Diff of the two buildlogs: -- --- b1/build.log 2025-03-06 07:32:14.649400925 +0000 +++ b2/build.log 2025-03-06 07:40:43.698461581 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Apr 8 01:50:21 -12 2026 -I: pbuilder-time-stamp: 1775656221 +I: Current time: Thu Mar 6 21:32:18 +14 2025 +I: pbuilder-time-stamp: 1741246338 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -22,52 +22,84 @@ dpkg-source: info: unpacking garli_2.1-9.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1169299/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2660829/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Mar 6 07:32 /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/2660829/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2660829/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='a419b35002c34a5cb0b9f082c3781380' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1169299' - PS1='# ' - PS2='> ' + INVOCATION_ID=8284e6613a074d61b53299ea09f54ec5 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2660829 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.ATTb9YRN/pbuilderrc_2CuS --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ATTb9YRN/b1 --logfile b1/build.log garli_2.1-9.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ATTb9YRN/pbuilderrc_uv4O --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ATTb9YRN/b2 --logfile b2/build.log garli_2.1-9.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1169299/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2660829/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -216,7 +248,7 @@ Get: 103 http://deb.debian.org/debian trixie/main arm64 libopenmpi-dev arm64 5.0.7-1 [1089 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 mpi-default-dev arm64 1.18 [3372 B] Get: 105 http://deb.debian.org/debian trixie/main arm64 ncl-tools arm64 2.1.21+git20210811.b1213a7-6 [166 kB] -Fetched 99.8 MB in 1s (133 MB/s) +Fetched 99.8 MB in 2s (42.7 MB/s) Preconfiguring packages ... Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19914 files and directories currently installed.) @@ -659,7 +691,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/garli-2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../garli_2.1-9_source.changes +I: user script /srv/workspace/pbuilder/2660829/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2660829/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/garli-2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../garli_2.1-9_source.changes dpkg-buildpackage: info: source package garli dpkg-buildpackage: info: source version 2.1-9 dpkg-buildpackage: info: source distribution unstable @@ -764,8 +800,8 @@ checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking for gcc... gcc @@ -944,11 +980,12 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, - from adaptation.cpp:25: + from funcs.cpp:30: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -958,7 +995,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from adaptation.cpp:18: + from population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1041,10 +1078,20 @@ /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{ | ^~~~~~~~~~~~~~~ @@ -1054,17 +1101,10 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from population.h:23: + from model.cpp:17: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -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:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -1103,16 +1143,7 @@ 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{ | ^~~~~~~~~~~~~~~ @@ -1223,75 +1249,11 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -1301,7 +1263,7 @@ 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 adaptation.cpp:18: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1339,13 +1301,19 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -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 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] @@ -1400,7 +1368,109 @@ optimization.cpp:1099:87: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1099 | pair Tree::CalcDerivativesRateHet(TreeNode *nd1, TreeNode *nd2){ | ^ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp +adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)': +adaptation.cpp:271:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 271 | fread((char *) this, 1, scalarSize, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:278:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 278 | fread((char *) improvetotal, sizeof(FLOAT_TYPE), intervalsToStore, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:280:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 280 | fread((char *) randNNI, sizeof(FLOAT_TYPE), intervalsToStore, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:281:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 281 | fread((char *) randNNInum, sizeof(int), intervalsToStore, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:283:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 283 | fread((char *) exNNI, sizeof(FLOAT_TYPE), intervalsToStore, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:284:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 284 | fread((char *) exNNInum, sizeof(int), intervalsToStore, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:286:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 286 | fread((char *) randSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:287:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 287 | fread((char *) randSPRnum, sizeof(int), intervalsToStore, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:289:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 289 | fread((char *) limSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:290:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 290 | fread((char *) limSPRnum, sizeof(int), intervalsToStore, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:292:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 292 | fread((char *) exlimSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:293:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 293 | fread((char *) exlimSPRnum, sizeof(int), intervalsToStore, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:295:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 295 | fread((char *) randRecom, sizeof(FLOAT_TYPE), intervalsToStore, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:296:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 296 | fread((char *) randRecomnum, sizeof(int), intervalsToStore, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:298:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 298 | fread((char *) bipartRecom, sizeof(FLOAT_TYPE), intervalsToStore, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:299:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | fread((char *) bipartRecomnum, sizeof(int), intervalsToStore, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:301:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 301 | fread((char *) onlyBrlen, sizeof(FLOAT_TYPE), intervalsToStore, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:302:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 302 | fread((char *) onlyBrlennum, sizeof(int), intervalsToStore, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:304:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 304 | fread((char *) anyModel, sizeof(FLOAT_TYPE), intervalsToStore, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +adaptation.cpp:305:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 305 | fread((char *) anyModelnum, sizeof(int), intervalsToStore, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': +model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3675:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3675 | fread(&o, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3677:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3677 | fread(&o, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3684:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3684 | fread((char*) &(b[i]), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3691:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3691 | fread((char*) &(rateMults[i]), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3692:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3692 | fread((char*) &(rateProbs[i]), sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3699:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3699 | fread((char*) &a, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3705:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3705 | fread((char*) &p, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3710:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3710 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp:3713:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 3713 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': +model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 population.h:31, @@ -1448,47 +1518,37 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.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' when C++17 is enabled changed to match C++14 in GCC 10.1 875 | tree0->CalcDerivativesRateHet(nd->anc, nd); @@ -1521,13 +1581,7 @@ from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from datamatr.cpp:20: + from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1539,11 +1593,12 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, - from /usr/include/c++/14/ext/string_conversions.h:45, - 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/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1559,15 +1614,7 @@ 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/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1596,7 +1643,16 @@ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, - from 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 datamatr.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1610,8 +1666,9 @@ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, - from /usr/include/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: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1624,10 +1681,7 @@ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, - from /usr/include/c++/14/cstdio:42, - from /usr/include/c++/14/ext/string_conversions.h:45, - from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54: + from configreader.cpp:18: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1655,7 +1709,6 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -1679,7 +1732,6 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp garlimain.cpp: In function 'int SubGarliMain(int)': @@ -1766,11 +1818,11 @@ funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE)': tree.cpp:8463:87: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 8463 | pair Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE optPrecision){ | ^ +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -1788,22 +1840,6 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -In file included from /usr/include/stdio.h:970, - from /usr/include/c++/14/cstdio:42, - from /usr/include/c++/14/ext/string_conversions.h:45, - from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] tree.cpp: In member function 'void Tree::ReadBinaryFormattedTree(FILE*)': tree.cpp:6808:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6808 | fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in); @@ -1871,6 +1907,43 @@ tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6881 | fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:970, + from /usr/include/c++/14/cstdio:42, + from /usr/include/c++/14/ext/string_conversions.h:45, + from /usr/include/c++/14/bits/basic_string.h:4154, + from /usr/include/c++/14/string:54, + from translatetable.h:24, + from translatetable.cpp:19: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +In file included from /usr/include/stdio.h:970, + from /usr/include/c++/14/cstdio:42, + from /usr/include/c++/14/ext/string_conversions.h:45, + from /usr/include/c++/14/bits/basic_string.h:4154, + from /usr/include/c++/14/string:54, + from datamatr.h:23, + from sequencedata.h:27, + from sequencedata.cpp:21: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -1927,25 +2000,6 @@ funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2306,7 +2340,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from configreader.cpp:21: + from model.cpp:17: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2344,11 +2378,11 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, - from funcs.h:25, - from funcs.cpp:30: + from garlimain.cpp:40: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2396,17 +2430,16 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2416,7 +2449,7 @@ 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 | ^~~~~~~~~~~~~~~ @@ -2454,7 +2487,10 @@ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.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] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2576,7 +2611,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, - from population.h:23: + from configreader.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2586,6 +2621,10 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2614,6 +2653,72 @@ /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] @@ -2723,6 +2815,11 @@ 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)': +datamatr.cpp:1390:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1390 | fscanf(inf, "%d %d", &num_taxa, &num_chars); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -2776,67 +2873,6 @@ 170 | for(register int i=0;i' when C++17 is enabled changed to match C++14 in GCC 10.1 - 875 | tree0->CalcDerivativesRateHet(nd->anc, nd); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -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, @@ -2922,19 +2930,6 @@ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, - from configreader.cpp:18: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, @@ -2950,6 +2945,34 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +population.cpp: In member function 'void Population::RunTests()': +population.cpp:875:46: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 875 | tree0->CalcDerivativesRateHet(nd->anc, nd); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +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, @@ -2966,6 +2989,7 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -2988,6 +3012,7 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/ncl/ncl.h:27, @@ -3003,19 +3028,12 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, 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/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3027,13 +3045,32 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp +In file included from /usr/include/stdio.h:970, + from configreader.cpp:18: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54: + from /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: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3045,8 +3082,6 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -3103,42 +3138,7 @@ tree.cpp:8463:87: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 8463 | pair Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE optPrecision){ | ^ -In file included from /usr/include/stdio.h:970, - from /usr/include/c++/14/cstdio:42, - from /usr/include/c++/14/ext/string_conversions.h:45, - from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54, - from datamatr.h:23, - from sequencedata.h:27, - from sequencedata.cpp:21: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -In file included from /usr/include/stdio.h:970, - from /usr/include/c++/14/cstdio:42, - from /usr/include/c++/14/ext/string_conversions.h:45, - from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54, - from population.cpp:25: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp tree.cpp: In member function 'void Tree::ReadBinaryFormattedTree(FILE*)': tree.cpp:6808:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6808 | fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in); @@ -3211,6 +3211,25 @@ from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, + from datamatr.h:23, + from sequencedata.h:27, + from sequencedata.cpp:21: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +In file included from /usr/include/stdio.h:970, + from /usr/include/c++/14/cstdio:42, + from /usr/include/c++/14/ext/string_conversions.h:45, + from /usr/include/c++/14/bits/basic_string.h:4154, + from /usr/include/c++/14/string:54, from translatetable.h:24, from translatetable.cpp:19: In function 'int sprintf(char*, const char*, ...)', @@ -3224,22 +3243,23 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': -population.cpp:3066:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] - 3066 | sprintf(oStr, "R(%d)", d + 1); - | ^~ -population.cpp:3066:47: note: directive argument in the range [1, 2147483647] - 3066 | sprintf(oStr, "R(%d)", d + 1); - | ^~~~~~~ +In file included from /usr/include/stdio.h:970, + from /usr/include/c++/14/cstdio:42, + from /usr/include/c++/14/ext/string_conversions.h:45, + from /usr/include/c++/14/bits/basic_string.h:4154, + from /usr/include/c++/14/string:54, + from population.cpp:25: In function 'int sprintf(char*, const char*, ...)', - inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10 + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -3262,6 +3282,22 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': +population.cpp:3066:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] + 3066 | sprintf(oStr, "R(%d)", d + 1); + | ^~ +population.cpp:3066:47: note: directive argument in the range [1, 2147483647] + 3066 | sprintf(oStr, "R(%d)", d + 1); + | ^~~~~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -5967,7 +6003,7 @@ 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 ... ####################################################### @@ -6264,7 +6300,7 @@ 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 10 seconds +Time used = 0 hours, 0 minutes and 18 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6416,7 +6452,7 @@ pass 10: -13269.2298 (branch= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13269.2298 -Time used = 0 hours, 0 minutes and 5 seconds +Time used = 0 hours, 0 minutes and 10 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7147,7 +7183,7 @@ pass 10: -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13931.0232 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7313,7 +7349,7 @@ pass 14: -14498.8854 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -14498.8854 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -7567,7 +7603,7 @@ pass 36: -13306.2061 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) Looking for minimum length branches... Final score = -13306.2061 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 5 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -9536,7 +9572,7 @@ pass 495: -208.3585 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... Final score = -208.3585 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 2 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -9800,7 +9836,7 @@ pass 373: -208.1243 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... Final score = -208.1243 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 3 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -10096,7 +10132,7 @@ pass 503: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... Final score = -208.3583 -Time used = 0 hours, 0 minutes and 2 seconds +Time used = 0 hours, 0 minutes and 3 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -10389,7 +10425,7 @@ pass 491: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.3583 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 3 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -13111,70 +13147,15 @@ 1300 -88.8312 0.010 879 1400 -88.8046 0.010 879 1500 -88.8000 0.010 879 -1600 -88.7604 0.010 879 -1700 -88.7532 0.010 879 -1800 -88.7145 0.010 879 -1900 -88.6979 0.010 879 -2000 -88.6746 0.010 879 -2100 -88.6394 0.010 879 -2200 -88.6224 0.010 879 -2300 -88.6154 0.010 879 -2400 -88.6058 0.010 879 -2500 -88.5913 0.010 879 -2600 -88.5622 0.010 879 -2700 -88.5467 0.010 879 -2800 -88.5396 0.010 879 -2900 -88.5337 0.010 879 -3000 -88.5266 0.010 879 -3100 -88.5249 0.010 879 -Reached termination condition! -last topological improvement at gen 879 -Improvement over last 500 gen = 0.03733 - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 20 (amino acid data) - Amino Acid Rate Matrix: Jones - Equilibrium State Frequencies: empirical (observed) values (+F) - (ACDEFGHIKLMNPQRSTVWY) - 0.0165 0.0083 0.0496 0.0909 0.0909 - 0.0083 0.0744 0.0083 0.0083 0.1074 - 0.1157 0.0248 0.1240 0.0331 0.0083 - 0.0826 0.0496 0.0579 0.0083 0.0331 - Rate Heterogeneity Model: - 3 discrete gamma distributed rate categories, alpha param estimated - 3.1526 - with an invariant (invariable) site category, proportion estimated - 0.2947 - Substitution rate categories under this model: - rate proportion - 0.0000 0.2947 - 0.4599 0.2351 - 0.9028 0.2351 - 1.6373 0.2351 - -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 2 branches were collapsed. - - -####################################################### - -Completed 1 replicate search(es) (of 1). -Results: -Replicate 1 : -88.5249 - -Parameter estimates: - alpha pinv -rep 1: 3.153 0.295 - -Treelengths: - TL -rep 1: 2.365 +NOTE: ****Specified time limit (5 seconds) reached... -Saving best tree to bootstrap file ch.a.G3.boot.tre +NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY +TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE +FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF +(set restart = 1 in the config file). IF YOU WANT TO USE THE +PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY +ADD "end;" TO THE TREE FILES. ->>>Completed Bootstrap rep 1<<< -####################################################### Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## @@ -13262,9 +13243,9 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 3100, seed 1872184071, best lnL -88.525 +Bootstrap rep 1 (of 1) generation 1574, seed 1873631793, best lnL -88.763 gen current_lnL precision last_tree_imp -3100 -88.5249 0.010 879 +1574 -88.7626 0.010 879 MODEL REPORT - Parameter values are FINAL Model 1 @@ -13278,33 +13259,33 @@ 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 3.1526 + 1.2326 with an invariant (invariable) site category, proportion estimated - 0.2947 + 0.1665 Substitution rate categories under this model: rate proportion - 0.0000 0.2947 - 0.4599 0.2351 - 0.9028 0.2351 - 1.6373 0.2351 + 0.0000 0.1665 + 0.2376 0.2778 + 0.7620 0.2778 + 2.0004 0.2778 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 2 branches were collapsed. + 1 branches were collapsed. ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -88.5249 +Replicate 1 : -88.7626 Parameter estimates: alpha pinv -rep 1: 3.153 0.295 +rep 1: 1.233 0.166 Treelengths: TL -rep 1: 2.365 +rep 1: 2.350 Saving best tree to bootstrap file ch.a.G3.boot.tre @@ -13440,15 +13421,6 @@ 900 -110.5555 0.010 707 1000 -110.5065 0.010 707 1100 -110.4789 0.010 707 -1200 -110.4460 0.010 707 -1300 -110.4042 0.010 707 -1400 -110.3747 0.010 707 -1500 -110.3652 0.010 707 -1600 -110.2967 0.010 707 -1700 -110.2780 0.010 707 -1800 -110.2329 0.010 707 -1900 -110.2137 0.010 707 -2000 -110.1884 0.010 707 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13535,9 +13507,9 @@ STARTING RUN Restarting from checkpoint... - generation 2036, seed 1990348747, best lnL -110.188 + generation 1149, seed 785158587, best lnL -110.476 gen current_lnL precision last_tree_imp -2036 -110.1883 0.010 707 +1149 -110.4756 0.010 707 MODEL REPORT - Parameter values are FINAL Model 1 @@ -13551,16 +13523,16 @@ 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 2.9338 + 1.3661 with an invariant (invariable) site category, proportion estimated - 0.1639 + 0.0935 Substitution rate categories under this model: rate proportion - 0.0000 0.1639 - 0.3841 0.2090 - 0.7278 0.2090 - 1.0822 0.2090 - 1.8060 0.2090 + 0.0000 0.0935 + 0.2039 0.2266 + 0.5646 0.2266 + 1.0415 0.2266 + 2.1900 0.2266 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. @@ -13571,15 +13543,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -110.1883 +Replicate 1 : -110.4756 Parameter estimates: alpha pinv -rep 1: 2.934 0.164 +rep 1: 1.366 0.094 Treelengths: TL -rep 1: 2.691 +rep 1: 2.614 Saving final tree from best search rep (#1) to ch.a.G4.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.G4.internalstates.log @@ -14008,18 +13980,6 @@ 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 -120 -205.3431 0.500 106 -130 -205.2505 0.500 121 -140 -205.2440 0.500 121 -150 -205.1047 0.500 121 -160 -205.0609 0.500 121 -170 -204.9813 0.500 121 NOTE: ****Specified time limit (10 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14106,15 +14066,21 @@ STARTING RUN Restarting from checkpoint... - generation 171, seed 1312101128, best lnL -204.981 + generation 58, seed 1611739816, best lnL -205.599 gen current_lnL precision last_tree_imp -171 -204.9813 0.500 121 +58 -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 - AC = 1.586, AG = 4.036, AT = 0.040, CG = 2.453, CT = 3.968, GT = 1.000 + AC = 1.586, AG = 3.999, AT = 0.040, CG = 2.453, CT = 3.968, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) @@ -14135,31 +14101,38 @@ 2 nonsynonymous rate categories, rate and proportion of each estimated (this is effectively the M3 model of PAML) dN/dS Proportion - 0.0473 0.5211 + 0.0490 0.5211 0.4995 0.4789 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file ch.c.M3x2.sitelikes.log ... +WARNING: Site likelihoods being output on prematurely terminated search ... + +NOTE: ***Search was terminated before full auto-termination condition was reached! +Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** + ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -204.9813 +Replicate 1 : -205.3829 Parameter estimates: w(0) p(0) w(1) p(1) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) -rep 1: 0.047 0.521 0.499 0.479 1.586 4.036 0.04 2.453 3.968 1 +rep 1: 0.049 0.521 0.499 0.479 1.586 3.999 0.04 2.453 3.968 1 Treelengths: TL -rep 1: 7.813 +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 @@ -14291,16 +14264,6 @@ 40 -195.2556 0.500 0 50 -195.2139 0.500 0 60 -195.1631 0.500 0 -70 -195.0045 0.500 0 -80 -194.9480 0.500 0 -90 -194.9094 0.500 0 -100 -194.9094 0.500 0 -110 -194.8988 0.500 0 -120 -194.8988 0.500 0 -130 -194.8986 0.500 0 -140 -194.8502 0.500 0 -150 -194.7087 0.500 0 -160 -194.7087 0.500 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14388,16 +14351,21 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 160, seed 375495465, best lnL -194.709 +Bootstrap rep 1 (of 1) generation 65, seed 432969045, best lnL -195.099 gen current_lnL precision last_tree_imp -160 -194.7087 0.500 0 +65 -195.0991 0.500 0 +70 -195.0045 0.500 0 +80 -194.9480 0.500 0 +90 -194.9094 0.500 0 +100 -194.9094 0.500 0 +NOTE: ****Specified generation limit (100) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 61 (codon data, standard code) One estimated dN/dS ratio (aka omega) = 0.120505 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates - AC = 1.637, AG = 5.802, AT = 0.011, CG = 4.174, CT = 2.324, GT = 1.000 + AC = 1.637, AG = 5.679, AT = 0.011, CG = 4.174, CT = 2.324, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) @@ -14421,23 +14389,27 @@ No branches were short enough to be collapsed. +NOTE: ***Search was terminated before full auto-termination condition was reached! +Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** + + ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -194.7087 +Replicate 1 : -194.9094 Parameter estimates: w(0) p(0) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) -rep 1: 0.121 1.000 1.637 5.802 0.01146 4.174 2.324 1 +rep 1: 0.121 1.000 1.637 5.679 0.01146 4.174 2.324 1 Treelengths: TL -rep 1: 9.839 +rep 1: 9.255 Saving best tree to bootstrap file ch.c.boot.tre ->>>Completed Bootstrap rep 1<<< +WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/g.dnaBnoZ.conf @@ -14611,23 +14583,6 @@ 2100 -3351.6185 0.010 0 2200 -3351.3743 0.010 0 2300 -3351.3495 0.010 0 -2400 -3351.3419 0.010 0 -2500 -3351.2390 0.010 0 -2600 -3351.1730 0.010 0 -2700 -3351.1728 0.010 0 -2800 -3351.1190 0.010 0 -2900 -3351.1178 0.010 0 -3000 -3351.1136 0.010 0 -3100 -3351.1012 0.010 0 -3200 -3351.0892 0.010 0 -3300 -3351.0874 0.010 0 -3400 -3351.0857 0.010 0 -3500 -3351.0846 0.010 0 -3600 -3351.0820 0.010 0 -3700 -3351.0489 0.010 0 -3800 -3351.0367 0.010 0 -3900 -3350.9821 0.010 0 -4000 -3350.9821 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14731,9 +14686,26 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 4084, seed 2103404515, best lnL -3350.976 +Search rep 1 (of 2) generation 2324, seed 1844487779, best lnL -3351.349 gen current_lnL precision last_tree_imp -4084 -3350.9755 0.010 0 +2324 -3351.3492 0.010 0 +2400 -3351.3419 0.010 0 +2500 -3351.2390 0.010 0 +2600 -3351.1730 0.010 0 +2700 -3351.1728 0.010 0 +2800 -3351.1190 0.010 0 +2900 -3351.1178 0.010 0 +3000 -3351.1136 0.010 0 +3100 -3351.1012 0.010 0 +3200 -3351.0892 0.010 0 +3300 -3351.0874 0.010 0 +3400 -3351.0857 0.010 0 +3500 -3351.0846 0.010 0 +3600 -3351.0820 0.010 0 +3700 -3351.0489 0.010 0 +3800 -3351.0367 0.010 0 +3900 -3350.9821 0.010 0 +4000 -3350.9821 0.010 0 4100 -3350.9752 0.010 0 4200 -3350.9687 0.010 0 4300 -3350.9681 0.010 0 @@ -14741,96 +14713,62 @@ 4500 -3350.9641 0.010 0 4600 -3350.9235 0.010 0 4700 -3350.9232 0.010 0 -4800 -3350.9222 0.010 0 -4900 -3350.9222 0.010 0 -5000 -3350.9212 0.010 0 -5100 -3350.8984 0.010 0 -5200 -3350.8802 0.010 0 -5300 -3350.8789 0.010 0 -5400 -3350.8598 0.010 0 -5500 -3350.8007 0.010 0 -5600 -3350.7520 0.010 0 -5700 -3350.7435 0.010 0 -5800 -3350.6967 0.010 0 -5900 -3350.6924 0.010 0 -6000 -3350.6869 0.010 0 -6100 -3350.6726 0.010 0 -6200 -3350.6726 0.010 0 -6300 -3350.6692 0.010 0 -6400 -3350.6687 0.010 0 -6500 -3350.6687 0.010 0 -6600 -3350.6647 0.010 0 -6700 -3350.6647 0.010 0 -6800 -3350.6599 0.010 0 -6900 -3350.6258 0.010 0 -7000 -3350.6223 0.010 0 -7100 -3350.6215 0.010 0 -7200 -3350.6215 0.010 0 -7300 -3350.6209 0.010 0 -7400 -3350.5924 0.010 0 -7500 -3350.5907 0.010 0 -7600 -3350.5865 0.010 0 -7700 -3350.5853 0.010 0 -7800 -3350.5834 0.010 0 -7900 -3350.5825 0.010 0 -8000 -3350.5695 0.010 0 -8100 -3350.5679 0.010 0 -8200 -3350.5643 0.010 0 -8300 -3350.5641 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3350.5561 +Current score = -3350.9232 Performing final optimizations... -pass 1 : -3350.5509 (branch= 0.0000 alpha= 0.0000 pinv= 0.0051 eq freqs= 0.0001 rel rates= 0.0000 subset rates= 0.0000) -pass 2 : -3350.5135 (branch= 0.0040 alpha= 0.0155 pinv= 0.0151 eq freqs= 0.0026 rel rates= 0.0001 subset rates= 0.0000) -pass 3 : -3350.4798 (branch= 0.0000 alpha= 0.0152 pinv= 0.0134 eq freqs= 0.0014 rel rates= 0.0038 subset rates= 0.0000) -pass 4 : -3350.4496 (branch= 0.0020 alpha= 0.0131 pinv= 0.0123 eq freqs= 0.0000 rel rates= 0.0008 subset rates= 0.0020) -pass 5 : -3350.4246 (branch= 0.0028 alpha= 0.0105 pinv= 0.0112 eq freqs= 0.0003 rel rates= 0.0000 subset rates= 0.0000) -pass 6 : -3350.4012 (branch= 0.0008 alpha= 0.0118 pinv= 0.0099 eq freqs= 0.0000 rel rates= 0.0009 subset rates= 0.0000) -pass 7 : -3350.3812 (branch= 0.0006 alpha= 0.0097 pinv= 0.0090 eq freqs= 0.0000 rel rates= 0.0007 subset rates= 0.0000) -pass 8 : -3350.3624 (branch= 0.0002 alpha= 0.0092 pinv= 0.0080 eq freqs= 0.0000 rel rates= 0.0005 subset rates= 0.0009) -pass 9 : -3350.3462 (branch= 0.0011 alpha= 0.0078 pinv= 0.0072 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) -pass 10: -3350.3326 (branch= 0.0001 alpha= 0.0068 pinv= 0.0064 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) -pass 11: -3350.3201 (branch= 0.0001 alpha= 0.0064 pinv= 0.0057 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) -pass 12: -3350.3090 (branch= 0.0000 alpha= 0.0058 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) -pass 13: -3350.2992 (branch= 0.0000 alpha= 0.0051 pinv= 0.0045 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) -pass 14: -3350.2905 (branch= 0.0000 alpha= 0.0045 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) -pass 15: -3350.2828 (branch= 0.0000 alpha= 0.0040 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) -pass 16: -3350.2761 (branch= 0.0000 alpha= 0.0035 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) -pass 17: -3350.2702 (branch= 0.0000 alpha= 0.0030 pinv= 0.0027 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) -pass 18: -3350.2651 (branch= 0.0000 alpha= 0.0027 pinv= 0.0023 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) -pass 19: -3350.2606 (branch= 0.0000 alpha= 0.0023 pinv= 0.0020 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) -pass 20: -3350.2567 (branch= 0.0000 alpha= 0.0020 pinv= 0.0018 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 1 : -3350.8569 (branch= 0.0000 alpha= 0.0000 pinv= 0.0256 eq freqs= 0.0001 rel rates= 0.0407 subset rates= 0.0000) +pass 2 : -3350.7889 (branch= 0.0056 alpha= 0.0097 pinv= 0.0189 eq freqs= 0.0000 rel rates= 0.0321 subset rates= 0.0017) +pass 3 : -3350.7223 (branch= 0.0065 alpha= 0.0164 pinv= 0.0167 eq freqs= 0.0047 rel rates= 0.0223 subset rates= 0.0000) +pass 4 : -3350.6658 (branch= 0.0031 alpha= 0.0152 pinv= 0.0152 eq freqs= 0.0007 rel rates= 0.0207 subset rates= 0.0017) +pass 5 : -3350.6154 (branch= 0.0046 alpha= 0.0143 pinv= 0.0139 eq freqs= 0.0000 rel rates= 0.0175 subset rates= 0.0000) +pass 6 : -3350.5703 (branch= 0.0008 alpha= 0.0132 pinv= 0.0127 eq freqs= 0.0004 rel rates= 0.0165 subset rates= 0.0015) +pass 7 : -3350.5310 (branch= 0.0024 alpha= 0.0120 pinv= 0.0116 eq freqs= 0.0000 rel rates= 0.0133 subset rates= 0.0000) +pass 8 : -3350.4953 (branch= 0.0004 alpha= 0.0107 pinv= 0.0105 eq freqs= 0.0000 rel rates= 0.0126 subset rates= 0.0014) +pass 9 : -3350.4639 (branch= 0.0016 alpha= 0.0099 pinv= 0.0096 eq freqs= 0.0001 rel rates= 0.0102 subset rates= 0.0000) +pass 10: -3350.4367 (branch= 0.0002 alpha= 0.0088 pinv= 0.0086 eq freqs= 0.0000 rel rates= 0.0095 subset rates= 0.0000) +pass 11: -3350.4117 (branch= 0.0001 alpha= 0.0086 pinv= 0.0077 eq freqs= 0.0000 rel rates= 0.0085 subset rates= 0.0000) +pass 12: -3350.3895 (branch= 0.0000 alpha= 0.0078 pinv= 0.0069 eq freqs= 0.0000 rel rates= 0.0074 subset rates= 0.0000) +pass 13: -3350.3698 (branch= 0.0000 alpha= 0.0070 pinv= 0.0062 eq freqs= 0.0000 rel rates= 0.0064 subset rates= 0.0000) +pass 14: -3350.3524 (branch= 0.0000 alpha= 0.0063 pinv= 0.0056 eq freqs= 0.0000 rel rates= 0.0056 subset rates= 0.0000) +pass 15: -3350.3370 (branch= 0.0000 alpha= 0.0056 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0048 subset rates= 0.0000) +pass 16: -3350.3235 (branch= 0.0000 alpha= 0.0050 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0041 subset rates= 0.0000) +pass 17: -3350.3116 (branch= 0.0000 alpha= 0.0044 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0036 subset rates= 0.0000) +pass 18: -3350.3012 (branch= 0.0000 alpha= 0.0039 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0031 subset rates= 0.0000) +pass 19: -3350.2921 (branch= 0.0000 alpha= 0.0034 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0026 subset rates= 0.0000) +pass 20: -3350.2842 (branch= 0.0000 alpha= 0.0030 pinv= 0.0027 eq freqs= 0.0000 rel rates= 0.0023 subset rates= 0.0000) + optimization up to ... +pass 30: -3350.2445 (branch= 0.0000 alpha= 0.0150 pinv= 0.0135 eq freqs= 0.0000 rel rates= 0.0110 subset rates= 0.0000) optimization up to ... -pass 30: -3350.2377 (branch= 0.0000 alpha= 0.0098 pinv= 0.0088 eq freqs= 0.0000 rel rates= 0.0004 subset rates= 0.0000) +pass 40: -3350.2356 (branch= 0.0000 alpha= 0.0033 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0026 subset rates= 0.0000) optimization up to ... -pass 40: -3350.2338 (branch= 0.0000 alpha= 0.0020 pinv= 0.0018 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 50: -3350.2338 (branch= 0.0000 alpha= 0.0006 pinv= 0.0006 eq freqs= 0.0000 rel rates= 0.0006 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2330 (branch= 0.0000 alpha= 0.0004 pinv= 0.0003 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 60: -3350.2335 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) optimization up to ... -pass 53: -3350.2330 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 65: -3350.2334 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -3350.2330 +Final score = -3350.2335 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.138, AG = 10.500, AT = 2.714, CG = 0.001, CT = 22.133, GT = 1.000 + AC = 3.114, AG = 10.409, AT = 2.688, CG = 0.001, CT = 21.882, 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 - 0.5739 + 0.5783 with an invariant (invariable) site category, proportion estimated - 0.3644 + 0.3658 Substitution rate categories under this model: rate proportion - 0.0000 0.3644 - 0.0478 0.1589 - 0.2974 0.1589 - 0.8674 0.1589 - 2.7874 0.1589 + 0.0000 0.3658 + 0.0487 0.1585 + 0.3000 0.1585 + 0.8698 0.1585 + 2.7815 0.1585 Model 2 Number of states = 2 (binary data) @@ -14855,20 +14793,20 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3350.2330 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3350.2335 (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: 3.138 10.5 2.714 0.001 22.13 1 0.333 0.222 0.157 0.288 0.574 0.364 +rep 1: 3.114 10.41 2.688 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 Treelengths and subset rate multipliers: TL R(1) R(2) -rep 1: 0.791 1.821 0.179 +rep 1: 0.788 1.820 0.180 Saving final tree from best search rep (#1) to ch.g.dnaBnoZ.best.tre ####################################################### @@ -15025,16 +14963,6 @@ Optimizing branchlengths... improved 0.023 lnL 700 -3321.3649 0.255 1 800 -3321.0294 0.255 1 -900 -3321.0142 0.255 1 -1000 -3320.9667 0.255 1 -1100 -3320.8654 0.255 1 -Optimization precision reduced - Optimizing parameters... improved 0.575 lnL - Optimizing branchlengths... improved 0.059 lnL -1200 -3320.1519 0.010 1 -1300 -3320.0935 0.010 1 -1400 -3320.0786 0.010 1 -1500 -3320.0251 0.010 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15135,77 +15063,75 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 1575, seed 1652149641, best lnL -3320.016 +Search rep 1 (of 2) generation 875, seed 508528929, best lnL -3321.014 gen current_lnL precision last_tree_imp -1575 -3320.0162 0.010 1 -1600 -3320.0162 0.010 1 -1700 -3320.0146 0.010 1 -1800 -3319.8207 0.010 1 -1900 -3319.6041 0.010 1 -2000 -3319.5586 0.010 1 -2100 -3319.5579 0.010 1 -2200 -3319.4756 0.010 1 -2300 -3319.3806 0.010 1 -2400 -3319.3433 0.010 1 -2500 -3319.3402 0.010 1 -2600 -3319.1370 0.010 1 -2700 -3319.1196 0.010 1 +875 -3321.0142 0.255 1 +900 -3321.0142 0.255 1 +1000 -3320.9667 0.255 1 +1100 -3320.8654 0.255 1 +Optimization precision reduced + Optimizing parameters... improved 0.575 lnL + Optimizing branchlengths... improved 0.059 lnL +1200 -3320.1519 0.010 1 +1300 -3320.0935 0.010 1 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3319.1057 +Current score = -3320.0786 Performing final optimizations... -pass 1 : -3318.9305 (branch= 0.0082 alpha= 0.0120 pinv= 0.0146 eq freqs= 0.0001 rel rates= 0.1105 ins/del rates= 0.0299) -pass 2 : -3318.7686 (branch= 0.0359 alpha= 0.0061 pinv= 0.0150 eq freqs= 0.0026 rel rates= 0.0922 ins/del rates= 0.0101) -pass 3 : -3318.6228 (branch= 0.0390 alpha= 0.0118 pinv= 0.0138 eq freqs= 0.0000 rel rates= 0.0707 ins/del rates= 0.0104) -pass 4 : -3318.5023 (branch= 0.0248 alpha= 0.0089 pinv= 0.0134 eq freqs= 0.0015 rel rates= 0.0638 ins/del rates= 0.0082) -pass 5 : -3318.4049 (branch= 0.0145 alpha= 0.0096 pinv= 0.0126 eq freqs= 0.0008 rel rates= 0.0540 ins/del rates= 0.0059) -pass 6 : -3318.3235 (branch= 0.0095 alpha= 0.0088 pinv= 0.0118 eq freqs= 0.0002 rel rates= 0.0473 ins/del rates= 0.0037) -pass 7 : -3318.2542 (branch= 0.0063 alpha= 0.0091 pinv= 0.0110 eq freqs= 0.0002 rel rates= 0.0403 ins/del rates= 0.0026) -pass 8 : -3318.1948 (branch= 0.0040 alpha= 0.0086 pinv= 0.0101 eq freqs= 0.0001 rel rates= 0.0349 ins/del rates= 0.0017) -pass 9 : -3318.1430 (branch= 0.0026 alpha= 0.0083 pinv= 0.0093 eq freqs= 0.0001 rel rates= 0.0305 ins/del rates= 0.0011) -pass 10: -3318.0978 (branch= 0.0017 alpha= 0.0079 pinv= 0.0085 eq freqs= 0.0001 rel rates= 0.0263 ins/del rates= 0.0007) -pass 11: -3318.0585 (branch= 0.0011 alpha= 0.0074 pinv= 0.0077 eq freqs= 0.0000 rel rates= 0.0227 ins/del rates= 0.0005) -pass 12: -3318.0240 (branch= 0.0007 alpha= 0.0068 pinv= 0.0069 eq freqs= 0.0000 rel rates= 0.0196 ins/del rates= 0.0003) -pass 13: -3317.9939 (branch= 0.0005 alpha= 0.0063 pinv= 0.0063 eq freqs= 0.0000 rel rates= 0.0168 ins/del rates= 0.0002) -pass 14: -3317.9674 (branch= 0.0003 alpha= 0.0057 pinv= 0.0056 eq freqs= 0.0000 rel rates= 0.0146 ins/del rates= 0.0001) -pass 15: -3317.9443 (branch= 0.0002 alpha= 0.0052 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0126 ins/del rates= 0.0001) -pass 16: -3317.9240 (branch= 0.0001 alpha= 0.0047 pinv= 0.0045 eq freqs= 0.0000 rel rates= 0.0109 ins/del rates= 0.0000) -pass 17: -3317.9062 (branch= 0.0001 alpha= 0.0042 pinv= 0.0040 eq freqs= 0.0000 rel rates= 0.0094 ins/del rates= 0.0000) -pass 18: -3317.8907 (branch= 0.0000 alpha= 0.0038 pinv= 0.0036 eq freqs= 0.0000 rel rates= 0.0081 ins/del rates= 0.0000) -pass 19: -3317.8771 (branch= 0.0000 alpha= 0.0034 pinv= 0.0032 eq freqs= 0.0000 rel rates= 0.0070 ins/del rates= 0.0000) -pass 20: -3317.8651 (branch= 0.0000 alpha= 0.0030 pinv= 0.0028 eq freqs= 0.0000 rel rates= 0.0061 ins/del rates= 0.0000) - optimization up to ... -pass 30: -3317.8053 (branch= 0.0000 alpha= 0.0158 pinv= 0.0145 eq freqs= 0.0001 rel rates= 0.0293 ins/del rates= 0.0000) +pass 1 : -3319.5777 (branch= 0.0258 alpha= 0.0000 pinv= 0.0168 eq freqs= 0.0001 rel rates= 0.4045 ins/del rates= 0.0538) +pass 2 : -3319.2846 (branch= 0.0355 alpha= 0.0242 pinv= 0.0144 eq freqs= 0.0036 rel rates= 0.2116 ins/del rates= 0.0038) +pass 3 : -3319.0611 (branch= 0.0273 alpha= 0.0110 pinv= 0.0149 eq freqs= 0.0000 rel rates= 0.1628 ins/del rates= 0.0075) +pass 4 : -3318.8652 (branch= 0.0233 alpha= 0.0112 pinv= 0.0146 eq freqs= 0.0025 rel rates= 0.1370 ins/del rates= 0.0072) +pass 5 : -3318.7073 (branch= 0.0121 alpha= 0.0103 pinv= 0.0139 eq freqs= 0.0012 rel rates= 0.1158 ins/del rates= 0.0048) +pass 6 : -3318.5760 (branch= 0.0095 alpha= 0.0109 pinv= 0.0130 eq freqs= 0.0002 rel rates= 0.0940 ins/del rates= 0.0036) +pass 7 : -3318.4658 (branch= 0.0064 alpha= 0.0098 pinv= 0.0122 eq freqs= 0.0003 rel rates= 0.0788 ins/del rates= 0.0027) +pass 8 : -3318.3716 (branch= 0.0037 alpha= 0.0101 pinv= 0.0113 eq freqs= 0.0003 rel rates= 0.0672 ins/del rates= 0.0016) +pass 9 : -3318.2905 (branch= 0.0028 alpha= 0.0093 pinv= 0.0104 eq freqs= 0.0003 rel rates= 0.0572 ins/del rates= 0.0012) +pass 10: -3318.2213 (branch= 0.0018 alpha= 0.0088 pinv= 0.0095 eq freqs= 0.0001 rel rates= 0.0481 ins/del rates= 0.0008) +pass 11: -3318.1622 (branch= 0.0012 alpha= 0.0084 pinv= 0.0087 eq freqs= 0.0001 rel rates= 0.0402 ins/del rates= 0.0005) +pass 12: -3318.1115 (branch= 0.0008 alpha= 0.0078 pinv= 0.0079 eq freqs= 0.0001 rel rates= 0.0337 ins/del rates= 0.0003) +pass 13: -3318.0686 (branch= 0.0005 alpha= 0.0074 pinv= 0.0072 eq freqs= 0.0001 rel rates= 0.0277 ins/del rates= 0.0002) +pass 14: -3318.0316 (branch= 0.0003 alpha= 0.0067 pinv= 0.0065 eq freqs= 0.0001 rel rates= 0.0233 ins/del rates= 0.0001) +pass 15: -3317.9995 (branch= 0.0002 alpha= 0.0060 pinv= 0.0058 eq freqs= 0.0000 rel rates= 0.0199 ins/del rates= 0.0001) +pass 16: -3317.9716 (branch= 0.0001 alpha= 0.0055 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0170 ins/del rates= 0.0000) +pass 17: -3317.9473 (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= 0.0001 alpha= 0.0045 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0124 ins/del rates= 0.0000) +pass 19: -3317.9078 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0106 ins/del rates= 0.0000) +pass 20: -3317.8918 (branch= 0.0000 alpha= 0.0036 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0091 ins/del rates= 0.0000) + optimization up to ... +pass 30: -3317.8117 (branch= 0.0001 alpha= 0.0189 pinv= 0.0174 eq freqs= 0.0001 rel rates= 0.0436 ins/del rates= 0.0000) + optimization up to ... +pass 40: -3317.7926 (branch= 0.0001 alpha= 0.0046 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0101 ins/del rates= 0.0000) optimization up to ... -pass 40: -3317.7911 (branch= 0.0001 alpha= 0.0038 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0069 ins/del rates= 0.0000) +pass 50: -3317.7883 (branch= 0.0000 alpha= 0.0010 pinv= 0.0009 eq freqs= 0.0000 rel rates= 0.0024 ins/del rates= 0.0000) optimization up to ... -pass 50: -3317.7879 (branch= 0.0000 alpha= 0.0008 pinv= 0.0007 eq freqs= 0.0000 rel rates= 0.0017 ins/del rates= 0.0000) +pass 60: -3317.7873 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0005 ins/del rates= 0.0000) optimization up to ... -pass 60: -3317.7872 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0003 ins/del rates= 0.0000) +pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) optimization up to ... -pass 69: -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 72: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3317.7871 -Time used so far = 0 hours, 0 minutes and 12 seconds +Time used so far = 0 hours, 0 minutes and 13 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.065, AG = 10.264, AT = 2.657, CG = 0.001, CT = 21.540, GT = 1.000 + AC = 3.065, AG = 10.261, AT = 2.655, CG = 0.001, CT = 21.532, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3328 0.2223 0.1567 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.5745 + 0.5751 with an invariant (invariable) site category, proportion estimated - 0.3611 + 0.3614 Substitution rate categories under this model: rate proportion - 0.0000 0.3611 - 0.0479 0.1597 - 0.2978 0.1597 - 0.8677 0.1597 - 2.7866 0.1597 + 0.0000 0.3614 + 0.0480 0.1596 + 0.2982 0.1596 + 0.8681 0.1596 + 2.7857 0.1596 Model 2 Number of states = 2 (0/1 coding of gaps) @@ -15237,7 +15163,7 @@ Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.065 10.26 2.657 0.001 21.54 1 0.333 0.222 0.157 0.288 0.574 0.361 +rep 1: 3.065 10.26 2.655 0.001 21.53 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del @@ -15247,7 +15173,7 @@ Treelengths: TL -rep 1: 1.419 +rep 1: 1.418 Saving final tree from best search rep (#1) to ch.g.dnaMix.best.tre ####################################################### @@ -16800,11 +16726,6 @@ Optimizing parameters... improved 0.001 lnL Optimizing branchlengths... improved 0.000 lnL 2600 -13370.3703 0.010 0 -2700 -13370.3695 0.010 0 -2800 -13370.3692 0.010 0 -2900 -13370.3688 0.010 0 -3000 -13370.3644 0.010 0 -3100 -13370.3583 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16927,18 +16848,18 @@ Subset 3: Random seed for bootstrap reweighting: 486988955 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 3177, seed 409498974, best lnL -13370.353 +Bootstrap rep 1 (of 1) generation 2603, seed 406718355, best lnL -13370.370 gen current_lnL precision last_tree_imp -3177 -13370.3526 0.010 0 +2603 -13370.3703 0.010 0 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) - AC = 1.717, AG = 2.662, AT = 1.270, CG = 1.270, CT = 4.337, GT = 1.000 + AC = 1.719, AG = 2.662, AT = 1.270, CG = 1.270, CT = 4.304, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3076 0.1804 0.3103 0.2017 + (ACGT) 0.3084 0.1807 0.3089 0.2021 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.3662 @@ -16953,7 +16874,7 @@ Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) - AC = 2.631, AG = 4.225, AT = 0.813, CG = 4.225, CT = 2.631, GT = 1.000 + AC = 2.622, AG = 4.243, AT = 0.820, CG = 4.243, CT = 2.622, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2819 0.1752 0.1596 0.3832 Rate Heterogeneity Model: @@ -16970,21 +16891,21 @@ Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) - AC = 1.000, AG = 5.303, AT = 4.268, CG = 0.630, CT = 5.303, GT = 1.000 + AC = 1.000, AG = 5.303, AT = 4.268, CG = 0.629, CT = 5.303, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1555 0.3463 0.2762 0.2219 + (ACGT) 0.1555 0.3463 0.2763 0.2219 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.1990 + 4.1267 with an invariant (invariable) site category, proportion estimated - 0.0491 + 0.0487 Substitution rate categories under this model: rate proportion - 0.0000 0.0491 - 0.4650 0.2377 - 0.7818 0.2377 - 1.0843 0.2377 - 1.6689 0.2377 + 0.0000 0.0487 + 0.4612 0.2378 + 0.7795 0.2378 + 1.0844 0.2378 + 1.6750 0.2378 Subset rate multipliers: 0.53 0.29 2.18 @@ -16996,25 +16917,25 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13370.3526 +Replicate 1 : -13370.3703 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: 1.717 2.662 1.27 1.27 4.337 1 0.308 0.180 0.310 0.202 0.366 +rep 1: 1.719 2.662 1.27 1.27 4.304 1 0.308 0.181 0.309 0.202 0.366 Partition model subset 2: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 2.631 4.225 0.813 4.225 2.631 1 0.282 0.175 0.160 0.383 0.245 +rep 1: 2.622 4.243 0.8202 4.243 2.622 1 0.282 0.175 0.160 0.383 0.245 Partition model subset 3: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 1 5.303 4.268 0.6297 5.303 1 0.155 0.346 0.276 0.222 4.199 0.049 +rep 1: 1 5.303 4.268 0.6292 5.303 1 0.155 0.346 0.276 0.222 4.127 0.049 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 1.767 0.530 0.287 2.183 +rep 1: 1.762 0.530 0.287 2.183 Saving best tree to bootstrap file ch.p.3diff.boot.tre @@ -17237,7 +17158,7 @@ pass 16: -467.6788 (branch= 0.0000 subset rates= 0.0011) Looking for minimum length branches... Final score = -467.6787 -Time used so far = 0 hours, 0 minutes and 1 seconds +Time used so far = 0 hours, 0 minutes and 2 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17365,7 +17286,7 @@ pass 17: -467.6782 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6782 -Time used so far = 0 hours, 0 minutes and 2 seconds +Time used so far = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17476,6 +17397,134 @@ 3300 -467.7014 0.010 0 3400 -467.7009 0.010 0 3500 -467.7000 0.010 0 +NOTE: ****Specified time limit (5 seconds) reached... + +NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY +TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE +FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF +(set restart = 1 in the config file). IF YOU WANT TO USE THE +PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY +ADD "end;" TO THE TREE FILES. + +Running GARLI Version 2.1. () +->Single processor version for 64-bit OS<- +############################################################## + This is GARLI 2.1: maximum likelihood phylogenetic inference + using nucleotide, amino acid, codon and morphology-like data, + as well as partitioned models. + General program usage is extensively documented here: + http://www.nescent.org/wg/garli/ + See this page for details on partitioned model usage: + http://www.nescent.org/wg_garli/Using_partitioned_models + and this page for details on Mkv mophology model usage: + http://www.nescent.org/wg_garli/Mkv_morphology_model + PLEASE LET ME KNOW OF ANY PROBLEMS AT: + garli.support@gmail.com +############################################################## +Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0 +Using NCL version 2.1.17 + +####################################################### +Reading config file ./restart/p.mk.ssr.conf +################################################### +READING OF DATA +Attempting to read data file in Nexus format (using NCL): + data/L2001.30x52.nex ... +Reading CHARACTERS block... +Warning: + Skipping command: OPTIONS +at line 23, column (approximately) 9 (file position 611) +storing implied block: TAXA +storing read block: CHARACTERS + found standard data... successful +Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS + successful + +################################################### +PARTITIONING OF DATA AND MODELS +GARLI data subset 1 + CHARACTERS block #1 ("Untitled CHARACTERS Block 1") + Data read as Standard k-state data, + modeled as Standard k-state data +NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. +Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 + + Subset of data with 2 states: + chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 + Summary of data: + 30 sequences. + 0 constant characters. + 39 parsimony-informative characters. + 0 uninformative variable characters. + 39 total characters. + 39 unique patterns in compressed data matrix. +NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. +Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 + + Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: + char 90 + Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: + char 90 + Subset of data with 3 states: + chars 54 61 62 64 71 72 83 90-102 \ 6 + Summary of data: + 30 sequences. + 0 constant characters. + 10 parsimony-informative characters. + 0 uninformative variable characters. + 10 total characters. + 10 unique patterns in compressed data matrix. +NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. +Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 + + Subset of data with 4 states: + chars 52 59 73 + Summary of data: + 30 sequences. + 0 constant characters. + 0 parsimony-informative characters. + 3 uninformative variable characters. + 3 total characters. + 3 unique patterns in compressed data matrix. +NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. +Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 + +NOTE: No characters found with 5 observed states. +NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. +Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 + +NOTE: No characters found with 6 observed states. + +################################################### +NOTE: Unlike many programs, the amount of system memory that Garli will +use can be controlled by the user. +(This comes from the availablememory setting in the configuration file. +Availablememory should NOT be set to more than the actual amount of +physical memory that your computer has installed) + +For this dataset: + Mem level availablememory setting + great >= 1 MB + good approx 0 MB to 1 MB + low approx 0 MB to 1 MB + very low approx 0 MB to 1 MB +the minimum required availablememory is 1 MB + +You specified that Garli should use at most 512.0 MB of memory. + +Garli will actually use approx. 0.5 MB of memory +**Your memory level is: great (you don't need to change anything)** + +####################################################### +Loading starting model and/or tree from file data/L.start +Reading TREES block...storing read block: TREES + successful +STARTING RUN + +Restarting from checkpoint... +Search rep 3 (of 5) generation 3508, seed 1436112128, best lnL -467.700 +gen current_lnL precision last_tree_imp +3508 -467.7000 0.010 0 3600 -467.6999 0.010 0 3700 -467.6995 0.010 0 3800 -467.6994 0.010 0 @@ -17507,7 +17556,7 @@ pass 15: -467.6783 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6783 -Time used so far = 0 hours, 0 minutes and 4 seconds +Time used so far = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17606,134 +17655,6 @@ 2200 -467.7117 0.010 0 2300 -467.7101 0.010 0 2400 -467.7097 0.010 0 -NOTE: ****Specified time limit (5 seconds) reached... - -NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY -TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE -FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF -(set restart = 1 in the config file). IF YOU WANT TO USE THE -PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY -ADD "end;" TO THE TREE FILES. - -Running GARLI Version 2.1. () -->Single processor version for 64-bit OS<- -############################################################## - This is GARLI 2.1: maximum likelihood phylogenetic inference - using nucleotide, amino acid, codon and morphology-like data, - as well as partitioned models. - General program usage is extensively documented here: - http://www.nescent.org/wg/garli/ - See this page for details on partitioned model usage: - http://www.nescent.org/wg_garli/Using_partitioned_models - and this page for details on Mkv mophology model usage: - http://www.nescent.org/wg_garli/Mkv_morphology_model - PLEASE LET ME KNOW OF ANY PROBLEMS AT: - garli.support@gmail.com -############################################################## -Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0 -Using NCL version 2.1.17 - -####################################################### -Reading config file ./restart/p.mk.ssr.conf -################################################### -READING OF DATA -Attempting to read data file in Nexus format (using NCL): - data/L2001.30x52.nex ... -Reading CHARACTERS block... -Warning: - Skipping command: OPTIONS -at line 23, column (approximately) 9 (file position 611) -storing implied block: TAXA -storing read block: CHARACTERS - found standard data... successful -Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS - successful - -################################################### -PARTITIONING OF DATA AND MODELS -GARLI data subset 1 - CHARACTERS block #1 ("Untitled CHARACTERS Block 1") - Data read as Standard k-state data, - modeled as Standard k-state data -NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. -Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 - - Subset of data with 2 states: - chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 - Summary of data: - 30 sequences. - 0 constant characters. - 39 parsimony-informative characters. - 0 uninformative variable characters. - 39 total characters. - 39 unique patterns in compressed data matrix. -NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. -Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 - - Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: - char 90 - Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: - char 90 - Subset of data with 3 states: - chars 54 61 62 64 71 72 83 90-102 \ 6 - Summary of data: - 30 sequences. - 0 constant characters. - 10 parsimony-informative characters. - 0 uninformative variable characters. - 10 total characters. - 10 unique patterns in compressed data matrix. -NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. -Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 - - Subset of data with 4 states: - chars 52 59 73 - Summary of data: - 30 sequences. - 0 constant characters. - 0 parsimony-informative characters. - 3 uninformative variable characters. - 3 total characters. - 3 unique patterns in compressed data matrix. -NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. -Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 - -NOTE: No characters found with 5 observed states. -NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. -Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 - -NOTE: No characters found with 6 observed states. - -################################################### -NOTE: Unlike many programs, the amount of system memory that Garli will -use can be controlled by the user. -(This comes from the availablememory setting in the configuration file. -Availablememory should NOT be set to more than the actual amount of -physical memory that your computer has installed) - -For this dataset: - Mem level availablememory setting - great >= 1 MB - good approx 0 MB to 1 MB - low approx 0 MB to 1 MB - very low approx 0 MB to 1 MB -the minimum required availablememory is 1 MB - -You specified that Garli should use at most 512.0 MB of memory. - -Garli will actually use approx. 0.5 MB of memory -**Your memory level is: great (you don't need to change anything)** - -####################################################### -Loading starting model and/or tree from file data/L.start -Reading TREES block...storing read block: TREES - successful -STARTING RUN - -Restarting from checkpoint... -Search rep 4 (of 5) generation 2420, seed 355175019, best lnL -467.710 -gen current_lnL precision last_tree_imp -2420 -467.7097 0.010 0 2500 -467.7091 0.010 0 2600 -467.7082 0.010 0 2700 -467.7078 0.010 0 @@ -17768,7 +17689,7 @@ pass 17: -467.6784 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6784 -Time used so far = 0 hours, 0 minutes and 6 seconds +Time used so far = 0 hours, 0 minutes and 8 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17904,7 +17825,7 @@ pass 14: -467.6783 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6783 -Time used = 0 hours, 0 minutes and 8 seconds +Time used = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18445,16 +18366,6 @@ 400 -477.7468 0.010 188 500 -477.7408 0.010 188 600 -477.7022 0.010 520 -700 -477.6898 0.010 520 -800 -477.6823 0.010 520 -900 -477.6795 0.010 520 -1000 -477.6777 0.010 520 -1100 -477.3824 0.010 1037 -1200 -477.3598 0.010 1037 -1300 -477.3536 0.010 1037 -1400 -477.3511 0.010 1037 -1500 -477.3003 0.010 1443 -1600 -477.2712 0.010 1502 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -18580,9 +18491,19 @@ STARTING RUN Restarting from checkpoint... -Search rep 3 (of 5) generation 1683, seed 1696949978, best lnL -477.269 +Search rep 3 (of 5) generation 639, seed 900643297, best lnL -477.695 gen current_lnL precision last_tree_imp -1683 -477.2687 0.010 1502 +639 -477.6949 0.010 520 +700 -477.6898 0.010 520 +800 -477.6823 0.010 520 +900 -477.6795 0.010 520 +1000 -477.6777 0.010 520 +1100 -477.3824 0.010 1037 +1200 -477.3598 0.010 1037 +1300 -477.3536 0.010 1037 +1400 -477.3511 0.010 1037 +1500 -477.3003 0.010 1443 +1600 -477.2712 0.010 1502 1700 -477.2687 0.010 1502 1800 -477.2676 0.010 1502 1900 -477.2646 0.010 1502 @@ -18652,7 +18573,7 @@ pass 13: -477.2119 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.2119 -Time used so far = 0 hours, 0 minutes and 8 seconds +Time used so far = 0 hours, 0 minutes and 9 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18782,170 +18703,26 @@ Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 0.000 lnL 5100 -477.4606 0.010 252 -5200 -477.4604 0.010 252 -5300 -477.4602 0.010 252 -5400 -477.4598 0.010 252 -5500 -477.4595 0.010 252 -5600 -477.4594 0.010 252 -5700 -477.4592 0.010 252 -5800 -477.4592 0.010 252 -Reached termination condition! -last topological improvement at gen 252 -Improvement over last 500 gen = 0.00098 -Current score = -477.4592 -Performing final optimizations... -pass 1 : -477.4573 (branch= 0.0000 subset rates= 0.0019) -pass 2 : -477.4520 (branch= 0.0052 subset rates= 0.0000) -pass 3 : -477.4385 (branch= 0.0113 subset rates= 0.0021) -pass 4 : -477.4368 (branch= 0.0018 subset rates= 0.0000) -pass 5 : -477.4353 (branch= 0.0015 subset rates= 0.0000) -pass 6 : -477.4342 (branch= 0.0011 subset rates= 0.0000) -pass 7 : -477.4327 (branch= 0.0007 subset rates= 0.0008) -pass 8 : -477.4322 (branch= 0.0005 subset rates= 0.0000) -pass 9 : -477.4319 (branch= 0.0002 subset rates= 0.0000) -pass 10: -477.4318 (branch= 0.0001 subset rates= 0.0000) -pass 11: -477.4317 (branch= 0.0001 subset rates= 0.0000) -pass 12: -477.4317 (branch= 0.0000 subset rates= 0.0000) -pass 13: -477.4316 (branch= 0.0000 subset rates= 0.0000) -pass 14: -477.4316 (branch= 0.0000 subset rates= 0.0000) -pass 15: -477.4316 (branch= 0.0000 subset rates= 0.0000) -pass 16: -477.4316 (branch= 0.0000 subset rates= 0.0000) -pass 17: -477.4316 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -477.4315 -Time used so far = 0 hours, 0 minutes and 10 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 1.91 2.74 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. - ->>>Completed Search rep 4 (of 5)<<< - ->>>Search rep 5 (of 5)<<< -Obtained starting tree 1 from Nexus -MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) -Model 1 - Number of states = 2 (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=328833807 - -Initial ln Likelihood: -660.1326 -optimizing: starting branch lengths, subset rates... -pass 1:+ 159.381 (branch= 147.15 scale= 2.32 subset rates= 9.91) -pass 2:+ 16.729 (branch= 12.80 scale= 0.00 subset rates= 3.93) -pass 3:+ 3.088 (branch= 1.77 scale= 0.02 subset rates= 1.30) -pass 4:+ 0.890 (branch= 0.55 scale= 0.00 subset rates= 0.34) -pass 5:+ 1.052 (branch= 1.02 scale= 0.00 subset rates= 0.03) -pass 6:+ 0.985 (branch= 0.98 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.201 (branch= 0.20 scale= 0.00 subset rates= 0.00) -pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -477.8081 -gen current_lnL precision last_tree_imp -0 -477.8081 0.010 0 -100 -477.7965 0.010 0 -200 -477.6034 0.010 125 -300 -477.5479 0.010 255 -400 -477.5332 0.010 255 -500 -477.5173 0.010 255 -600 -477.5149 0.010 255 -700 -477.5046 0.010 255 -800 -477.4977 0.010 255 -900 -477.4956 0.010 255 -1000 -477.4912 0.010 255 -1100 -477.4900 0.010 255 -1200 -477.4877 0.010 255 -1300 -477.4857 0.010 255 -1400 -477.4814 0.010 255 -1500 -477.4795 0.010 255 -1600 -477.4765 0.010 255 -1700 -477.4765 0.010 255 -1800 -477.4741 0.010 255 -1900 -477.4739 0.010 255 -2000 -477.4730 0.010 255 -2100 -477.4719 0.010 255 -2200 -477.4719 0.010 255 -2300 -477.4718 0.010 255 -2400 -477.4715 0.010 255 -2500 -477.4707 0.010 255 -2600 -477.4701 0.010 255 -2700 -477.4685 0.010 255 -2800 -477.4684 0.010 255 -2900 -477.4678 0.010 255 -3000 -477.4675 0.010 255 -3100 -477.4673 0.010 255 -3200 -477.4672 0.010 255 -3300 -477.4668 0.010 255 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -477.4668 +Current score = -477.4606 Performing final optimizations... -pass 1 : -477.4591 (branch= 0.0050 subset rates= 0.0027) -pass 2 : -477.4485 (branch= 0.0087 subset rates= 0.0018) -pass 3 : -477.4454 (branch= 0.0023 subset rates= 0.0008) -pass 4 : -477.4397 (branch= 0.0039 subset rates= 0.0019) -pass 5 : -477.4364 (branch= 0.0033 subset rates= 0.0000) -pass 6 : -477.4352 (branch= 0.0012 subset rates= 0.0000) -pass 7 : -477.4338 (branch= 0.0012 subset rates= 0.0001) -pass 8 : -477.4328 (branch= 0.0008 subset rates= 0.0003) -pass 9 : -477.4322 (branch= 0.0005 subset rates= 0.0000) -pass 10: -477.4319 (branch= 0.0003 subset rates= 0.0000) -pass 11: -477.4318 (branch= 0.0001 subset rates= 0.0000) -pass 12: -477.4317 (branch= 0.0001 subset rates= 0.0000) -pass 13: -477.4317 (branch= 0.0000 subset rates= 0.0000) -pass 14: -477.4317 (branch= 0.0000 subset rates= 0.0000) -pass 15: -477.4316 (branch= 0.0000 subset rates= 0.0000) -pass 16: -477.4316 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -477.4573 (branch= 0.0000 subset rates= 0.0034) +pass 2 : -477.4465 (branch= 0.0108 subset rates= 0.0000) +pass 3 : -477.4397 (branch= 0.0067 subset rates= 0.0000) +pass 4 : -477.4390 (branch= 0.0007 subset rates= 0.0000) +pass 5 : -477.4358 (branch= 0.0020 subset rates= 0.0013) +pass 6 : -477.4337 (branch= 0.0021 subset rates= 0.0000) +pass 7 : -477.4330 (branch= 0.0006 subset rates= 0.0000) +pass 8 : -477.4326 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -477.4324 (branch= 0.0003 subset rates= 0.0000) +pass 10: -477.4322 (branch= 0.0001 subset rates= 0.0000) +pass 11: -477.4321 (branch= 0.0001 subset rates= 0.0000) +pass 12: -477.4321 (branch= 0.0000 subset rates= 0.0000) +pass 13: -477.4321 (branch= 0.0000 subset rates= 0.0000) +pass 14: -477.4320 (branch= 0.0000 subset rates= 0.0001) Looking for minimum length branches... -Final score = -477.4316 -Time used = 0 hours, 0 minutes and 12 seconds +Final score = -477.4318 +Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 @@ -18973,11 +18750,11 @@ no rate heterogeneity Subset rate multipliers: - 0.63 1.91 2.75 + 0.63 1.91 2.73 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. ->>>Terminated Search rep 5 (of 5)<<< +>>>Terminated Search rep 4 (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!*** @@ -18985,7 +18762,7 @@ ####################################################### -Completed 5 replicate search(es) (of 5). +Completed 4 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. @@ -18993,8 +18770,7 @@ Replicate 1 : -477.4316 Replicate 2 : -477.2120 Replicate 3 : -477.2119 (best) (same topology as 2) -Replicate 4 : -477.4315 (same topology as 1) -Replicate 5 : -477.4316 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 4 : -477.4318 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -19012,8 +18788,7 @@ rep 1: 4.928 0.632 1.916 2.734 rep 2: 4.672 0.642 1.910 2.621 rep 3: 4.671 0.643 1.910 2.613 -rep 4: 4.929 0.632 1.913 2.743 -rep 5: 4.930 0.632 1.911 2.750 +rep 4: 4.925 0.633 1.910 2.734 Saving final tree from best search rep (#3) to ch.p.mkO.ssr.best.tre ####################################################### @@ -19360,7 +19135,7 @@ pass 13: -425.5487 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.5487 -Time used so far = 0 hours, 0 minutes and 3 seconds +Time used so far = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -19447,93 +19222,6 @@ 3600 -425.3438 0.010 611 3700 -425.3437 0.010 611 3800 -425.3436 0.010 611 -3900 -425.3433 0.010 611 -4000 -425.3433 0.010 611 -4100 -425.3433 0.010 611 -Reached termination condition! -last topological improvement at gen 611 -Improvement over last 500 gen = 0.00055 -Current score = -425.3433 -Performing final optimizations... -pass 1 : -425.3433 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -425.3303 (branch= 0.0130 subset rates= 0.0000) -pass 3 : -425.3242 (branch= 0.0061 subset rates= 0.0000) -pass 4 : -425.3230 (branch= 0.0011 subset rates= 0.0000) -pass 5 : -425.3223 (branch= 0.0005 subset rates= 0.0002) -pass 6 : -425.3223 (branch= 0.0000 subset rates= 0.0000) -pass 7 : -425.3214 (branch= 0.0009 subset rates= 0.0000) -pass 8 : -425.3210 (branch= 0.0005 subset rates= 0.0000) -pass 9 : -425.3206 (branch= 0.0003 subset rates= 0.0000) -pass 10: -425.3201 (branch= 0.0001 subset rates= 0.0004) -pass 11: -425.3201 (branch= 0.0000 subset rates= 0.0000) -pass 12: -425.3201 (branch= 0.0000 subset rates= 0.0000) -pass 13: -425.3200 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -425.3200 -Time used so far = 0 hours, 0 minutes and 5 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (standard data) - Character change matrix: - One rate (symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (standard data) - Character change matrix: - One rate (symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (standard data) - Character change matrix: - One rate (symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 0.86 1.54 1.15 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 9 branches were collapsed. - ->>>Completed Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< - ->>>Bootstrap rep 1 (of 1) Search rep 4 (of 5)<<< -Obtained starting tree 1 from Nexus -Starting with seed=2070757799 - -Initial ln Likelihood: -550.3246 -optimizing: starting branch lengths, subset rates... -pass 1:+ 102.933 (branch= 102.64 scale= 0.09 subset rates= 0.20) -pass 2:+ 5.507 (branch= 5.49 scale= 0.00 subset rates= 0.02) -pass 3:+ 2.290 (branch= 2.25 scale= 0.04 subset rates= 0.00) -pass 4:+ 0.292 (branch= 0.29 scale= 0.00 subset rates= 0.00) -pass 5:+ 0.071 (branch= 0.06 scale= 0.00 subset rates= 0.01) -pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -439.2316 -gen current_lnL precision last_tree_imp -0 -439.2316 0.010 0 -100 -433.6971 0.010 75 -200 -432.2075 0.010 188 -300 -429.7506 0.010 212 -400 -427.9705 0.010 391 -500 -427.8319 0.010 409 -600 -425.6450 0.010 594 -700 -425.6393 0.010 594 -800 -425.6316 0.010 594 -900 -425.6267 0.010 594 -1000 -425.6213 0.010 594 -1100 -425.6180 0.010 594 -1200 -425.6150 0.010 594 -1300 -425.6135 0.010 594 -1400 -425.6117 0.010 594 -1500 -425.6100 0.010 594 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -19662,9 +19350,96 @@ Subset 3: Random seed for bootstrap reweighting: 974568031 Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 4 (of 5) generation 1582, seed 2116577696, best lnL -425.608 +Bootstrap rep 1 (of 1) Search rep 3 (of 5) generation 3860, seed 1005162342, best lnL -425.343 gen current_lnL precision last_tree_imp -1582 -425.6085 0.010 594 +3860 -425.3434 0.010 611 +3900 -425.3433 0.010 611 +4000 -425.3433 0.010 611 +4100 -425.3433 0.010 611 +Reached termination condition! +last topological improvement at gen 611 +Improvement over last 500 gen = 0.00055 +Current score = -425.3433 +Performing final optimizations... +pass 1 : -425.3433 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -425.3303 (branch= 0.0130 subset rates= 0.0000) +pass 3 : -425.3242 (branch= 0.0061 subset rates= 0.0000) +pass 4 : -425.3230 (branch= 0.0011 subset rates= 0.0000) +pass 5 : -425.3223 (branch= 0.0005 subset rates= 0.0002) +pass 6 : -425.3223 (branch= 0.0000 subset rates= 0.0000) +pass 7 : -425.3214 (branch= 0.0009 subset rates= 0.0000) +pass 8 : -425.3210 (branch= 0.0005 subset rates= 0.0000) +pass 9 : -425.3206 (branch= 0.0003 subset rates= 0.0000) +pass 10: -425.3201 (branch= 0.0001 subset rates= 0.0004) +pass 11: -425.3201 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.3201 (branch= 0.0000 subset rates= 0.0000) +pass 13: -425.3200 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -425.3200 +Time used so far = 0 hours, 0 minutes and 6 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.86 1.54 1.15 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 9 branches were collapsed. + +>>>Completed Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< + +>>>Bootstrap rep 1 (of 1) Search rep 4 (of 5)<<< +Obtained starting tree 1 from Nexus +Starting with seed=2070757799 + +Initial ln Likelihood: -550.3246 +optimizing: starting branch lengths, subset rates... +pass 1:+ 102.933 (branch= 102.64 scale= 0.09 subset rates= 0.20) +pass 2:+ 5.507 (branch= 5.49 scale= 0.00 subset rates= 0.02) +pass 3:+ 2.290 (branch= 2.25 scale= 0.04 subset rates= 0.00) +pass 4:+ 0.292 (branch= 0.29 scale= 0.00 subset rates= 0.00) +pass 5:+ 0.071 (branch= 0.06 scale= 0.00 subset rates= 0.01) +pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -439.2316 +gen current_lnL precision last_tree_imp +0 -439.2316 0.010 0 +100 -433.6971 0.010 75 +200 -432.2075 0.010 188 +300 -429.7506 0.010 212 +400 -427.9705 0.010 391 +500 -427.8319 0.010 409 +600 -425.6450 0.010 594 +700 -425.6393 0.010 594 +800 -425.6316 0.010 594 +900 -425.6267 0.010 594 +1000 -425.6213 0.010 594 +1100 -425.6180 0.010 594 +1200 -425.6150 0.010 594 +1300 -425.6135 0.010 594 +1400 -425.6117 0.010 594 +1500 -425.6100 0.010 594 1600 -425.6084 0.010 594 1700 -425.6069 0.010 594 1800 -425.6062 0.010 594 @@ -19716,7 +19491,7 @@ pass 14: -425.3202 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.3202 -Time used so far = 0 hours, 0 minutes and 7 seconds +Time used so far = 0 hours, 0 minutes and 8 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -19823,7 +19598,7 @@ pass 13: -425.5486 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.5486 -Time used = 0 hours, 0 minutes and 8 seconds +Time used = 0 hours, 0 minutes and 9 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -20341,117 +20116,6 @@ 2300 -473.9850 0.010 593 2400 -473.9843 0.010 593 2500 -473.9843 0.010 593 -2600 -473.9840 0.010 593 -2700 -473.9838 0.010 593 -2800 -473.9838 0.010 593 -2900 -473.9835 0.010 593 -Reached termination condition! -last topological improvement at gen 593 -Improvement over last 500 gen = 0.00081 -Current score = -473.9835 -Performing final optimizations... -pass 1 : -473.9820 (branch= 0.0000 subset rates= 0.0015) -pass 2 : -473.9648 (branch= 0.0172 subset rates= 0.0000) -pass 3 : -473.9599 (branch= 0.0038 subset rates= 0.0010) -pass 4 : -473.9559 (branch= 0.0015 subset rates= 0.0025) -pass 5 : -473.9533 (branch= 0.0026 subset rates= 0.0000) -pass 6 : -473.9522 (branch= 0.0012 subset rates= 0.0000) -pass 7 : -473.9513 (branch= 0.0009 subset rates= 0.0000) -pass 8 : -473.9509 (branch= 0.0004 subset rates= 0.0000) -pass 9 : -473.9509 (branch= 0.0001 subset rates= 0.0000) -pass 10: -473.9508 (branch= 0.0001 subset rates= 0.0000) -pass 11: -473.9508 (branch= 0.0000 subset rates= 0.0000) -pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9508 (branch= 0.0000 subset rates= 0.0000) -pass 14: -473.9507 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -473.9507 -Time used so far = 0 hours, 0 minutes and 5 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 0.59 2.07 2.81 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. - ->>>Completed Search rep 3 (of 5)<<< - ->>>Search rep 4 (of 5)<<< -Obtained starting tree 1 from Nexus -MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 1.00 1.00 1.00 -Starting with seed=274781070 - -Initial ln Likelihood: -666.9404 -optimizing: starting branch lengths, subset rates... -pass 1:+ 166.009 (branch= 155.23 scale= 0.87 subset rates= 9.91) -pass 2:+ 16.814 (branch= 12.53 scale= 0.00 subset rates= 4.29) -pass 3:+ 7.072 (branch= 5.49 scale= 0.00 subset rates= 1.58) -pass 4:+ 1.900 (branch= 1.29 scale= 0.01 subset rates= 0.59) -pass 5:+ 0.210 (branch= 0.19 scale= 0.00 subset rates= 0.02) -pass 6:+ 0.043 (branch= 0.03 scale= 0.01 subset rates= 0.00) -pass 7:+ 0.018 (branch= 0.02 scale= 0.00 subset rates= 0.00) -pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8745 -gen current_lnL precision last_tree_imp -0 -474.8745 0.010 0 -100 -474.8391 0.010 0 -200 -474.7434 0.010 147 -300 -474.0572 0.010 266 -400 -474.0437 0.010 266 -500 -474.0285 0.010 266 -600 -474.0173 0.010 266 -700 -474.0063 0.010 266 -800 -474.0054 0.010 266 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -20577,9 +20241,120 @@ STARTING RUN Restarting from checkpoint... -Search rep 4 (of 5) generation 815, seed 2117739374, best lnL -474.005 +Search rep 3 (of 5) generation 2577, seed 350861161, best lnL -473.984 +gen current_lnL precision last_tree_imp +2577 -473.9841 0.010 593 +2600 -473.9840 0.010 593 +2700 -473.9838 0.010 593 +2800 -473.9838 0.010 593 +2900 -473.9835 0.010 593 +Reached termination condition! +last topological improvement at gen 593 +Improvement over last 500 gen = 0.00081 +Current score = -473.9835 +Performing final optimizations... +pass 1 : -473.9820 (branch= 0.0000 subset rates= 0.0015) +pass 2 : -473.9648 (branch= 0.0172 subset rates= 0.0000) +pass 3 : -473.9599 (branch= 0.0038 subset rates= 0.0010) +pass 4 : -473.9559 (branch= 0.0015 subset rates= 0.0025) +pass 5 : -473.9533 (branch= 0.0026 subset rates= 0.0000) +pass 6 : -473.9522 (branch= 0.0012 subset rates= 0.0000) +pass 7 : -473.9513 (branch= 0.0009 subset rates= 0.0000) +pass 8 : -473.9509 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -473.9509 (branch= 0.0001 subset rates= 0.0000) +pass 10: -473.9508 (branch= 0.0001 subset rates= 0.0000) +pass 11: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 13: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 14: -473.9507 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -473.9507 +Time used so far = 0 hours, 0 minutes and 6 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.59 2.07 2.81 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 8 branches were collapsed. + +>>>Completed Search rep 3 (of 5)<<< + +>>>Search rep 4 (of 5)<<< +Obtained starting tree 1 from Nexus +MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 1.00 1.00 1.00 +Starting with seed=274781070 + +Initial ln Likelihood: -666.9404 +optimizing: starting branch lengths, subset rates... +pass 1:+ 166.009 (branch= 155.23 scale= 0.87 subset rates= 9.91) +pass 2:+ 16.814 (branch= 12.53 scale= 0.00 subset rates= 4.29) +pass 3:+ 7.072 (branch= 5.49 scale= 0.00 subset rates= 1.58) +pass 4:+ 1.900 (branch= 1.29 scale= 0.01 subset rates= 0.59) +pass 5:+ 0.210 (branch= 0.19 scale= 0.00 subset rates= 0.02) +pass 6:+ 0.043 (branch= 0.03 scale= 0.01 subset rates= 0.00) +pass 7:+ 0.018 (branch= 0.02 scale= 0.00 subset rates= 0.00) +pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -474.8745 gen current_lnL precision last_tree_imp -815 -474.0046 0.010 266 +0 -474.8745 0.010 0 +100 -474.8391 0.010 0 +200 -474.7434 0.010 147 +300 -474.0572 0.010 266 +400 -474.0437 0.010 266 +500 -474.0285 0.010 266 +600 -474.0173 0.010 266 +700 -474.0063 0.010 266 +800 -474.0054 0.010 266 900 -473.9993 0.010 266 1000 -473.9988 0.010 266 1100 -473.9969 0.010 266 @@ -20628,7 +20403,7 @@ pass 13: -473.9483 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -473.9483 -Time used so far = 0 hours, 0 minutes and 7 seconds +Time used so far = 0 hours, 0 minutes and 8 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -20765,7 +20540,7 @@ pass 12: -473.9511 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -473.9511 -Time used = 0 hours, 0 minutes and 9 seconds +Time used = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -20907,8 +20682,8 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-9_arm64.deb'. -dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-9_all.deb'. dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-9_arm64.deb'. +dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-9_all.deb'. dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-9_arm64.deb'. dpkg-deb: building package 'garli' in '../garli_2.1-9_arm64.deb'. dpkg-genbuildinfo --build=binary -O../garli_2.1-9_arm64.buildinfo @@ -20918,12 +20693,14 @@ 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/2660829/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2660829/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/1169299 and its subdirectories -I: Current time: Wed Apr 8 01:55:13 -12 2026 -I: pbuilder-time-stamp: 1775656513 +I: removing directory /srv/workspace/pbuilder/2660829 and its subdirectories +I: Current time: Thu Mar 6 21:40:42 +14 2025 +I: pbuilder-time-stamp: 1741246842