 0.010 75 +1000 -467.7309 0.010 75 +1100 -467.7251 0.010 75 +1200 -467.7223 0.010 75 +1300 -467.7207 0.010 75 +1400 -467.7202 0.010 75 +1500 -467.7181 0.010 75 +1600 -467.7176 0.010 75 +1700 -467.7164 0.010 75 +1800 -467.7139 0.010 75 +1900 -467.7123 0.010 75 +2000 -467.7117 0.010 75 +2100 -467.7106 0.010 75 +2200 -467.7093 0.010 75 +2300 -467.7084 0.010 75 +2400 -467.7070 0.010 75 +2500 -467.7068 0.010 75 +2600 -467.7054 0.010 75 +2700 -467.7045 0.010 75 +2800 -467.7041 0.010 75 +2900 -467.7040 0.010 75 +3000 -467.7029 0.010 75 +3100 -467.7026 0.010 75 +3200 -467.7026 0.010 75 +3300 -467.7023 0.010 75 +3400 -467.7015 0.010 75 +3500 -467.7013 0.010 75 +3600 -467.7011 0.010 75 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -467.7467 +Current score = -467.7010 Performing final optimizations... -pass 1 : -467.7454 (branch= 0.0000 subset rates= 0.0013) -pass 2 : -467.7115 (branch= 0.0338 subset rates= 0.0001) -pass 3 : -467.7005 (branch= 0.0107 subset rates= 0.0003) -pass 4 : -467.6892 (branch= 0.0113 subset rates= 0.0000) -pass 5 : -467.6833 (branch= 0.0058 subset rates= 0.0000) -pass 6 : -467.6808 (branch= 0.0026 subset rates= 0.0000) -pass 7 : -467.6795 (branch= 0.0012 subset rates= 0.0000) -pass 8 : -467.6789 (branch= 0.0006 subset rates= 0.0000) -pass 9 : -467.6786 (branch= 0.0003 subset rates= 0.0000) +pass 1 : -467.7004 (branch= 0.0000 subset rates= 0.0006) +pass 2 : -467.6874 (branch= 0.0122 subset rates= 0.0008) +pass 3 : -467.6819 (branch= 0.0055 subset rates= 0.0000) +pass 4 : -467.6810 (branch= 0.0009 subset rates= 0.0000) +pass 5 : -467.6803 (branch= 0.0007 subset rates= 0.0000) +pass 6 : -467.6800 (branch= 0.0003 subset rates= 0.0000) +pass 7 : -467.6794 (branch= 0.0006 subset rates= 0.0000) +pass 8 : -467.6788 (branch= 0.0006 subset rates= 0.0000) +pass 9 : -467.6786 (branch= 0.0002 subset rates= 0.0000) pass 10: -467.6785 (branch= 0.0001 subset rates= 0.0000) -pass 11: -467.6784 (branch= 0.0001 subset rates= 0.0000) +pass 11: -467.6785 (branch= 0.0000 subset rates= 0.0000) pass 12: -467.6784 (branch= 0.0000 subset rates= 0.0000) pass 13: -467.6784 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6783 (branch= 0.0000 subset rates= 0.0000) -pass 15: -467.6783 (branch= 0.0000 subset rates= 0.0001) +pass 14: -467.6784 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -467.6783 +Final score = -467.6784 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -16952,7 +17194,7 @@ no rate heterogeneity Subset rate multipliers: - 0.79 1.48 2.18 + 0.78 1.48 2.19 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. @@ -16969,9 +17211,9 @@ NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -467.6782 +Replicate 1 : -467.6789 Replicate 2 : -467.6782 (best) (same topology as 1) -Replicate 3 : -467.6783 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 3 : -467.6784 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -16986,9 +17228,9 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 3.843 0.786 1.480 2.181 +rep 1: 3.841 0.787 1.482 2.160 rep 2: 3.843 0.786 1.477 2.187 -rep 3: 3.841 0.787 1.475 2.183 +rep 3: 3.844 0.785 1.482 2.187 Saving final tree from best search rep (#2) to ch.p.mk.ssr.best.tre ####################################################### @@ -17207,7 +17449,7 @@ pass 16: -477.4317 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.4316 -Time used so far = 0 hours, 0 minutes and 5 seconds +Time used so far = 0 hours, 0 minutes and 3 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17286,6 +17528,28 @@ gen current_lnL precision last_tree_imp 0 -477.8517 0.010 0 100 -477.7860 0.010 74 +200 -477.7643 0.010 74 +300 -477.7463 0.010 74 +400 -477.7402 0.010 74 +500 -477.7271 0.010 74 +600 -477.7244 0.010 74 +700 -477.7189 0.010 74 +800 -477.7180 0.010 74 +900 -477.7173 0.010 74 +1000 -477.7111 0.010 74 +1100 -477.7093 0.010 74 +1200 -477.7091 0.010 74 +1300 -477.7049 0.010 74 +1400 -477.7022 0.010 74 +1500 -477.6989 0.010 74 +1600 -477.6967 0.010 74 +1700 -477.6956 0.010 74 +1800 -477.6946 0.010 74 +1900 -477.6945 0.010 74 +2000 -477.6902 0.010 74 +2100 -477.6899 0.010 74 +2200 -477.6898 0.010 74 +2300 -477.6894 0.010 74 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17411,31 +17675,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 154, seed 1639935539, best lnL -477.776 +Search rep 2 (of 5) generation 2327, seed 66501600, best lnL -477.689 gen current_lnL precision last_tree_imp -154 -477.7757 0.010 74 -200 -477.7643 0.010 74 -300 -477.7463 0.010 74 -400 -477.7402 0.010 74 -500 -477.7271 0.010 74 -600 -477.7244 0.010 74 -700 -477.7189 0.010 74 -800 -477.7180 0.010 74 -900 -477.7173 0.010 74 -1000 -477.7111 0.010 74 -1100 -477.7093 0.010 74 -1200 -477.7091 0.010 74 -1300 -477.7049 0.010 74 -1400 -477.7022 0.010 74 -1500 -477.6989 0.010 74 -1600 -477.6967 0.010 74 -1700 -477.6956 0.010 74 -1800 -477.6946 0.010 74 -1900 -477.6945 0.010 74 -2000 -477.6902 0.010 74 -2100 -477.6899 0.010 74 -2200 -477.6898 0.010 74 -2300 -477.6894 0.010 74 +2327 -477.6890 0.010 74 2400 -477.6889 0.010 74 2500 -477.6883 0.010 74 2600 -477.6879 0.010 74 @@ -17449,27 +17691,167 @@ 3400 -477.6806 0.010 74 3500 -477.6782 0.010 74 3600 -477.6776 0.010 74 +3700 -477.5167 0.010 3640 +3800 -477.5121 0.010 3640 +3900 -477.5087 0.010 3640 +4000 -477.5077 0.010 3640 +4100 -477.5055 0.010 3640 +4200 -477.5046 0.010 3640 +4300 -477.4990 0.010 3640 +4400 -477.4985 0.010 3640 +4500 -477.4959 0.010 3640 +4600 -477.4934 0.010 3640 +4700 -477.4934 0.010 3640 +4800 -477.4928 0.010 3640 +4900 -477.4905 0.010 3640 +5000 -477.4897 0.010 3640 + Optimizing parameters... improved 0.012 lnL + Optimizing branchlengths... improved 0.000 lnL +5100 -477.4735 0.010 3640 +5200 -477.4721 0.010 3640 +5300 -477.4710 0.010 3640 +5400 -477.4705 0.010 3640 +5500 -477.4701 0.010 3640 +5600 -477.4700 0.010 3640 +5700 -477.4688 0.010 3640 +5800 -477.4676 0.010 3640 +5900 -477.4659 0.010 3640 +6000 -477.4654 0.010 3640 +6100 -477.4651 0.010 3640 +6200 -477.4651 0.010 3640 +6300 -477.4647 0.010 3640 +6400 -477.4646 0.010 3640 +6500 -477.4638 0.010 3640 +6600 -477.4637 0.010 3640 +6700 -477.4633 0.010 3640 +6800 -477.4633 0.010 3640 +6900 -477.4630 0.010 3640 +7000 -477.4630 0.010 3640 +Reached termination condition! +last topological improvement at gen 3640 +Improvement over last 500 gen = 0.00082 +Current score = -477.4630 +Performing final optimizations... +pass 1 : -477.4630 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -477.4568 (branch= 0.0063 subset rates= 0.0000) +pass 3 : -477.4423 (branch= 0.0145 subset rates= 0.0000) +pass 4 : -477.4394 (branch= 0.0029 subset rates= 0.0000) +pass 5 : -477.4375 (branch= 0.0019 subset rates= 0.0000) +pass 6 : -477.4357 (branch= 0.0017 subset rates= 0.0000) +pass 7 : -477.4351 (branch= 0.0006 subset rates= 0.0000) +pass 8 : -477.4343 (branch= 0.0008 subset rates= 0.0000) +pass 9 : -477.4339 (branch= 0.0004 subset rates= 0.0000) +pass 10: -477.4337 (branch= 0.0002 subset rates= 0.0000) +pass 11: -477.4336 (branch= 0.0001 subset rates= 0.0000) +pass 12: -477.4335 (branch= 0.0001 subset rates= 0.0000) +pass 13: -477.4335 (branch= 0.0000 subset rates= 0.0000) +pass 14: -477.4335 (branch= 0.0000 subset rates= 0.0000) +pass 15: -477.4334 (branch= 0.0000 subset rates= 0.0000) +pass 16: -477.4334 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -477.4334 +Time used so far = 0 hours, 0 minutes and 11 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.63 1.90 2.79 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 7 branches were collapsed. + +>>>Completed Search rep 2 (of 5)<<< + +>>>Search rep 3 (of 5)<<< +Obtained starting tree 1 from Nexus +MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 1.00 1.00 1.00 +Starting with seed=142730073 + +Initial ln Likelihood: -629.9190 +optimizing: starting branch lengths, subset rates... +pass 1:+ 130.937 (branch= 120.28 scale= 1.19 subset rates= 9.47) +pass 2:+ 17.167 (branch= 13.05 scale= 0.01 subset rates= 4.10) +pass 3:+ 3.157 (branch= 1.89 scale= 0.00 subset rates= 1.27) +pass 4:+ 0.670 (branch= 0.38 scale= 0.01 subset rates= 0.28) +pass 5:+ 0.070 (branch= 0.07 scale= 0.00 subset rates= 0.00) +pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -477.9174 +gen current_lnL precision last_tree_imp +0 -477.9174 0.010 0 +100 -477.8787 0.010 0 +200 -477.8578 0.010 0 +300 -477.8324 0.010 0 +400 -477.5256 0.010 400 +500 -477.3126 0.010 461 +600 -477.3016 0.010 461 +700 -477.2868 0.010 461 +800 -477.2838 0.010 461 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -477.5171 +Current score = -477.2815 Performing final optimizations... -pass 1 : -477.4999 (branch= 0.0103 subset rates= 0.0069) -pass 2 : -477.4623 (branch= 0.0308 subset rates= 0.0067) -pass 3 : -477.4441 (branch= 0.0171 subset rates= 0.0011) -pass 4 : -477.4416 (branch= 0.0026 subset rates= 0.0000) -pass 5 : -477.4375 (branch= 0.0040 subset rates= 0.0000) -pass 6 : -477.4356 (branch= 0.0019 subset rates= 0.0001) -pass 7 : -477.4343 (branch= 0.0012 subset rates= 0.0000) -pass 8 : -477.4334 (branch= 0.0010 subset rates= 0.0000) -pass 9 : -477.4327 (branch= 0.0007 subset rates= 0.0000) -pass 10: -477.4324 (branch= 0.0003 subset rates= 0.0000) -pass 11: -477.4322 (branch= 0.0002 subset rates= 0.0000) -pass 12: -477.4321 (branch= 0.0001 subset rates= 0.0000) -pass 13: -477.4320 (branch= 0.0001 subset rates= 0.0000) -pass 14: -477.4320 (branch= 0.0000 subset rates= 0.0000) -pass 15: -477.4320 (branch= 0.0000 subset rates= 0.0000) -pass 16: -477.4320 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -477.2704 (branch= 0.0082 subset rates= 0.0029) +pass 2 : -477.2385 (branch= 0.0237 subset rates= 0.0082) +pass 3 : -477.2259 (branch= 0.0126 subset rates= 0.0000) +pass 4 : -477.2161 (branch= 0.0098 subset rates= 0.0000) +pass 5 : -477.2099 (branch= 0.0053 subset rates= 0.0009) +pass 6 : -477.2067 (branch= 0.0023 subset rates= 0.0010) +pass 7 : -477.2056 (branch= 0.0011 subset rates= 0.0000) +pass 8 : -477.2054 (branch= 0.0002 subset rates= 0.0000) +pass 9 : -477.2051 (branch= 0.0003 subset rates= 0.0000) +pass 10: -477.2050 (branch= 0.0001 subset rates= 0.0000) +pass 11: -477.2050 (branch= 0.0000 subset rates= 0.0000) +pass 12: -477.2050 (branch= 0.0000 subset rates= 0.0000) +pass 13: -477.2050 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.4320 +Final score = -477.2050 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -17498,11 +17880,11 @@ no rate heterogeneity Subset rate multipliers: - 0.63 1.91 2.75 + 0.63 1.93 2.66 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. + 8 branches were collapsed. ->>>Terminated Search rep 2 (of 5)<<< +>>>Terminated Search rep 3 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -17510,13 +17892,14 @@ ####################################################### -Completed 2 replicate search(es) (of 5). +Completed 3 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -477.4316 (best) -Replicate 2 : -477.4320 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 1 : -477.4316 +Replicate 2 : -477.4334 (same topology as 1) +Replicate 3 : -477.2050 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17532,9 +17915,10 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.930 0.631 1.918 2.736 -rep 2: 4.926 0.633 1.906 2.747 +rep 2: 4.933 0.631 1.902 2.786 +rep 3: 4.699 0.634 1.930 2.656 -Saving final tree from best search rep (#1) to ch.p.mkO.ssr.best.tre +Saving final tree from best search rep (#3) to ch.p.mkO.ssr.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkv.ssr.conf @@ -17732,6 +18116,106 @@ 3000 -425.5867 0.010 365 3100 -425.5858 0.010 365 3200 -425.5857 0.010 365 +3300 -425.5849 0.010 365 +3400 -425.5842 0.010 365 +3500 -425.5842 0.010 365 +3600 -425.5840 0.010 365 +3700 -425.5839 0.010 365 +3800 -425.5838 0.010 365 +3900 -425.5838 0.010 365 +Reached termination condition! +last topological improvement at gen 365 +Improvement over last 500 gen = 0.00044 +Current score = -425.5838 +Performing final optimizations... +pass 1 : -425.5746 (branch= 0.0000 subset rates= 0.0092) +pass 2 : -425.5588 (branch= 0.0144 subset rates= 0.0014) +pass 3 : -425.5516 (branch= 0.0070 subset rates= 0.0002) +pass 4 : -425.5509 (branch= 0.0007 subset rates= 0.0000) +pass 5 : -425.5505 (branch= 0.0004 subset rates= 0.0000) +pass 6 : -425.5498 (branch= 0.0007 subset rates= 0.0000) +pass 7 : -425.5494 (branch= 0.0004 subset rates= 0.0000) +pass 8 : -425.5490 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -425.5487 (branch= 0.0003 subset rates= 0.0000) +pass 10: -425.5487 (branch= 0.0001 subset rates= 0.0000) +pass 11: -425.5487 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.5487 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -425.5486 +Time used so far = 0 hours, 0 minutes and 4 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.87 1.53 1.12 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 10 branches were collapsed. + +>>>Completed Bootstrap rep 1 (of 1) Search rep 1 (of 5)<<< + +>>>Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< +Obtained starting tree 1 from Nexus +Starting with seed=222492842 + +Initial ln Likelihood: -586.0233 +optimizing: starting branch lengths, subset rates... +pass 1:+ 129.358 (branch= 127.50 scale= 1.82 subset rates= 0.04) +pass 2:+ 11.580 (branch= 11.46 scale= 0.04 subset rates= 0.07) +pass 3:+ 3.728 (branch= 3.71 scale= 0.00 subset rates= 0.02) +pass 4:+ 1.685 (branch= 1.66 scale= 0.02 subset rates= 0.01) +pass 5:+ 0.130 (branch= 0.13 scale= 0.00 subset rates= 0.00) +pass 6:+ 0.037 (branch= 0.04 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.031 (branch= 0.03 scale= 0.00 subset rates= 0.00) +pass 8:+ 0.037 (branch= 0.04 scale= 0.00 subset rates= 0.00) +pass 9:+ 0.043 (branch= 0.04 scale= 0.00 subset rates= 0.00) +pass10:+ 0.052 (branch= 0.05 scale= 0.00 subset rates= 0.00) +pass11:+ 0.061 (branch= 0.06 scale= 0.00 subset rates= 0.00) +pass12:+ 0.042 (branch= 0.04 scale= 0.00 subset rates= 0.00) +pass13:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) +pass14:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -439.2273 +gen current_lnL precision last_tree_imp +0 -439.2273 0.010 0 +100 -428.8676 0.010 98 +200 -428.0498 0.010 164 +300 -427.6002 0.010 249 +400 -427.5648 0.010 249 +500 -427.4910 0.010 499 +600 -427.3863 0.010 511 +700 -425.7187 0.010 668 +800 -425.6950 0.010 722 +900 -425.6794 0.010 722 +1000 -425.6689 0.010 722 +1100 -425.6640 0.010 722 +1200 -425.6430 0.010 722 +1300 -425.6381 0.010 722 +1400 -425.6345 0.010 722 +1500 -425.6342 0.010 722 +1600 -425.6274 0.010 722 +1700 -425.6240 0.010 722 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17860,31 +18344,43 @@ Subset 3: Random seed for bootstrap reweighting: 974568031 Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 1 (of 5) generation 3273, seed 1700330852, best lnL -425.585 +Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 1765, seed 2051031173, best lnL -425.624 gen current_lnL precision last_tree_imp -3273 -425.5849 0.010 365 -3300 -425.5849 0.010 365 -3400 -425.5842 0.010 365 -3500 -425.5842 0.010 365 -3600 -425.5840 0.010 365 -3700 -425.5839 0.010 365 -3800 -425.5838 0.010 365 -3900 -425.5838 0.010 365 +1765 -425.6239 0.010 722 +1800 -425.6236 0.010 722 +1900 -425.6226 0.010 722 +2000 -425.6202 0.010 722 +2100 -425.6197 0.010 722 +2200 -425.6174 0.010 722 +2300 -425.6146 0.010 722 +2400 -425.6135 0.010 722 +2500 -425.6104 0.010 722 +2600 -425.6099 0.010 722 +2700 -425.6088 0.010 722 +2800 -425.6077 0.010 722 +2900 -425.6074 0.010 722 +3000 -425.6059 0.010 722 +3100 -425.6056 0.010 722 +3200 -425.6055 0.010 722 +3300 -425.6051 0.010 722 +3400 -425.6049 0.010 722 +3500 -425.6048 0.010 722 +3600 -425.6048 0.010 722 Reached termination condition! -last topological improvement at gen 365 -Improvement over last 500 gen = 0.00044 -Current score = -425.5838 +last topological improvement at gen 722 +Improvement over last 500 gen = 0.00085 +Current score = -425.6048 Performing final optimizations... -pass 1 : -425.5804 (branch= 0.0000 subset rates= 0.0033) -pass 2 : -425.5633 (branch= 0.0144 subset rates= 0.0027) -pass 3 : -425.5516 (branch= 0.0070 subset rates= 0.0047) -pass 4 : -425.5509 (branch= 0.0007 subset rates= 0.0000) -pass 5 : -425.5505 (branch= 0.0004 subset rates= 0.0000) -pass 6 : -425.5498 (branch= 0.0007 subset rates= 0.0000) -pass 7 : -425.5494 (branch= 0.0004 subset rates= 0.0000) -pass 8 : -425.5490 (branch= 0.0004 subset rates= 0.0000) +pass 1 : -425.5761 (branch= 0.0000 subset rates= 0.0286) +pass 2 : -425.5574 (branch= 0.0188 subset rates= 0.0000) +pass 3 : -425.5532 (branch= 0.0041 subset rates= 0.0000) +pass 4 : -425.5520 (branch= 0.0012 subset rates= 0.0000) +pass 5 : -425.5503 (branch= 0.0016 subset rates= 0.0000) +pass 6 : -425.5498 (branch= 0.0005 subset rates= 0.0000) +pass 7 : -425.5490 (branch= 0.0008 subset rates= 0.0000) +pass 8 : -425.5490 (branch= 0.0000 subset rates= 0.0000) pass 9 : -425.5487 (branch= 0.0003 subset rates= 0.0000) -pass 10: -425.5487 (branch= 0.0001 subset rates= 0.0000) +pass 10: -425.5486 (branch= 0.0001 subset rates= 0.0000) pass 11: -425.5486 (branch= 0.0000 subset rates= 0.0000) pass 12: -425.5486 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... @@ -17919,74 +18415,79 @@ Subset rate multipliers: 0.87 1.53 1.12 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 10 branches were collapsed. + 9 branches were collapsed. ->>>Completed Bootstrap rep 1 (of 1) Search rep 1 (of 5)<<< +>>>Completed Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< ->>>Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< +>>>Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< Obtained starting tree 1 from Nexus -Starting with seed=222492842 +Starting with seed=2129292874 -Initial ln Likelihood: -586.0233 +Initial ln Likelihood: -588.2493 optimizing: starting branch lengths, subset rates... -pass 1:+ 129.358 (branch= 127.50 scale= 1.82 subset rates= 0.04) -pass 2:+ 11.580 (branch= 11.46 scale= 0.04 subset rates= 0.07) -pass 3:+ 3.728 (branch= 3.71 scale= 0.00 subset rates= 0.02) -pass 4:+ 1.685 (branch= 1.66 scale= 0.02 subset rates= 0.01) -pass 5:+ 0.130 (branch= 0.13 scale= 0.00 subset rates= 0.00) -pass 6:+ 0.037 (branch= 0.04 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.031 (branch= 0.03 scale= 0.00 subset rates= 0.00) -pass 8:+ 0.037 (branch= 0.04 scale= 0.00 subset rates= 0.00) -pass 9:+ 0.043 (branch= 0.04 scale= 0.00 subset rates= 0.00) -pass10:+ 0.052 (branch= 0.05 scale= 0.00 subset rates= 0.00) -pass11:+ 0.061 (branch= 0.06 scale= 0.00 subset rates= 0.00) -pass12:+ 0.042 (branch= 0.04 scale= 0.00 subset rates= 0.00) -pass13:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) -pass14:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -439.2273 +pass 1:+ 141.030 (branch= 140.49 scale= 0.38 subset rates= 0.17) +pass 2:+ 6.536 (branch= 6.52 scale= 0.00 subset rates= 0.02) +pass 3:+ 1.051 (branch= 1.03 scale= 0.00 subset rates= 0.02) +pass 4:+ 0.061 (branch= 0.06 scale= 0.00 subset rates= 0.00) +pass 5:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -439.5713 gen current_lnL precision last_tree_imp -0 -439.2273 0.010 0 -100 -428.8676 0.010 98 -200 -428.0498 0.010 164 -300 -427.6002 0.010 249 -400 -427.5648 0.010 249 -500 -427.4910 0.010 499 -600 -427.3863 0.010 511 -700 -425.7187 0.010 668 -800 -425.6950 0.010 722 -900 -425.6794 0.010 722 -1000 -425.6689 0.010 722 -1100 -425.6640 0.010 722 -1200 -425.6430 0.010 722 -1300 -425.6381 0.010 722 -1400 -425.6345 0.010 722 -1500 -425.6342 0.010 722 -1600 -425.6274 0.010 722 -1700 -425.6240 0.010 722 -1800 -425.6236 0.010 722 -1900 -425.6226 0.010 722 -2000 -425.6202 0.010 722 -2100 -425.6197 0.010 722 -2200 -425.6174 0.010 722 -2300 -425.6146 0.010 722 -2400 -425.6135 0.010 722 -2500 -425.6104 0.010 722 +0 -439.5713 0.010 0 +100 -431.1390 0.010 95 +200 -428.6585 0.010 167 +300 -427.6515 0.010 295 +400 -427.2440 0.010 295 +500 -427.2139 0.010 295 +600 -427.1679 0.010 568 +700 -427.1487 0.010 568 +800 -425.4818 0.010 762 +900 -425.4264 0.010 803 +1000 -425.4085 0.010 803 +1100 -425.4058 0.010 803 +1200 -425.3915 0.010 803 +1300 -425.3912 0.010 803 +1400 -425.3887 0.010 803 +1500 -425.3865 0.010 803 +1600 -425.3820 0.010 803 +1700 -425.3760 0.010 803 +1800 -425.3758 0.010 803 +1900 -425.3750 0.010 803 +2000 -425.3712 0.010 803 +2100 -425.3702 0.010 803 +2200 -425.3666 0.010 803 +2300 -425.3654 0.010 803 +2400 -425.3635 0.010 803 +2500 -425.3629 0.010 803 +2600 -425.3622 0.010 803 +2700 -425.3619 0.010 803 +2800 -425.3613 0.010 803 +2900 -425.3592 0.010 803 +3000 -425.3583 0.010 803 +3100 -425.3581 0.010 803 +3200 -425.3571 0.010 803 +3300 -425.3567 0.010 803 +3400 -425.3566 0.010 803 +3500 -425.3562 0.010 803 +3600 -425.3554 0.010 803 +3700 -425.3549 0.010 803 +3800 -425.3546 0.010 803 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -425.6103 +Current score = -425.3546 Performing final optimizations... -pass 1 : -425.5974 (branch= 0.0000 subset rates= 0.0129) -pass 2 : -425.5619 (branch= 0.0206 subset rates= 0.0150) -pass 3 : -425.5565 (branch= 0.0042 subset rates= 0.0012) -pass 4 : -425.5537 (branch= 0.0028 subset rates= 0.0000) -pass 5 : -425.5520 (branch= 0.0017 subset rates= 0.0000) -pass 6 : -425.5503 (branch= 0.0017 subset rates= 0.0000) -pass 7 : -425.5496 (branch= 0.0007 subset rates= 0.0000) -pass 8 : -425.5493 (branch= 0.0004 subset rates= 0.0000) -pass 9 : -425.5490 (branch= 0.0002 subset rates= 0.0000) -pass 10: -425.5489 (branch= 0.0001 subset rates= 0.0000) -pass 11: -425.5489 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -425.3509 (branch= 0.0000 subset rates= 0.0036) +pass 2 : -425.3326 (branch= 0.0165 subset rates= 0.0018) +pass 3 : -425.3242 (branch= 0.0085 subset rates= 0.0000) +pass 4 : -425.3223 (branch= 0.0019 subset rates= 0.0000) +pass 5 : -425.3223 (branch= 0.0000 subset rates= 0.0000) +pass 6 : -425.3223 (branch= 0.0000 subset rates= 0.0000) +pass 7 : -425.3209 (branch= 0.0014 subset rates= 0.0000) +pass 8 : -425.3202 (branch= 0.0007 subset rates= 0.0000) +pass 9 : -425.3202 (branch= 0.0000 subset rates= 0.0000) +pass 10: -425.3201 (branch= 0.0001 subset rates= 0.0000) +pass 11: -425.3201 (branch= 0.0001 subset rates= 0.0000) +pass 12: -425.3201 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -425.5489 +Final score = -425.3200 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -18015,11 +18516,11 @@ no rate heterogeneity Subset rate multipliers: - 0.87 1.53 1.13 + 0.86 1.54 1.15 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 9 branches were collapsed. ->>>Terminated Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< +>>>Terminated Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -18027,13 +18528,14 @@ ####################################################### -Completed 2 replicate search(es) (of 5). +Completed 3 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -425.5486 (best) -Replicate 2 : -425.5489 (TERMINATED PREMATURELY) +Replicate 1 : -425.5486 +Replicate 2 : -425.5486 +Replicate 3 : -425.3200 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -18048,11 +18550,13 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 3.038 0.868 1.529 1.123 -rep 2: 3.036 0.868 1.527 1.132 +rep 1: 3.039 0.869 1.528 1.122 +rep 2: 3.037 0.868 1.532 1.121 +rep 3: 2.979 0.865 1.538 1.148 -Saving tree from best search rep (#1) to bootstrap file ch.p.mkv.ssr.boot.tre +Saving tree from best search rep (#3) to bootstrap file ch.p.mkv.ssr.boot.tre +WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkvO.ssr.conf @@ -18243,6 +18747,125 @@ 2500 -473.9804 0.010 653 2600 -473.9801 0.010 653 2700 -473.9793 0.010 653 +2800 -473.9779 0.010 653 +2900 -473.9777 0.010 653 +3000 -473.9777 0.010 653 +3100 -473.9773 0.010 653 +3200 -473.9772 0.010 653 +3300 -473.9771 0.010 653 +Reached termination condition! +last topological improvement at gen 653 +Improvement over last 500 gen = 0.00088 +Current score = -473.9771 +Performing final optimizations... +pass 1 : -473.9742 (branch= 0.0000 subset rates= 0.0029) +pass 2 : -473.9558 (branch= 0.0183 subset rates= 0.0000) +pass 3 : -473.9558 (branch= 0.0000 subset rates= 0.0000) +pass 4 : -473.9548 (branch= 0.0011 subset rates= 0.0000) +pass 5 : -473.9529 (branch= 0.0018 subset rates= 0.0000) +pass 6 : -473.9525 (branch= 0.0004 subset rates= 0.0000) +pass 7 : -473.9517 (branch= 0.0008 subset rates= 0.0000) +pass 8 : -473.9513 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -473.9511 (branch= 0.0003 subset rates= 0.0000) +pass 10: -473.9510 (branch= 0.0001 subset rates= 0.0000) +pass 11: -473.9510 (branch= 0.0000 subset rates= 0.0000) +pass 12: -473.9509 (branch= 0.0000 subset rates= 0.0000) +pass 13: -473.9509 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -473.9509 +Time used so far = 0 hours, 0 minutes and 4 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.59 2.07 2.82 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 8 branches were collapsed. + +>>>Completed Search rep 1 (of 5)<<< + +>>>Search rep 2 (of 5)<<< +Obtained starting tree 1 from Nexus +MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 1.00 1.00 1.00 +Starting with seed=2125680066 + +Initial ln Likelihood: -649.8224 +optimizing: starting branch lengths, subset rates... +pass 1:+ 148.288 (branch= 136.88 scale= 0.96 subset rates= 10.45) +pass 2:+ 18.126 (branch= 13.41 scale= 0.03 subset rates= 4.69) +pass 3:+ 5.650 (branch= 3.93 scale= 0.00 subset rates= 1.72) +pass 4:+ 2.344 (branch= 1.67 scale= 0.00 subset rates= 0.67) +pass 5:+ 0.473 (branch= 0.43 scale= 0.01 subset rates= 0.03) +pass 6:+ 0.135 (branch= 0.13 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -474.8070 +gen current_lnL precision last_tree_imp +0 -474.8070 0.010 0 +100 -474.7912 0.010 0 +200 -474.7022 0.010 123 +300 -474.5643 0.010 272 +400 -474.5191 0.010 272 +500 -474.5075 0.010 272 +600 -474.5034 0.010 272 +700 -474.4997 0.010 272 +800 -474.4937 0.010 272 +900 -474.4914 0.010 272 +1000 -474.4880 0.010 272 +1100 -474.4855 0.010 272 +1200 -474.4848 0.010 272 +1300 -474.4839 0.010 272 +1400 -474.4822 0.010 272 +1500 -474.4805 0.010 272 +1600 -474.4799 0.010 272 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -18368,36 +18991,74 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 5) generation 2754, seed 1747510246, best lnL -473.979 +Search rep 2 (of 5) generation 1614, seed 986383439, best lnL -474.480 gen current_lnL precision last_tree_imp -2754 -473.9791 0.010 653 -2800 -473.9779 0.010 653 -2900 -473.9777 0.010 653 -3000 -473.9777 0.010 653 -3100 -473.9773 0.010 653 -3200 -473.9772 0.010 653 -3300 -473.9771 0.010 653 +1614 -474.4799 0.010 272 +1700 -474.4796 0.010 272 +1800 -474.4791 0.010 272 +1900 -474.4787 0.010 272 +2000 -474.4786 0.010 272 +2100 -474.4782 0.010 272 +2200 -474.4775 0.010 272 +2300 -474.4768 0.010 272 +2400 -474.4765 0.010 272 +2500 -474.4765 0.010 272 +2600 -474.4747 0.010 272 +2700 -474.4737 0.010 272 +2800 -474.4721 0.010 272 +2900 -474.4720 0.010 272 +3000 -474.4653 0.010 272 +3100 -474.4597 0.010 272 +3200 -474.4561 0.010 272 +3300 -474.4551 0.010 272 +3400 -474.4539 0.010 272 +3500 -474.4525 0.010 272 +3600 -474.4522 0.010 272 +3700 -474.4507 0.010 272 +3800 -474.4505 0.010 272 +3900 -474.4501 0.010 272 +4000 -474.4501 0.010 272 +4100 -474.4499 0.010 272 +4200 -474.4490 0.010 272 +4300 -474.4489 0.010 272 +4400 -474.4484 0.010 272 +4500 -474.4482 0.010 272 +4600 -474.4481 0.010 272 +4700 -474.4472 0.010 272 +4800 -474.4468 0.010 272 +4900 -474.4462 0.010 272 +5000 -474.4461 0.010 272 + Optimizing parameters... improved 0.000 lnL + Optimizing branchlengths... improved 0.000 lnL +5100 -474.4451 0.010 272 +5200 -474.4451 0.010 272 +5300 -474.4451 0.010 272 +5400 -474.4450 0.010 272 +5500 -474.4450 0.010 272 +5600 -474.4442 0.010 272 Reached termination condition! -last topological improvement at gen 653 -Improvement over last 500 gen = 0.00088 -Current score = -473.9771 +last topological improvement at gen 272 +Improvement over last 500 gen = 0.00090 +Current score = -474.4442 Performing final optimizations... -pass 1 : -473.9742 (branch= 0.0000 subset rates= 0.0029) -pass 2 : -473.9558 (branch= 0.0183 subset rates= 0.0000) -pass 3 : -473.9558 (branch= 0.0000 subset rates= 0.0000) -pass 4 : -473.9548 (branch= 0.0011 subset rates= 0.0000) -pass 5 : -473.9529 (branch= 0.0018 subset rates= 0.0000) -pass 6 : -473.9525 (branch= 0.0004 subset rates= 0.0000) -pass 7 : -473.9517 (branch= 0.0008 subset rates= 0.0000) -pass 8 : -473.9513 (branch= 0.0004 subset rates= 0.0000) -pass 9 : -473.9511 (branch= 0.0003 subset rates= 0.0000) -pass 10: -473.9510 (branch= 0.0001 subset rates= 0.0000) -pass 11: -473.9510 (branch= 0.0000 subset rates= 0.0000) -pass 12: -473.9509 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9509 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -474.4442 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -474.4349 (branch= 0.0093 subset rates= 0.0000) +pass 3 : -474.4349 (branch= 0.0000 subset rates= 0.0000) +pass 4 : -474.4314 (branch= 0.0036 subset rates= 0.0000) +pass 5 : -474.4301 (branch= 0.0013 subset rates= 0.0000) +pass 6 : -474.4297 (branch= 0.0003 subset rates= 0.0000) +pass 7 : -474.4289 (branch= 0.0008 subset rates= 0.0000) +pass 8 : -474.4285 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -474.4283 (branch= 0.0002 subset rates= 0.0000) +pass 10: -474.4282 (branch= 0.0001 subset rates= 0.0000) +pass 11: -474.4282 (branch= 0.0001 subset rates= 0.0000) +pass 12: -474.4281 (branch= 0.0000 subset rates= 0.0000) +pass 13: -474.4281 (branch= 0.0000 subset rates= 0.0000) +pass 14: -474.4281 (branch= 0.0000 subset rates= 0.0000) +pass 15: -474.4281 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -473.9509 -Time used so far = 0 hours, 0 minutes and 7 seconds +Final score = -474.4281 +Time used so far = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18425,13 +19086,13 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.07 2.82 + 0.59 2.03 2.92 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. + 7 branches were collapsed. ->>>Completed Search rep 1 (of 5)<<< +>>>Completed Search rep 2 (of 5)<<< ->>>Search rep 2 (of 5)<<< +>>>Search rep 3 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 @@ -18460,64 +19121,53 @@ Subset rate multipliers: 1.00 1.00 1.00 -Starting with seed=2125680066 +Starting with seed=962219047 -Initial ln Likelihood: -649.8224 +Initial ln Likelihood: -627.7847 optimizing: starting branch lengths, subset rates... -pass 1:+ 148.288 (branch= 136.88 scale= 0.96 subset rates= 10.45) -pass 2:+ 18.126 (branch= 13.41 scale= 0.03 subset rates= 4.69) -pass 3:+ 5.650 (branch= 3.93 scale= 0.00 subset rates= 1.72) -pass 4:+ 2.344 (branch= 1.67 scale= 0.00 subset rates= 0.67) -pass 5:+ 0.473 (branch= 0.43 scale= 0.01 subset rates= 0.03) -pass 6:+ 0.135 (branch= 0.13 scale= 0.00 subset rates= 0.00) +pass 1:+ 131.737 (branch= 120.88 scale= 0.56 subset rates= 10.29) +pass 2:+ 14.701 (branch= 9.85 scale= 0.02 subset rates= 4.83) +pass 3:+ 5.363 (branch= 3.65 scale= 0.00 subset rates= 1.71) +pass 4:+ 1.030 (branch= 0.39 scale= 0.03 subset rates= 0.61) +pass 5:+ 0.053 (branch= 0.02 scale= 0.00 subset rates= 0.03) +pass 6:+ 0.023 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8070 +lnL after optimization: -474.8769 gen current_lnL precision last_tree_imp -0 -474.8070 0.010 0 -100 -474.7912 0.010 0 -200 -474.7022 0.010 123 -300 -474.5643 0.010 272 -400 -474.5191 0.010 272 -500 -474.5075 0.010 272 -600 -474.5034 0.010 272 -700 -474.4997 0.010 272 -800 -474.4937 0.010 272 -900 -474.4914 0.010 272 -1000 -474.4880 0.010 272 -1100 -474.4855 0.010 272 -1200 -474.4848 0.010 272 -1300 -474.4839 0.010 272 -1400 -474.4822 0.010 272 -1500 -474.4805 0.010 272 -1600 -474.4799 0.010 272 -1700 -474.4796 0.010 272 -1800 -474.4791 0.010 272 -1900 -474.4787 0.010 272 -2000 -474.4786 0.010 272 -2100 -474.4782 0.010 272 -2200 -474.4775 0.010 272 -2300 -474.4768 0.010 272 -2400 -474.4765 0.010 272 -2500 -474.4765 0.010 272 +0 -474.8769 0.010 0 +100 -474.8469 0.010 0 +200 -474.8166 0.010 0 +300 -474.8105 0.010 0 +400 -474.5903 0.010 373 +500 -474.5388 0.010 474 +600 -474.5224 0.010 474 +700 -474.5152 0.010 474 +800 -474.5091 0.010 474 +900 -474.5063 0.010 474 +1000 -474.5042 0.010 474 +1100 -474.5023 0.010 474 +1200 -474.4970 0.010 474 +1300 -474.4950 0.010 474 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -474.4752 +Current score = -474.4926 Performing final optimizations... -pass 1 : -474.4686 (branch= 0.0066 subset rates= 0.0000) -pass 2 : -474.4452 (branch= 0.0234 subset rates= 0.0000) -pass 3 : -474.4368 (branch= 0.0083 subset rates= 0.0000) -pass 4 : -474.4353 (branch= 0.0015 subset rates= 0.0000) -pass 5 : -474.4334 (branch= 0.0019 subset rates= 0.0000) -pass 6 : -474.4309 (branch= 0.0020 subset rates= 0.0006) -pass 7 : -474.4295 (branch= 0.0014 subset rates= 0.0000) -pass 8 : -474.4287 (branch= 0.0008 subset rates= 0.0000) -pass 9 : -474.4285 (branch= 0.0002 subset rates= 0.0000) -pass 10: -474.4284 (branch= 0.0001 subset rates= 0.0000) -pass 11: -474.4282 (branch= 0.0001 subset rates= 0.0000) -pass 12: -474.4282 (branch= 0.0000 subset rates= 0.0000) -pass 13: -474.4282 (branch= 0.0000 subset rates= 0.0000) -pass 14: -474.4282 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -474.4784 (branch= 0.0119 subset rates= 0.0023) +pass 2 : -474.4482 (branch= 0.0302 subset rates= 0.0000) +pass 3 : -474.4439 (branch= 0.0039 subset rates= 0.0004) +pass 4 : -474.4393 (branch= 0.0031 subset rates= 0.0015) +pass 5 : -474.4345 (branch= 0.0047 subset rates= 0.0000) +pass 6 : -474.4311 (branch= 0.0034 subset rates= 0.0000) +pass 7 : -474.4299 (branch= 0.0012 subset rates= 0.0000) +pass 8 : -474.4292 (branch= 0.0007 subset rates= 0.0000) +pass 9 : -474.4289 (branch= 0.0003 subset rates= 0.0000) +pass 10: -474.4288 (branch= 0.0001 subset rates= 0.0000) +pass 11: -474.4287 (branch= 0.0001 subset rates= 0.0000) +pass 12: -474.4287 (branch= 0.0000 subset rates= 0.0000) +pass 13: -474.4287 (branch= 0.0000 subset rates= 0.0000) +pass 14: -474.4287 (branch= 0.0000 subset rates= 0.0000) +pass 15: -474.4287 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -474.4282 +Final score = -474.4287 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -18546,11 +19196,11 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.03 2.92 + 0.59 2.03 2.90 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. ->>>Terminated Search rep 2 (of 5)<<< +>>>Terminated Search rep 3 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -18558,13 +19208,14 @@ ####################################################### -Completed 2 replicate search(es) (of 5). +Completed 3 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -473.9509 (best) -Replicate 2 : -474.4282 (TERMINATED PREMATURELY) +Replicate 2 : -474.4281 +Replicate 3 : -474.4287 (same topology as 2) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -18580,7 +19231,8 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.351 0.587 2.065 2.818 -rep 2: 4.599 0.588 2.031 2.920 +rep 2: 4.601 0.587 2.032 2.923 +rep 3: 4.596 0.589 2.030 2.905 Saving final tree from best search rep (#1) to ch.p.mkvO.ssr.best.tre ####################################################### @@ -18598,7 +19250,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j11 install DESTDIR=/build/reproducible-path/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no + make -j21 install DESTDIR=/build/reproducible-path/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/garli-2.1' Making install in src make[2]: Entering directory '/build/reproducible-path/garli-2.1/src' @@ -18647,11 +19299,11 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'garli' in '../garli_2.1-9_i386.deb'. -dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-9_i386.deb'. -dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-9_i386.deb'. dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-9_all.deb'. +dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-9_i386.deb'. dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-9_i386.deb'. +dpkg-deb: building package 'garli' in '../garli_2.1-9_i386.deb'. +dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-9_i386.deb'. dpkg-genbuildinfo --build=binary -O../garli_2.1-9_i386.buildinfo dpkg-genchanges --build=binary -O../garli_2.1-9_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -18659,12 +19311,14 @@ 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/4345/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4345/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/34980 and its subdirectories -I: Current time: Fri Dec 20 11:38:15 -12 2024 -I: pbuilder-time-stamp: 1734737895 +I: removing directory /srv/workspace/pbuilder/4345 and its subdirectories +I: Current time: Fri Jan 23 20:06:38 +14 2026 +I: pbuilder-time-stamp: 1769148398