Diff of the two buildlogs: -- --- b1/build.log 2024-11-11 07:22:50.306195877 +0000 +++ b2/build.log 2024-11-11 07:31:38.155347027 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Dec 14 01:40:39 -12 2025 -I: pbuilder-time-stamp: 1765719639 +I: Current time: Mon Nov 11 21:22:54 +14 2024 +I: pbuilder-time-stamp: 1731309774 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_2.1-8.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/77655/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/8894/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-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 Nov 11 07:23 /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/8894/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/8894/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=22 ' - 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]="32" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.32(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=10 ' + 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='4820d191ba4047cc8949a49cb941a3bf' - 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='77655' - PS1='# ' - PS2='> ' + INVOCATION_ID=a2d982868f2e4dd28d9c4c651209284e + 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=8894 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.rBfFWdLu/pbuilderrc_nDBd --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.rBfFWdLu/b1 --logfile b1/build.log garli_2.1-8.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://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.rBfFWdLu/pbuilderrc_PJHB --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.rBfFWdLu/b2 --logfile b2/build.log garli_2.1-8.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://46.16.76.132:3128 I: uname -a - Linux ionos16-i386 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/77655/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/8894/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 2s (22.3 MB/s) +Fetched 42.1 MB in 1s (38.1 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 ... 19955 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_2.1-8_source.changes +I: user script /srv/workspace/pbuilder/8894/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/8894/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_2.1-8_source.changes dpkg-buildpackage: info: source package garli dpkg-buildpackage: info: source version 2.1-8 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 -j22 + make -j10 make[2]: Entering directory '/build/reproducible-path/garli-2.1' make all-recursive make[3]: Entering directory '/build/reproducible-path/garli-2.1' @@ -583,21 +619,6 @@ 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 garlimain.o garlimain.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 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__); | ^~~~~~~~ @@ -626,22 +647,6 @@ | ~~~~~~~~~~~~~~~~~ /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=] -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 bipartition.cpp:20: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ @@ -686,56 +691,22 @@ /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 - | ^~~~~~~~~~~~~~~ -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) - | ^~~~~~~ -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{ | ^~~~~~~~~~~~~~~ @@ -801,7 +777,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from mpitrick.cpp:21: + from configreader.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -839,11 +815,6 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from garlimain.cpp:46: -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 58 | class DistEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/string:49, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from adaptation.cpp:18: -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -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 individual.h:21, - from model.cpp:26: + from funcs.cpp:30: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -905,7 +833,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from model.cpp:17: + from population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -929,13 +857,6 @@ /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) - | ^~~~~~~ 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)); @@ -954,33 +875,7 @@ 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 - | ^~~~~~~~~~~~~~~ -In file included from tree.h:35, - from individual.h:21, - from population.h:31, - from funcs.h:25, - from configreader.cpp:30: + from adaptation.cpp:25: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -990,7 +885,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from configreader.cpp:21: + from adaptation.cpp:18: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1021,28 +916,6 @@ /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 '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) - | ^~~~~~~ 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; @@ -1050,36 +923,15 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from 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 - | ^~~~~~~~~~~~~~~ +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 +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] 65 | class DistEqualsWithinCutSubtree:public 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)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/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: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)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ -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) - | ^~~~~~~ -In file included from tree.h:35, - from individual.h:21, - from population.h:31, - from population.cpp:45: -reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 58 | class DistEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/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 - | ^~~~~~~~~~~~~~~ -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 | ^~~~~~~~~~~~~~~ @@ -1163,13 +960,6 @@ /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)); @@ -1192,42 +982,15 @@ /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 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) + | ^~~~~~~ +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) + | ^~~~~~~ model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); @@ -1394,41 +1144,24 @@ model.cpp:3713:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3713 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -reconnode.h: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)': -reconnode.h:388:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 388 | fread(&unique, scalarSize, 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -reconnode.h: In constructor 'Swap::Swap(FILE*&)': -reconnode.h:264:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 264 | fread(&count, scalarSize, 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from treenode.h:30, - from tree.h:31: -bipartition.h: In member function 'void Bipartition::BinaryInput(FILE*&)': -bipartition.h:518:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 518 | fread((char*) rep, sizeof(unsigned int), nBlocks, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp: In member function 'void Population::ReadPopulationCheckpoint()': -population.cpp:1880:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1880 | fread((char *) &seed, sizeof(seed), 1, pin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp:1887:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1887 | fread((char *) &t, sizeof(t), 1, pin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp:1896:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(this, scalarSize, 1, pin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, 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/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] @@ -1444,14 +1177,7 @@ 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 rng.h:36, - from tree.h:30: + 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] @@ -1464,9 +1190,10 @@ /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=] In file included from /usr/include/stdio.h:970, - 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: + 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] @@ -1533,15 +1260,7 @@ from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from model.h:25, - from clamanager.h:25, - from condlike.cpp:22: + from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1553,11 +1272,55 @@ | ~~~~~~~~~~~~~~~~~ /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=] +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: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) + | ^~~~~~~ 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/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] @@ -1569,10 +1332,18 @@ | ~~~~~~~~~~~~~~~~~ /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=] +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: +/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) + | ^~~~~~~ +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 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{ + | ^~~~~~~~~~~~~~~ +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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 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, @@ -1641,11 +1630,68 @@ | ~~~~~~~~~~~~~~~~~ /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/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 - | ^~~~~~~~~~~~~~~ -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/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: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) - | ^~~~~~~ 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); @@ -2119,67 +2039,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -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/string:49, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from adaptation.cpp:18: -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -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/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) - | ^~~~~~~ -In file included from tree.h:35, - from individual.h:21, - from population.h:31, - from garlimain.cpp:40: + from adaptation.cpp:25: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2291,7 +2103,7 @@ 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 | ^~~~~~~~~~~~~~~ @@ -2322,10 +2134,6 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; @@ -2337,18 +2145,14 @@ funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2396,10 +2200,6 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2417,7 +2219,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from model.cpp:17: + from configreader.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2458,13 +2260,18 @@ In file included from tree.h:35, from individual.h:21, from population.h:31, - from population.cpp:45: + 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/bits/refwrap.h:39, - from /usr/include/c++/14/vector:68, - from population.cpp:23: +In file included from /usr/include/c++/14/string:49, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2502,11 +2309,20 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from 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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)': +configreader.cpp:602:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 602 | fread(&ch, sizeof(char), 1, file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +configreader.cpp:605:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(&ch, sizeof(char), 1, file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from tree.h:35, + from 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) + | ^~~~~~~ +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) + | ^~~~~~~ +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 optimization.o optimization.cpp model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); @@ -2670,36 +2477,19 @@ model.cpp:3713:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3713 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': -model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -reconnode.h: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)': -reconnode.h:388:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 388 | fread(&unique, scalarSize, 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -reconnode.h: In constructor 'Swap::Swap(FILE*&)': -reconnode.h:264:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 264 | fread(&count, scalarSize, 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from treenode.h:30, - from tree.h:31: -bipartition.h: In member function 'void Bipartition::BinaryInput(FILE*&)': -bipartition.h:518:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 518 | fread((char*) rep, sizeof(unsigned int), nBlocks, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp: In member function 'void Population::ReadPopulationCheckpoint()': -population.cpp:1880:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1880 | fread((char *) &seed, sizeof(seed), 1, pin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp:1887:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1887 | fread((char *) &t, sizeof(t), 1, pin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp:1896:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(this, scalarSize, 1, pin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, - from configreader.cpp:18: + from /usr/include/c++/14/cstdio:42, + from /usr/include/c++/14/ext/string_conversions.h:45, + from /usr/include/c++/14/bits/basic_string.h:4154, + from /usr/include/c++/14/string:54, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from 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] @@ -2715,13 +2505,7 @@ 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] @@ -2733,14 +2517,15 @@ | ~~~~~~~~~~~~~~~~~ /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=] +model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': +model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54, - from datamatr.h:23, - from sequencedata.h:27, - from sequencedata.cpp:21: + from /usr/include/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] @@ -2754,9 +2539,8 @@ /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/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] @@ -2784,13 +2568,58 @@ | ~~~~~~~~~~~~~~~~~ /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 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: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) + | ^~~~~~~ +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: +/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) + | ^~~~~~~ +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 +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{ + | ^~~~~~~~~~~~~~~ +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 /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 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] @@ -2905,8 +2931,12 @@ /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 /usr/include/c++/14/ext/string_conversions.h:45, + from /usr/include/c++/14/bits/basic_string.h:4154, + from /usr/include/c++/14/string:54, + from datamatr.h:23, + from sequencedata.h:27, + from sequencedata.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2922,7 +2952,8 @@ 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 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] @@ -2939,9 +2970,12 @@ 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 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] @@ -2958,7 +2992,9 @@ from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, - from population.cpp:25: + from datamatr.h:23, + from sequencedata.h:27, + from tree.cpp:31: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -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 -j22 check "TESTSUITEFLAGS=-j22 --verbose" VERBOSE=1 + make -j10 check "TESTSUITEFLAGS=-j10 --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' @@ -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 0 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 13 seconds +Time used = 0 hours, 0 minutes and 26 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 10 seconds +Time used = 0 hours, 0 minutes and 17 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: -3350.5337 (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 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 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= 0.0059 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) +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) 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 ... @@ -6320,14 +6356,12 @@ 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: -3350.2338 (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 80: -3350.2336 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +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) 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) +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) Looking for minimum length branches... Final score = -3350.2336 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6340,7 +6374,7 @@ 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: 3.114 10.41 2.689 0.001 21.88 1 0.333 0.222 0.157 0.288 0.580 0.366 +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 Partition model subset 2: Model contains no estimated parameters @@ -6353,9 +6387,9 @@ Writing optimized trees and models to scr.g.dnaBnoZ.best.all.tre ***********TEST************** -***Score is 3350.23358 +***Score is 3350.23362 ***Expected is 3350.2345 -***SCORE DIFFERENCE IS -.00092 +***SCORE DIFFERENCE IS -.00088 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/g.dnaBnoZ.conf *** Running scoring test ./scoring/g.dnaMix.conf @@ -6535,7 +6569,7 @@ 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 1 seconds +Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7019,7 +7053,7 @@ 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 4 seconds +Time used = 0 hours, 0 minutes and 11 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -7273,7 +7307,7 @@ 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 4 seconds +Time used = 0 hours, 0 minutes and 7 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7700,7 +7734,7 @@ pass 17: -467.6787 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6787 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -9125,53 +9159,53 @@ 3000 -210.5163 0.010 1215 Reached termination condition! last topological improvement at gen 1215 -Improvement over last 500 gen = 0.03350 -Current score = -210.5120 +Improvement over last 500 gen = 0.03351 +Current score = -210.5119 Performing final optimizations... -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) +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) optimization up to ... -pass 80: -208.5380 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0356) +pass 80: -208.5378 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0356) optimization up to ... -pass 90: -208.5108 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0270) +pass 90: -208.5107 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0269) optimization up to ... -pass 100: -208.4896 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0211) +pass 100: -208.4896 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0210) optimization up to ... -pass 110: -208.4727 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0168) +pass 110: -208.4726 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0169) 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: -208.4473 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0115) +pass 130: -208.4472 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0115) optimization up to ... -pass 140: -208.4376 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0097) +pass 140: -208.4375 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0096) 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 ... @@ -9187,27 +9221,27 @@ 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= 0.0033) +pass 220: -208.3947 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) optimization up to ... -pass 230: -208.3917 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0030) +pass 230: -208.3916 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0031) optimization up to ... pass 240: -208.3889 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0028) optimization up to ... -pass 250: -208.3864 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0025) +pass 250: -208.3863 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0025) optimization up to ... -pass 260: -208.3841 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0023) +pass 260: -208.3840 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0023) optimization up to ... -pass 270: -208.3820 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) +pass 270: -208.3819 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) optimization up to ... -pass 280: -208.3800 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) +pass 280: -208.3800 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... -pass 290: -208.3782 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) +pass 290: -208.3781 (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: -208.3750 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) +pass 310: -208.3749 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... -pass 320: -208.3735 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) +pass 320: -208.3734 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 330: -208.3721 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... @@ -9223,40 +9257,38 @@ 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: -208.3647 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) +pass 400: -208.3646 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 410: -208.3638 (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= 0.0007) +pass 430: -208.3623 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) 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= 0.0007) +pass 460: -208.3602 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 470: -208.3596 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... -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: -208.3589 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) +pass 480: -208.3593 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... -pass 500: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) +pass 490: -208.3590 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... -pass 510: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) +pass 500: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... -pass 512: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) +pass 509: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... -Final score = -208.3583 -Time used = 0 hours, 0 minutes and 4 seconds +Final score = -208.3584 +Time used = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 123.075, AG = 189.929, AT = 7.010, CG = 206.213, CT = 196.176, GT = 1.000 + AC = 122.311, AG = 188.753, AT = 6.967, CG = 204.934, CT = 194.972, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2225 0.2906 0.2035 0.2835 Rate Heterogeneity Model: @@ -9280,11 +9312,11 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -208.3583 +Replicate 1 : -208.3584 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 123.1 189.9 7.01 206.2 196.2 1 0.223 0.291 0.203 0.283 999.900 0.278 +rep 1: 122.3 188.8 6.967 204.9 195 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL @@ -9421,43 +9453,43 @@ 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 : -208.5667 (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) +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) optimization up to ... -pass 30: -208.2568 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0440) +pass 30: -208.2567 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0439) optimization up to ... -pass 40: -208.2294 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0273) +pass 40: -208.2293 (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= 0.0189) +pass 50: -208.2105 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0187) optimization up to ... -pass 60: -208.1968 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0137) +pass 60: -208.1969 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0136) 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: -208.1716 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) +pass 90: -208.1715 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) 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: -208.1615 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) +pass 110: -208.1614 (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 ... @@ -9467,7 +9499,7 @@ 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= 0.0024) +pass 160: -208.1461 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0023) 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 ... @@ -9503,7 +9535,7 @@ 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: -208.1260 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 340: -208.1259 (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 ... @@ -9511,16 +9543,16 @@ 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 372: -208.1243 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) +pass 373: -208.1243 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... Final score = -208.1243 -Time used = 0 hours, 0 minutes and 5 seconds +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 = 22.239, AG = 32.314, AT = 0.001, CG = 36.402, CT = 80.320, GT = 1.000 + AC = 22.244, AG = 32.321, AT = 0.001, CG = 36.409, CT = 80.319, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2210 0.3445 0.2161 0.2184 Rate Heterogeneity Model: @@ -9548,7 +9580,7 @@ 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 32.31 0.001 36.4 80.32 1 0.221 0.344 0.216 0.218 999.900 0.338 +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 Treelengths: TL @@ -9676,158 +9708,148 @@ Optimization precision reduced Optimizing parameters... improved 1.908 lnL Optimizing branchlengths... improved 0.702 lnL -2000 -210.9688 0.010 1502 +2000 -210.9689 0.010 1502 2500 -210.8711 0.010 1502 -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 +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 Reached termination condition! -last topological improvement at gen 9713 -Improvement over last 500 gen = 0.01208 -Current score = -209.3469 +last topological improvement at gen 4692 +Improvement over last 500 gen = 0.02291 +Current score = -210.4049 Performing final optimizations... -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) +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) optimization up to ... -pass 30: -208.7099 (branch= 0.0200 alpha= 0.0000 pinv= 0.0018 eq freqs= 0.0077 rel rates= 0.1306) +pass 40: -208.7374 (branch= 0.0228 alpha= 0.0000 pinv= 0.0019 eq freqs= 0.0081 rel rates= 0.1377) optimization up to ... -pass 40: -208.6301 (branch= 0.0017 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0010 rel rates= 0.0768) +pass 50: -208.6461 (branch= 0.0028 alpha= 0.0000 pinv= 0.0004 eq freqs= 0.0016 rel rates= 0.0865) optimization up to ... -pass 50: -208.5785 (branch= 0.0003 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0510) +pass 60: -208.5898 (branch= 0.0004 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0556) optimization up to ... -pass 60: -208.5414 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0367) +pass 70: -208.5497 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0397) optimization up to ... -pass 70: -208.5134 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0278) +pass 80: -208.5198 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0297) optimization up to ... -pass 80: -208.4917 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0215) +pass 90: -208.4966 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0230) optimization up to ... -pass 90: -208.4743 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0173) +pass 100: -208.4783 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0182) optimization up to ... -pass 100: -208.4602 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0140) +pass 110: -208.4635 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0147) optimization up to ... -pass 110: -208.4485 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0117) +pass 120: -208.4511 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0123) optimization up to ... -pass 120: -208.4386 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0098) +pass 130: -208.4408 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0102) optimization up to ... -pass 130: -208.4301 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0084) +pass 140: -208.4321 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0087) optimization up to ... -pass 140: -208.4229 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0071) +pass 150: -208.4246 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0074) optimization up to ... -pass 150: -208.4167 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0062) +pass 160: -208.4181 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0065) optimization up to ... -pass 160: -208.4112 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0054) +pass 170: -208.4125 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0056) optimization up to ... -pass 170: -208.4065 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) +pass 180: -208.4076 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) optimization up to ... -pass 180: -208.4022 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0042) +pass 190: -208.4033 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0043) optimization up to ... -pass 190: -208.3984 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0038) +pass 200: -208.3994 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0039) optimization up to ... -pass 200: -208.3950 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) +pass 210: -208.3959 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) optimization up to ... -pass 210: -208.3919 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0031) +pass 220: -208.3928 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0031) optimization up to ... -pass 220: -208.3892 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0028) +pass 230: -208.3898 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) optimization up to ... -pass 230: -208.3866 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) +pass 240: -208.3872 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) optimization up to ... -pass 240: -208.3843 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0023) +pass 250: -208.3848 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... -pass 250: -208.3821 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) +pass 260: -208.3826 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... -pass 260: -208.3801 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) +pass 270: -208.3806 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... -pass 270: -208.3783 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) +pass 280: -208.3788 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... -pass 280: -208.3766 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) +pass 290: -208.3771 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... -pass 290: -208.3751 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) +pass 300: -208.3754 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... -pass 300: -208.3736 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) +pass 310: -208.3740 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... -pass 310: -208.3722 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) +pass 320: -208.3726 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... -pass 320: -208.3710 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) +pass 330: -208.3713 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... -pass 330: -208.3698 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) +pass 340: -208.3700 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... -pass 340: -208.3686 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) +pass 350: -208.3689 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... -pass 350: -208.3676 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) +pass 360: -208.3678 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... -pass 360: -208.3666 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) +pass 370: -208.3668 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... -pass 370: -208.3656 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) +pass 380: -208.3659 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... -pass 380: -208.3647 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) +pass 390: -208.3650 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... -pass 390: -208.3639 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) +pass 400: -208.3641 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... -pass 400: -208.3631 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) +pass 410: -208.3633 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... -pass 410: -208.3623 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) +pass 420: -208.3625 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... -pass 420: -208.3616 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 430: -208.3618 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 430: -208.3609 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) +pass 440: -208.3611 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 440: -208.3603 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 450: -208.3604 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... -pass 450: -208.3596 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) +pass 460: -208.3598 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... -pass 460: -208.3592 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) +pass 470: -208.3592 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... -pass 470: -208.3589 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) +pass 480: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) optimization up to ... -pass 480: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) +pass 490: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... -pass 490: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) +pass 491: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... -Final score = -208.3583 +Final score = -208.3584 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 = 122.734, AG = 189.877, AT = 7.006, CG = 205.815, CT = 195.714, GT = 1.000 + AC = 122.675, AG = 189.304, AT = 6.999, CG = 205.533, CT = 195.564, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2225 0.2906 0.2034 0.2835 + (ACGT) 0.2225 0.2906 0.2035 0.2835 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 999.9000 @@ -9854,11 +9876,11 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -208.3583 +Replicate 1 : -208.3584 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 122.7 189.9 7.006 205.8 195.7 1 0.223 0.291 0.203 0.283 999.900 0.278 +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 Treelengths: TL @@ -9985,73 +10007,73 @@ Optimization precision reduced Optimizing parameters... improved 1.494 lnL Optimizing branchlengths... improved 0.350 lnL -1500 -210.9425 0.010 1230 +1500 -210.9424 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 = 0.03867 +Improvement over last 500 gen = 0.03865 Current score = -210.5968 Performing final optimizations... -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) +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) optimization up to ... -pass 70: -208.5550 (branch= 0.0002 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0417) +pass 70: -208.5553 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0416) optimization up to ... -pass 80: -208.5239 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0309) +pass 80: -208.5239 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0311) optimization up to ... -pass 90: -208.4998 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0239) +pass 90: -208.4999 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0238) optimization up to ... -pass 100: -208.4809 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0188) +pass 100: -208.4809 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0189) 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: -208.4424 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0105) +pass 130: -208.4423 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0105) optimization up to ... -pass 140: -208.4333 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0090) +pass 140: -208.4334 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0089) optimization up to ... -pass 150: -208.4256 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0076) +pass 150: -208.4257 (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= 0.0065) +pass 160: -208.4191 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) 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: -208.4084 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) +pass 180: -208.4083 (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: -208.4000 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0039) +pass 200: -208.3999 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) optimization up to ... -pass 210: -208.3964 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0035) +pass 210: -208.3963 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0036) 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 ... @@ -10065,7 +10087,7 @@ 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: -208.3791 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) +pass 280: -208.3790 (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 ... @@ -10105,20 +10127,22 @@ 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: -208.3588 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) +pass 480: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) + 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 490: -208.3585 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) +pass 492: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... -Final score = -208.3585 -Time used = 0 hours, 0 minutes and 4 seconds +Final score = -208.3584 +Time used = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 121.995, AG = 188.263, AT = 6.960, CG = 204.402, CT = 194.488, GT = 1.000 + AC = 122.522, AG = 189.082, AT = 6.990, CG = 205.290, CT = 195.326, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2225 0.2905 0.2035 0.2835 + (ACGT) 0.2225 0.2906 0.2035 0.2835 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 999.9000 @@ -10145,11 +10169,11 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -208.3585 +Replicate 1 : -208.3584 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 122 188.3 6.96 204.4 194.5 1 0.223 0.291 0.203 0.283 999.900 0.278 +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 Treelengths: TL @@ -12825,11 +12849,6 @@ 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 -1200 -88.8463 0.010 879 -1300 -88.8312 0.010 879 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12926,11 +12945,14 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 1301, seed 716847524, best lnL -88.831 +Bootstrap rep 1 (of 1) generation 872, seed 1874256898, best lnL -89.637 gen current_lnL precision last_tree_imp -1301 -88.8312 0.010 879 +872 -89.6373 0.010 840 +900 -88.9507 0.010 879 +1000 -88.8871 0.010 879 +NOTE: ****Specified generation limit (1000) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones @@ -12942,37 +12964,41 @@ 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 0.9984 + 0.9045 with an invariant (invariable) site category, proportion estimated - 0.1371 + 0.1355 Substitution rate categories under this model: rate proportion - 0.0000 0.1371 - 0.1887 0.2876 - 0.7119 0.2876 - 2.0994 0.2876 + 0.0000 0.1355 + 0.1669 0.2882 + 0.6855 0.2882 + 2.1476 0.2882 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 : -88.8312 +Replicate 1 : -88.8871 Parameter estimates: alpha pinv -rep 1: 0.998 0.137 +rep 1: 0.904 0.136 Treelengths: TL -rep 1: 2.337 +rep 1: 2.441 Saving best tree to bootstrap file ch.a.G3.boot.tre ->>>Completed Bootstrap rep 1<<< +WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/a.G4.conf @@ -13095,12 +13121,6 @@ 300 -112.3224 0.500 84 400 -112.1061 0.500 84 500 -111.8129 0.500 84 -600 -111.7788 0.500 84 -Optimization precision reduced - Optimizing parameters... improved 0.386 lnL - Optimizing branchlengths... improved 0.390 lnL -700 -110.8142 0.010 615 -800 -110.5642 0.010 707 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13187,9 +13207,15 @@ STARTING RUN Restarting from checkpoint... - generation 878, seed 1874256898, best lnL -110.555 + generation 593, seed 1456445603, best lnL -111.779 gen current_lnL precision last_tree_imp -878 -110.5555 0.010 707 +593 -111.7788 0.500 84 +600 -111.7788 0.500 84 +Optimization precision reduced + Optimizing parameters... improved 0.386 lnL + Optimizing branchlengths... improved 0.390 lnL +700 -110.8142 0.010 615 +800 -110.5642 0.010 707 900 -110.5555 0.010 707 1000 -110.5065 0.010 707 NOTE: ****Specified generation limit (1000) reached... @@ -13376,19 +13402,6 @@ 1600 -111.6818 0.010 563 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 -3100 -111.6815 0.010 563 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13474,9 +13487,9 @@ STARTING RUN Restarting from checkpoint... - generation 3103, seed 1524232791, best lnL -111.682 + generation 1802, seed 1519431587, best lnL -111.682 gen current_lnL precision last_tree_imp -3103 -111.6815 0.010 563 +1802 -111.6818 0.010 563 MODEL REPORT - Parameter values are FINAL Model 1 @@ -13500,14 +13513,14 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -111.6815 +Replicate 1 : -111.6818 Parameter estimates: Model contains no estimated parameters Treelengths: TL -rep 1: 2.607 +rep 1: 2.606 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 @@ -13639,12 +13652,6 @@ 30 -205.6499 0.500 18 40 -205.6371 0.500 18 50 -205.6175 0.500 18 -60 -205.5990 0.500 53 -70 -205.5741 0.500 53 -80 -205.4022 0.500 76 -90 -205.3871 0.500 76 -100 -205.3829 0.500 76 -110 -205.3431 0.500 106 NOTE: ****Specified time limit (10 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13731,11 +13738,17 @@ STARTING RUN Restarting from checkpoint... - generation 116, seed 1919088460, best lnL -205.343 + generation 54, seed 227725811, best lnL -205.599 gen current_lnL precision last_tree_imp -116 -205.3431 0.500 106 +54 -205.5990 0.500 53 +60 -205.5990 0.500 53 +70 -205.5741 0.500 53 +80 -205.4022 0.500 76 +90 -205.3871 0.500 76 +100 -205.3829 0.500 76 +NOTE: ****Specified generation limit (100) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates @@ -13767,12 +13780,17 @@ 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 : -205.3431 +Replicate 1 : -205.3829 Parameter estimates: w(0) p(0) w(1) p(1) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) @@ -13780,11 +13798,13 @@ Treelengths: TL -rep 1: 7.779 +rep 1: 7.371 Saving final tree from best search rep (#1) to ch.c.M3x2.best.tre Inferring internal state probabilities on best tree... saving to file ch.c.M3x2.internalstates.log +WARNING: Internal states inferred on tree from prematurely terminated search + ####################################################### TREEFILES PASS Running checkpoint test ./check/c.conf @@ -13913,13 +13933,6 @@ 10 -195.3553 0.500 0 20 -195.3340 0.500 0 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 @@ -14007,11 +14020,19 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 106, seed 1626872889, best lnL -194.909 +Bootstrap rep 1 (of 1) generation 31, seed 166052708, best lnL -195.278 gen current_lnL precision last_tree_imp -106 -194.9092 0.500 0 +31 -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 generation limit (100) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 61 (codon data, standard code) One estimated dN/dS ratio (aka omega) = 0.120505 @@ -14040,6 +14061,10 @@ 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). @@ -14056,7 +14081,7 @@ Saving best tree to bootstrap file ch.c.boot.tre ->>>Completed Bootstrap rep 1<<< +WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/g.dnaBnoZ.conf @@ -14220,19 +14245,6 @@ 1100 -3352.7219 0.010 0 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 -2500 -3351.1237 0.010 0 -2600 -3351.0612 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14336,88 +14348,75 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 2677, seed 1130685511, best lnL -3351.061 +Search rep 1 (of 2) generation 1330, seed 952342344, best lnL -3352.545 gen current_lnL precision last_tree_imp -2677 -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 -4700 -3350.8150 0.010 0 -4800 -3350.8148 0.010 0 -4900 -3350.8148 0.010 0 +1330 -3352.5453 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 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3350.8136 +Current score = -3351.2511 Performing final optimizations... -pass 1 : -3350.7660 (branch= 0.0000 alpha= 0.0000 pinv= 0.0220 eq freqs= 0.0001 rel rates= 0.0255 subset rates= 0.0000) -pass 2 : -3350.7213 (branch= 0.0025 alpha= 0.0101 pinv= 0.0168 eq freqs= 0.0000 rel rates= 0.0153 subset rates= 0.0000) -pass 3 : -3350.6668 (branch= 0.0048 alpha= 0.0167 pinv= 0.0148 eq freqs= 0.0000 rel rates= 0.0153 subset rates= 0.0029) -pass 4 : -3350.6127 (branch= 0.0083 alpha= 0.0130 pinv= 0.0139 eq freqs= 0.0015 rel rates= 0.0163 subset rates= 0.0012) -pass 5 : -3350.5677 (branch= 0.0055 alpha= 0.0115 pinv= 0.0128 eq freqs= 0.0000 rel rates= 0.0140 subset rates= 0.0012) -pass 6 : -3350.5277 (branch= 0.0041 alpha= 0.0110 pinv= 0.0117 eq freqs= 0.0000 rel rates= 0.0123 subset rates= 0.0010) -pass 7 : -3350.4938 (branch= 0.0022 alpha= 0.0098 pinv= 0.0106 eq freqs= 0.0000 rel rates= 0.0113 subset rates= 0.0000) -pass 8 : -3350.4623 (branch= 0.0004 alpha= 0.0099 pinv= 0.0095 eq freqs= 0.0000 rel rates= 0.0107 subset rates= 0.0010) -pass 9 : -3350.4345 (branch= 0.0012 alpha= 0.0090 pinv= 0.0086 eq freqs= 0.0001 rel rates= 0.0088 subset rates= 0.0000) -pass 10: -3350.4103 (branch= 0.0002 alpha= 0.0081 pinv= 0.0077 eq freqs= 0.0000 rel rates= 0.0083 subset rates= 0.0000) -pass 11: -3350.3883 (branch= 0.0001 alpha= 0.0076 pinv= 0.0069 eq freqs= 0.0000 rel rates= 0.0073 subset rates= 0.0000) -pass 12: -3350.3687 (branch= 0.0000 alpha= 0.0070 pinv= 0.0062 eq freqs= 0.0000 rel rates= 0.0065 subset rates= 0.0000) -pass 13: -3350.3514 (branch= 0.0000 alpha= 0.0062 pinv= 0.0055 eq freqs= 0.0000 rel rates= 0.0055 subset rates= 0.0000) -pass 14: -3350.3362 (branch= 0.0000 alpha= 0.0055 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0048 subset rates= 0.0000) -pass 15: -3350.3227 (branch= 0.0000 alpha= 0.0049 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0042 subset rates= 0.0000) -pass 16: -3350.3110 (branch= 0.0000 alpha= 0.0044 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0036 subset rates= 0.0000) -pass 17: -3350.3006 (branch= 0.0000 alpha= 0.0038 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0031 subset rates= 0.0000) -pass 18: -3350.2916 (branch= 0.0000 alpha= 0.0034 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0027 subset rates= 0.0000) -pass 19: -3350.2837 (branch= 0.0000 alpha= 0.0030 pinv= 0.0026 eq freqs= 0.0000 rel rates= 0.0023 subset rates= 0.0000) -pass 20: -3350.2768 (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: -3350.2427 (branch= 0.0000 alpha= 0.0129 pinv= 0.0116 eq freqs= 0.0000 rel rates= 0.0096 subset rates= 0.0000) +pass 1 : -3351.0980 (branch= 0.0000 alpha= 0.0293 pinv= 0.0165 eq freqs= 0.0245 rel rates= 0.0701 subset rates= 0.0127) +pass 2 : -3350.9809 (branch= 0.0105 alpha= 0.0099 pinv= 0.0177 eq freqs= 0.0000 rel rates= 0.0777 subset rates= 0.0013) +pass 3 : -3350.8827 (branch= 0.0109 alpha= 0.0148 pinv= 0.0159 eq freqs= 0.0000 rel rates= 0.0545 subset rates= 0.0021) +pass 4 : -3350.8009 (branch= 0.0077 alpha= 0.0136 pinv= 0.0148 eq freqs= 0.0007 rel rates= 0.0434 subset rates= 0.0016) +pass 5 : -3350.7309 (branch= 0.0052 alpha= 0.0117 pinv= 0.0137 eq freqs= 0.0000 rel rates= 0.0380 subset rates= 0.0012) +pass 6 : -3350.6702 (branch= 0.0032 alpha= 0.0119 pinv= 0.0126 eq freqs= 0.0004 rel rates= 0.0326 subset rates= 0.0000) +pass 7 : -3350.6151 (branch= 0.0008 alpha= 0.0115 pinv= 0.0114 eq freqs= 0.0000 rel rates= 0.0298 subset rates= 0.0016) +pass 8 : -3350.5677 (branch= 0.0015 alpha= 0.0105 pinv= 0.0104 eq freqs= 0.0002 rel rates= 0.0248 subset rates= 0.0000) +pass 9 : -3350.5252 (branch= 0.0002 alpha= 0.0097 pinv= 0.0094 eq freqs= 0.0000 rel rates= 0.0221 subset rates= 0.0011) +pass 10: -3350.4879 (branch= 0.0011 alpha= 0.0088 pinv= 0.0091 eq freqs= 0.0001 rel rates= 0.0182 subset rates= 0.0000) +pass 11: -3350.4560 (branch= 0.0002 alpha= 0.0079 pinv= 0.0077 eq freqs= 0.0000 rel rates= 0.0162 subset rates= 0.0000) +pass 12: -3350.4273 (branch= 0.0000 alpha= 0.0075 pinv= 0.0068 eq freqs= 0.0000 rel rates= 0.0142 subset rates= 0.0000) +pass 13: -3350.4021 (branch= 0.0000 alpha= 0.0068 pinv= 0.0061 eq freqs= 0.0000 rel rates= 0.0122 subset rates= 0.0000) +pass 14: -3350.3800 (branch= 0.0000 alpha= 0.0061 pinv= 0.0055 eq freqs= 0.0000 rel rates= 0.0104 subset rates= 0.0000) +pass 15: -3350.3607 (branch= 0.0000 alpha= 0.0055 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0089 subset rates= 0.0000) +pass 16: -3350.3438 (branch= 0.0000 alpha= 0.0049 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0077 subset rates= 0.0000) +pass 17: -3350.3291 (branch= 0.0000 alpha= 0.0043 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0065 subset rates= 0.0000) +pass 18: -3350.3163 (branch= 0.0000 alpha= 0.0038 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0056 subset rates= 0.0000) +pass 19: -3350.3051 (branch= 0.0000 alpha= 0.0034 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0048 subset rates= 0.0000) +pass 20: -3350.2954 (branch= 0.0000 alpha= 0.0029 pinv= 0.0026 eq freqs= 0.0000 rel rates= 0.0041 subset rates= 0.0000) + optimization up to ... +pass 30: -3350.2472 (branch= 0.0000 alpha= 0.0147 pinv= 0.0133 eq freqs= 0.0001 rel rates= 0.0200 subset rates= 0.0000) optimization up to ... -pass 40: -3350.2351 (branch= 0.0000 alpha= 0.0028 pinv= 0.0025 eq freqs= 0.0000 rel rates= 0.0023 subset rates= 0.0000) +pass 40: -3350.2363 (branch= 0.0000 alpha= 0.0032 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0047 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2336 (branch= 0.0000 alpha= 0.0005 pinv= 0.0005 eq freqs= 0.0000 rel rates= 0.0005 subset rates= 0.0000) +pass 50: -3350.2339 (branch= 0.0000 alpha= 0.0006 pinv= 0.0006 eq freqs= 0.0000 rel rates= 0.0012 subset rates= 0.0000) optimization up to ... -pass 60: -3350.2333 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +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) optimization up to ... -pass 64: -3350.2333 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 69: -3350.2334 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) Looking for minimum length branches... -Final score = -3350.2333 -Time used so far = 0 hours, 0 minutes and 12 seconds +Final score = -3350.2334 +Time used so far = 0 hours, 0 minutes and 13 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.112, AG = 10.407, AT = 2.687, CG = 0.001, CT = 21.883, GT = 1.000 + AC = 3.113, AG = 10.404, AT = 2.686, CG = 0.001, CT = 21.876, 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 - 0.5780 + 0.5784 with an invariant (invariable) site category, proportion estimated - 0.3658 + 0.3659 Substitution rate categories under this model: rate proportion - 0.0000 0.3658 - 0.0486 0.1586 - 0.2998 0.1586 - 0.8697 0.1586 - 2.7819 0.1586 + 0.0000 0.3659 + 0.0487 0.1585 + 0.3001 0.1585 + 0.8699 0.1585 + 2.7814 0.1585 Model 2 Number of states = 2 (binary data) @@ -14442,13 +14441,13 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3350.2333 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3350.2334 (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: 3.112 10.41 2.687 0.001 21.88 1 0.333 0.222 0.157 0.288 0.578 0.366 +rep 1: 3.113 10.4 2.686 0.001 21.88 1 0.333 0.222 0.157 0.288 0.578 0.366 Partition model subset 2: Model contains no estimated parameters @@ -14605,13 +14604,6 @@ 200 -3324.7543 0.500 1 300 -3324.3007 0.500 1 400 -3323.9848 0.500 1 -500 -3323.6818 0.500 1 -600 -3323.3459 0.500 1 -Optimization precision reduced - Optimizing parameters... improved 1.812 lnL - Optimizing branchlengths... improved 0.023 lnL -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 @@ -14712,77 +14704,74 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 883, seed 1039573528, best lnL -3321.014 +Search rep 1 (of 2) generation 411, seed 381960656, best lnL -3323.925 gen current_lnL precision last_tree_imp -883 -3321.0142 0.255 1 -900 -3321.0142 0.255 1 -1000 -3320.9667 0.255 1 -1100 -3320.8654 0.255 1 +411 -3323.9255 0.500 1 +500 -3323.6818 0.500 1 +600 -3323.3459 0.500 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 + 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... -Current score = -3320.0123 +Current score = -3321.0142 Performing final optimizations... -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) +pass 1 : -3320.3940 (branch= 0.0389 alpha= 0.0000 pinv= 0.0127 eq freqs= 0.0124 rel rates= 0.5392 ins/del rates= 0.0170) +pass 2 : -3319.9303 (branch= 0.0587 alpha= 0.0040 pinv= 0.0163 eq freqs= 0.0045 rel rates= 0.3634 ins/del rates= 0.0168) +pass 3 : -3319.5727 (branch= 0.0425 alpha= 0.0109 pinv= 0.0156 eq freqs= 0.0060 rel rates= 0.2688 ins/del rates= 0.0138) +pass 4 : -3319.2837 (branch= 0.0315 alpha= 0.0099 pinv= 0.0153 eq freqs= 0.0018 rel rates= 0.2191 ins/del rates= 0.0115) +pass 5 : -3319.0435 (branch= 0.0214 alpha= 0.0087 pinv= 0.0147 eq freqs= 0.0009 rel rates= 0.1856 ins/del rates= 0.0087) +pass 6 : -3318.8454 (branch= 0.0132 alpha= 0.0111 pinv= 0.0138 eq freqs= 0.0010 rel rates= 0.1538 ins/del rates= 0.0053) +pass 7 : -3318.6809 (branch= 0.0094 alpha= 0.0094 pinv= 0.0132 eq freqs= 0.0007 rel rates= 0.1278 ins/del rates= 0.0039) +pass 8 : -3318.5458 (branch= 0.0061 alpha= 0.0102 pinv= 0.0122 eq freqs= 0.0003 rel rates= 0.1036 ins/del rates= 0.0026) +pass 9 : -3318.4330 (branch= 0.0040 alpha= 0.0099 pinv= 0.0113 eq freqs= 0.0003 rel rates= 0.0856 ins/del rates= 0.0017) +pass 10: -3318.3375 (branch= 0.0026 alpha= 0.0095 pinv= 0.0110 eq freqs= 0.0002 rel rates= 0.0709 ins/del rates= 0.0011) +pass 11: -3318.2590 (branch= 0.0017 alpha= 0.0090 pinv= 0.0095 eq freqs= 0.0002 rel rates= 0.0574 ins/del rates= 0.0007) +pass 12: -3318.1931 (branch= 0.0011 alpha= 0.0084 pinv= 0.0087 eq freqs= 0.0001 rel rates= 0.0470 ins/del rates= 0.0005) +pass 13: -3318.1370 (branch= 0.0008 alpha= 0.0078 pinv= 0.0079 eq freqs= 0.0001 rel rates= 0.0392 ins/del rates= 0.0003) +pass 14: -3318.0890 (branch= 0.0005 alpha= 0.0072 pinv= 0.0072 eq freqs= 0.0001 rel rates= 0.0327 ins/del rates= 0.0002) +pass 15: -3318.0485 (branch= 0.0003 alpha= 0.0068 pinv= 0.0065 eq freqs= 0.0001 rel rates= 0.0268 ins/del rates= 0.0001) +pass 16: -3318.0137 (branch= 0.0002 alpha= 0.0061 pinv= 0.0058 eq freqs= 0.0001 rel rates= 0.0225 ins/del rates= 0.0001) +pass 17: -3317.9836 (branch= 0.0001 alpha= 0.0055 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0191 ins/del rates= 0.0000) +pass 18: -3317.9574 (branch= 0.0001 alpha= 0.0050 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0163 ins/del rates= 0.0000) +pass 19: -3317.9347 (branch= 0.0000 alpha= 0.0045 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0139 ins/del rates= 0.0000) +pass 20: -3317.9151 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0119 ins/del rates= 0.0000) + optimization up to ... +pass 30: -3317.8172 (branch= 0.0001 alpha= 0.0216 pinv= 0.0199 eq freqs= 0.0001 rel rates= 0.0562 ins/del rates= 0.0000) + optimization up to ... +pass 40: -3317.7939 (branch= 0.0001 alpha= 0.0054 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0129 ins/del rates= 0.0000) optimization up to ... -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) +pass 50: -3317.7886 (branch= 0.0000 alpha= 0.0011 pinv= 0.0010 eq freqs= 0.0000 rel rates= 0.0031 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= 0.0005 ins/del rates= 0.0000) +pass 60: -3317.7874 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0007 ins/del rates= 0.0000) optimization up to ... -pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) +pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 ins/del rates= 0.0000) optimization up to ... -pass 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) +pass 75: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... -Final score = -3317.7870 -Time used so far = 0 hours, 0 minutes and 12 seconds +Final score = -3317.7871 +Time used so far = 0 hours, 0 minutes and 13 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.068, AG = 10.268, AT = 2.657, CG = 0.001, CT = 21.552, GT = 1.000 + AC = 3.064, AG = 10.256, AT = 2.653, CG = 0.001, CT = 21.521, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3328 0.2223 0.1567 0.2882 + (ACGT) 0.3328 0.2223 0.1566 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.5750 + 0.5748 with an invariant (invariable) site category, proportion estimated 0.3613 Substitution rate categories under this model: rate proportion 0.0000 0.3613 0.0480 0.1597 - 0.2981 0.1597 - 0.8680 0.1597 - 2.7859 0.1597 + 0.2980 0.1597 + 0.8679 0.1597 + 2.7862 0.1597 Model 2 Number of states = 2 (0/1 coding of gaps) @@ -14808,13 +14797,13 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3317.7870 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3317.7871 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.068 10.27 2.657 0.001 21.55 1 0.333 0.222 0.157 0.288 0.575 0.361 +rep 1: 3.064 10.26 2.653 0.001 21.52 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del @@ -14964,19 +14953,6 @@ 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 -7600 -210.2625 0.010 1104 -7800 -210.1873 0.010 1104 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15056,42 +15032,35 @@ STARTING RUN Restarting from checkpoint... - generation 7807, seed 705038715, best lnL -210.183 + generation 5300, seed 343343948, best lnL -210.567 gen current_lnL precision last_tree_imp -7807 -210.1826 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 +5300 -210.5675 0.010 1104 +5400 -210.5461 0.010 1104 Reached termination condition! last topological improvement at gen 1104 -Improvement over last 500 gen = 0.04891 +Improvement over last 500 gen = 0.03202 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.918, AG = 6.882, AT = 0.186, CG = 6.998, CT = 11.153, GT = 1.000 + AC = 2.798, AG = 5.231, AT = 0.196, CG = 4.937, CT = 8.094, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2363 0.3327 0.2105 0.2206 + (ACGT) 0.2331 0.3366 0.2107 0.2196 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 1.8479 + 1.2636 with an invariant (invariable) site category, proportion estimated - 0.1921 + 0.1401 Substitution rate categories under this model: rate proportion - 0.0000 0.1921 - 0.3353 0.2693 - 0.8372 0.2693 - 1.8275 0.2693 + 0.0000 0.1401 + 0.2435 0.2866 + 0.7674 0.2866 + 1.9891 0.2866 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - No branches were short enough to be collapsed. + 1 branches were collapsed. Saving site likelihoods to file ch.n.G3.sitelikes.log ... @@ -15099,15 +15068,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -210.0895 +Replicate 1 : -210.5461 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: 3.918 6.882 0.186 6.998 11.15 1 0.236 0.333 0.210 0.221 1.848 0.192 +rep 1: 2.798 5.231 0.1964 4.937 8.094 1 0.233 0.337 0.211 0.220 1.264 0.140 Treelengths: TL -rep 1: 2.358 +rep 1: 2.244 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 @@ -15230,44 +15199,33 @@ 800 -169.9099 0.500 296 Optimization precision reduced Optimizing parameters... improved 2.192 lnL - 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 -5200 -165.6633 0.010 843 -5400 -165.5975 0.010 843 -5600 -165.4766 0.010 843 -5800 -165.3724 0.010 843 -6000 -165.3454 0.010 843 -6200 -165.2645 0.010 843 -6400 -165.1352 0.010 843 -6600 -165.0587 0.010 843 -6800 -165.0560 0.010 843 -7000 -164.9213 0.010 843 -7200 -164.8005 0.010 843 -7400 -164.7206 0.010 7384 -7600 -164.6623 0.010 7384 -7800 -164.5214 0.010 7384 -8000 -164.4386 0.010 7384 -8200 -164.2994 0.010 7384 + 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 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15348,50 +15306,71 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 8200, seed 1610546417, best lnL -164.299 +Bootstrap rep 1 (of 1) generation 6126, seed 135321861, best lnL -165.154 gen current_lnL precision last_tree_imp -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 +6126 -165.1537 0.010 843 +6200 -165.1217 0.010 843 +6300 -165.0111 0.010 843 +6400 -164.9323 0.010 843 +6500 -164.8800 0.010 843 +6600 -164.7902 0.010 843 +6700 -164.7892 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 NOTE: ****Specified generation limit (10000) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 0.623, AG = 8.556, AT = 1.923, CG = 3.484, CT = 32.886, GT = 1.000 + AC = 0.840, AG = 12.212, AT = 2.930, CG = 4.820, CT = 55.192, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1298 0.4236 0.2357 0.2109 + (ACGT) 0.1330 0.4224 0.2438 0.2008 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 526.3244 + 39.2376 with an invariant (invariable) site category, proportion estimated - 0.3606 + 0.3493 Substitution rate categories under this model: rate proportion - 0.0000 0.3606 - 0.9452 0.1599 - 0.9853 0.1599 - 1.0136 0.1599 - 1.0559 0.1599 + 0.0000 0.3493 + 0.8050 0.1627 + 0.9411 0.1627 + 1.0443 0.1627 + 1.2095 0.1627 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 3 branches were collapsed. @@ -15405,15 +15384,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -162.0354 +Replicate 1 : -161.9932 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 0.6227 8.556 1.923 3.484 32.89 1 0.130 0.424 0.236 0.211 526.324 0.361 +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 Treelengths: TL -rep 1: 3.168 +rep 1: 3.542 Saving best tree to bootstrap file ch.n.G4.boot.tre @@ -15556,62 +15535,15 @@ 7200 -212.7024 0.010 3769 7400 -212.6754 0.010 3769 7600 -212.6692 0.010 3769 -7800 -212.6655 0.010 3769 -8000 -212.6638 0.010 3769 -8200 -212.6580 0.010 3769 -8400 -212.6570 0.010 3769 -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... - -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 +NOTE: ****Specified time limit (5 seconds) reached... -WARNING: Internal states inferred on tree from prematurely terminated search +NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY +TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE +FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF +(set restart = 1 in the config file). IF YOU WANT TO USE THE +PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY +ADD "end;" TO THE TREE FILES. -####################################################### Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## @@ -15682,17 +15614,21 @@ STARTING RUN Restarting from checkpoint... - generation 10001, seed 1459438551, best lnL -212.501 + generation 7695, seed 2028716398, best lnL -212.668 gen current_lnL precision last_tree_imp -10001 -212.5014 0.010 3769 +7695 -212.6684 0.010 3769 +7700 -212.6684 0.010 3769 +Reached termination condition! +last topological improvement at gen 3769 +Improvement over last 500 gen = 0.03397 MODEL REPORT - Parameter values are FINAL 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 + AC = 5.421, AG = 10.376, AT = 0.430, CG = 10.683, CT = 6.839, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2189 0.2871 0.1831 0.3108 + (ACGT) 0.2215 0.2881 0.1827 0.3076 Rate Heterogeneity Model: no rate heterogeneity @@ -15705,15 +15641,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -212.5014 +Replicate 1 : -212.6684 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 +rep 1: 5.421 10.38 0.4295 10.68 6.839 1 0.222 0.288 0.183 0.308 Treelengths: TL -rep 1: 1.722 +rep 1: 1.728 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 @@ -15843,108 +15779,47 @@ Optimization precision reduced Optimizing parameters... improved 1.908 lnL Optimizing branchlengths... improved 0.702 lnL -1600 -211.2006 0.010 1502 -1800 -211.0868 0.010 1502 -2000 -210.9688 0.010 1502 +1600 -211.2008 0.010 1502 +1800 -211.0870 0.010 1502 +2000 -210.9689 0.010 1502 2200 -210.8961 0.010 1502 2400 -210.8906 0.010 1502 -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... - -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 +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 +7200 -210.3950 0.010 4692 +7400 -210.3738 0.010 4692 +7600 -210.3657 0.010 4692 +7800 -210.2747 0.010 7782 +NOTE: ****Specified time limit (5 seconds) reached... -WARNING: Internal states inferred on tree from prematurely terminated search +NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY +TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE +FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF +(set restart = 1 in the config file). IF YOU WANT TO USE THE +PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY +ADD "end;" TO THE TREE FILES. -####################################################### Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## @@ -16023,29 +15898,53 @@ STARTING RUN Restarting from checkpoint... - generation 10001, seed 1730967105, best lnL -209.410 + generation 7958, seed 981057004, best lnL -210.270 gen current_lnL precision last_tree_imp -10001 -209.4100 0.010 9713 +7958 -210.2703 0.010 7782 +8000 -210.2702 0.010 7782 +8100 -210.2701 0.010 7782 +8200 -210.2666 0.010 7782 +8300 -210.2522 0.010 7782 +8400 -210.2509 0.010 7782 +8500 -210.2011 0.010 8499 +8600 -210.1983 0.010 8499 +8700 -210.1818 0.010 8499 +8800 -210.1582 0.010 8499 +8900 -210.1468 0.010 8499 +9000 -210.1192 0.010 8499 +9100 -210.0959 0.010 8499 +9200 -210.0879 0.010 8499 +9300 -210.0865 0.010 8499 +9400 -210.0862 0.010 8499 +9500 -210.0719 0.010 8499 +9600 -210.0719 0.010 8499 +9700 -210.0719 0.010 8499 +9800 -210.0664 0.010 8499 +9900 -210.0660 0.010 8499 +10000 -210.0540 0.010 8499 + Optimizing parameters... improved 0.467 lnL + Optimizing branchlengths... improved 0.000 lnL +NOTE: ****Specified generation limit (10000) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 2.658, AG = 4.802, AT = 0.044, CG = 4.939, CT = 9.263, GT = 1.000 + AC = 2.598, AG = 4.738, AT = 0.043, CG = 4.858, CT = 9.008, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2412 0.3354 0.2106 0.2128 + (ACGT) 0.2435 0.3332 0.2111 0.2122 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.4382 + 2.9066 with an invariant (invariable) site category, proportion estimated - 0.3025 + 0.2846 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 + 0.0000 0.2846 + 0.3819 0.1788 + 0.7262 0.1788 + 1.0820 0.1788 + 1.8099 0.1788 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. @@ -16056,24 +15955,31 @@ 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 +Replicate 1 : -209.5871 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 +rep 1: 2.598 4.738 0.04288 4.858 9.008 1 0.243 0.333 0.211 0.212 2.907 0.285 Treelengths: TL -rep 1: 2.411 +rep 1: 2.408 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 + ####################################################### TREEFILES PASS Running checkpoint test ./check/p.3diff.conf @@ -16277,20 +16183,6 @@ Optimizing branchlengths... improved 0.000 lnL 600 -13371.2064 0.402 0 700 -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 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16413,79 +16305,78 @@ Subset 3: Random seed for bootstrap reweighting: 486988955 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 1579, seed 1767420404, best lnL -13370.482 +Bootstrap rep 1 (of 1) generation 792, seed 1676266441, best lnL -13370.949 gen current_lnL precision last_tree_imp -1579 -13370.4816 0.206 0 -1600 -13370.4816 0.206 0 -1700 -13370.4688 0.206 0 -1800 -13370.4569 0.206 0 -1900 -13370.4339 0.206 0 -2000 -13370.4174 0.206 0 +792 -13370.9490 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 0.006 lnL + Optimizing parameters... improved 0.037 lnL Optimizing branchlengths... improved 0.000 lnL -NOTE: ****Specified generation limit (2000) reached... +NOTE: ****Specified time limit (1 seconds) reached... -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) - AC = 1.663, AG = 2.558, AT = 1.235, CG = 1.235, CT = 4.221, GT = 1.000 + AC = 1.545, AG = 2.495, AT = 1.160, CG = 1.160, CT = 4.035, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3082 0.1810 0.3087 0.2020 + (ACGT) 0.3110 0.1818 0.3061 0.2010 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.3662 + 0.3640 Substitution rate categories under this model: rate proportion - 0.0122 0.2500 - 0.1561 0.2500 - 0.6919 0.2500 - 3.1398 0.2500 + 0.0119 0.2500 + 0.1544 0.2500 + 0.6892 0.2500 + 3.1446 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 = 2.621, AG = 4.245, AT = 0.820, CG = 4.245, CT = 2.621, GT = 1.000 + AC = 2.627, AG = 4.239, AT = 0.821, CG = 4.239, CT = 2.627, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2814 0.1768 0.1593 0.3825 + (ACGT) 0.2791 0.1777 0.1601 0.3830 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.2457 + 0.2460 Substitution rate categories under this model: rate proportion 0.0019 0.2500 - 0.0636 0.2500 - 0.4923 0.2500 - 3.4422 0.2500 + 0.0638 0.2500 + 0.4929 0.2500 + 3.4413 0.2500 Model 3 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) - AC = 1.000, AG = 5.311, AT = 4.291, CG = 0.629, CT = 5.311, GT = 1.000 + AC = 1.000, AG = 5.382, AT = 4.304, CG = 0.635, CT = 5.382, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1554 0.3464 0.2763 0.2219 + (ACGT) 0.1557 0.3453 0.2772 0.2218 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.1264 + 4.1101 with an invariant (invariable) site category, proportion estimated - 0.0487 + 0.0486 Substitution rate categories under this model: rate proportion - 0.0000 0.0487 - 0.4612 0.2378 - 0.7795 0.2378 - 1.0844 0.2378 - 1.6750 0.2378 + 0.0000 0.0486 + 0.4603 0.2379 + 0.7789 0.2379 + 1.0844 0.2379 + 1.6764 0.2379 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!*** @@ -16495,25 +16386,25 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13370.4112 +Replicate 1 : -13370.6003 (TERMINATED PREMATURELY) Parameter estimates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 1.663 2.558 1.235 1.235 4.221 1 0.308 0.181 0.309 0.202 0.366 +rep 1: 1.545 2.495 1.16 1.16 4.035 1 0.311 0.182 0.306 0.201 0.364 Partition model subset 2: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 2.621 4.245 0.8204 4.245 2.621 1 0.281 0.177 0.159 0.382 0.246 +rep 1: 2.627 4.239 0.8212 4.239 2.627 1 0.279 0.178 0.160 0.383 0.246 Partition model subset 3: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 1 5.311 4.291 0.6292 5.311 1 0.155 0.346 0.276 0.222 4.126 0.049 +rep 1: 1 5.382 4.304 0.6346 5.382 1 0.156 0.345 0.277 0.222 4.110 0.049 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 1.762 0.530 0.287 2.183 +rep 1: 1.772 0.530 0.285 2.185 Saving best tree to bootstrap file ch.p.3diff.boot.tre @@ -16728,12 +16619,13 @@ 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: -467.6790 (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) +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) Looking for minimum length branches... -Final score = -467.6789 +Final score = -467.6782 Time used so far = 0 hours, 0 minutes and 5 seconds MODEL REPORT - Parameter values are FINAL @@ -16762,7 +16654,7 @@ no rate heterogeneity Subset rate multipliers: - 0.79 1.48 2.16 + 0.79 1.48 2.18 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. @@ -16812,9 +16704,6 @@ 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 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16940,9 +16829,12 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 616, seed 929135131, best lnL -467.772 +Search rep 2 (of 5) generation 339, seed 1611590179, best lnL -467.793 gen current_lnL precision last_tree_imp -616 -467.7723 0.010 0 +339 -467.7929 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 @@ -16989,7 +16881,7 @@ 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 8 seconds +Time used so far = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17074,47 +16966,24 @@ 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 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -467.7029 +Current score = -467.7381 Performing final optimizations... -pass 1 : -467.7020 (branch= 0.0000 subset rates= 0.0009) -pass 2 : -467.6894 (branch= 0.0126 subset rates= 0.0000) -pass 3 : -467.6837 (branch= 0.0057 subset rates= 0.0000) -pass 4 : -467.6821 (branch= 0.0016 subset rates= 0.0000) -pass 5 : -467.6821 (branch= 0.0000 subset rates= 0.0000) -pass 6 : -467.6809 (branch= 0.0013 subset rates= 0.0000) -pass 7 : -467.6797 (branch= 0.0012 subset rates= 0.0000) -pass 8 : -467.6791 (branch= 0.0007 subset rates= 0.0000) -pass 9 : -467.6788 (branch= 0.0002 subset rates= 0.0000) -pass 10: -467.6787 (branch= 0.0001 subset rates= 0.0000) -pass 11: -467.6786 (branch= 0.0001 subset rates= 0.0000) -pass 12: -467.6785 (branch= 0.0001 subset rates= 0.0000) -pass 13: -467.6785 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6784 (branch= 0.0000 subset rates= 0.0001) -pass 15: -467.6783 (branch= 0.0001 subset rates= 0.0000) -pass 16: -467.6782 (branch= 0.0000 subset rates= 0.0000) -pass 17: -467.6782 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -467.7371 (branch= 0.0000 subset rates= 0.0009) +pass 2 : -467.7128 (branch= 0.0243 subset rates= 0.0000) +pass 3 : -467.7040 (branch= 0.0088 subset rates= 0.0000) +pass 4 : -467.6908 (branch= 0.0132 subset rates= 0.0000) +pass 5 : -467.6831 (branch= 0.0073 subset rates= 0.0004) +pass 6 : -467.6808 (branch= 0.0023 subset rates= 0.0000) +pass 7 : -467.6792 (branch= 0.0016 subset rates= 0.0000) +pass 8 : -467.6787 (branch= 0.0005 subset rates= 0.0000) +pass 9 : -467.6785 (branch= 0.0002 subset rates= 0.0000) +pass 10: -467.6784 (branch= 0.0001 subset rates= 0.0000) +pass 11: -467.6783 (branch= 0.0001 subset rates= 0.0000) +pass 12: -467.6782 (branch= 0.0000 subset rates= 0.0000) +pass 13: -467.6782 (branch= 0.0000 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) Looking for minimum length branches... Final score = -467.6782 Time used so far = 0 hours, 0 minutes and 12 seconds @@ -17162,7 +17031,7 @@ NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -467.6789 +Replicate 1 : -467.6782 Replicate 2 : -467.6782 (best) (same topology as 1) Replicate 3 : -467.6782 (same topology as 1) (TERMINATED PREMATURELY) @@ -17179,9 +17048,9 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 3.841 0.787 1.482 2.160 +rep 1: 3.843 0.786 1.480 2.181 rep 2: 3.843 0.786 1.477 2.187 -rep 3: 3.843 0.786 1.480 2.181 +rep 3: 3.843 0.786 1.478 2.183 Saving final tree from best search rep (#2) to ch.p.mk.ssr.best.tre ####################################################### @@ -17400,7 +17269,7 @@ 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 3 seconds +Time used so far = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17485,22 +17354,6 @@ 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 @@ -17626,9 +17479,25 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 2302, seed 1899633739, best lnL -477.689 +Search rep 2 (of 5) generation 758, seed 1316951799, best lnL -477.718 gen current_lnL precision last_tree_imp -2302 -477.6894 0.010 74 +758 -477.7180 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 2400 -477.6889 0.010 74 2500 -477.6883 0.010 74 2600 -477.6879 0.010 74 @@ -17652,156 +17521,26 @@ 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 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -477.2838 +Current score = -477.4934 Performing final optimizations... -pass 1 : -477.2632 (branch= 0.0082 subset rates= 0.0123) -pass 2 : -477.2373 (branch= 0.0259 subset rates= 0.0000) -pass 3 : -477.2226 (branch= 0.0147 subset rates= 0.0000) -pass 4 : -477.2125 (branch= 0.0101 subset rates= 0.0000) -pass 5 : -477.2082 (branch= 0.0042 subset rates= 0.0001) -pass 6 : -477.2063 (branch= 0.0018 subset rates= 0.0001) -pass 7 : -477.2052 (branch= 0.0011 subset rates= 0.0000) -pass 8 : -477.2048 (branch= 0.0003 subset rates= 0.0000) -pass 9 : -477.2046 (branch= 0.0002 subset rates= 0.0000) -pass 10: -477.2045 (branch= 0.0001 subset rates= 0.0000) -pass 11: -477.2045 (branch= 0.0000 subset rates= 0.0000) -pass 12: -477.2045 (branch= 0.0000 subset rates= 0.0000) -pass 13: -477.2045 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -477.4809 (branch= 0.0044 subset rates= 0.0081) +pass 2 : -477.4636 (branch= 0.0113 subset rates= 0.0060) +pass 3 : -477.4450 (branch= 0.0173 subset rates= 0.0013) +pass 4 : -477.4409 (branch= 0.0041 subset rates= 0.0000) +pass 5 : -477.4378 (branch= 0.0031 subset rates= 0.0000) +pass 6 : -477.4353 (branch= 0.0025 subset rates= 0.0000) +pass 7 : -477.4346 (branch= 0.0007 subset rates= 0.0000) +pass 8 : -477.4339 (branch= 0.0007 subset rates= 0.0000) +pass 9 : -477.4336 (branch= 0.0003 subset rates= 0.0000) +pass 10: -477.4335 (branch= 0.0001 subset rates= 0.0000) +pass 11: -477.4334 (branch= 0.0001 subset rates= 0.0000) +pass 12: -477.4333 (branch= 0.0000 subset rates= 0.0000) +pass 13: -477.4333 (branch= 0.0000 subset rates= 0.0000) +pass 14: -477.4333 (branch= 0.0000 subset rates= 0.0000) +pass 15: -477.4333 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.2045 +Final score = -477.4333 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -17830,11 +17569,11 @@ no rate heterogeneity Subset rate multipliers: - 0.63 1.94 2.63 + 0.63 1.90 2.78 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. + 7 branches were collapsed. ->>>Terminated Search rep 3 (of 5)<<< +>>>Terminated Search rep 2 (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!*** @@ -17842,14 +17581,13 @@ ####################################################### -Completed 3 replicate search(es) (of 5). +Completed 2 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -477.4316 -Replicate 2 : -477.4334 (same topology as 1) -Replicate 3 : -477.2045 (best) (TERMINATED PREMATURELY) +Replicate 1 : -477.4316 (best) +Replicate 2 : -477.4333 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17865,10 +17603,9 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.930 0.631 1.918 2.736 -rep 2: 4.933 0.631 1.902 2.786 -rep 3: 4.699 0.633 1.941 2.629 +rep 2: 4.933 0.631 1.902 2.784 -Saving final tree from best search rep (#3) to ch.p.mkO.ssr.best.tre +Saving final tree from best search rep (#1) to ch.p.mkO.ssr.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkv.ssr.conf @@ -18078,9 +17815,9 @@ 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 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) @@ -18088,11 +17825,11 @@ 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) +pass 11: -425.5486 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.5486 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.5486 -Time used so far = 0 hours, 0 minutes and 4 seconds +Time used so far = 0 hours, 0 minutes and 5 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18150,22 +17887,6 @@ 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 @@ -18294,9 +18015,25 @@ Subset 3: Random seed for bootstrap reweighting: 974568031 Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 1728, seed 448857339, best lnL -425.624 +Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 166, seed 1685324100, best lnL -428.232 gen current_lnL precision last_tree_imp -1728 -425.6239 0.010 722 +166 -428.2325 0.010 164 +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 @@ -18321,21 +18058,21 @@ Improvement over last 500 gen = 0.00085 Current score = -425.6048 Performing final optimizations... -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: -425.5486 (branch= 0.0001 subset rates= 0.0000) -pass 11: -425.5486 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -425.5762 (branch= 0.0000 subset rates= 0.0285) +pass 2 : -425.5575 (branch= 0.0188 subset rates= 0.0000) +pass 3 : -425.5533 (branch= 0.0041 subset rates= 0.0000) +pass 4 : -425.5521 (branch= 0.0012 subset rates= 0.0000) +pass 5 : -425.5505 (branch= 0.0017 subset rates= 0.0000) +pass 6 : -425.5500 (branch= 0.0005 subset rates= 0.0000) +pass 7 : -425.5491 (branch= 0.0008 subset rates= 0.0000) +pass 8 : -425.5491 (branch= 0.0000 subset rates= 0.0000) +pass 9 : -425.5488 (branch= 0.0003 subset rates= 0.0000) +pass 10: -425.5487 (branch= 0.0001 subset rates= 0.0000) +pass 11: -425.5486 (branch= 0.0000 subset rates= 0.0001) pass 12: -425.5486 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.5486 -Time used so far = 0 hours, 0 minutes and 7 seconds +Time used so far = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18390,55 +18127,24 @@ 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 = -425.3537 +Current score = -425.4818 Performing final optimizations... -pass 1 : -425.3498 (branch= 0.0000 subset rates= 0.0039) -pass 2 : -425.3320 (branch= 0.0164 subset rates= 0.0015) -pass 3 : -425.3251 (branch= 0.0069 subset rates= 0.0000) -pass 4 : -425.3224 (branch= 0.0026 subset rates= 0.0000) -pass 5 : -425.3224 (branch= 0.0000 subset rates= 0.0000) -pass 6 : -425.3224 (branch= 0.0000 subset rates= 0.0000) -pass 7 : -425.3212 (branch= 0.0012 subset rates= 0.0000) -pass 8 : -425.3203 (branch= 0.0009 subset rates= 0.0000) -pass 9 : -425.3203 (branch= 0.0000 subset rates= 0.0000) -pass 10: -425.3202 (branch= 0.0001 subset rates= 0.0000) -pass 11: -425.3202 (branch= 0.0000 subset rates= 0.0000) -pass 12: -425.3202 (branch= 0.0000 subset rates= 0.0000) -pass 13: -425.3202 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -425.4247 (branch= 0.0516 subset rates= 0.0055) +pass 2 : -425.3538 (branch= 0.0709 subset rates= 0.0000) +pass 3 : -425.3310 (branch= 0.0228 subset rates= 0.0000) +pass 4 : -425.3229 (branch= 0.0081 subset rates= 0.0000) +pass 5 : -425.3220 (branch= 0.0006 subset rates= 0.0004) +pass 6 : -425.3217 (branch= 0.0003 subset rates= 0.0000) +pass 7 : -425.3209 (branch= 0.0008 subset rates= 0.0000) +pass 8 : -425.3207 (branch= 0.0002 subset rates= 0.0000) +pass 9 : -425.3206 (branch= 0.0001 subset rates= 0.0000) +pass 10: -425.3206 (branch= 0.0000 subset rates= 0.0000) +pass 11: -425.3206 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.3204 (branch= 0.0000 subset rates= 0.0001) +pass 13: -425.3204 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -425.3202 +Final score = -425.3204 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -18467,9 +18173,9 @@ no rate heterogeneity Subset rate multipliers: - 0.87 1.54 1.15 + 0.86 1.54 1.15 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 9 branches were collapsed. + 10 branches were collapsed. >>>Terminated Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< @@ -18486,7 +18192,7 @@ Results: Replicate 1 : -425.5486 Replicate 2 : -425.5486 -Replicate 3 : -425.3202 (best) (TERMINATED PREMATURELY) +Replicate 3 : -425.3204 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -18501,9 +18207,9 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 3.039 0.869 1.528 1.122 -rep 2: 3.037 0.868 1.532 1.121 -rep 3: 2.980 0.866 1.535 1.147 +rep 1: 3.038 0.868 1.529 1.123 +rep 2: 3.037 0.868 1.532 1.119 +rep 3: 2.980 0.864 1.541 1.146 Saving tree from best search rep (#3) to bootstrap file ch.p.mkv.ssr.boot.tre @@ -18700,120 +18406,6 @@ 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 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -18939,77 +18531,34 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 1312, seed 90226361, best lnL -474.484 +Search rep 1 (of 5) generation 2902, seed 1026971122, best lnL -473.978 gen current_lnL precision last_tree_imp -1312 -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 -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 +2902 -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 272 -Improvement over last 500 gen = 0.00090 -Current score = -474.4442 +last topological improvement at gen 653 +Improvement over last 500 gen = 0.00088 +Current score = -473.9771 Performing final optimizations... -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) +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 = -474.4281 -Time used so far = 0 hours, 0 minutes and 10 seconds +Final score = -473.9509 +Time used so far = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -19037,13 +18586,13 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.03 2.92 + 0.59 2.07 2.82 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. + 8 branches were collapsed. ->>>Completed Search rep 2 (of 5)<<< +>>>Completed Search rep 1 (of 5)<<< ->>>Search rep 3 (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 @@ -19072,47 +18621,67 @@ Subset rate multipliers: 1.00 1.00 1.00 -Starting with seed=962219047 +Starting with seed=2125680066 -Initial ln Likelihood: -627.7847 +Initial ln Likelihood: -649.8224 optimizing: starting branch lengths, subset rates... -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 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: -474.8769 +lnL after optimization: -474.8070 gen current_lnL precision last_tree_imp -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 +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 +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 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -474.5052 +Current score = -474.4621 Performing final optimizations... -pass 1 : -474.4837 (branch= 0.0179 subset rates= 0.0035) -pass 2 : -474.4569 (branch= 0.0259 subset rates= 0.0010) -pass 3 : -474.4457 (branch= 0.0111 subset rates= 0.0000) -pass 4 : -474.4376 (branch= 0.0081 subset rates= 0.0000) -pass 5 : -474.4340 (branch= 0.0036 subset rates= 0.0000) -pass 6 : -474.4314 (branch= 0.0026 subset rates= 0.0000) -pass 7 : -474.4298 (branch= 0.0016 subset rates= 0.0000) -pass 8 : -474.4290 (branch= 0.0007 subset rates= 0.0000) -pass 9 : -474.4287 (branch= 0.0004 subset rates= 0.0000) -pass 10: -474.4285 (branch= 0.0002 subset rates= 0.0000) -pass 11: -474.4284 (branch= 0.0001 subset rates= 0.0000) +pass 1 : -474.4621 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -474.4415 (branch= 0.0206 subset rates= 0.0000) +pass 3 : -474.4342 (branch= 0.0073 subset rates= 0.0000) +pass 4 : -474.4327 (branch= 0.0014 subset rates= 0.0000) +pass 5 : -474.4318 (branch= 0.0010 subset rates= 0.0000) +pass 6 : -474.4294 (branch= 0.0023 subset rates= 0.0000) +pass 7 : -474.4292 (branch= 0.0002 subset rates= 0.0000) +pass 8 : -474.4289 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -474.4286 (branch= 0.0002 subset rates= 0.0000) +pass 10: -474.4286 (branch= 0.0001 subset rates= 0.0000) +pass 11: -474.4285 (branch= 0.0001 subset rates= 0.0000) pass 12: -474.4284 (branch= 0.0000 subset rates= 0.0000) pass 13: -474.4284 (branch= 0.0000 subset rates= 0.0000) pass 14: -474.4284 (branch= 0.0000 subset rates= 0.0000) -pass 15: -474.4284 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -474.4284 Time used so far = 0 hours, 0 minutes and 12 seconds @@ -19143,11 +18712,11 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.03 2.91 + 0.59 2.03 2.92 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. ->>>Terminated Search rep 3 (of 5)<<< +>>>Terminated Search rep 2 (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!*** @@ -19155,14 +18724,13 @@ ####################################################### -Completed 3 replicate search(es) (of 5). +Completed 2 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 : -474.4281 -Replicate 3 : -474.4284 (same topology as 2) (TERMINATED PREMATURELY) +Replicate 2 : -474.4284 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -19178,8 +18746,7 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.351 0.587 2.065 2.818 -rep 2: 4.601 0.587 2.032 2.923 -rep 3: 4.598 0.589 2.030 2.912 +rep 2: 4.598 0.589 2.029 2.916 Saving final tree from best search rep (#1) to ch.p.mkvO.ssr.best.tre ####################################################### @@ -19197,7 +18764,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j22 install DESTDIR=/build/reproducible-path/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no + make -j10 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' @@ -19258,12 +18825,14 @@ 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/8894/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/8894/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/77655 and its subdirectories -I: Current time: Sun Dec 14 01:45:48 -12 2025 -I: pbuilder-time-stamp: 1765719948 +I: removing directory /srv/workspace/pbuilder/8894 and its subdirectories +I: Current time: Mon Nov 11 21:31:37 +14 2024 +I: pbuilder-time-stamp: 1731310297