Fri Dec 20 23:29:18 UTC 2024 I: starting to build garli/unstable/i386 on jenkins on '2024-12-20 23:28' Fri Dec 20 23:29:18 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_5/44276/console.log Fri Dec 20 23:29:18 UTC 2024 I: Downloading source for unstable/garli=2.1-9 --2024-12-20 23:29:18-- http://deb.debian.org/debian/pool/main/g/garli/garli_2.1-9.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2186 (2.1K) [text/prs.lines.tag] Saving to: ‘garli_2.1-9.dsc’ 0K .. 100% 324M=0s 2024-12-20 23:29:18 (324 MB/s) - ‘garli_2.1-9.dsc’ saved [2186/2186] Fri Dec 20 23:29:18 UTC 2024 I: garli_2.1-9.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: garli Binary: garli, garli-mpi, garli-examples Architecture: any all Version: 2.1-9 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/Ashod/garli Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/garli Vcs-Git: https://salsa.debian.org/med-team/garli.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libncl-dev, mpi-default-dev, ncl-tools, bc Package-List: garli deb science optional arch=any garli-examples deb science optional arch=all garli-mpi deb science optional arch=any Checksums-Sha1: a7a5cb81f92ed19672324b5aacf8c7da1f6a2df3 1248730 garli_2.1.orig.tar.gz 03357cb420644769d7123b89aeb933dca5f02fc6 5072 garli_2.1-9.debian.tar.xz Checksums-Sha256: 00aa31af5d8ecc2cb9bd276ce93b6580ae6cff93f4f5e1145d95d5fe6359e1b6 1248730 garli_2.1.orig.tar.gz 11ae86ea4dcf9b875b85761819eb466c627e32912073a5dc08c28f19cea8e0af 5072 garli_2.1-9.debian.tar.xz Files: 83d6720df816365182291306383d056c 1248730 garli_2.1.orig.tar.gz c01e4bc42638d26bb8ef30388b77a867 5072 garli_2.1-9.debian.tar.xz Dgit: 81831dac4c7f11278ba4d060cc3632f00bf4ccc2 debian archive/debian/2.1-9 https://git.dgit.debian.org/garli -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmdkfooUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdq2ghAAr/k4+RQEPAaE17wimNfH2ot8xnhD bex0rBkdzNEeP31Rzp48RuSw0ea6z7GQOIkfE81cFOmRbhx02AnKU0nW4ooeHMof Uc7FsLpf99CeMY4QOM0vgpeGhBRytUWTJOB5uigqJhic22WzOD1/8lFUwHVY9lKw U9bx2k/2+3p/A1fg9C4zowu0DQmIvmx5wRWxgyAqR/hk/Xj1GYfm0EbD8DxH5AC0 Ay+yxSjpC70C165ZKRz/2m8NVKHJY3QNaRy5NcVwAtvWMvrxUuwr6WpriAUWlkn8 mjGX3jjK7njNruWVx6mYZ4nvrnsR4kgjUOHjR+Y+AAjxocTRGPQL7HxljhJTOAad 8cO4Hgr+tE/NI5W7DoLrPmNvkgzmu8lxsF8HERpmYuNP70z9FHCETKR/rD76YWFh MztoI1i0J1fTt1W7ZcE86MkDl1E3I+JPFz2HnsIpbYya8C7LwKmVZHtwYTXvySEZ TubYmg6NCD0KsnZMFuxfjWfkCymOcRsp7zbls3Ezf9Zr4WgOeYU7n3vQIm9OL7YI a+bkzDPPl3yD4+ih/Lb791u+e7ZsD8B+9X3q1ybZDyP1oqtNUqeW2tmY1bK7pbXm DXJxZLRsOgoeJq49HkRtMmC/HZXVpDrD+90c6O8a5FwOexzPwF/bdar4X/l51Edp gOUJVVt2ALk7oC0= =ksP3 -----END PGP SIGNATURE----- Fri Dec 20 23:29:18 UTC 2024 I: Checking whether the package is not for us Fri Dec 20 23:29:18 UTC 2024 I: Starting 1st build on remote node ionos12-i386.debian.net. Fri Dec 20 23:29:18 UTC 2024 I: Preparing to do remote build '1' on ionos12-i386.debian.net. Fri Dec 20 23:38:16 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Dec 20 11:29:21 -12 2024 I: pbuilder-time-stamp: 1734737361 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [garli_2.1-9.dsc] I: copying [./garli_2.1.orig.tar.gz] I: copying [./garli_2.1-9.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Dec 19 20:14:02 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./garli_2.1-9.dsc: no acceptable signature found dpkg-source: info: extracting garli in garli-2.1 dpkg-source: info: unpacking garli_2.1.orig.tar.gz dpkg-source: info: unpacking garli_2.1-9.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/34980/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='35af8123dc9649f0b942a98b5036d8dc' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='34980' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.L6wO1cWn/pbuilderrc_L3KR --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.L6wO1cWn/b1 --logfile b1/build.log garli_2.1-9.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos12-i386 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/34980/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libncl-dev, mpi-default-dev, ncl-tools, bc dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19953 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libncl-dev; however: Package libncl-dev is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-dev; however: Package mpi-default-dev is not installed. pbuilder-satisfydepends-dummy depends on ncl-tools; however: Package ncl-tools is not installed. pbuilder-satisfydepends-dummy depends on bc; however: Package bc is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bc{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran-14{a} gfortran-14-i686-linux-gnu{a} groff-base{a} hwloc-nox{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libhwloc-dev{a} libhwloc15{a} libicu72{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmpich-dev{a} libmpich12{a} libncl-dev{a} libncl2{a} libnuma-dev{a} libnuma1{a} libpipeline1{a} libreadline8t64{a} libslurm42t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mpi-default-dev{a} mpich{a} ncl-tools{a} po-debconf{a} readline-common{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libhwloc-plugins libmail-sendmail-perl lynx wget 0 packages upgraded, 51 newly installed, 0 to remove and 0 not upgraded. Need to get 42.1 MB of archives. After unpacking 158 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-6 [69.4 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.22.5-3 [201 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-6 [1198 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.2-12 [95.9 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 autopoint all 0.22.5-3 [723 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-6 [173 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 bc i386 1.07.1-4 [105 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.22 [90.5 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-8 [517 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 25 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 gettext i386 0.22.5-3 [1631 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 debhelper all 13.22 [919 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14.2.0-11 [735 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 libgfortran-14-dev i386 14.2.0-11 [801 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 gfortran-14-i686-linux-gnu i386 14.2.0-11 [12.5 MB] Get: 36 http://deb.debian.org/debian unstable/main i386 gfortran-14 i386 14.2.0-11 [13.2 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 libhwloc15 i386 2.11.2-1 [177 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 hwloc-nox i386 2.11.2-1 [229 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 libnuma1 i386 2.0.18-1+b1 [23.9 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 libnuma-dev i386 2.0.18-1+b1 [38.8 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 libltdl7 i386 2.4.7-8 [395 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 libltdl-dev i386 2.4.7-8 [167 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 libhwloc-dev i386 2.11.2-1 [271 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 libmpich12 i386 4.2.1-4 [1519 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 libslurm42t64 i386 24.11.0-1 [753 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 mpich i386 4.2.1-4 [236 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 libmpich-dev i386 4.2.1-4 [2499 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 libncl2 i386 2.1.21+git20210811.b1213a7-6 [405 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 libncl-dev i386 2.1.21+git20210811.b1213a7-6 [642 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 mpi-default-dev i386 1.17 [3144 B] Get: 51 http://deb.debian.org/debian unstable/main i386 ncl-tools i386 2.1.21+git20210811.b1213a7-6 [199 kB] Fetched 42.1 MB in 1s (35.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19953 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3+b1_i386.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.22.5-3_i386.deb ... Unpacking gettext-base (0.22.5-3) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-6_i386.deb ... Unpacking groff-base (1.23.0-6) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40.2-12_i386.deb ... Unpacking bsdextrautils (2.40.2-12) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../09-libpipeline1_1.5.8-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.0-1_i386.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.22.5-3_all.deb ... Unpacking autopoint (0.22.5-3) ... Selecting previously unselected package libreadline8t64:i386. Preparing to unpack .../16-libreadline8t64_8.2-6_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-6) ... Selecting previously unselected package bc. Preparing to unpack .../17-bc_1.07.1-4_i386.deb ... Unpacking bc (1.07.1-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../18-libdebhelper-perl_13.22_all.deb ... Unpacking libdebhelper-perl (13.22) ... Selecting previously unselected package libtool. Preparing to unpack .../19-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../20-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../21-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../22-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:i386. Preparing to unpack .../24-libelf1t64_0.192-4_i386.deb ... Unpacking libelf1t64:i386 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.15-1+b1_i386.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../26-libicu72_72.1-5+b1_i386.deb ... Unpacking libicu72:i386 (72.1-5+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../27-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_i386.deb ... Unpacking libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.22.5-3_i386.deb ... Unpacking gettext (0.22.5-3) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. 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Setting up libncl-dev:i386 (2.1.21+git20210811.b1213a7-6) ... Setting up autotools-dev (20220109.1) ... Setting up libslurm42t64 (24.11.0-1) ... Setting up libhwloc15:i386 (2.11.2-1) ... Setting up autopoint (0.22.5-3) ... Setting up libltdl7:i386 (2.4.7-8) ... Setting up libgfortran5:i386 (14.2.0-11) ... Setting up autoconf (2.72-3) ... Setting up libnuma1:i386 (2.0.18-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up libmpich12:i386 (4.2.1-4) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:i386 (0.0.8-1+b2) ... Setting up readline-common (8.2-6) ... Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libgfortran-14-dev:i386 (14.2.0-11) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-3) ... Setting up libtool (2.4.7-8) ... Setting up hwloc-nox (2.11.2-1) ... Setting up ncl-tools (2.1.21+git20210811.b1213a7-6) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:i386 (2.0.18-1+b1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:i386 (2.4.7-8) ... Setting up gfortran-14-i686-linux-gnu (14.2.0-11) ... Setting up libreadline8t64:i386 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-6) ... Setting up libhwloc-dev:i386 (2.11.2-1) ... Setting up gfortran-14 (14.2.0-11) ... Setting up mpich (4.2.1-4) ... update-alternatives: using /usr/bin/mpicc.mpich to provide /usr/bin/mpicc (mpi) in auto mode update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up bc (1.07.1-4) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libmpich-dev:i386 (4.2.1-4) ... update-alternatives: using /usr/include/i386-linux-gnu/mpich to provide /usr/include/i386-linux-gnu/mpi (mpi-i386-linux-gnu) in auto mode Setting up mpi-default-dev (1.17) ... Setting up debhelper (13.22) ... Processing triggers for libc-bin (2.40-4) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... 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 dpkg-buildpackage: info: source package garli dpkg-buildpackage: info: source version 2.1-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf aclocal: warning: couldn't open directory 'config/m4': No such file or directory configure.ac:8: warning: The macro 'AC_CONFIG_HEADER' is obsolete. configure.ac:8: You should run autoupdate. ./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from... configure.ac:8: the top level configure.ac:47: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.ac:47: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.ac:47: the top level configure.ac:64: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:64: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:64: the top level configure.ac:68: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:68: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:68: the top level configure.ac:80: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:80: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:80: the top level configure.ac:92: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:92: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:92: the top level configure.ac:104: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:104: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:104: the top level configure.ac:113: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:113: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:113: the top level configure.ac:122: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:122: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:122: the top level configure.ac:131: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:131: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:131: the top level configure.ac:140: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:140: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:140: the top level configure.ac:224: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.ac:224: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... config/acx_mpi.m4:74: ACX_MPI is expanded from... configure.ac:224: the top level configure.ac:249: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:249: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:249: the top level configure.ac:280: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:280: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:280: the top level configure.ac:339: warning: The macro 'AC_TRY_LINK' is obsolete. configure.ac:339: You should run autoupdate. ./lib/autoconf/general.m4:2918: AC_TRY_LINK is expanded from... configure.ac:339: the top level configure.ac:349: warning: The macro 'AC_TRY_LINK' is obsolete. configure.ac:349: You should run autoupdate. ./lib/autoconf/general.m4:2918: AC_TRY_LINK is expanded from... configure.ac:349: the top level configure.ac:355: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ./lib/autoconf/lang.m4:199: AC_LANG_CONFTEST is expanded from... ./lib/autoconf/general.m4:2821: _AC_COMPILE_IFELSE is expanded from... ./lib/autoconf/general.m4:2837: AC_COMPILE_IFELSE is expanded from... configure.ac:355: the top level configure.ac:25: warning: support for distribution archives compressed with legacy program 'compress' is deprecated. configure.ac:25: It will be removed in Automake 2.0 debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/garli-2.1' # First build MPI version of Garli dh_auto_configure -- --with-ncl=/usr --enable-mpi ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-ncl=/usr --enable-mpi checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking target system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '1111' is supported by ustar format... yes checking whether GID '1111' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking for ranlib... ranlib checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for float.h... yes checking for malloc.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for sys/time.h... yes checking for _Bool... yes checking for stdbool.h that conforms to C99 or later... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for error_at_line... yes checking for GNU libc compatible malloc... yes checking for working strtod... yes checking for floor... no checking for memmove... yes checking for memset... yes checking for pow... no checking for sqrt... no checking for strchr... yes checking for strdup... yes checking for strtol... yes configure: *** NOTE: compiling MPI run distributing version checking for mpic++... mpic++ checking for MPI_Init... yes checking for mpi.h... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating tests/Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build make -j11 make[2]: Entering directory '/build/reproducible-path/garli-2.1' make all-recursive make[3]: Entering directory '/build/reproducible-path/garli-2.1' Making all in src make[4]: Entering directory '/build/reproducible-path/garli-2.1/src' mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o adaptation.o adaptation.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o bipartition.o bipartition.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o condlike.o condlike.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configoptions.o configoptions.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configreader.o configreader.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o datamatr.o datamatr.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o funcs.o funcs.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlimain.o garlimain.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlireader.o garlireader.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o individual.o individual.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp garlimain.cpp:434:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ garlimain.cpp:434:76: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)': linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1322 | register int nsq = n * n; | ^~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, 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 configoptions.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, from funcs.cpp:30: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from bipartition.cpp:20: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from bipartition.h:23, from bipartition.cpp:19: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from adaptation.cpp:18: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from garlimain.cpp:46: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/iomanip:42, from individual.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from configreader.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from model.cpp:17: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from tree.h:35, from optimization.cpp:19: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from tree.h:24: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from optimization.cpp:21: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from population.cpp:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from population.cpp:49: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from tree.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;idlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6845:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6845 | fread(&dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6849:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6849 | fread(&dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6855:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6855 | fread(&dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6858:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6858 | fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6862:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6862 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6865:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6865 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6868:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6868 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6872:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6872 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6878:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6878 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6881 | fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from translatetable.h:24, from translatetable.cpp:19: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, from mpitrick.cpp:27: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from mpitrick.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from bipartition.h:23, from bipartition.cpp:19: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': configoptions.cpp:337:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 337 | sprintf(modName, "model%d", modelNum); | ^~ configoptions.cpp:337:34: note: directive argument in the range [0, 2147483647] 337 | sprintf(modName, "model%d", modelNum); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)' at configoptions.cpp:337:10: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, from individual.cpp:28: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/iomanip:42, from individual.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, from adaptation.cpp:25: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from adaptation.cpp:18: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, from funcs.cpp:30: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from configreader.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from garlimain.cpp:46: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from tree.h:24: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from population.cpp:45: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from population.cpp:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from model.cpp:26: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from model.cpp:17: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from optimization.cpp:21: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from population.cpp:49: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from tree.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;idlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6845:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6845 | fread(&dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6849:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6849 | fread(&dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6855:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6855 | fread(&dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6858:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6858 | fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6862:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6862 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6865:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6865 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6868:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6868 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6872:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6872 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6878:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6878 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6881 | fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from translatetable.h:24, from translatetable.cpp:19: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': population.cpp:3066:50: warning: '%d' directive writing between 1 and 9 bytes into a region of size 8 [-Wformat-overflow=] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~ population.cpp:3066:47: note: directive argument in the range [1, 536870911] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 13 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from datamatr.h:23, from sequencedata.h:27, from sequencedata.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from treenode.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from datamatr.h:23, from sequencedata.h:27, from tree.cpp:31: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-z,relro -Wl,-z,now -L/usr/lib -o Garli adaptation.o bipartition.o condlike.o configoptions.o configreader.o datamatr.o funcs.o garlimain.o garlireader.o individual.o linalg.o model.o optimization.o population.o rng.o sequencedata.o set.o translatetable.o tree.o treenode.o mpitrick.o -lncl -lncl make[3]: Leaving directory '/build/reproducible-path/garli-2.1/src' Making all in tests make[3]: Entering directory '/build/reproducible-path/garli-2.1/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/garli-2.1/tests' make[3]: Entering directory '/build/reproducible-path/garli-2.1' make[3]: Leaving directory '/build/reproducible-path/garli-2.1' make[2]: Leaving directory '/build/reproducible-path/garli-2.1' make[1]: Leaving directory '/build/reproducible-path/garli-2.1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/garli-2.1' cp -a tests tests.bak # get (mostly!) reproducible test results and avoid failures as described in bug #907905 find tests -name "*.conf" -exec sed -i~ 's/randseed *= *-1/randseed = 1\nbootstrapseed = 42/' \{\} \; dh_auto_test make -j11 check "TESTSUITEFLAGS=-j11 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/garli-2.1' Making check in src make[3]: Entering directory '/build/reproducible-path/garli-2.1/src' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/garli-2.1/src' Making check in tests make[3]: Entering directory '/build/reproducible-path/garli-2.1/tests' make check-local make[4]: Entering directory '/build/reproducible-path/garli-2.1/tests' ./runtests.sh . ../src/Garli /usr/bin/NEXUSvalidator Linking to data .... data folder already exists ************************** Running internal tests ... ************************** Running internal test ./internal/a.G3.conf Running internal test ./internal/a.G3.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./internal/a.G3.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/moore.matK90-120.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 86 sequences. 2 constant characters. 6 parsimony-informative characters. 2 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### 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 >= 5 MB good approx 4 MB to 2 MB low approx 2 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. 5.8 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/moore.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0088 0.0022 0.0131 0.3020 0.0985 0.0088 0.0109 0.0284 0.0810 0.0503 0.1794 0.0022 0.0044 0.1575 0.0109 0.0109 0.0044 0.0044 0.0022 0.0197 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0500 Substitution rate categories under this model: rate proportion 0.0000 0.0500 0.0603 0.3167 0.4894 0.3167 2.4503 0.3167 Starting with seed=1 WARNING: Polytomies found in start tree. These were arbitrarily resolved. Initial ln Likelihood: -534.6163 optimizing: starting branch lengths, alpha shape, prop. invar... pass 1:+ 97.093 (branch= 90.61 scale= 6.48 alpha= 0.00 pinv= 0.00) pass 2:+ 26.504 (branch= 20.56 scale= 5.94 alpha= 0.00 pinv= 0.00) pass 3:+ 7.183 (branch= 6.27 scale= 0.91 alpha= 0.00 pinv= 0.00) pass 4:+ 2.513 (branch= 1.73 scale= 0.78 alpha= 0.00 pinv= 0.00) pass 5:+ 1.030 (branch= 0.48 scale= 0.55 alpha= 0.00 pinv= 0.00) pass 6:+ 0.375 (branch= 0.37 scale= 0.00 alpha= 0.00 pinv= 0.00) lnL after optimization: -399.9190 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/a.G4.conf Running internal test ./internal/a.G4.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./internal/a.G4.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/moore.matK90-120.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 86 sequences. 2 constant characters. 6 parsimony-informative characters. 2 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### 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 >= 6 MB good approx 5 MB to 4 MB low approx 3 MB to 2 MB very low approx 2 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. 7.7 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/moore.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0088 0.0022 0.0131 0.3020 0.0985 0.0088 0.0109 0.0284 0.0810 0.0503 0.1794 0.0022 0.0044 0.1575 0.0109 0.0109 0.0044 0.0044 0.0022 0.0197 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0500 Substitution rate categories under this model: rate proportion 0.0000 0.0500 0.0334 0.2375 0.2519 0.2375 0.8203 0.2375 2.8944 0.2375 Starting with seed=1 WARNING: Polytomies found in start tree. These were arbitrarily resolved. Initial ln Likelihood: -532.4673 optimizing: starting branch lengths, alpha shape, prop. invar... pass 1:+ 92.949 (branch= 88.74 scale= 4.20 alpha= 0.00 pinv= 0.00) pass 2:+ 25.801 (branch= 20.07 scale= 5.73 alpha= 0.00 pinv= 0.00) pass 3:+ 9.142 (branch= 7.26 scale= 1.88 alpha= 0.00 pinv= 0.00) pass 4:+ 3.445 (branch= 2.67 scale= 0.78 alpha= 0.00 pinv= 0.00) pass 5:+ 0.802 (branch= 0.25 scale= 0.55 alpha= 0.00 pinv= 0.00) pass 6:+ 0.294 (branch= 0.29 scale= 0.00 alpha= 0.00 pinv= 0.00) lnL after optimization: -400.0333 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/a.conf Running internal test ./internal/a.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./internal/a.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/moore.matK90-120.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 86 sequences. 2 constant characters. 6 parsimony-informative characters. 2 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### 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 >= 2 MB good approx 2 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. 2.0 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/moore.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0088 0.0022 0.0131 0.3020 0.0985 0.0088 0.0109 0.0284 0.0810 0.0503 0.1794 0.0022 0.0044 0.1575 0.0109 0.0109 0.0044 0.0044 0.0022 0.0197 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 WARNING: Polytomies found in start tree. These were arbitrarily resolved. NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -567.2416 optimizing: starting branch lengths... pass 1:+ 135.572 (branch= 118.31 scale= 17.26) pass 2:+ 21.497 (branch= 16.34 scale= 5.15) pass 3:+ 6.821 (branch= 6.09 scale= 0.73) pass 4:+ 2.066 (branch= 1.47 scale= 0.59) pass 5:+ 1.595 (branch= 1.59 scale= 0.00) pass 6:+ 1.322 (branch= 0.81 scale= 0.51) pass 7:+ 0.354 (branch= 0.35 scale= 0.00) lnL after optimization: -398.0145 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/c.M3x2.conf Running internal test ./internal/c.M3x2.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./internal/c.M3x2.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x30.stop.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Codon data Warning: stop codon TAA found at codon site 11 (nuc site 31) in taxon MorNa6. Treating as missing data because ignorestopcodons = 1 is set in configuration file. Warning: stop codon TAA found at codon site 11 (nuc site 31) in taxon ClownNa6. Treating as missing data because ignorestopcodons = 1 is set in configuration file. Base usage at codon positions: A C G T pos 1 0.27184 0.35922 0.21359 0.15534 pos 2 0.32039 0.20388 0.07767 0.39806 pos 3 0.12621 0.37864 0.26214 0.23301 all pos 0.23948 0.31392 0.18447 0.26214 Summary of data: 11 sequences. 0 constant characters. 9 parsimony-informative characters. 1 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 10 total characters (11 before removing empty columns). 10 unique patterns in compressed data matrix. ################################################### 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. 1.3 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### STARTING RUN starting internal tests... MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0112 0.0337 0.0233 0.0207 0.0071 0.0214 0.0148 0.0132 0.0027 0.0082 0.0057 0.0050 0.0139 0.0418 0.0290 0.0258 0.0148 0.0445 0.0308 0.0274 0.0094 0.0283 0.0196 0.0174 0.0036 0.0108 0.0075 0.0066 0.0184 0.0553 0.0383 0.0340 0.0088 0.0265 0.0183 0.0163 0.0056 0.0168 0.0117 0.0104 0.0021 0.0064 0.0044 0.0039 0.0110 0.0329 0.0228 0.0202 0.0192 0.0118 0.0041 0.0122 0.0085 0.0075 0.0047 0.0032 0.0029 0.0080 0.0239 0.0166 0.0147 Rate Heterogeneity Model: 2 nonsynonymous rate categories, rate and proportion of each estimated (this is effectively the M3 model of PAML) dN/dS Proportion 0.2500 0.5000 0.5000 0.5000 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 4.421 lnL Optimizing branchlengths... improved 0.690 lnL 7 8 9 10 11 Initial ln Likelihood: -215.5693 optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters... pass 1:+ 6.143 (branch= 0.00 scale= 0.00 omega= 0.01 rel rates= 6.13) pass 2:+ 0.420 (branch= 0.00 scale= 0.00 omega= 0.01 rel rates= 0.41) lnL after optimization: -209.0069 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/c.conf Running internal test ./internal/c.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./internal/c.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Codon data Base usage at codon positions: A C G T pos 1 0.27723 0.36634 0.21782 0.13861 pos 2 0.30693 0.20792 0.07921 0.40594 pos 3 0.10891 0.38614 0.26733 0.23762 all pos 0.23102 0.32013 0.18812 0.26073 Summary of data: 11 sequences. 0 constant characters. 9 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### STARTING RUN starting internal tests... MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 61 (codon data, standard code) One estimated dN/dS ratio (aka omega) = 0.250000 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0094 0.0334 0.0231 0.0206 0.0064 0.0226 0.0157 0.0139 0.0024 0.0086 0.0060 0.0053 0.0125 0.0442 0.0306 0.0272 0.0125 0.0442 0.0306 0.0272 0.0084 0.0299 0.0207 0.0184 0.0032 0.0114 0.0079 0.0070 0.0165 0.0584 0.0405 0.0360 0.0074 0.0263 0.0182 0.0162 0.0050 0.0178 0.0123 0.0110 0.0019 0.0068 0.0047 0.0042 0.0098 0.0347 0.0241 0.0214 0.0167 0.0103 0.0032 0.0113 0.0078 0.0070 0.0043 0.0030 0.0027 0.0062 0.0221 0.0153 0.0136 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.001 lnL Optimizing branchlengths... improved 0.000 lnL 7 8 9 10 11 Initial ln Likelihood: -225.6424 optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters... pass 1:+ 10.932 (branch= 2.26 scale= 0.50 omega= 0.00 rel rates= 8.17) pass 2:+ 0.926 (branch= 0.64 scale= 0.00 omega= 0.28 rel rates= 0.00) pass 3:+ 0.732 (branch= 0.04 scale= 0.68 omega= 0.01 rel rates= 0.00) pass 4:+ 0.015 (branch= 0.00 scale= 0.00 omega= 0.01 rel rates= 0.00) lnL after optimization: -213.0373 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/n.G3.conf Running internal test ./internal/n.G3.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./internal/n.G3.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/moore.matK90-120.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 86 sequences. 10 constant characters. 13 parsimony-informative characters. 7 uninformative variable characters. 30 total characters. 24 unique patterns in compressed data matrix. ################################################### 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 >= 2 MB good approx 2 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. 2.9 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN starting internal tests... MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.4638 0.0976 0.2304 0.2082 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0833 Substitution rate categories under this model: rate proportion 0.0000 0.0833 0.0603 0.3056 0.4894 0.3056 2.4503 0.3056 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 Optimizing parameters... improved 2.070 lnL Optimizing branchlengths... improved 1.544 lnL 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 Initial ln Likelihood: -351.3160 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 11.635 (branch= 3.88 scale= 0.50 alpha= 0.97 freqs= 0.05 rel rates= 6.23 pinv= 0.01) pass 2:+ 1.385 (branch= 0.93 scale= 0.41 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.01) pass 3:+ 0.338 (branch= 0.30 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.01) lnL after optimization: -337.9573 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/n.G4.conf Running internal test ./internal/n.G4.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./internal/n.G4.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/moore.matK90-120.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 86 sequences. 10 constant characters. 13 parsimony-informative characters. 7 uninformative variable characters. 30 total characters. 24 unique patterns in compressed data matrix. ################################################### 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 >= 4 MB good approx 3 MB to 2 MB low approx 2 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. 3.8 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN starting internal tests... MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.4638 0.0976 0.2304 0.2082 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0833 Substitution rate categories under this model: rate proportion 0.0000 0.0833 0.0334 0.2292 0.2519 0.2292 0.8203 0.2292 2.8944 0.2292 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 Optimizing parameters... improved 2.099 lnL Optimizing branchlengths... improved 1.492 lnL 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 Initial ln Likelihood: -363.1701 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 13.147 (branch= 2.38 scale= 2.97 alpha= 0.67 freqs= 1.24 rel rates= 5.88 pinv= 0.01) pass 2:+ 2.663 (branch= 2.63 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.00) pass 3:+ 0.035 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.00) lnL after optimization: -347.3249 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/n.conf Running internal test ./internal/n.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./internal/n.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/moore.matK90-120.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 86 sequences. 10 constant characters. 13 parsimony-informative characters. 7 uninformative variable characters. 30 total characters. 24 unique patterns in compressed data matrix. ################################################### 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. 1.0 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN starting internal tests... MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 1 rate Equilibrium State Frequencies: estimated (ACGT) 0.4638 0.0976 0.2304 0.2082 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 2.038 lnL 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 Initial ln Likelihood: -371.0442 optimizing: starting branch lengths, eq freqs... pass 1:+ 3.897 (branch= 2.20 scale= 0.00 freqs= 1.70) pass 2:+ 0.641 (branch= 0.60 scale= 0.00 freqs= 0.04) pass 3:+ 0.073 (branch= 0.03 scale= 0.00 freqs= 0.04) lnL after optimization: -366.4339 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.3diff.conf Running internal test ./internal/p.3diff.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./internal/p.3diff.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.byPos.11x2178.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful Reading SETS block...storing read block: SETS successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #1 ("1stpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 4 Summary of data: 11 sequences. 441 constant characters. 171 parsimony-informative characters. 113 uninformative variable characters. 725 total characters. 237 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #2 ("2ndpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 5 Summary of data: 11 sequences. 527 constant characters. 90 parsimony-informative characters. 108 uninformative variable characters. 725 total characters. 158 unique patterns in compressed data matrix. GARLI data subset 3 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #3 ("3rdpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 6 Summary of data: 11 sequences. 102 constant characters. 507 parsimony-informative characters. 116 uninformative variable characters. 725 total characters. 548 unique patterns in compressed data matrix. ################################################### 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 >= 11 MB good approx 10 MB to 9 MB low approx 8 MB to 5 MB very low approx 4 MB to 4 MB the minimum required availablememory is 4 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 16.0 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### STARTING RUN starting internal tests... MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3150 0.1749 0.3006 0.2095 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 Substitution rate categories under this model: rate proportion 0.0334 0.2500 0.2519 0.2500 0.8203 0.2500 2.8944 0.2500 Model 2 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) AC = 4.000, AG = 4.000, AT = 1.000, CG = 4.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2706 0.1568 0.1630 0.4096 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 Substitution rate categories under this model: rate proportion 0.0334 0.2500 0.2519 0.2500 0.8203 0.2500 2.8944 0.2500 Model 3 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1462 0.3614 0.2906 0.2018 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0352 Substitution rate categories under this model: rate proportion 0.0000 0.0352 0.0334 0.2412 0.2519 0.2412 0.8203 0.2412 2.8944 0.2412 Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 168.526 lnL Optimizing branchlengths... improved 66.084 lnL 7 8 9 10 11 Initial ln Likelihood: -13699.7841 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates... pass 1:+ 209.568 (branch= 7.95 scale= 0.00 alpha= 35.56 freqs= 28.70 rel rates= 62.31 pinv= 0.00 subset rates= 75.04) pass 2:+ 77.744 (branch= 2.27 scale= 0.00 alpha= 4.14 freqs= 11.78 rel rates= 3.62 pinv= 0.00 subset rates= 55.94) pass 3:+ 48.023 (branch= 7.13 scale= 0.72 alpha= 2.17 freqs= 1.08 rel rates= 1.34 pinv= 0.98 subset rates= 34.60) pass 4:+ 16.656 (branch= 0.00 scale= 0.55 alpha= 1.38 freqs= 1.19 rel rates= 1.51 pinv= 0.01 subset rates= 12.02) pass 5:+ 6.312 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.10 rel rates= 1.34 pinv= 0.01 subset rates= 4.85) pass 6:+ 0.120 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.09 rel rates= 0.01 pinv= 0.01 subset rates= 0.00) lnL after optimization: -13341.3609 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mk.conf Running internal test ./internal/p.mk.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./internal/p.mk.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 NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk 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 Mk 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 Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -609.1934 optimizing: starting branch lengths... pass 1:+ 125.912 (branch= 124.97 scale= 0.94) pass 2:+ 7.205 (branch= 7.20 scale= 0.00) pass 3:+ 1.518 (branch= 1.48 scale= 0.03) pass 4:+ 0.225 (branch= 0.22 scale= 0.00) pass 5:+ 0.014 (branch= 0.01 scale= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -474.3188 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mk.ssr.conf Running internal test ./internal/p.mk.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./internal/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 NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk 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 Mk 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 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=1 Initial ln Likelihood: -609.1934 optimizing: starting branch lengths, subset rates... pass 1:+ 130.207 (branch= 124.97 scale= 0.94 subset rates= 4.29) pass 2:+ 9.056 (branch= 8.14 scale= 0.00 subset rates= 0.91) pass 3:+ 1.801 (branch= 1.66 scale= 0.02 subset rates= 0.12) pass 4:+ 0.302 (branch= 0.30 scale= 0.00 subset rates= 0.00) pass 5:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -467.8159 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mkO.conf Running internal test ./internal/p.mkO.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./internal/p.mkO.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, modeled as Standard ordered k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... 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 Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -641.9257 optimizing: starting branch lengths... pass 1:+ 137.411 (branch= 136.58 scale= 0.83) pass 2:+ 7.774 (branch= 7.77 scale= 0.00) pass 3:+ 1.542 (branch= 1.52 scale= 0.02) pass 4:+ 0.091 (branch= 0.09 scale= 0.00) pass 5:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -495.1076 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mkO.ssr.conf Running internal test ./internal/p.mkO.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./internal/p.mkO.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, modeled as Standard ordered k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... 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=1 Initial ln Likelihood: -641.9257 optimizing: starting branch lengths, subset rates... pass 1:+ 147.096 (branch= 136.58 scale= 0.83 subset rates= 9.68) pass 2:+ 12.451 (branch= 8.46 scale= 0.00 subset rates= 3.99) pass 3:+ 3.549 (branch= 2.32 scale= 0.03 subset rates= 1.20) pass 4:+ 0.759 (branch= 0.51 scale= 0.00 subset rates= 0.25) pass 5:+ 0.120 (branch= 0.11 scale= 0.00 subset rates= 0.01) pass 6:+ 0.011 (branch= 0.01 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -477.9403 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mkv.conf Running internal test ./internal/p.mkv.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./internal/p.mkv.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, variable only, modeled as Standard k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) 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 Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -605.5989 optimizing: starting branch lengths... pass 1:+ 124.584 (branch= 123.99 scale= 0.59) pass 2:+ 6.980 (branch= 6.98 scale= 0.00) pass 3:+ 1.324 (branch= 1.31 scale= 0.02) pass 4:+ 0.161 (branch= 0.16 scale= 0.00) pass 5:+ 0.013 (branch= 0.01 scale= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -472.5370 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mkv.ssr.conf Running internal test ./internal/p.mkv.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./internal/p.mkv.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, variable only, modeled as Standard k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) 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: 1.00 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -605.5989 optimizing: starting branch lengths, subset rates... pass 1:+ 129.563 (branch= 123.99 scale= 0.59 subset rates= 4.98) pass 2:+ 9.277 (branch= 7.97 scale= 0.00 subset rates= 1.31) pass 3:+ 1.737 (branch= 1.57 scale= 0.00 subset rates= 0.16) pass 4:+ 0.310 (branch= 0.31 scale= 0.00 subset rates= 0.00) pass 5:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -464.7121 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mkvO.conf Running internal test ./internal/p.mkvO.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./internal/p.mkvO.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, variable only, modeled as Standard ordered k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... 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 Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -637.9212 optimizing: starting branch lengths... pass 1:+ 134.883 (branch= 134.40 scale= 0.48) pass 2:+ 7.290 (branch= 7.29 scale= 0.00) pass 3:+ 1.758 (branch= 1.73 scale= 0.03) pass 4:+ 0.187 (branch= 0.19 scale= 0.00) pass 5:+ 0.011 (branch= 0.01 scale= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -493.7915 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mkvO.ssr.conf Running internal test ./internal/p.mkvO.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./internal/p.mkvO.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, variable only, modeled as Standard ordered k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... 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=1 Initial ln Likelihood: -637.9212 optimizing: starting branch lengths, subset rates... pass 1:+ 144.867 (branch= 134.40 scale= 0.48 subset rates= 9.98) pass 2:+ 12.967 (branch= 8.30 scale= 0.00 subset rates= 4.67) pass 3:+ 3.847 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.162 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.156 (branch= 0.12 scale= 0.00 subset rates= 0.03) pass 6:+ 0.044 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 7:+ 0.015 (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: -474.8631 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** ************************** Running scoring tests ... ************************** Running scoring test ./scoring/a.G3.conf Running scoring test ./scoring/a.G3.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./scoring/a.G3.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x2178.AA.nex ... Reading TAXA block...storing read block: TAXA successful Reading CHARACTERS block...storing read block: CHARACTERS found protein data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful Reading CODONS block...storing read block: CODONS successful Reading MESQUITECHARMODELS block...storing read block: MESQUITECHARMODELS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Protein translation of Character Matrix") Data read as Amino acid data, modeled as Amino acid data Found wtset "equal" with data, applying... Summary of data: 11 sequences. 389 constant characters. 190 parsimony-informative characters. 147 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 726 total characters (727 before removing empty columns). 343 unique patterns in compressed data matrix. ################################################### 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 >= 13 MB good approx 12 MB to 9 MB low approx 8 MB to 5 MB very low approx 4 MB to 2 MB the minimum required availablememory is 2 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 5 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 18.0 MB of memory ####################################################### Found outgroup specification: 1 2 ####################################################### Loading starting model and/or tree from file data/a.G3.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus Obtained starting or fixed model parameter values from configuration file: MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: WAG Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0500 0.0252 0.0458 0.0579 0.0750 0.0561 0.0078 0.0882 0.0489 0.1128 0.0438 0.0500 0.0296 0.0252 0.0373 0.0552 0.0444 0.0906 0.0217 0.0346 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.4368 Substitution rate categories under this model: rate proportion 0.0437 0.3333 0.4372 0.3333 2.5190 0.3333 Starting with seed=1 Initial ln Likelihood: -6242.8631 optimizing: starting branch lengths, alpha shape... pass 1:+ 0.000 (branch= 0.00 scale= 0.00 alpha= 0.00) lnL after optimization: -6242.8629 Current score = -6242.8629 Performing final optimizations... pass 1 : -6242.8629 (branch= 0.0000 alpha= 0.0000) pass 2 : -6242.8595 (branch= 0.0034 alpha= 0.0000) pass 3 : -6242.8595 (branch= 0.0000 alpha= 0.0000) pass 4 : -6242.8595 (branch= 0.0000 alpha= 0.0000) pass 5 : -6242.8591 (branch= 0.0004 alpha= 0.0000) pass 6 : -6242.8586 (branch= 0.0005 alpha= 0.0000) pass 7 : -6242.8585 (branch= 0.0001 alpha= 0.0000) pass 8 : -6242.8583 (branch= 0.0002 alpha= 0.0000) pass 9 : -6242.8582 (branch= 0.0001 alpha= 0.0000) pass 10: -6242.8581 (branch= 0.0001 alpha= 0.0000) pass 11: -6242.8580 (branch= 0.0000 alpha= 0.0000) pass 12: -6242.8580 (branch= 0.0000 alpha= 0.0000) pass 13: -6242.8580 (branch= 0.0000 alpha= 0.0000) Looking for minimum length branches... Final score = -6242.8580 Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -6242.8580 Parameter estimates: alpha rep 1: 0.436 Treelengths: TL rep 1: 1.345 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.a.G3.best.all.tre ***********TEST************** ***Score is 6242.85802 ***Expected is 6242.85802 ***SCORE DIFFERENCE IS 0 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/a.G3.conf *** Running scoring test ./scoring/a.G4.conf Running scoring test ./scoring/a.G4.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./scoring/a.G4.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x2178.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data Some sites treated as missing data for taxon SterNa6 due to ambiguity in translation. Aminoacids coded as missing for that taxon: 708 Summary of data: 11 sequences. 389 constant characters. 190 parsimony-informative characters. 147 uninformative variable characters. 726 total characters. 343 unique patterns in compressed data matrix. ################################################### 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 >= 17 MB good approx 16 MB to 13 MB low approx 12 MB to 6 MB very low approx 5 MB to 3 MB the minimum required availablememory is 3 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 6 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 23.9 MB of memory ####################################################### Found outgroup specification: 1-5 ####################################################### Loading starting model and/or tree from file data/a.G4.start Reading TREES block...storing read block: TREES successful Reading GARLI block...storing read block: GARLI successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus Obtained starting or fixed model parameter values from Nexus: MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: values specified by user (fixed) Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0500 0.0252 0.0458 0.0579 0.0750 0.0561 0.0078 0.0882 0.0489 0.1128 0.0438 0.0500 0.0296 0.0252 0.0373 0.0552 0.0444 0.0906 0.0217 0.0346 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.4616 Substitution rate categories under this model: rate proportion 0.0265 0.2500 0.2261 0.2500 0.7902 0.2500 2.9572 0.2500 Starting with seed=1 Initial ln Likelihood: -6249.1664 optimizing: starting branch lengths, alpha shape... pass 1:+ 1.482 (branch= 0.00 scale= 1.47 alpha= 0.01) pass 2:+ 0.010 (branch= 0.00 scale= 0.00 alpha= 0.01) lnL after optimization: -6247.6743 Current score = -6247.6743 Performing final optimizations... pass 1 : -6247.0539 (branch= 0.2066 alpha= 0.4138) pass 2 : -6247.0347 (branch= 0.0192 alpha= 0.0000) pass 3 : -6247.0279 (branch= 0.0068 alpha= 0.0000) pass 4 : -6247.0255 (branch= 0.0023 alpha= 0.0000) pass 5 : -6247.0234 (branch= 0.0022 alpha= 0.0000) pass 6 : -6247.0228 (branch= 0.0005 alpha= 0.0000) pass 7 : -6247.0226 (branch= 0.0002 alpha= 0.0000) pass 8 : -6247.0223 (branch= 0.0002 alpha= 0.0000) pass 9 : -6247.0222 (branch= 0.0001 alpha= 0.0000) pass 10: -6247.0222 (branch= 0.0000 alpha= 0.0000) Looking for minimum length branches... Final score = -6247.0222 Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -6247.0222 Parameter estimates: alpha rep 1: 0.423 Treelengths: TL rep 1: 1.467 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.a.G4.best.all.tre ***********TEST************** ***Score is 6247.02222 ***Expected is 6247.02222 ***SCORE DIFFERENCE IS 0 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/a.G4.conf *** Running scoring test ./scoring/a.conf Running scoring test ./scoring/a.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./scoring/a.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x2178.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data Some sites treated as missing data for taxon SterNa6 due to ambiguity in translation. Aminoacids coded as missing for that taxon: 708 Summary of data: 11 sequences. 389 constant characters. 190 parsimony-informative characters. 147 uninformative variable characters. 726 total characters. 343 unique patterns in compressed data matrix. ################################################### 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 >= 4 MB good approx 3 MB to 3 MB low approx 2 MB to 2 MB very low approx 1 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 2 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 6.1 MB of memory ####################################################### Found outgroup specification: 1 ####################################################### Loading starting model and/or tree from file data/a.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: WAG Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0500 0.0252 0.0458 0.0579 0.0750 0.0561 0.0078 0.0882 0.0489 0.1128 0.0438 0.0500 0.0296 0.0252 0.0373 0.0552 0.0444 0.0906 0.0217 0.0346 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -6434.5146 optimizing: starting branch lengths... pass 1:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -6434.5146 Current score = -6434.5146 Performing final optimizations... pass 1 : -6434.5146 (branch= 0.0000) pass 2 : -6434.5101 (branch= 0.0045) pass 3 : -6434.5101 (branch= 0.0000) pass 4 : -6434.5101 (branch= 0.0000) pass 5 : -6434.5101 (branch= 0.0000) pass 6 : -6434.5092 (branch= 0.0009) pass 7 : -6434.5092 (branch= 0.0000) pass 8 : -6434.5092 (branch= 0.0000) pass 9 : -6434.5092 (branch= 0.0000) pass 10: -6434.5092 (branch= 0.0000) pass 11: -6434.5092 (branch= 0.0000) Looking for minimum length branches... Final score = -6434.5092 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -6434.5092 Parameter estimates: Model contains no estimated parameters Treelengths: TL rep 1: 1.143 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.a.best.all.tre ***********TEST************** ***Score is 6434.50916 ***Expected is 6434.50916 ***SCORE DIFFERENCE IS 0 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/a.conf *** Running scoring test ./scoring/c.M3x2.conf Running scoring test ./scoring/c.M3x2.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./scoring/c.M3x2.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x2178.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Codon data Gaps or ambiguity codes found within codon for taxon SterNa6. Codons coded as missing for that taxon: 708 Gaps or ambiguity codes found within codon for taxon PinniNa6. Codons coded as missing for that taxon: 513 646 Summary of data: 11 sequences. 72 constant characters. 527 parsimony-informative characters. 127 uninformative variable characters. 726 total characters. 668 unique patterns in compressed data matrix. ################################################### 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 >= 47 MB good approx 46 MB to 36 MB low approx 35 MB to 18 MB very low approx 17 MB to 7 MB the minimum required availablememory is 7 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 15 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 70.8 MB of memory ####################################################### Found outgroup specification: 1 2 ####################################################### Loading starting model and/or tree from file data/c.M3x2.start Reading TREES block...storing read block: TREES successful Reading GARLI block...storing read block: GARLI successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus Obtained starting or fixed model parameter values from Nexus: MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates Values specified by user (fixed) AC = 1.260, AG = 2.449, AT = 1.259, CG = 0.687, CT = 1.396, GT = 1.000 Equilibrium State Frequencies: empirical (observed) values, fixed: (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0179 0.0349 0.0309 0.0152 0.0114 0.0181 0.0065 0.0084 0.0095 0.0122 0.0083 0.0104 0.0094 0.0507 0.0438 0.0281 0.0078 0.0049 0.0174 0.0029 0.0087 0.0102 0.0023 0.0085 0.0034 0.0080 0.0029 0.0051 0.0072 0.0286 0.0417 0.0152 0.0204 0.0307 0.0375 0.0151 0.0119 0.0221 0.0043 0.0118 0.0166 0.0168 0.0134 0.0093 0.0080 0.0260 0.0435 0.0130 0.0220 0.0127 0.0077 0.0130 0.0034 0.0085 0.0159 0.0217 0.0093 0.0061 0.0469 0.0139 0.0281 Rate Heterogeneity Model: 2 nonsynonymous rate categories, rate and proportion of each estimated (this is effectively the M3 model of PAML) dN/dS Proportion 0.0200 0.6965 0.2936 0.3035 Starting with seed=1 Initial ln Likelihood: -12956.1235 Current score = -12956.1235 Performing final optimizations... pass 1 : -12956.1235 (branch= 0.0000 omega= 0.0000) pass 2 : -12956.1235 (branch= 0.0000 omega= 0.0000) pass 3 : -12956.1235 (branch= 0.0000 omega= 0.0000) pass 4 : -12956.1235 (branch= 0.0000 omega= 0.0000) pass 5 : -12956.1235 (branch= 0.0000 omega= 0.0000) pass 6 : -12956.1235 (branch= 0.0000 omega= 0.0000) pass 7 : -12956.1235 (branch= 0.0000 omega= 0.0000) pass 8 : -12956.1235 (branch= 0.0000 omega= 0.0000) pass 9 : -12956.1235 (branch= 0.0000 omega= 0.0000) pass 10: -12956.1235 (branch= 0.0000 omega= 0.0000) Looking for minimum length branches... Final score = -12956.1235 Time used = 0 hours, 0 minutes and 25 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -12956.1235 Parameter estimates: w(0) p(0) w(1) p(1) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) rep 1: 0.020 0.696 0.294 0.304 1.26 2.449 1.259 0.6866 1.396 1 Treelengths: TL rep 1: 5.371 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.c.M3x2.best.all.tre ***********TEST************** ***Score is 12956.12351 ***Expected is 12956.1235 ***SCORE DIFFERENCE IS .00001 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/c.M3x2.conf *** Running scoring test ./scoring/c.conf Running scoring test ./scoring/c.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./scoring/c.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x2178.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Codon data Gaps or ambiguity codes found within codon for taxon SterNa6. Codons coded as missing for that taxon: 708 Gaps or ambiguity codes found within codon for taxon PinniNa6. Codons coded as missing for that taxon: 513 646 Summary of data: 11 sequences. 72 constant characters. 527 parsimony-informative characters. 127 uninformative variable characters. 726 total characters. 668 unique patterns in compressed data matrix. ################################################### 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 >= 24 MB good approx 23 MB to 18 MB low approx 17 MB to 9 MB very low approx 8 MB to 4 MB the minimum required availablememory is 4 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 8 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 35.5 MB of memory ####################################################### Found outgroup specification: 1 2 ####################################################### Loading starting model and/or tree from file data/c.start Reading TREES block...storing read block: TREES successful Reading GARLI block...storing read block: GARLI successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus Obtained starting or fixed model parameter values from Nexus: MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 61 (codon data, standard code) One dN/dS ratio (aka omega). Value provided by user (fixed) = 0.087400 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.265, AG = 2.362, AT = 1.151, CG = 0.706, CT = 1.402, GT = 1.000 Equilibrium State Frequencies: empirical (observed) values, fixed: (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0179 0.0349 0.0309 0.0152 0.0114 0.0181 0.0065 0.0084 0.0095 0.0122 0.0083 0.0104 0.0094 0.0507 0.0438 0.0281 0.0078 0.0049 0.0174 0.0029 0.0087 0.0102 0.0023 0.0085 0.0034 0.0080 0.0029 0.0051 0.0072 0.0286 0.0417 0.0152 0.0204 0.0307 0.0375 0.0151 0.0119 0.0221 0.0043 0.0118 0.0166 0.0168 0.0134 0.0093 0.0080 0.0260 0.0435 0.0130 0.0220 0.0127 0.0077 0.0130 0.0034 0.0085 0.0159 0.0217 0.0093 0.0061 0.0469 0.0139 0.0281 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 Initial ln Likelihood: -13269.2298 Current score = -13269.2298 Performing final optimizations... pass 1 : -13269.2298 (branch= 0.0000 rel rates= 0.0000) pass 2 : -13269.2298 (branch= 0.0000 rel rates= 0.0000) pass 3 : -13269.2298 (branch= 0.0000 rel rates= 0.0000) pass 4 : -13269.2298 (branch= 0.0000 rel rates= 0.0000) pass 5 : -13269.2298 (branch= 0.0000 rel rates= 0.0000) pass 6 : -13269.2298 (branch= 0.0000 rel rates= 0.0000) pass 7 : -13269.2298 (branch= 0.0000 rel rates= 0.0000) pass 8 : -13269.2298 (branch= 0.0000 rel rates= 0.0000) pass 9 : -13269.2298 (branch= 0.0000 rel rates= 0.0000) pass 10: -13269.2298 (branch= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13269.2298 Time used = 0 hours, 0 minutes and 18 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -13269.2298 Parameter estimates: w(0) p(0) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) rep 1: 0.087 1.000 1.265 2.362 1.151 0.7058 1.402 1 Treelengths: TL rep 1: 5.169 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.c.best.all.tre ***********TEST************** ***Score is 13269.22979 ***Expected is 13269.229793 ***SCORE DIFFERENCE IS -.000003 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/c.conf *** Running scoring test ./scoring/g.dnaBnoZ.conf Running scoring test ./scoring/g.dnaBnoZ.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./scoring/g.dnaBnoZ.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/dnaGap.8x1K.nex ... Reading TAXA block...storing read block: TAXA successful Reading CHARACTERS block...storing read block: CHARACTERS found dna data... successful Reading CHARACTERS block...storing read block: CHARACTERS found standard data... successful Reading TREES block...storing read block: TREES successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1GapsAsMissing") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 8 sequences. 428 constant characters. 129 parsimony-informative characters. 100 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 239 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #2 ("Untitled DATA Block 1GapsAsBinary") Data read as Binary data, no constant state 0 chars, modeled as Binary data, no constant state 0 chars NOTE: entirely missing characters removed from matrix: 1 25 29-34 36 37 52-54 61 67-69 84 85 87 95 96 99 106 110-116 125 138-145 163-165 167 169-177 188 197-199 202-210 213 216-218 228-231 233-236 238-240 247 249 256 257 260 266-270 \ 2 271-277 281-285 290-294 298-300 311 312 322 325 331 332 336-338 344 359 369 373-378 397 404-406 413 416 417 420-426 439-442 450-454 \ 2 455-460 462 471 474-479 487-490 492 494 495 497 502-506 510 521-526 532 533 538-541 544 547 551-553 562 570-572 577 579 609 610 614 615 622 624-626 639 640 647-650 653 655-660 667 668 673-676 679 680 685 695 696 701-705 708-713 716 717 731 742-749 751-755 762 763 770 771 783 788 791-793 804 806-808 813 821-825 827 830-832 840 842 843 845 850 851 856-865 886-894 896 897 903-905 913 914 924 927 948-956 963-971 976-981 991-993 996 Subset of data with 2 states: chars 1-1000 Summary of data: 8 sequences. 502 constant characters. 39 parsimony-informative characters. 116 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 24 unique patterns in compressed data matrix. ################################################### 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 >= 2 MB good approx 1 MB to 2 MB low approx 1 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 2.3 MB of memory ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3220 0.2180 0.1602 0.2999 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.1629 Substitution rate categories under this model: rate proportion 0.0000 0.1629 0.0334 0.2093 0.2519 0.2093 0.8203 0.2093 2.8944 0.2093 Model 2 Number of states = 2 (binary data) Character change matrix: Binary, no all-zero columns (2-state symmetric one rate model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -4043.7391 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates... pass 1:+ 532.047 (branch= 438.84 scale= 6.77 alpha= 15.79 freqs= 3.30 rel rates= 8.48 pinv= 0.00 subset rates= 58.86) pass 2:+ 88.209 (branch= 42.39 scale= 0.83 alpha= 0.82 freqs= 0.72 rel rates= 0.01 pinv= 0.00 subset rates= 43.45) pass 3:+ 34.899 (branch= 0.70 scale= 2.02 alpha= 1.89 freqs= 0.04 rel rates= 0.72 pinv= 0.00 subset rates= 29.52) pass 4:+ 17.437 (branch= 4.66 scale= 2.38 alpha= 1.70 freqs= 0.05 rel rates= 0.01 pinv= 0.00 subset rates= 8.64) pass 5:+ 10.201 (branch= 4.19 scale= 1.64 alpha= 0.69 freqs= 0.05 rel rates= 2.14 pinv= 0.00 subset rates= 1.49) pass 6:+ 1.986 (branch= 0.00 scale= 1.92 alpha= 0.00 freqs= 0.06 rel rates= 0.01 pinv= 0.00 subset rates= 0.00) pass 7:+ 0.532 (branch= 0.47 scale= 0.00 alpha= 0.00 freqs= 0.06 rel rates= 0.01 pinv= 0.00 subset rates= 0.00) pass 8:+ 0.057 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.05 rel rates= 0.01 pinv= 0.00 subset rates= 0.00) lnL after optimization: -3358.3708 Current score = -3358.3708 Performing final optimizations... pass 1 : -3355.4786 (branch= 0.9931 alpha= 0.0078 pinv= 0.0071 eq freqs= 0.1960 rel rates= 1.3027 subset rates= 0.3855) pass 2 : -3354.0845 (branch= 0.5096 alpha= 0.0087 pinv= 0.0116 eq freqs= 0.0202 rel rates= 0.6704 subset rates= 0.1736) pass 3 : -3353.2216 (branch= 0.2838 alpha= 0.0000 pinv= 0.0085 eq freqs= 0.0161 rel rates= 0.4611 subset rates= 0.0933) pass 4 : -3352.5952 (branch= 0.1909 alpha= 0.0023 pinv= 0.0160 eq freqs= 0.0043 rel rates= 0.3690 subset rates= 0.0439) pass 5 : -3352.1456 (branch= 0.0893 alpha= 0.0058 pinv= 0.0163 eq freqs= 0.0021 rel rates= 0.3064 subset rates= 0.0296) pass 6 : -3351.7989 (branch= 0.0483 alpha= 0.0070 pinv= 0.0164 eq freqs= 0.0009 rel rates= 0.2560 subset rates= 0.0182) pass 7 : -3351.5275 (branch= 0.0312 alpha= 0.0089 pinv= 0.0158 eq freqs= 0.0008 rel rates= 0.2042 subset rates= 0.0105) pass 8 : -3351.3129 (branch= 0.0189 alpha= 0.0099 pinv= 0.0149 eq freqs= 0.0005 rel rates= 0.1637 subset rates= 0.0067) pass 9 : -3351.1410 (branch= 0.0122 alpha= 0.0104 pinv= 0.0140 eq freqs= 0.0005 rel rates= 0.1310 subset rates= 0.0039) pass 10: -3350.9999 (branch= 0.0075 alpha= 0.0103 pinv= 0.0138 eq freqs= 0.0004 rel rates= 0.1065 subset rates= 0.0026) pass 11: -3350.8835 (branch= 0.0048 alpha= 0.0102 pinv= 0.0127 eq freqs= 0.0003 rel rates= 0.0868 subset rates= 0.0016) pass 12: -3350.7869 (branch= 0.0030 alpha= 0.0098 pinv= 0.0116 eq freqs= 0.0002 rel rates= 0.0710 subset rates= 0.0010) pass 13: -3350.7072 (branch= 0.0019 alpha= 0.0093 pinv= 0.0106 eq freqs= 0.0002 rel rates= 0.0577 subset rates= 0.0000) pass 14: -3350.6389 (branch= 0.0005 alpha= 0.0090 pinv= 0.0090 eq freqs= 0.0001 rel rates= 0.0486 subset rates= 0.0012) pass 15: -3350.5822 (branch= 0.0009 alpha= 0.0082 pinv= 0.0081 eq freqs= 0.0001 rel rates= 0.0392 subset rates= 0.0000) pass 16: -3350.5338 (branch= 0.0003 alpha= 0.0075 pinv= 0.0073 eq freqs= 0.0001 rel rates= 0.0333 subset rates= 0.0000) pass 17: -3350.4923 (branch= 0.0001 alpha= 0.0072 pinv= 0.0066 eq freqs= 0.0001 rel rates= 0.0275 subset rates= 0.0000) pass 18: -3350.4567 (branch= 0.0000 alpha= 0.0066 pinv= 0.0059 eq freqs= 0.0001 rel rates= 0.0231 subset rates= 0.0000) pass 19: -3350.4262 (branch= 0.0000 alpha= 0.0058 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0193 subset rates= 0.0000) pass 20: -3350.3998 (branch= 0.0000 alpha= 0.0052 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0165 subset rates= 0.0000) optimization up to ... pass 30: -3350.2717 (branch= 0.0000 alpha= 0.0276 pinv= 0.0250 eq freqs= 0.0002 rel rates= 0.0754 subset rates= 0.0000) optimization up to ... pass 40: -3350.2422 (branch= 0.0000 alpha= 0.0065 pinv= 0.0061 eq freqs= 0.0000 rel rates= 0.0168 subset rates= 0.0000) optimization up to ... pass 50: -3350.2355 (branch= 0.0000 alpha= 0.0013 pinv= 0.0012 eq freqs= 0.0000 rel rates= 0.0041 subset rates= 0.0000) optimization up to ... pass 60: -3350.2340 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0011 subset rates= 0.0000) optimization up to ... pass 70: -3350.2337 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) optimization up to ... pass 77: -3350.2336 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) Looking for minimum length branches... Final score = -3350.2336 Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -3350.2336 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 pinv rep 1: 3.11 10.4 2.687 0.001 21.85 1 0.333 0.222 0.157 0.288 0.579 0.366 Partition model subset 2: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) rep 1: 0.787 1.820 0.180 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.g.dnaBnoZ.best.all.tre ***********TEST************** ***Score is 3350.23362 ***Expected is 3350.2345 ***SCORE DIFFERENCE IS -.00088 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/g.dnaBnoZ.conf *** Running scoring test ./scoring/g.dnaMix.conf Running scoring test ./scoring/g.dnaMix.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./scoring/g.dnaMix.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/dnaGap.8x1K.nex ... Reading TAXA block...storing read block: TAXA successful Reading CHARACTERS block...storing read block: CHARACTERS found dna data... successful Reading CHARACTERS block...storing read block: CHARACTERS found standard data... successful Reading TREES block...storing read block: TREES successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1GapsAsMissing") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 8 sequences. 428 constant characters. 129 parsimony-informative characters. 100 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 239 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #2 ("Untitled DATA Block 1GapsAsBinary") Data read as Gap-coded data, oriented with respect to time, modeled as Gap-coded data, oriented with respect to time Summary of data: 8 sequences. 502 constant characters. 39 parsimony-informative characters. 116 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 24 unique patterns in compressed data matrix. ################################################### 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 >= 2 MB good approx 1 MB to 2 MB low approx 1 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 2.7 MB of memory ####################################################### WARNING - specified outgroup (1) being ignored due to inference of a rooted true ####################################################### STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3220 0.2180 0.1602 0.2999 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.1629 Substitution rate categories under this model: rate proportion 0.0000 0.1629 0.0334 0.2093 0.2519 0.2093 0.8203 0.2093 2.8944 0.2093 Model 2 Number of states = 2 (0/1 coding of gaps) Character change matrix: irreversible matrix deletion rate parameter only estimated if using a partitioned model without subset rates deletion rate = 1.000 Equilibrium State Frequencies: proportion of inserted sites parameter insert proportion = 0.500 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 Initial ln Likelihood: -4257.0961 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, ins rate, del rate... pass 1:+ 640.405 (branch= 431.06 scale= 2.03 alpha= 9.92 freqs= 3.07 rel rates= 7.29 pinv= 0.00 ins/del=187.03) pass 2:+ 169.102 (branch= 75.12 scale= 1.32 alpha= 0.88 freqs= 0.65 rel rates= 0.01 pinv= 0.00 ins/del= 91.12) pass 3:+ 55.144 (branch= 7.14 scale= 1.85 alpha= 1.09 freqs= 0.05 rel rates= 0.90 pinv= 0.00 ins/del= 44.12) pass 4:+ 25.231 (branch= 7.02 scale= 1.52 alpha= 0.69 freqs= 0.06 rel rates= 0.01 pinv= 0.00 ins/del= 15.94) pass 5:+ 14.361 (branch= 7.97 scale= 1.87 alpha= 0.01 freqs= 0.05 rel rates= 2.45 pinv= 0.00 ins/del= 2.01) pass 6:+ 10.438 (branch= 7.36 scale= 2.34 alpha= 0.01 freqs= 0.07 rel rates= 0.00 pinv= 0.00 ins/del= 0.66) pass 7:+ 6.158 (branch= 5.23 scale= 0.83 alpha= 0.01 freqs= 0.06 rel rates= 0.00 pinv= 0.00 ins/del= 0.03) pass 8:+ 3.640 (branch= 2.31 scale= 0.00 alpha= 0.00 freqs= 0.05 rel rates= 0.60 pinv= 0.00 ins/del= 0.67) pass 9:+ 0.148 (branch= 0.08 scale= 0.00 alpha= 0.00 freqs= 0.06 rel rates= 0.00 pinv= 0.00 ins/del= 0.00) lnL after optimization: -3332.4700 Current score = -3332.4700 Performing final optimizations... pass 1 : -3329.9917 (branch= 1.3745 alpha= 0.0217 pinv= 0.0099 eq freqs= 0.2403 rel rates= 0.7565 ins/del rates= 0.0754) pass 2 : -3329.0479 (branch= 0.3511 alpha= 0.0000 pinv= 0.0096 eq freqs= 0.0000 rel rates= 0.5199 ins/del rates= 0.0631) pass 3 : -3328.4344 (branch= 0.1467 alpha= 0.0038 pinv= 0.0146 eq freqs= 0.0183 rel rates= 0.3878 ins/del rates= 0.0424) pass 4 : -3327.9727 (branch= 0.0856 alpha= 0.0068 pinv= 0.0148 eq freqs= 0.0030 rel rates= 0.3224 ins/del rates= 0.0291) pass 5 : -3327.6171 (branch= 0.0530 alpha= 0.0080 pinv= 0.0147 eq freqs= 0.0018 rel rates= 0.2601 ins/del rates= 0.0179) pass 6 : -3327.3315 (branch= 0.0344 alpha= 0.0079 pinv= 0.0146 eq freqs= 0.0009 rel rates= 0.2163 ins/del rates= 0.0115) pass 7 : -3327.1095 (branch= 0.0220 alpha= 0.0095 pinv= 0.0139 eq freqs= 0.0008 rel rates= 0.1679 ins/del rates= 0.0078) pass 8 : -3326.9287 (branch= 0.0143 alpha= 0.0096 pinv= 0.0133 eq freqs= 0.0005 rel rates= 0.1380 ins/del rates= 0.0051) pass 9 : -3326.7826 (branch= 0.0095 alpha= 0.0099 pinv= 0.0125 eq freqs= 0.0004 rel rates= 0.1106 ins/del rates= 0.0034) pass 10: -3326.6620 (branch= 0.0063 alpha= 0.0098 pinv= 0.0123 eq freqs= 0.0003 rel rates= 0.0896 ins/del rates= 0.0023) pass 11: -3326.5620 (branch= 0.0042 alpha= 0.0094 pinv= 0.0114 eq freqs= 0.0002 rel rates= 0.0731 ins/del rates= 0.0015) pass 12: -3326.4797 (branch= 0.0028 alpha= 0.0090 pinv= 0.0099 eq freqs= 0.0002 rel rates= 0.0594 ins/del rates= 0.0010) pass 13: -3326.4106 (branch= 0.0019 alpha= 0.0085 pinv= 0.0091 eq freqs= 0.0001 rel rates= 0.0488 ins/del rates= 0.0007) pass 14: -3326.3519 (branch= 0.0013 alpha= 0.0080 pinv= 0.0083 eq freqs= 0.0001 rel rates= 0.0406 ins/del rates= 0.0005) pass 15: -3326.3016 (branch= 0.0009 alpha= 0.0074 pinv= 0.0076 eq freqs= 0.0001 rel rates= 0.0341 ins/del rates= 0.0003) pass 16: -3326.2590 (branch= 0.0005 alpha= 0.0070 pinv= 0.0069 eq freqs= 0.0001 rel rates= 0.0279 ins/del rates= 0.0002) pass 17: -3326.2225 (branch= 0.0004 alpha= 0.0063 pinv= 0.0062 eq freqs= 0.0001 rel rates= 0.0234 ins/del rates= 0.0001) pass 18: -3326.1908 (branch= 0.0002 alpha= 0.0057 pinv= 0.0056 eq freqs= 0.0000 rel rates= 0.0200 ins/del rates= 0.0001) pass 19: -3326.1633 (branch= 0.0002 alpha= 0.0052 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0171 ins/del rates= 0.0000) pass 20: -3326.1394 (branch= 0.0001 alpha= 0.0047 pinv= 0.0045 eq freqs= 0.0000 rel rates= 0.0146 ins/del rates= 0.0000) optimization up to ... pass 30: -3326.0197 (branch= 0.0002 alpha= 0.0262 pinv= 0.0244 eq freqs= 0.0002 rel rates= 0.0687 ins/del rates= 0.0001) optimization up to ... pass 40: -3325.9908 (branch= 0.0001 alpha= 0.0068 pinv= 0.0063 eq freqs= 0.0000 rel rates= 0.0157 ins/del rates= 0.0000) optimization up to ... pass 50: -3325.9841 (branch= 0.0001 alpha= 0.0015 pinv= 0.0014 eq freqs= 0.0000 rel rates= 0.0037 ins/del rates= 0.0000) optimization up to ... pass 60: -3325.9826 (branch= 0.0000 alpha= 0.0003 pinv= 0.0003 eq freqs= 0.0000 rel rates= 0.0009 ins/del rates= 0.0000) optimization up to ... pass 70: -3325.9823 (branch= 0.0000 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 ins/del rates= 0.0000) optimization up to ... pass 75: -3325.9822 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3325.9822 Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -3325.9822 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 pinv rep 1: 3.061 10.25 2.654 0.001 21.52 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del rep 1: 0.053 0.145 **ins = proportion of columns that experienced an insertion **del = deletion rate relative to nucleotide substitution rate Treelengths: TL rep 1: 1.417 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.g.dnaMix.best.all.tre ***********TEST************** ***Score is 3325.98221 ***Expected is 3325.98222 ***SCORE DIFFERENCE IS -.00001 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/g.dnaMix.conf *** Running scoring test ./scoring/n.G4.conf Running scoring test ./scoring/n.G4.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./scoring/n.G4.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x2178.wtset.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 816 1012 1019 1022 1995 2180 Found wtset "compensate" with data, applying... Summary of data: 11 sequences. 1072 constant characters. 768 parsimony-informative characters. 338 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 2178 total characters (2179 before removing empty columns). 845 unique patterns in compressed data matrix. ################################################### 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 >= 8 MB good approx 7 MB to 6 MB low approx 5 MB to 3 MB very low approx 2 MB to 2 MB the minimum required availablememory is 2 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 4 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 12.1 MB of memory ####################################################### Found outgroup specification: 2 ####################################################### Loading starting model and/or tree from file data/n.G4.start Reading TREES block...storing read block: TREES successful Reading PAUP block...storing read block: PAUP successful Reading GARLI block...storing read block: GARLI successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus Obtained starting or fixed model parameter values from Nexus: MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.532, AG = 3.880, AT = 1.559, CG = 1.283, CT = 4.738, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2442 0.2425 0.2497 0.2635 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 1.2505 with an invariant (invariable) site category, proportion estimated 0.3018 Substitution rate categories under this model: rate proportion 0.0000 0.3018 0.1841 0.1746 0.5410 0.1746 1.0317 0.1746 2.2433 0.1746 Starting with seed=1 Initial ln Likelihood: -13930.5181 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 0.000 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.00 rel rates= 0.00 pinv= 0.00) lnL after optimization: -13930.5181 Current score = -13930.5181 Performing final optimizations... pass 1 : -13930.5181 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 2 : -13930.5181 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 3 : -13930.5181 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 4 : -13930.5181 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 5 : -13930.5180 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 6 : -13930.5180 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 7 : -13930.5180 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 8 : -13930.5180 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 9 : -13930.5180 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 10: -13930.5180 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13930.5180 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -13930.5180 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 1.531 3.879 1.558 1.283 4.736 1 0.244 0.243 0.250 0.263 1.252 0.302 Treelengths: TL rep 1: 1.577 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.n.G4.best.all.tre ***********TEST************** ***Score is 13917.56622 ***Expected is 13917.56622 ***SCORE DIFFERENCE IS 0 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/n.G4.conf *** Running scoring test ./scoring/n.G5.conf Running scoring test ./scoring/n.G5.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./scoring/n.G5.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x2178.wtset.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 816 1012 1019 1022 1995 2180 Found wtset "compensate" with data, applying... Summary of data: 11 sequences. 1072 constant characters. 768 parsimony-informative characters. 338 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 2178 total characters (2179 before removing empty columns). 845 unique patterns in compressed data matrix. ################################################### 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 >= 10 MB good approx 10 MB to 8 MB low approx 7 MB to 4 MB very low approx 3 MB to 2 MB the minimum required availablememory is 2 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 4 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 15.0 MB of memory ####################################################### Found outgroup specification: 1 ####################################################### Loading starting model and/or tree from file data/n.G5.start Reading TREES block...storing read block: TREES successful Reading GARLI block...storing read block: GARLI successful Reading PAUP block...storing read block: PAUP successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus Obtained starting or fixed model parameter values from Nexus: MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.530, AG = 3.881, AT = 1.553, CG = 1.285, CT = 4.742, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2445 0.2424 0.2496 0.2636 Rate Heterogeneity Model: 5 discrete gamma distributed rate categories, alpha param estimated 1.3438 with an invariant (invariable) site category, proportion estimated 0.3098 Substitution rate categories under this model: rate proportion 0.0000 0.3098 0.1655 0.1380 0.4459 0.1380 0.7709 0.1380 1.2349 0.1380 2.3828 0.1380 Starting with seed=1 Initial ln Likelihood: -13931.0233 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 0.000 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.00 rel rates= 0.00 pinv= 0.00) lnL after optimization: -13931.0233 Current score = -13931.0233 Performing final optimizations... pass 1 : -13931.0233 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 2 : -13931.0233 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 3 : -13931.0233 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 4 : -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 5 : -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 6 : -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 7 : -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 8 : -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 9 : -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 10: -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13931.0232 Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -13931.0232 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 1.53 3.88 1.552 1.284 4.739 1 0.244 0.242 0.250 0.264 1.346 0.310 Treelengths: TL rep 1: 1.581 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.n.G5.best.all.tre ***********TEST************** ***Score is 13918.08407 ***Expected is 13918.08407 ***SCORE DIFFERENCE IS 0 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/n.G5.conf *** Running scoring test ./scoring/n.conf Running scoring test ./scoring/n.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./scoring/n.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x2178.wtset.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 816 1012 1019 1022 1995 2180 Found wtset "compensate" with data, applying... Summary of data: 11 sequences. 1072 constant characters. 768 parsimony-informative characters. 338 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 2178 total characters (2179 before removing empty columns). 845 unique patterns in compressed data matrix. ################################################### 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 >= 4 MB good approx 3 MB to 2 MB low approx 2 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. 3.9 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1-3 ####################################################### Loading starting model and/or tree from file data/n.start Reading GARLI block...storing read block: GARLI successful STARTING RUN Obtained starting or fixed model parameter values from Nexus: MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.869, AG = 3.671, AT = 1.221, CG = 1.853, CT = 4.414, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2554 0.2086 0.2382 0.2978 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating random starting tree... Initial ln Likelihood: -18359.9501 optimizing: starting branch lengths, rel rates, eq freqs... pass 1:+ 2061.638 (branch=1982.89 scale= 74.28 freqs= 0.89 rel rates= 3.59) pass 2:+ 221.910 (branch= 220.59 scale= 0.00 freqs= 0.86 rel rates= 0.45) pass 3:+ 4.934 (branch= 4.75 scale= 0.00 freqs= 0.06 rel rates= 0.12) pass 4:+ 0.338 (branch= 0.30 scale= 0.00 freqs= 0.00 rel rates= 0.03) pass 5:+ 0.068 (branch= 0.07 scale= 0.00 freqs= 0.00 rel rates= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00 freqs= 0.00 rel rates= 0.00) lnL after optimization: -16071.0615 gen current_lnL precision last_tree_imp 0 -16071.0615 0.010 0 100 -14502.0548 0.010 73 200 -14502.0273 0.010 73 300 -14501.0234 0.010 73 400 -14500.3936 0.010 73 500 -14499.9895 0.010 73 600 -14499.5150 0.010 73 700 -14499.2251 0.010 73 800 -14499.0577 0.010 73 900 -14499.0511 0.010 73 1000 -14499.0511 0.010 73 1100 -14498.9760 0.010 73 1200 -14498.9758 0.010 73 1300 -14498.9756 0.010 73 1400 -14498.9756 0.010 73 1500 -14498.9756 0.010 73 1600 -14498.9607 0.010 73 Reached termination condition! last topological improvement at gen 73 Improvement over last 500 gen = 0.01521 Current score = -14498.9607 Performing final optimizations... pass 1 : -14498.9272 (branch= 0.0118 eq freqs= 0.0156 rel rates= 0.0061) pass 2 : -14498.8998 (branch= 0.0172 eq freqs= 0.0064 rel rates= 0.0038) pass 3 : -14498.8933 (branch= 0.0062 eq freqs= 0.0001 rel rates= 0.0002) pass 4 : -14498.8887 (branch= 0.0009 eq freqs= 0.0013 rel rates= 0.0024) pass 5 : -14498.8879 (branch= 0.0006 eq freqs= 0.0001 rel rates= 0.0001) pass 6 : -14498.8868 (branch= 0.0004 eq freqs= 0.0004 rel rates= 0.0003) pass 7 : -14498.8861 (branch= 0.0003 eq freqs= 0.0002 rel rates= 0.0001) pass 8 : -14498.8859 (branch= 0.0001 eq freqs= 0.0000 rel rates= 0.0001) pass 9 : -14498.8857 (branch= 0.0001 eq freqs= 0.0000 rel rates= 0.0001) pass 10: -14498.8856 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) pass 11: -14498.8855 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) pass 12: -14498.8854 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) pass 13: -14498.8854 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 14: -14498.8854 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 15: -14498.8854 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -14498.8854 Time used = 0 hours, 0 minutes and 12 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.871, AG = 3.674, AT = 1.223, CG = 1.855, CT = 4.418, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2554 0.2085 0.2382 0.2978 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file scr.n.sitelikes.log ... WARNING: Site likelihoods are being output when wtset compensate is in effect. Sites with weight > 1 will only be output once! ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -14498.8854 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 1.871 3.674 1.223 1.855 4.418 1 0.255 0.209 0.238 0.298 Treelengths: TL rep 1: 1.298 Saving final tree from best search rep (#1) to scr.n.best.tre ####################################################### ***********TEST************** ***Score is 14486.03887 ***Expected is 14486.03829 ***SCORE DIFFERENCE IS .00058 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/n.conf *** Running scoring test ./scoring/p.3diff.conf Running scoring test ./scoring/p.3diff.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./scoring/p.3diff.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.byPos.11x2178.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful Reading SETS block...storing read block: SETS successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #1 ("1stpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 4 Summary of data: 11 sequences. 441 constant characters. 171 parsimony-informative characters. 113 uninformative variable characters. 725 total characters. 237 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #2 ("2ndpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 5 Summary of data: 11 sequences. 527 constant characters. 90 parsimony-informative characters. 108 uninformative variable characters. 725 total characters. 158 unique patterns in compressed data matrix. GARLI data subset 3 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #3 ("3rdpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 6 Summary of data: 11 sequences. 102 constant characters. 507 parsimony-informative characters. 116 uninformative variable characters. 725 total characters. 548 unique patterns in compressed data matrix. ################################################### 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 >= 9 MB good approx 8 MB to 7 MB low approx 6 MB to 4 MB very low approx 3 MB to 2 MB the minimum required availablememory is 2 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 4 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 13.5 MB of memory ####################################################### Loading starting model and/or tree from file data/p.3diff.start Reading TREES block...storing read block: TREES successful Reading GARLI block...storing read block: GARLI successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus Obtained starting or fixed model parameter values from Nexus: MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) AC = 1.000, AG = 10.000, AT = 2.000, CG = 2.000, CT = 0.010, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3150 0.1749 0.3006 0.2095 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.6000 Substitution rate categories under this model: rate proportion 0.0531 0.2500 0.3123 0.2500 0.8813 0.2500 2.7533 0.2500 Model 2 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) AC = 4.000, AG = 4.000, AT = 1.000, CG = 4.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1000 0.2000 0.3000 0.4000 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.4000 Substitution rate categories under this model: rate proportion 0.0167 0.2500 0.1818 0.2500 0.7313 0.2500 3.0702 0.2500 Model 3 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) AC = 1.000, AG = 2.000, AT = 3.000, CG = 5.000, CT = 2.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.4000 0.2000 0.3000 0.1000 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0100 Substitution rate categories under this model: rate proportion 0.0000 0.0100 0.0334 0.2475 0.2519 0.2475 0.8203 0.2475 2.8944 0.2475 Subset rate multipliers: 0.54 0.30 2.16 Starting with seed=1 Initial ln Likelihood: -17270.1042 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates... pass 1:+ 3387.561 (branch=2073.05 scale= 39.85 alpha=118.40 freqs=413.09 rel rates=737.83 pinv= 0.00 subset rates= 5.33) pass 2:+ 327.989 (branch= 41.53 scale= 0.00 alpha= 19.91 freqs=187.33 rel rates= 77.79 pinv= 0.74 subset rates= 0.69) pass 3:+ 196.574 (branch= 1.56 scale= 1.04 alpha= 7.14 freqs= 83.86 rel rates=102.19 pinv= 0.01 subset rates= 0.77) pass 4:+ 36.659 (branch= 1.45 scale= 0.00 alpha= 0.68 freqs= 18.87 rel rates= 15.00 pinv= 0.00 subset rates= 0.65) pass 5:+ 4.518 (branch= 0.00 scale= 0.00 alpha= 0.02 freqs= 3.51 rel rates= 0.99 pinv= 0.01 subset rates= 0.00) pass 6:+ 0.902 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.10 rel rates= 0.78 pinv= 0.01 subset rates= 0.00) pass 7:+ 0.107 (branch= 0.00 scale= 0.00 alpha= 0.02 freqs= 0.08 rel rates= 0.01 pinv= 0.01 subset rates= 0.00) lnL after optimization: -13315.7940 Current score = -13315.7940 Performing final optimizations... pass 1 : -13309.4865 (branch= 2.8300 alpha= 0.8831 pinv= 0.0158 eq freqs= 0.2323 rel rates= 1.8499 subset rates= 0.4965) pass 2 : -13307.8382 (branch= 0.4528 alpha= 0.2105 pinv= 0.0138 eq freqs= 0.1137 rel rates= 0.6944 subset rates= 0.1630) pass 3 : -13307.2493 (branch= 0.0930 alpha= 0.0566 pinv= 0.0029 eq freqs= 0.0115 rel rates= 0.4153 subset rates= 0.0097) pass 4 : -13306.8898 (branch= 0.0271 alpha= 0.0170 pinv= 0.0027 eq freqs= 0.0114 rel rates= 0.2997 subset rates= 0.0015) pass 5 : -13306.6681 (branch= 0.0049 alpha= 0.0050 pinv= 0.0011 eq freqs= 0.0058 rel rates= 0.2020 subset rates= 0.0029) pass 6 : -13306.5170 (branch= 0.0044 alpha= 0.0016 pinv= 0.0003 eq freqs= 0.0042 rel rates= 0.1405 subset rates= 0.0000) pass 7 : -13306.4178 (branch= 0.0010 alpha= 0.0006 pinv= 0.0001 eq freqs= 0.0032 rel rates= 0.0943 subset rates= 0.0000) pass 8 : -13306.3503 (branch= 0.0005 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0023 rel rates= 0.0645 subset rates= 0.0000) pass 9 : -13306.3039 (branch= 0.0004 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0013 rel rates= 0.0434 subset rates= 0.0013) pass 10: -13306.2725 (branch= 0.0002 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0010 rel rates= 0.0297 subset rates= 0.0003) pass 11: -13306.2510 (branch= 0.0002 alpha= 0.0002 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0203 subset rates= 0.0000) pass 12: -13306.2368 (branch= 0.0001 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0138 subset rates= 0.0000) pass 13: -13306.2270 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0094 subset rates= 0.0000) pass 14: -13306.2204 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0064 subset rates= 0.0000) pass 15: -13306.2159 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0044 subset rates= 0.0000) pass 16: -13306.2129 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0029 subset rates= 0.0000) pass 17: -13306.2107 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0021 subset rates= 0.0000) pass 18: -13306.2093 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014 subset rates= 0.0000) pass 19: -13306.2083 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010 subset rates= 0.0000) pass 20: -13306.2076 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007 subset rates= 0.0000) optimization up to ... pass 30: -13306.2062 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0014 subset rates= 0.0000) optimization up to ... pass 35: -13306.2061 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) Looking for minimum length branches... Final score = -13306.2061 Time used = 0 hours, 0 minutes and 8 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -13306.2061 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: 1.974 2.576 1.414 1.414 3.719 1 0.310 0.177 0.297 0.216 0.407 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: 4.373 7.058 1.609 7.058 4.373 1 0.270 0.164 0.161 0.406 0.362 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 4.939 3.387 0.4595 4.939 1 0.157 0.354 0.287 0.202 4.037 0.033 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 1.694 0.541 0.301 2.159 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.p.3diff.best.all.tre ***********TEST************** ***Score is 13306.20612 ***Expected is 13306.20608 ***SCORE DIFFERENCE IS .00004 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.3diff.conf *** Running scoring test ./scoring/p.mk.conf Running scoring test ./scoring/p.mk.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./scoring/p.mk.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 NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk 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 Mk 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 Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -609.1934 optimizing: starting branch lengths... pass 1:+ 125.912 (branch= 124.97 scale= 0.94) pass 2:+ 7.205 (branch= 7.20 scale= 0.00) pass 3:+ 1.518 (branch= 1.48 scale= 0.03) pass 4:+ 0.225 (branch= 0.22 scale= 0.00) pass 5:+ 0.014 (branch= 0.01 scale= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -474.3188 Current score = -474.3188 Performing final optimizations... pass 1 : -474.2925 (branch= 0.0264) pass 2 : -474.2170 (branch= 0.0755) pass 3 : -474.1996 (branch= 0.0173) pass 4 : -474.1939 (branch= 0.0057) pass 5 : -474.1908 (branch= 0.0031) pass 6 : -474.1886 (branch= 0.0022) pass 7 : -474.1872 (branch= 0.0014) pass 8 : -474.1869 (branch= 0.0003) pass 9 : -474.1867 (branch= 0.0002) pass 10: -474.1865 (branch= 0.0002) pass 11: -474.1864 (branch= 0.0001) pass 12: -474.1864 (branch= 0.0000) pass 13: -474.1864 (branch= 0.0000) pass 14: -474.1864 (branch= 0.0000) Looking for minimum length branches... Final score = -474.1864 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -474.1864 Parameter estimates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths: TL rep 1: 3.854 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.p.mk.best.all.tre ***********TEST************** ***Score is 474.18638 ***Expected is 474.1864 ***SCORE DIFFERENCE IS -.00002 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mk.conf *** Running scoring test ./scoring/p.mk.ssr.conf Running scoring test ./scoring/p.mk.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./scoring/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 NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk 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 Mk 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 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=1 Initial ln Likelihood: -609.1934 optimizing: starting branch lengths, subset rates... pass 1:+ 130.207 (branch= 124.97 scale= 0.94 subset rates= 4.29) pass 2:+ 9.056 (branch= 8.14 scale= 0.00 subset rates= 0.91) pass 3:+ 1.801 (branch= 1.66 scale= 0.02 subset rates= 0.12) pass 4:+ 0.302 (branch= 0.30 scale= 0.00 subset rates= 0.00) pass 5:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -467.8159 Current score = -467.8159 Performing final optimizations... pass 1 : -467.7865 (branch= 0.0211 subset rates= 0.0082) pass 2 : -467.7144 (branch= 0.0700 subset rates= 0.0021) pass 3 : -467.7035 (branch= 0.0110 subset rates= 0.0000) pass 4 : -467.6950 (branch= 0.0067 subset rates= 0.0018) pass 5 : -467.6884 (branch= 0.0066 subset rates= 0.0000) pass 6 : -467.6850 (branch= 0.0034 subset rates= 0.0000) pass 7 : -467.6837 (branch= 0.0013 subset rates= 0.0000) pass 8 : -467.6812 (branch= 0.0002 subset rates= 0.0023) pass 9 : -467.6807 (branch= 0.0005 subset rates= 0.0000) pass 10: -467.6804 (branch= 0.0002 subset rates= 0.0000) pass 11: -467.6804 (branch= 0.0001 subset rates= 0.0000) pass 12: -467.6804 (branch= 0.0000 subset rates= 0.0000) pass 13: -467.6790 (branch= 0.0000 subset rates= 0.0014) pass 14: -467.6788 (branch= 0.0002 subset rates= 0.0000) pass 15: -467.6787 (branch= 0.0001 subset rates= 0.0000) pass 16: -467.6787 (branch= 0.0000 subset rates= 0.0000) pass 17: -467.6787 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6787 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -467.6787 Parameter estimates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 3.841 0.787 1.483 2.165 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.p.mk.ssr.best.all.tre ***********TEST************** ***Score is 467.67872 ***Expected is 467.6783 ***SCORE DIFFERENCE IS .00042 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mk.ssr.conf *** Running scoring test ./scoring/p.mkO.conf Running scoring test ./scoring/p.mkO.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./scoring/p.mkO.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, modeled as Standard ordered k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... 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 Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -641.9257 optimizing: starting branch lengths... pass 1:+ 137.411 (branch= 136.58 scale= 0.83) pass 2:+ 7.774 (branch= 7.77 scale= 0.00) pass 3:+ 1.542 (branch= 1.52 scale= 0.02) pass 4:+ 0.091 (branch= 0.09 scale= 0.00) pass 5:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -495.1076 Current score = -495.1076 Performing final optimizations... pass 1 : -495.0677 (branch= 0.0399) pass 2 : -494.9999 (branch= 0.0678) pass 3 : -494.9820 (branch= 0.0179) pass 4 : -494.9768 (branch= 0.0051) pass 5 : -494.9724 (branch= 0.0044) pass 6 : -494.9711 (branch= 0.0013) pass 7 : -494.9709 (branch= 0.0002) pass 8 : -494.9703 (branch= 0.0006) pass 9 : -494.9702 (branch= 0.0001) pass 10: -494.9701 (branch= 0.0001) pass 11: -494.9701 (branch= 0.0000) pass 12: -494.9700 (branch= 0.0000) pass 13: -494.9700 (branch= 0.0000) Looking for minimum length branches... Final score = -494.9700 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -494.9700 Parameter estimates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths: TL rep 1: 4.503 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.p.mkO.best.all.tre ***********TEST************** ***Score is 494.97003 ***Expected is 494.9700 ***SCORE DIFFERENCE IS .00003 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mkO.conf *** Running scoring test ./scoring/p.mkO.ssr.conf Running scoring test ./scoring/p.mkO.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./scoring/p.mkO.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, modeled as Standard ordered k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... 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=1 Initial ln Likelihood: -641.9257 optimizing: starting branch lengths, subset rates... pass 1:+ 147.096 (branch= 136.58 scale= 0.83 subset rates= 9.68) pass 2:+ 12.451 (branch= 8.46 scale= 0.00 subset rates= 3.99) pass 3:+ 3.549 (branch= 2.32 scale= 0.03 subset rates= 1.20) pass 4:+ 0.759 (branch= 0.51 scale= 0.00 subset rates= 0.25) pass 5:+ 0.120 (branch= 0.11 scale= 0.00 subset rates= 0.01) pass 6:+ 0.011 (branch= 0.01 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -477.9403 Current score = -477.9403 Performing final optimizations... pass 1 : -477.8556 (branch= 0.0847 subset rates= 0.0000) pass 2 : -477.7621 (branch= 0.0916 subset rates= 0.0020) pass 3 : -477.7285 (branch= 0.0325 subset rates= 0.0010) pass 4 : -477.7065 (branch= 0.0220 subset rates= 0.0000) pass 5 : -477.6981 (branch= 0.0084 subset rates= 0.0000) pass 6 : -477.6914 (branch= 0.0039 subset rates= 0.0027) pass 7 : -477.6890 (branch= 0.0025 subset rates= 0.0000) pass 8 : -477.6873 (branch= 0.0016 subset rates= 0.0000) pass 9 : -477.6863 (branch= 0.0010 subset rates= 0.0000) pass 10: -477.6858 (branch= 0.0005 subset rates= 0.0000) pass 11: -477.6856 (branch= 0.0003 subset rates= 0.0000) pass 12: -477.6854 (branch= 0.0002 subset rates= 0.0000) pass 13: -477.6853 (branch= 0.0001 subset rates= 0.0000) pass 14: -477.6853 (branch= 0.0001 subset rates= 0.0000) pass 15: -477.6853 (branch= 0.0000 subset rates= 0.0000) pass 16: -477.6852 (branch= 0.0000 subset rates= 0.0000) pass 17: -477.6852 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.6852 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -477.6852 Parameter estimates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.909 0.632 1.897 2.791 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.p.mkO.ssr.best.all.tre ***********TEST************** ***Score is 477.68522 ***Expected is 477.6848 ***SCORE DIFFERENCE IS .00042 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mkO.ssr.conf *** Running scoring test ./scoring/p.mkv.conf Running scoring test ./scoring/p.mkv.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./scoring/p.mkv.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, variable only, modeled as Standard k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) 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 Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -605.5989 optimizing: starting branch lengths... pass 1:+ 124.584 (branch= 123.99 scale= 0.59) pass 2:+ 6.980 (branch= 6.98 scale= 0.00) pass 3:+ 1.324 (branch= 1.31 scale= 0.02) pass 4:+ 0.161 (branch= 0.16 scale= 0.00) pass 5:+ 0.013 (branch= 0.01 scale= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -472.5370 Current score = -472.5370 Performing final optimizations... pass 1 : -472.4890 (branch= 0.0480) pass 2 : -472.4195 (branch= 0.0694) pass 3 : -472.4053 (branch= 0.0142) pass 4 : -472.3958 (branch= 0.0095) pass 5 : -472.3935 (branch= 0.0024) pass 6 : -472.3921 (branch= 0.0013) pass 7 : -472.3917 (branch= 0.0005) pass 8 : -472.3912 (branch= 0.0004) pass 9 : -472.3908 (branch= 0.0004) pass 10: -472.3907 (branch= 0.0001) pass 11: -472.3906 (branch= 0.0001) pass 12: -472.3906 (branch= 0.0000) pass 13: -472.3906 (branch= 0.0000) pass 14: -472.3906 (branch= 0.0000) Looking for minimum length branches... Final score = -472.3906 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -472.3906 Parameter estimates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths: TL rep 1: 3.621 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.p.mkv.best.all.tre ***********TEST************** ***Score is 472.39058 ***Expected is 472.3906 ***SCORE DIFFERENCE IS -.00002 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mkv.conf *** Running scoring test ./scoring/p.mkv.ssr.conf Running scoring test ./scoring/p.mkv.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./scoring/p.mkv.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, variable only, modeled as Standard k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) 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: 1.00 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -605.5989 optimizing: starting branch lengths, subset rates... pass 1:+ 129.563 (branch= 123.99 scale= 0.59 subset rates= 4.98) pass 2:+ 9.277 (branch= 7.97 scale= 0.00 subset rates= 1.31) pass 3:+ 1.737 (branch= 1.57 scale= 0.00 subset rates= 0.16) pass 4:+ 0.310 (branch= 0.31 scale= 0.00 subset rates= 0.00) pass 5:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -464.7121 Current score = -464.7121 Performing final optimizations... pass 1 : -464.6742 (branch= 0.0275 subset rates= 0.0105) pass 2 : -464.5899 (branch= 0.0814 subset rates= 0.0030) pass 3 : -464.5708 (branch= 0.0166 subset rates= 0.0025) pass 4 : -464.5618 (branch= 0.0090 subset rates= 0.0000) pass 5 : -464.5569 (branch= 0.0050 subset rates= 0.0000) pass 6 : -464.5549 (branch= 0.0019 subset rates= 0.0000) pass 7 : -464.5539 (branch= 0.0010 subset rates= 0.0000) pass 8 : -464.5537 (branch= 0.0002 subset rates= 0.0000) pass 9 : -464.5534 (branch= 0.0002 subset rates= 0.0000) pass 10: -464.5533 (branch= 0.0001 subset rates= 0.0000) pass 11: -464.5533 (branch= 0.0001 subset rates= 0.0000) pass 12: -464.5506 (branch= 0.0000 subset rates= 0.0027) pass 13: -464.5482 (branch= 0.0023 subset rates= 0.0000) pass 14: -464.5476 (branch= 0.0006 subset rates= 0.0000) pass 15: -464.5474 (branch= 0.0002 subset rates= 0.0000) pass 16: -464.5474 (branch= 0.0000 subset rates= 0.0000) pass 17: -464.5474 (branch= 0.0000 subset rates= 0.0000) pass 18: -464.5474 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -464.5474 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -464.5474 Parameter estimates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 3.400 0.771 1.638 2.479 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.p.mkv.ssr.best.all.tre ***********TEST************** ***Score is 464.54737 ***Expected is 464.5473 ***SCORE DIFFERENCE IS .00007 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mkv.ssr.conf *** Running scoring test ./scoring/p.mkvO.conf Running scoring test ./scoring/p.mkvO.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./scoring/p.mkvO.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, variable only, modeled as Standard ordered k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... 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 Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -637.9212 optimizing: starting branch lengths... pass 1:+ 134.883 (branch= 134.40 scale= 0.48) pass 2:+ 7.290 (branch= 7.29 scale= 0.00) pass 3:+ 1.758 (branch= 1.73 scale= 0.03) pass 4:+ 0.187 (branch= 0.19 scale= 0.00) pass 5:+ 0.011 (branch= 0.01 scale= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -493.7915 Current score = -493.7915 Performing final optimizations... pass 1 : -493.7599 (branch= 0.0316) pass 2 : -493.6921 (branch= 0.0678) pass 3 : -493.6791 (branch= 0.0130) pass 4 : -493.6729 (branch= 0.0062) pass 5 : -493.6703 (branch= 0.0026) pass 6 : -493.6691 (branch= 0.0012) pass 7 : -493.6680 (branch= 0.0011) pass 8 : -493.6679 (branch= 0.0001) pass 9 : -493.6678 (branch= 0.0001) pass 10: -493.6677 (branch= 0.0000) pass 11: -493.6677 (branch= 0.0001) pass 12: -493.6676 (branch= 0.0000) pass 13: -493.6676 (branch= 0.0000) Looking for minimum length branches... Final score = -493.6676 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -493.6676 Parameter estimates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths: TL rep 1: 4.301 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.p.mkvO.best.all.tre ***********TEST************** ***Score is 493.66764 ***Expected is 493.667 ***SCORE DIFFERENCE IS .00064 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mkvO.conf *** Running scoring test ./scoring/p.mkvO.ssr.conf Running scoring test ./scoring/p.mkvO.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./scoring/p.mkvO.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, variable only, modeled as Standard ordered k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... 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=1 Initial ln Likelihood: -637.9212 optimizing: starting branch lengths, subset rates... pass 1:+ 144.867 (branch= 134.40 scale= 0.48 subset rates= 9.98) pass 2:+ 12.967 (branch= 8.30 scale= 0.00 subset rates= 4.67) pass 3:+ 3.847 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.162 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.156 (branch= 0.12 scale= 0.00 subset rates= 0.03) pass 6:+ 0.044 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 7:+ 0.015 (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: -474.8631 Current score = -474.8631 Performing final optimizations... pass 1 : -474.7985 (branch= 0.0574 subset rates= 0.0072) pass 2 : -474.7025 (branch= 0.0912 subset rates= 0.0048) pass 3 : -474.6743 (branch= 0.0240 subset rates= 0.0042) pass 4 : -474.6584 (branch= 0.0156 subset rates= 0.0003) pass 5 : -474.6521 (branch= 0.0063 subset rates= 0.0000) pass 6 : -474.6490 (branch= 0.0031 subset rates= 0.0000) pass 7 : -474.6472 (branch= 0.0018 subset rates= 0.0000) pass 8 : -474.6465 (branch= 0.0007 subset rates= 0.0000) pass 9 : -474.6461 (branch= 0.0004 subset rates= 0.0000) pass 10: -474.6459 (branch= 0.0002 subset rates= 0.0000) pass 11: -474.6458 (branch= 0.0001 subset rates= 0.0000) pass 12: -474.6457 (branch= 0.0001 subset rates= 0.0000) pass 13: -474.6457 (branch= 0.0000 subset rates= 0.0000) pass 14: -474.6457 (branch= 0.0000 subset rates= 0.0000) pass 15: -474.6456 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -474.6456 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -474.6456 Parameter estimates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.584 0.586 2.013 3.001 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.p.mkvO.ssr.best.all.tre ***********TEST************** ***Score is 474.64558 ***Expected is 474.6455633 ***SCORE DIFFERENCE IS .0000167 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mkvO.ssr.conf *** ************************** Running constraint tests ... ************************** Running constraint test n.neg.const Running constraint test n.neg.const Running GARLI Version 2.1. () ->Single processor version for 32-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 ./const/n.neg.const.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### 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. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### Loading constraints from file data/z.neg.const.tre Found 1 negatively (conversely) constrained bipartition Bipartition 1: (1,2,3,4,5,11) | (6,7,8,9,10) STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0334 0.2271 0.2519 0.2271 0.8203 0.2271 2.8944 0.2271 Starting with seed=1 creating likelihood stepwise addition starting tree (compatible with constraints)... number of taxa added: 4 5 6 Optimizing parameters... improved 0.004 lnL Optimizing branchlengths... improved 0.000 lnL 7 8 9 10 11 Initial ln Likelihood: -227.5619 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 4.671 (branch= 0.06 scale= 0.00 alpha= 0.00 freqs= 2.00 rel rates= 2.60 pinv= 0.00) pass 2:+ 0.025 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.02 rel rates= 0.00 pinv= 0.00) lnL after optimization: -222.8653 gen current_lnL precision last_tree_imp 0 -222.8653 0.500 0 500 -213.0501 0.500 495 1000 -212.5074 0.500 628 Optimization precision reduced Optimizing parameters... improved 1.330 lnL Optimizing branchlengths... improved 0.015 lnL 1500 -210.8785 0.010 1215 2000 -210.6586 0.010 1215 2500 -210.6113 0.010 1215 3000 -210.5163 0.010 1215 Reached termination condition! last topological improvement at gen 1215 Improvement over last 500 gen = 0.03351 Current score = -210.5119 Performing final optimizations... pass 1 : -210.1432 (branch= 0.0000 alpha= 0.0976 pinv= 0.2252 eq freqs= 0.0000 rel rates= 0.0459) pass 2 : -209.5398 (branch= 0.0000 alpha= 0.3289 pinv= 0.2490 eq freqs= 0.0028 rel rates= 0.0227) pass 3 : -209.3300 (branch= 0.0346 alpha= 0.1445 pinv= 0.0169 eq freqs= 0.0069 rel rates= 0.0069) pass 4 : -209.2583 (branch= 0.0471 alpha= 0.0154 pinv= 0.0019 eq freqs= 0.0011 rel rates= 0.0061) pass 5 : -209.2211 (branch= 0.0234 alpha= 0.0069 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0069) pass 6 : -209.1987 (branch= 0.0105 alpha= 0.0024 pinv= 0.0009 eq freqs= 0.0002 rel rates= 0.0084) pass 7 : -209.1782 (branch= 0.0070 alpha= 0.0024 pinv= 0.0003 eq freqs= 0.0003 rel rates= 0.0104) pass 8 : -209.1601 (branch= 0.0044 alpha= 0.0012 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0117) pass 9 : -209.1461 (branch= 0.0023 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0111) pass 10: -209.1349 (branch= 0.0009 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0099) pass 11: -209.1252 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0089) pass 12: -209.1165 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0082) pass 13: -209.1087 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0075) pass 14: -209.1016 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0069) pass 15: -209.0948 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0065) pass 16: -209.0886 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0061) pass 17: -209.0827 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) pass 18: -209.0772 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0054) pass 19: -209.0719 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0052) pass 20: -209.0671 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) optimization up to ... pass 30: -208.9998 (branch= 0.0075 alpha= 0.0000 pinv= 0.0003 eq freqs= 0.0012 rel rates= 0.0583) optimization up to ... pass 40: -208.8391 (branch= 0.0297 alpha= 0.0000 pinv= 0.0015 eq freqs= 0.0076 rel rates= 0.1218) optimization up to ... pass 50: -208.6974 (branch= 0.0133 alpha= 0.0000 pinv= 0.0014 eq freqs= 0.0057 rel rates= 0.1212) optimization up to ... pass 60: -208.6231 (branch= 0.0012 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0007 rel rates= 0.0722) optimization up to ... pass 70: -208.5738 (branch= 0.0003 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0488) optimization up to ... pass 80: -208.5378 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0356) optimization up to ... pass 90: -208.5107 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0269) optimization up to ... pass 100: -208.4896 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0210) optimization up to ... pass 110: -208.4726 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0169) optimization up to ... pass 120: -208.4588 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0137) optimization up to ... pass 130: -208.4472 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0115) optimization up to ... pass 140: -208.4375 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0096) optimization up to ... pass 150: -208.4292 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0083) optimization up to ... pass 160: -208.4222 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0070) optimization up to ... pass 170: -208.4160 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0061) optimization up to ... pass 180: -208.4107 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0053) optimization up to ... pass 190: -208.4060 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) optimization up to ... pass 200: -208.4018 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0041) optimization up to ... pass 210: -208.3981 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0037) optimization up to ... pass 220: -208.3947 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) optimization up to ... pass 230: -208.3916 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0031) optimization up to ... pass 240: -208.3889 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0028) optimization up to ... pass 250: -208.3863 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0025) optimization up to ... pass 260: -208.3840 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0023) optimization up to ... pass 270: -208.3819 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) optimization up to ... pass 280: -208.3800 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 290: -208.3781 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) optimization up to ... pass 300: -208.3765 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 310: -208.3749 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 320: -208.3734 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 330: -208.3721 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 340: -208.3708 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... pass 350: -208.3696 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 360: -208.3685 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 370: -208.3675 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 380: -208.3665 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 390: -208.3655 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 400: -208.3646 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 410: -208.3638 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 420: -208.3630 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 430: -208.3623 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 440: -208.3615 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 450: -208.3609 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 460: -208.3602 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 470: -208.3596 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 480: -208.3593 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... pass 490: -208.3590 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... pass 500: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... pass 509: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... Final score = -208.3584 Time used = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 122.311, AG = 188.753, AT = 6.967, CG = 204.934, CT = 194.972, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2225 0.2906 0.2035 0.2835 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 999.8998 with an invariant (invariable) site category, proportion estimated 0.2780 Substitution rate categories under this model: rate proportion 0.0000 0.2780 0.9601 0.1805 0.9894 0.1805 1.0100 0.1805 1.0405 0.1805 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 2 branches were collapsed. ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -208.3584 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 122.3 188.8 6.967 204.9 195 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL rep 1: 1.881 Saving final tree from best search rep (#1) to con.n.neg.const.best.tre ####################################################### TREEFILES PASS Running constraint test n.negBack.const Running constraint test n.negBack.const Running GARLI Version 2.1. () ->Single processor version for 32-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 ./const/n.negBack.const.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### 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. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1-3 ####################################################### Loading constraints from file data/z.negBack.const.tre All constraints are backbone All constraints involve the same backbone set of taxa Found 1 negatively (conversely) constrained bipartition Bipartition 1 (backbone): (1,2,3,5,8,9,10) | (4,11) STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0334 0.2271 0.2519 0.2271 0.8203 0.2271 2.8944 0.2271 Starting with seed=1 creating likelihood stepwise addition starting tree (compatible with constraints)... number of taxa added: 4 5 6 Optimizing parameters... improved 0.005 lnL Optimizing branchlengths... improved 0.292 lnL 7 8 9 10 11 Initial ln Likelihood: -238.2863 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 6.219 (branch= 2.07 scale= 0.00 alpha= 0.00 freqs= 1.61 rel rates= 2.53 pinv= 0.00) pass 2:+ 1.027 (branch= 0.47 scale= 0.00 alpha= 0.00 freqs= 0.55 rel rates= 0.00 pinv= 0.00) pass 3:+ 0.029 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.02 rel rates= 0.00 pinv= 0.00) lnL after optimization: -231.0119 gen current_lnL precision last_tree_imp 0 -231.0119 0.500 0 500 -214.6598 0.500 276 Optimization precision reduced Optimizing parameters... improved 1.752 lnL Optimizing branchlengths... improved 0.106 lnL 1000 -212.3289 0.010 825 1500 -212.1957 0.010 825 2000 -211.9099 0.010 825 2500 -211.7709 0.010 825 3000 -211.6570 0.010 825 3500 -211.4394 0.010 825 4000 -211.3137 0.010 825 Reached termination condition! last topological improvement at gen 825 Improvement over last 500 gen = 0.03821 Current score = -211.2855 Performing final optimizations... pass 1 : -208.9741 (branch= 0.0000 alpha= 0.7616 pinv= 1.4574 eq freqs= 0.0064 rel rates= 0.0860) pass 2 : -208.5660 (branch= 0.0406 alpha= 0.3181 pinv= 0.0098 eq freqs= 0.0118 rel rates= 0.0278) pass 3 : -208.5065 (branch= 0.0302 alpha= 0.0021 pinv= 0.0000 eq freqs= 0.0017 rel rates= 0.0254) pass 4 : -208.4811 (branch= 0.0032 alpha= 0.0000 pinv= 0.0017 eq freqs= 0.0000 rel rates= 0.0206) pass 5 : -208.4602 (branch= 0.0023 alpha= 0.0007 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0175) pass 6 : -208.4415 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0178) pass 7 : -208.4245 (branch= 0.0009 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0158) pass 8 : -208.4098 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0145) pass 9 : -208.3958 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0136) pass 10: -208.3830 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0126) pass 11: -208.3715 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0114) pass 12: -208.3611 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0104) pass 13: -208.3514 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0096) pass 14: -208.3425 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0089) pass 15: -208.3343 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0082) pass 16: -208.3268 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0075) pass 17: -208.3195 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0073) pass 18: -208.3129 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) pass 19: -208.3065 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0063) pass 20: -208.3007 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) optimization up to ... pass 30: -208.2567 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0439) optimization up to ... pass 40: -208.2293 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0273) optimization up to ... pass 50: -208.2105 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0187) optimization up to ... pass 60: -208.1969 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0136) optimization up to ... pass 70: -208.1864 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0104) optimization up to ... pass 80: -208.1782 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0082) optimization up to ... pass 90: -208.1715 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) optimization up to ... pass 100: -208.1661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0055) optimization up to ... pass 110: -208.1614 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) optimization up to ... pass 120: -208.1575 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0039) optimization up to ... pass 130: -208.1541 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) optimization up to ... pass 140: -208.1511 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0030) optimization up to ... pass 150: -208.1485 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) optimization up to ... pass 160: -208.1461 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0023) optimization up to ... pass 170: -208.1440 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) optimization up to ... pass 180: -208.1421 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 190: -208.1404 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 200: -208.1389 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 210: -208.1374 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 220: -208.1361 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... pass 230: -208.1349 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 240: -208.1338 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 250: -208.1328 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 260: -208.1318 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 270: -208.1309 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 280: -208.1301 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 290: -208.1293 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 300: -208.1285 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 310: -208.1278 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 320: -208.1272 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 330: -208.1265 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 340: -208.1259 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 350: -208.1254 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 360: -208.1249 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) optimization up to ... pass 370: -208.1244 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) optimization up to ... pass 373: -208.1243 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... Final score = -208.1243 Time used = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 22.244, AG = 32.321, AT = 0.001, CG = 36.409, CT = 80.319, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2210 0.3445 0.2161 0.2184 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 999.9000 with an invariant (invariable) site category, proportion estimated 0.3383 Substitution rate categories under this model: rate proportion 0.0000 0.3383 0.9601 0.1654 0.9894 0.1654 1.0100 0.1654 1.0405 0.1654 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -208.1243 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 22.24 32.32 0.001 36.41 80.32 1 0.221 0.344 0.216 0.218 999.900 0.338 Treelengths: TL rep 1: 2.421 Saving final tree from best search rep (#1) to con.n.negBack.const.best.tre ####################################################### TREEFILES PASS Running constraint test n.pos.const Running constraint test n.pos.const Running GARLI Version 2.1. () ->Single processor version for 32-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 ./const/n.pos.const.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### 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. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1-5 ####################################################### Loading constraints from file data/z.pos.const.tre Found 6 positively constrained bipartition(s) Bipartition 1: (1,2,3,5,6,7,8,9,10) | (4,11) Bipartition 2: (1,3,5,6,7,8,9,10) | (2,4,11) Bipartition 3: (1,5,6,7,8,9,10) | (2,3,4,11) Bipartition 4: (1,2,3,4,5,8,9,10,11) | (6,7) Bipartition 5: (1,2,3,4,5,8,9,11) | (6,7,10) Bipartition 6: (1,5) | (2,3,4,6,7,8,9,10,11) STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0334 0.2271 0.2519 0.2271 0.8203 0.2271 2.8944 0.2271 Starting with seed=1 creating likelihood stepwise addition starting tree (compatible with constraints)... number of taxa added: 4 5 6 Optimizing parameters... improved 0.006 lnL Optimizing branchlengths... improved 11.173 lnL 7 8 9 10 11 Initial ln Likelihood: -225.0726 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 5.893 (branch= 2.29 scale= 0.89 alpha= 0.00 freqs= 1.20 rel rates= 1.50 pinv= 0.00) pass 2:+ 0.035 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.00) lnL after optimization: -219.1445 gen current_lnL precision last_tree_imp 0 -219.1445 0.500 0 500 -216.3491 0.500 474 1000 -215.0098 0.500 936 1500 -213.9531 0.500 936 Optimization precision reduced Optimizing parameters... improved 1.908 lnL Optimizing branchlengths... improved 0.702 lnL 2000 -210.9689 0.010 1502 2500 -210.8711 0.010 1502 3000 -210.7511 0.010 2883 3500 -210.7006 0.010 2883 4000 -210.6776 0.010 2883 4500 -210.6528 0.010 2883 5000 -210.5910 0.010 4692 5500 -210.5256 0.010 4692 6000 -210.4351 0.010 4692 6500 -210.4174 0.010 4692 Reached termination condition! last topological improvement at gen 4692 Improvement over last 500 gen = 0.02291 Current score = -210.4049 Performing final optimizations... pass 1 : -209.9406 (branch= 0.0001 alpha= 0.0823 pinv= 0.2856 eq freqs= 0.0000 rel rates= 0.0962) pass 2 : -209.3924 (branch= 0.0062 alpha= 0.3452 pinv= 0.1692 eq freqs= 0.0000 rel rates= 0.0276) pass 3 : -209.2775 (branch= 0.0331 alpha= 0.0616 pinv= 0.0125 eq freqs= 0.0043 rel rates= 0.0032) pass 4 : -209.2277 (branch= 0.0299 alpha= 0.0092 pinv= 0.0000 eq freqs= 0.0031 rel rates= 0.0077) pass 5 : -209.1812 (branch= 0.0279 alpha= 0.0113 pinv= 0.0007 eq freqs= 0.0008 rel rates= 0.0058) pass 6 : -209.1484 (branch= 0.0164 alpha= 0.0062 pinv= 0.0006 eq freqs= 0.0007 rel rates= 0.0089) pass 7 : -209.1265 (branch= 0.0077 alpha= 0.0037 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0100) pass 8 : -209.1126 (branch= 0.0038 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0092) pass 9 : -209.1029 (branch= 0.0012 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0080) pass 10: -209.0949 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0071) pass 11: -209.0879 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0064) pass 12: -209.0819 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0057) pass 13: -209.0762 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0054) pass 14: -209.0710 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0049) pass 15: -209.0658 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) pass 16: -209.0606 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0048) pass 17: -209.0550 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) pass 18: -209.0489 (branch= 0.0007 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0053) pass 19: -209.0423 (branch= 0.0010 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0055) pass 20: -209.0349 (branch= 0.0013 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0060) optimization up to ... pass 30: -208.9078 (branch= 0.0251 alpha= 0.0000 pinv= 0.0009 eq freqs= 0.0049 rel rates= 0.0960) optimization up to ... pass 40: -208.7374 (branch= 0.0228 alpha= 0.0000 pinv= 0.0019 eq freqs= 0.0081 rel rates= 0.1377) optimization up to ... pass 50: -208.6461 (branch= 0.0028 alpha= 0.0000 pinv= 0.0004 eq freqs= 0.0016 rel rates= 0.0865) optimization up to ... pass 60: -208.5898 (branch= 0.0004 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0556) optimization up to ... pass 70: -208.5497 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0397) optimization up to ... pass 80: -208.5198 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0297) optimization up to ... pass 90: -208.4966 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0230) optimization up to ... pass 100: -208.4783 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0182) optimization up to ... pass 110: -208.4635 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0147) optimization up to ... pass 120: -208.4511 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0123) optimization up to ... pass 130: -208.4408 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0102) optimization up to ... pass 140: -208.4321 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0087) optimization up to ... pass 150: -208.4246 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0074) optimization up to ... pass 160: -208.4181 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0065) optimization up to ... pass 170: -208.4125 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0056) optimization up to ... pass 180: -208.4076 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) optimization up to ... pass 190: -208.4033 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0043) optimization up to ... pass 200: -208.3994 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0039) optimization up to ... pass 210: -208.3959 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) optimization up to ... pass 220: -208.3928 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0031) optimization up to ... pass 230: -208.3898 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) optimization up to ... pass 240: -208.3872 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) optimization up to ... pass 250: -208.3848 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... pass 260: -208.3826 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... pass 270: -208.3806 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... pass 280: -208.3788 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 290: -208.3771 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 300: -208.3754 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 310: -208.3740 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... pass 320: -208.3726 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 330: -208.3713 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... pass 340: -208.3700 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 350: -208.3689 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 360: -208.3678 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 370: -208.3668 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 380: -208.3659 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 390: -208.3650 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 400: -208.3641 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 410: -208.3633 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 420: -208.3625 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 430: -208.3618 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 440: -208.3611 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 450: -208.3604 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 460: -208.3598 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 470: -208.3592 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 480: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) optimization up to ... pass 490: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... pass 491: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.3584 Time used = 0 hours, 0 minutes and 8 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 122.675, AG = 189.304, AT = 6.999, CG = 205.533, CT = 195.564, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2225 0.2906 0.2035 0.2835 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 999.9000 with an invariant (invariable) site category, proportion estimated 0.2781 Substitution rate categories under this model: rate proportion 0.0000 0.2781 0.9601 0.1805 0.9894 0.1805 1.0100 0.1805 1.0405 0.1805 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 2 branches were collapsed. NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with a positive constraint, it is possible for a constrained branch itself to be collapsed. If you care, be careful to check whether this has happened or turn off branch collapsing. ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -208.3584 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 122.7 189.3 6.999 205.5 195.6 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL rep 1: 1.881 Saving final tree from best search rep (#1) to con.n.pos.const.best.tre ####################################################### TREEFILES PASS Running constraint test n.posBack.const Running constraint test n.posBack.const Running GARLI Version 2.1. () ->Single processor version for 32-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 ./const/n.posBack.const.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### 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. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 2 ####################################################### Loading constraints from file data/z.posBack.const.tre All constraints are backbone All constraints involve the same backbone set of taxa Found 4 positively constrained bipartition(s) Bipartition 1 (backbone): (1,2,3,5,8,9,10) | (4,11) Bipartition 2 (backbone): (1,3,5,8,9,10) | (2,4,11) Bipartition 3 (backbone): (1,5,8,9,10) | (2,3,4,11) Bipartition 4 (backbone): (1,5) | (2,3,4,8,9,10,11) STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0334 0.2271 0.2519 0.2271 0.8203 0.2271 2.8944 0.2271 Starting with seed=1 creating likelihood stepwise addition starting tree (compatible with constraints)... number of taxa added: 4 5 6 Optimizing parameters... improved 0.006 lnL Optimizing branchlengths... improved 11.173 lnL 7 8 9 10 11 Initial ln Likelihood: -221.7983 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 5.406 (branch= 2.03 scale= 0.00 alpha= 0.00 freqs= 1.20 rel rates= 2.17 pinv= 0.00) pass 2:+ 0.072 (branch= 0.04 scale= 0.00 alpha= 0.00 freqs= 0.02 rel rates= 0.00 pinv= 0.00) lnL after optimization: -216.3203 gen current_lnL precision last_tree_imp 0 -216.3203 0.500 0 500 -213.9944 0.500 208 1000 -213.0248 0.500 547 Optimization precision reduced Optimizing parameters... improved 1.494 lnL Optimizing branchlengths... improved 0.350 lnL 1500 -210.9424 0.010 1230 2000 -210.7769 0.010 1230 2500 -210.6534 0.010 1230 3000 -210.6127 0.010 1230 Reached termination condition! last topological improvement at gen 1230 Improvement over last 500 gen = 0.03865 Current score = -210.5968 Performing final optimizations... pass 1 : -210.1948 (branch= 0.0000 alpha= 0.1301 pinv= 0.2110 eq freqs= 0.0000 rel rates= 0.0609) pass 2 : -209.5704 (branch= 0.0039 alpha= 0.3419 pinv= 0.2425 eq freqs= 0.0034 rel rates= 0.0327) pass 3 : -209.3335 (branch= 0.0544 alpha= 0.1398 pinv= 0.0224 eq freqs= 0.0092 rel rates= 0.0111) pass 4 : -209.2507 (branch= 0.0578 alpha= 0.0172 pinv= 0.0013 eq freqs= 0.0022 rel rates= 0.0042) pass 5 : -209.2005 (branch= 0.0351 alpha= 0.0090 pinv= 0.0011 eq freqs= 0.0004 rel rates= 0.0046) pass 6 : -209.1719 (branch= 0.0156 alpha= 0.0050 pinv= 0.0004 eq freqs= 0.0005 rel rates= 0.0072) pass 7 : -209.1457 (branch= 0.0098 alpha= 0.0033 pinv= 0.0002 eq freqs= 0.0013 rel rates= 0.0115) pass 8 : -209.1242 (branch= 0.0072 alpha= 0.0015 pinv= 0.0000 eq freqs= 0.0011 rel rates= 0.0117) pass 9 : -209.1104 (branch= 0.0030 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0009 rel rates= 0.0098) pass 10: -209.1003 (branch= 0.0011 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0084) pass 11: -209.0921 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0074) pass 12: -209.0851 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0065) pass 13: -209.0788 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0059) pass 14: -209.0733 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0054) pass 15: -209.0680 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0051) pass 16: -209.0632 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 17: -209.0583 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 18: -209.0534 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 19: -209.0481 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) pass 20: -209.0424 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0052) optimization up to ... pass 30: -208.9333 (branch= 0.0198 alpha= 0.0000 pinv= 0.0007 eq freqs= 0.0039 rel rates= 0.0847) optimization up to ... pass 40: -208.7577 (branch= 0.0266 alpha= 0.0000 pinv= 0.0020 eq freqs= 0.0087 rel rates= 0.1383) optimization up to ... pass 50: -208.6571 (branch= 0.0041 alpha= 0.0000 pinv= 0.0006 eq freqs= 0.0023 rel rates= 0.0936) optimization up to ... pass 60: -208.5973 (branch= 0.0005 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0589) optimization up to ... pass 70: -208.5553 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0416) optimization up to ... pass 80: -208.5239 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0311) optimization up to ... pass 90: -208.4999 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0238) optimization up to ... pass 100: -208.4809 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0189) optimization up to ... pass 110: -208.4656 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0152) optimization up to ... pass 120: -208.4529 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0126) optimization up to ... pass 130: -208.4423 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0105) optimization up to ... pass 140: -208.4334 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0089) optimization up to ... pass 150: -208.4257 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0076) optimization up to ... pass 160: -208.4191 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) optimization up to ... pass 170: -208.4134 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0057) optimization up to ... pass 180: -208.4083 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) optimization up to ... pass 190: -208.4039 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0044) optimization up to ... pass 200: -208.3999 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) optimization up to ... pass 210: -208.3963 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0036) optimization up to ... pass 220: -208.3932 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... pass 230: -208.3903 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) optimization up to ... pass 240: -208.3876 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0027) optimization up to ... pass 250: -208.3852 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... pass 260: -208.3830 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... pass 270: -208.3809 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... pass 280: -208.3790 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 290: -208.3773 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 300: -208.3757 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 310: -208.3742 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... pass 320: -208.3728 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 330: -208.3715 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... pass 340: -208.3702 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 350: -208.3691 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 360: -208.3680 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 370: -208.3670 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 380: -208.3660 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 390: -208.3651 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 400: -208.3642 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 410: -208.3634 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 420: -208.3626 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 430: -208.3619 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 440: -208.3612 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 450: -208.3605 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 460: -208.3599 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 470: -208.3593 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 480: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 490: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) optimization up to ... pass 492: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.3584 Time used = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 122.522, AG = 189.082, AT = 6.990, CG = 205.290, CT = 195.326, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2225 0.2906 0.2035 0.2835 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 999.9000 with an invariant (invariable) site category, proportion estimated 0.2781 Substitution rate categories under this model: rate proportion 0.0000 0.2781 0.9601 0.1805 0.9894 0.1805 1.0100 0.1805 1.0405 0.1805 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 2 branches were collapsed. NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with a positive constraint, it is possible for a constrained branch itself to be collapsed. If you care, be careful to check whether this has happened or turn off branch collapsing. ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -208.3584 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 122.5 189.1 6.99 205.3 195.3 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL rep 1: 1.881 Saving final tree from best search rep (#1) to con.n.posBack.const.best.tre ####################################################### TREEFILES PASS ************************** Running output tests ... ************************** Running output test a.G3 Running output test a.G3 Running GARLI Version 2.1. () ->Single processor version for 32-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 ./output/a.G3.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 11 sequences. 3 constant characters. 6 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) 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 0.5000 with an invariant (invariable) site category, proportion estimated 0.0750 Substitution rate categories under this model: rate proportion 0.0000 0.0750 0.0603 0.3083 0.4894 0.3083 2.4503 0.3083 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.002 lnL Optimizing branchlengths... improved 0.000 lnL 7 8 9 10 11 Initial ln Likelihood: -116.5267 optimizing: starting branch lengths, alpha shape, prop. invar... pass 1:+ 0.949 (branch= 0.95 scale= 0.00 alpha= 0.00 pinv= 0.00) pass 2:+ 0.099 (branch= 0.10 scale= 0.00 alpha= 0.00 pinv= 0.00) lnL after optimization: -115.4785 gen current_lnL precision last_tree_imp 0 -115.4785 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT 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 0.5015 with an invariant (invariable) site category, proportion estimated 0.0735 Substitution rate categories under this model: rate proportion 0.0000 0.0735 0.0607 0.3088 0.4905 0.3088 2.4487 0.3088 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.a.G3.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 : -114.0488 Parameter estimates: alpha pinv rep 1: 0.501 0.073 Treelengths: TL rep 1: 1.377 Saving final tree from best search rep (#1) to out.a.G3.best.tre Inferring internal state probabilities on best tree... saving to file out.a.G3.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.a.G3.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found 11 instead at line 1, column (approximately) 4 (file position 3) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 16, column (approximately) 1 (file position 470) storing implied block: TAXA storing read block: TREES TREEFILES PASS Running output test a.G4 Running output test a.G4 Running GARLI Version 2.1. () ->Single processor version for 32-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 ./output/a.G4.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 11 sequences. 3 constant characters. 6 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### 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. 0.8 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 2 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) 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: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0750 Substitution rate categories under this model: rate proportion 0.0000 0.0750 0.0334 0.2313 0.2519 0.2313 0.8203 0.2313 2.8944 0.2313 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.001 lnL Optimizing branchlengths... improved 0.006 lnL 7 8 9 10 11 Initial ln Likelihood: -117.7431 optimizing: starting branch lengths, alpha shape, prop. invar... pass 1:+ 1.466 (branch= 1.13 scale= 0.33 alpha= 0.00 pinv= 0.00) pass 2:+ 0.134 (branch= 0.13 scale= 0.00 alpha= 0.00 pinv= 0.00) lnL after optimization: -116.1434 gen current_lnL precision last_tree_imp 0 -116.1434 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT 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: 4 discrete gamma distributed rate categories, alpha param estimated 0.5015 with an invariant (invariable) site category, proportion estimated 0.0735 Substitution rate categories under this model: rate proportion 0.0000 0.0735 0.0337 0.2316 0.2529 0.2316 0.8214 0.2316 2.8921 0.2316 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.a.G4.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 : -114.3787 Parameter estimates: alpha pinv rep 1: 0.501 0.073 Treelengths: TL rep 1: 1.339 Saving final tree from best search rep (#1) to out.a.G4.best.tre Inferring internal state probabilities on best tree... saving to file out.a.G4.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.a.G4.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found 11 instead at line 1, column (approximately) 4 (file position 3) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 16, column (approximately) 1 (file position 470) storing implied block: TAXA storing read block: TREES TREEFILES PASS Running output test a Running output test a Running GARLI Version 2.1. () ->Single processor version for 32-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 ./output/a.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.AA.fas as Fasta amino acid format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Amino acid data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 11 sequences. 3 constant characters. 6 parsimony-informative characters. 1 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 10 total characters (11 before removing empty columns). 10 unique patterns in compressed data matrix. ################################################### 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. 0.2 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1-3 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) 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: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 0.121 lnL 7 8 9 10 11 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -117.7533 optimizing: starting branch lengths... pass 1:+ 0.632 (branch= 0.63 scale= 0.00) pass 2:+ 0.134 (branch= 0.13 scale= 0.00) lnL after optimization: -116.9881 gen current_lnL precision last_tree_imp 0 -116.9881 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT 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: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.a.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 : -115.6197 Parameter estimates: Model contains no estimated parameters Treelengths: TL rep 1: 2.324 Saving final tree from best search rep (#1) to out.a.best.tre Inferring internal state probabilities on best tree... saving to file out.a.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.a.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found > instead at line 1, column (approximately) 2 (file position 1) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 26, column (approximately) 1 (file position 310) storing implied block: TAXA storing read block: TREES TREEFILES PASS Running output test c.M3x2 Running output test c.M3x2 Running GARLI Version 2.1. () ->Single processor version for 32-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 ./output/c.M3x2.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Codon data Base usage at codon positions: A C G T pos 1 0.27723 0.36634 0.21782 0.13861 pos 2 0.30693 0.20792 0.07921 0.40594 pos 3 0.10891 0.38614 0.26733 0.23762 all pos 0.23102 0.32013 0.18812 0.26073 Summary of data: 11 sequences. 0 constant characters. 9 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### 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. 1.3 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1-5 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0094 0.0334 0.0231 0.0206 0.0064 0.0226 0.0157 0.0139 0.0024 0.0086 0.0060 0.0053 0.0125 0.0442 0.0306 0.0272 0.0125 0.0442 0.0306 0.0272 0.0084 0.0299 0.0207 0.0184 0.0032 0.0114 0.0079 0.0070 0.0165 0.0584 0.0405 0.0360 0.0074 0.0263 0.0182 0.0162 0.0050 0.0178 0.0123 0.0110 0.0019 0.0068 0.0047 0.0042 0.0098 0.0347 0.0241 0.0214 0.0167 0.0103 0.0032 0.0113 0.0078 0.0070 0.0043 0.0030 0.0027 0.0062 0.0221 0.0153 0.0136 Rate Heterogeneity Model: 2 nonsynonymous rate categories, rate and proportion of each estimated (this is effectively the M3 model of PAML) dN/dS Proportion 0.2500 0.5000 0.5000 0.5000 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 4.461 lnL Optimizing branchlengths... improved 0.701 lnL 7 8 9 10 11 Initial ln Likelihood: -215.8071 optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters... pass 1:+ 6.388 (branch= 0.00 scale= 0.44 omega= 0.01 rel rates= 5.93) pass 2:+ 0.434 (branch= 0.00 scale= 0.00 omega= 0.01 rel rates= 0.42) lnL after optimization: -208.9856 gen current_lnL precision last_tree_imp 0 -208.9856 0.500 0 NOTE: ****Specified generation limit (5) reached... 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 = 3.999, AT = 0.040, CG = 2.453, CT = 3.999, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0094 0.0334 0.0231 0.0206 0.0064 0.0226 0.0157 0.0139 0.0024 0.0086 0.0060 0.0053 0.0125 0.0442 0.0306 0.0272 0.0125 0.0442 0.0306 0.0272 0.0084 0.0299 0.0207 0.0184 0.0032 0.0114 0.0079 0.0070 0.0165 0.0584 0.0405 0.0360 0.0074 0.0263 0.0182 0.0162 0.0050 0.0178 0.0123 0.0110 0.0019 0.0068 0.0047 0.0042 0.0098 0.0347 0.0241 0.0214 0.0167 0.0103 0.0032 0.0113 0.0078 0.0070 0.0043 0.0030 0.0027 0.0062 0.0221 0.0153 0.0136 Rate Heterogeneity Model: 2 nonsynonymous rate categories, rate and proportion of each estimated (this is effectively the M3 model of PAML) dN/dS Proportion 0.0490 0.5030 0.4995 0.4970 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.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 : -208.2373 Parameter estimates: w(0) p(0) w(1) p(1) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) rep 1: 0.049 0.503 0.499 0.497 1.586 3.999 0.04 2.453 3.999 1 Treelengths: TL rep 1: 9.626 Saving final tree from best search rep (#1) to out.c.M3x2.best.tre Inferring internal state probabilities on best tree... saving to file out.c.M3x2.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.c.M3x2.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found 11 instead at line 1, column (approximately) 4 (file position 3) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 16, column (approximately) 1 (file position 470) storing implied block: TAXA storing read block: TREES TREEFILES PASS Running output test c Running output test c Running GARLI Version 2.1. () ->Single processor version for 32-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 ./output/c.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Codon data Base usage at codon positions: A C G T pos 1 0.27723 0.36634 0.21782 0.13861 pos 2 0.30693 0.20792 0.07921 0.40594 pos 3 0.10891 0.38614 0.26733 0.23762 all pos 0.23102 0.32013 0.18812 0.26073 Summary of data: 11 sequences. 0 constant characters. 9 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 5 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 61 (codon data, standard code) One estimated dN/dS ratio (aka omega) = 0.250000 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0094 0.0334 0.0231 0.0206 0.0064 0.0226 0.0157 0.0139 0.0024 0.0086 0.0060 0.0053 0.0125 0.0442 0.0306 0.0272 0.0125 0.0442 0.0306 0.0272 0.0084 0.0299 0.0207 0.0184 0.0032 0.0114 0.0079 0.0070 0.0165 0.0584 0.0405 0.0360 0.0074 0.0263 0.0182 0.0162 0.0050 0.0178 0.0123 0.0110 0.0019 0.0068 0.0047 0.0042 0.0098 0.0347 0.0241 0.0214 0.0167 0.0103 0.0032 0.0113 0.0078 0.0070 0.0043 0.0030 0.0027 0.0062 0.0221 0.0153 0.0136 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.001 lnL Optimizing branchlengths... improved 0.000 lnL 7 8 9 10 11 Initial ln Likelihood: -225.6424 optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters... pass 1:+ 10.932 (branch= 2.26 scale= 0.50 omega= 0.00 rel rates= 8.17) pass 2:+ 0.926 (branch= 0.64 scale= 0.00 omega= 0.28 rel rates= 0.00) pass 3:+ 0.732 (branch= 0.04 scale= 0.68 omega= 0.01 rel rates= 0.00) pass 4:+ 0.015 (branch= 0.00 scale= 0.00 omega= 0.01 rel rates= 0.00) lnL after optimization: -213.0373 gen current_lnL precision last_tree_imp 0 -213.0373 0.500 0 NOTE: ****Specified generation limit (5) reached... 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) = 0.130483 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 2.468, AG = 4.008, AT = 0.588, CG = 2.683, CT = 2.283, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0094 0.0334 0.0231 0.0206 0.0064 0.0226 0.0157 0.0139 0.0024 0.0086 0.0060 0.0053 0.0125 0.0442 0.0306 0.0272 0.0125 0.0442 0.0306 0.0272 0.0084 0.0299 0.0207 0.0184 0.0032 0.0114 0.0079 0.0070 0.0165 0.0584 0.0405 0.0360 0.0074 0.0263 0.0182 0.0162 0.0050 0.0178 0.0123 0.0110 0.0019 0.0068 0.0047 0.0042 0.0098 0.0347 0.0241 0.0214 0.0167 0.0103 0.0032 0.0113 0.0078 0.0070 0.0043 0.0030 0.0027 0.0062 0.0221 0.0153 0.0136 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.c.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 : -210.2319 Parameter estimates: w(0) p(0) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) rep 1: 0.130 1.000 2.468 4.008 0.588 2.683 2.283 1 Treelengths: TL rep 1: 8.650 Saving final tree from best search rep (#1) to out.c.best.tre Inferring internal state probabilities on best tree... saving to file out.c.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.c.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found 11 instead at line 1, column (approximately) 4 (file position 3) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 16, column (approximately) 1 (file position 470) storing implied block: TAXA storing read block: TREES TREEFILES PASS Running output test n.G3 Running output test n.G3 Running GARLI Version 2.1. () ->Single processor version for 32-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 ./output/n.G3.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### 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. 0.3 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0603 0.3028 0.4894 0.3028 2.4503 0.3028 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.004 lnL Optimizing branchlengths... improved 0.000 lnL 7 8 9 10 11 Initial ln Likelihood: -226.8217 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 3.951 (branch= 0.75 scale= 0.00 alpha= 0.00 freqs= 1.76 rel rates= 1.44 pinv= 0.00) pass 2:+ 0.586 (branch= 0.56 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.00) pass 3:+ 1.297 (branch= 0.66 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.61 pinv= 0.00) pass 4:+ 0.021 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.02 rel rates= 0.00 pinv= 0.00) lnL after optimization: -220.9660 gen current_lnL precision last_tree_imp 0 -220.9660 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.002, AG = 3.998, AT = 0.998, CG = 2.322, CT = 3.998, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2184 0.3566 0.2049 0.2201 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.5025 with an invariant (invariable) site category, proportion estimated 0.0892 Substitution rate categories under this model: rate proportion 0.0000 0.0892 0.0610 0.3036 0.4913 0.3036 2.4477 0.3036 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.n.G3.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 : -220.9571 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 1.002 3.998 0.998 2.322 3.998 1 0.218 0.357 0.205 0.220 0.502 0.089 Treelengths: TL rep 1: 2.169 Saving final tree from best search rep (#1) to out.n.G3.best.tre Inferring internal state probabilities on best tree... saving to file out.n.G3.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.n.G3.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found 11 instead at line 1, column (approximately) 4 (file position 3) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 16, column (approximately) 1 (file position 470) storing implied block: TAXA storing read block: TREES storing read block: PAUP TREEFILES PASS Running output test n.G4 Running output test n.G4 Running GARLI Version 2.1. () ->Single processor version for 32-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 ./output/n.G4.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### 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. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1-4 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0334 0.2271 0.2519 0.2271 0.8203 0.2271 2.8944 0.2271 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.005 lnL Optimizing branchlengths... improved 0.292 lnL 7 8 9 10 11 Initial ln Likelihood: -226.2799 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 5.831 (branch= 2.05 scale= 0.00 alpha= 0.00 freqs= 1.45 rel rates= 2.33 pinv= 0.00) pass 2:+ 0.107 (branch= 0.07 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.00) lnL after optimization: -220.3414 gen current_lnL precision last_tree_imp 0 -220.3414 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.001, AG = 2.400, AT = 0.589, CG = 1.512, CT = 4.001, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2259 0.3629 0.1852 0.2261 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5015 with an invariant (invariable) site category, proportion estimated 0.0902 Substitution rate categories under this model: rate proportion 0.0000 0.0902 0.0337 0.2275 0.2529 0.2275 0.8214 0.2275 2.8921 0.2275 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.n.G4.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 : -217.4380 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 1.001 2.4 0.589 1.512 4.001 1 0.226 0.363 0.185 0.226 0.501 0.090 Treelengths: TL rep 1: 1.694 Saving final tree from best search rep (#1) to out.n.G4.best.tre Inferring internal state probabilities on best tree... saving to file out.n.G4.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.n.G4.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found 11 instead at line 1, column (approximately) 4 (file position 3) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 16, column (approximately) 1 (file position 470) storing implied block: TAXA storing read block: TREES storing read block: PAUP TREEFILES PASS Running output test n Running output test n Running GARLI Version 2.1. () ->Single processor version for 32-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 ./output/n.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### 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. 0.1 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 2 3 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 3.458 lnL 7 8 9 10 11 Initial ln Likelihood: -225.5327 optimizing: starting branch lengths, rel rates, eq freqs... pass 1:+ 7.466 (branch= 0.77 scale= 0.00 freqs= 0.02 rel rates= 6.68) pass 2:+ 0.468 (branch= 0.45 scale= 0.00 freqs= 0.02 rel rates= 0.00) lnL after optimization: -217.5990 gen current_lnL precision last_tree_imp 0 -217.5990 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.511, AG = 3.999, AT = 0.200, CG = 2.619, CT = 2.047, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2300 0.3205 0.1884 0.2611 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.n.sitelikes.log ... WARNING: Site likelihoods being output on prematurely terminated search ... NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -217.2394 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 1.511 3.999 0.1995 2.619 2.047 1 0.230 0.321 0.188 0.261 Treelengths: TL rep 1: 1.686 Saving final tree from best search rep (#1) to out.n.best.tre Inferring internal state probabilities on best tree... saving to file out.n.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.n.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found 11 instead at line 1, column (approximately) 4 (file position 3) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 16, column (approximately) 1 (file position 470) storing implied block: TAXA storing read block: TREES storing read block: PAUP TREEFILES PASS Running output test n.wackyNames Running output test n.wackyNames Running GARLI Version 2.1. () ->Single processor version for 32-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 ./output/n.wackyNames.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x30.wackyNames.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### 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. 0.1 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 3.458 lnL 7 8 9 10 11 Initial ln Likelihood: -225.5327 optimizing: starting branch lengths, rel rates, eq freqs... pass 1:+ 7.466 (branch= 0.77 scale= 0.00 freqs= 0.02 rel rates= 6.68) pass 2:+ 0.468 (branch= 0.45 scale= 0.00 freqs= 0.02 rel rates= 0.00) lnL after optimization: -217.5990 gen current_lnL precision last_tree_imp 0 -217.5990 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.511, AG = 3.999, AT = 0.200, CG = 2.619, CT = 2.047, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2300 0.3205 0.1884 0.2611 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.n.sitelikes.log ... WARNING: Site likelihoods being output on prematurely terminated search ... NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -217.2394 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 1.511 3.999 0.1995 2.619 2.047 1 0.230 0.321 0.188 0.261 Treelengths: TL rep 1: 1.686 Saving final tree from best search rep (#1) to out.n.best.tre ####################################################### cat: out.n.wackyNames.best.tre: No such file or directory [Reading test.out.n.wackyNames.nex ] Executing storing implied block: TAXA storing read block: DATA TREEFILES PASS Running output test p.3diff Running output test p.3diff Running GARLI Version 2.1. () ->Single processor version for 32-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 ./output/p.3diff.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.byPos.11x2178.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful Reading SETS block...storing read block: SETS successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #1 ("1stpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 4 Summary of data: 11 sequences. 441 constant characters. 171 parsimony-informative characters. 113 uninformative variable characters. 725 total characters. 237 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #2 ("2ndpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 5 Summary of data: 11 sequences. 527 constant characters. 90 parsimony-informative characters. 108 uninformative variable characters. 725 total characters. 158 unique patterns in compressed data matrix. GARLI data subset 3 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #3 ("3rdpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 6 Summary of data: 11 sequences. 102 constant characters. 507 parsimony-informative characters. 116 uninformative variable characters. 725 total characters. 548 unique patterns in compressed data matrix. ################################################### 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 >= 11 MB good approx 10 MB to 9 MB low approx 8 MB to 5 MB very low approx 4 MB to 4 MB the minimum required availablememory is 4 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 16.0 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 2 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3150 0.1749 0.3006 0.2095 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 Substitution rate categories under this model: rate proportion 0.0334 0.2500 0.2519 0.2500 0.8203 0.2500 2.8944 0.2500 Model 2 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) AC = 4.000, AG = 4.000, AT = 1.000, CG = 4.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2706 0.1568 0.1630 0.4096 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 Substitution rate categories under this model: rate proportion 0.0334 0.2500 0.2519 0.2500 0.8203 0.2500 2.8944 0.2500 Model 3 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1462 0.3614 0.2906 0.2018 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0352 Substitution rate categories under this model: rate proportion 0.0000 0.0352 0.0334 0.2412 0.2519 0.2412 0.8203 0.2412 2.8944 0.2412 Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 168.526 lnL Optimizing branchlengths... improved 66.084 lnL 7 8 9 10 11 Initial ln Likelihood: -13699.7841 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates... pass 1:+ 209.568 (branch= 7.95 scale= 0.00 alpha= 35.56 freqs= 28.70 rel rates= 62.31 pinv= 0.00 subset rates= 75.04) pass 2:+ 77.744 (branch= 2.27 scale= 0.00 alpha= 4.14 freqs= 11.78 rel rates= 3.62 pinv= 0.00 subset rates= 55.94) pass 3:+ 48.023 (branch= 7.13 scale= 0.72 alpha= 2.17 freqs= 1.08 rel rates= 1.34 pinv= 0.98 subset rates= 34.60) pass 4:+ 16.656 (branch= 0.00 scale= 0.55 alpha= 1.38 freqs= 1.19 rel rates= 1.51 pinv= 0.01 subset rates= 12.02) pass 5:+ 6.312 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.10 rel rates= 1.34 pinv= 0.01 subset rates= 4.85) pass 6:+ 0.120 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.09 rel rates= 0.01 pinv= 0.01 subset rates= 0.00) lnL after optimization: -13341.3609 gen current_lnL precision last_tree_imp 0 -13341.3609 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) AC = 1.951, AG = 2.401, AT = 1.336, CG = 1.336, CT = 3.999, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3135 0.1755 0.2988 0.2123 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.3662 Substitution rate categories under this model: rate proportion 0.0122 0.2500 0.1561 0.2500 0.6920 0.2500 3.1397 0.2500 Model 2 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) AC = 3.969, AG = 6.059, AT = 1.216, CG = 6.059, CT = 3.969, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2816 0.1661 0.1575 0.3948 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.3382 Substitution rate categories under this model: rate proportion 0.0089 0.2500 0.1344 0.2500 0.6547 0.2500 3.2020 0.2500 Model 3 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) AC = 1.000, AG = 4.615, AT = 2.859, CG = 0.444, CT = 4.615, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1590 0.3518 0.2849 0.2043 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 3.7873 with an invariant (invariable) site category, proportion estimated 0.0222 Substitution rate categories under this model: rate proportion 0.0000 0.0222 0.4423 0.2444 0.7675 0.2444 1.0844 0.2444 1.7058 0.2444 Subset rate multipliers: 0.54 0.33 2.14 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.p.3diff.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 : -13323.6174 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: 1.951 2.401 1.336 1.336 3.999 1 0.313 0.176 0.299 0.212 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: 3.969 6.059 1.216 6.059 3.969 1 0.282 0.166 0.158 0.395 0.338 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 4.615 2.859 0.4442 4.615 1 0.159 0.352 0.285 0.204 3.787 0.022 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 1.706 0.537 0.325 2.138 Saving final tree from best search rep (#1) to out.p.3diff.best.tre Inferring internal state probabilities on best tree... saving to file out.p.3diff.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.p.3diff.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: SETS storing read block: ASSUMPTIONS storing read block: TREES TREEFILES PASS Running output test p.mkvO.ssr Running output test p.mkvO.ssr Running GARLI Version 2.1. () ->Single processor version for 32-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 ./output/p.mkvO.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, variable only, modeled as Standard ordered k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 5 ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN >>>Search rep 1 (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=1 Initial ln Likelihood: -637.9212 optimizing: starting branch lengths, subset rates... pass 1:+ 144.867 (branch= 134.40 scale= 0.48 subset rates= 9.98) pass 2:+ 12.967 (branch= 8.30 scale= 0.00 subset rates= 4.67) pass 3:+ 3.847 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.162 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.156 (branch= 0.12 scale= 0.00 subset rates= 0.03) pass 6:+ 0.044 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 7:+ 0.015 (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: -474.8631 gen current_lnL precision last_tree_imp 0 -474.8631 0.010 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT 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: 0.60 2.02 2.82 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 2 branches were collapsed. NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 5). Results: Replicate 1 : -474.8623 (best) Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.474 0.599 2.020 2.815 Saving final tree from best search rep (#1) to out.p.mkvO.ssr.best.tre ####################################################### >>>Search rep 2 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1351934195 Initial ln Likelihood: -668.6258 optimizing: starting branch lengths, subset rates... pass 1:+ 167.892 (branch= 157.14 scale= 1.13 subset rates= 9.62) pass 2:+ 19.859 (branch= 15.03 scale= 0.02 subset rates= 4.81) pass 3:+ 5.107 (branch= 3.29 scale= 0.00 subset rates= 1.82) pass 4:+ 0.825 (branch= 0.20 scale= 0.00 subset rates= 0.62) pass 5:+ 0.065 (branch= 0.04 scale= 0.00 subset rates= 0.03) pass 6:+ 0.027 (branch= 0.03 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -474.8512 gen current_lnL precision last_tree_imp 0 -474.8512 0.010 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT 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: 0.60 2.01 2.84 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 6 branches were collapsed. NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 2 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -474.8623 Replicate 2 : -474.8505 (best) Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.474 0.599 2.020 2.815 rep 2: 4.516 0.599 2.014 2.838 Saving final trees from all search reps to out.p.mkvO.ssr.best.all.tre Saving final tree from best search rep (#2) to out.p.mkvO.ssr.best.tre ####################################################### >>>Search rep 3 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate 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=290145159 Initial ln Likelihood: -605.1903 optimizing: starting branch lengths, subset rates... pass 1:+ 116.111 (branch= 105.75 scale= 0.22 subset rates= 10.14) pass 2:+ 10.329 (branch= 5.57 scale= 0.02 subset rates= 4.75) pass 3:+ 2.693 (branch= 1.07 scale= 0.00 subset rates= 1.62) pass 4:+ 0.940 (branch= 0.38 scale= 0.00 subset rates= 0.56) pass 5:+ 0.206 (branch= 0.17 scale= 0.00 subset rates= 0.04) pass 6:+ 0.019 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -474.8926 gen current_lnL precision last_tree_imp 0 -474.8926 0.010 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT 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: 0.60 2.01 2.84 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 3 branches were collapsed. NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 3 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -474.8623 Replicate 2 : -474.8505 (best) Replicate 3 : -474.8833 Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.474 0.599 2.020 2.815 rep 2: 4.516 0.599 2.014 2.838 rep 3: 4.460 0.600 2.010 2.837 Saving final trees from all search reps to out.p.mkvO.ssr.best.all.tre Saving final tree from best search rep (#2) to out.p.mkvO.ssr.best.tre ####################################################### >>>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=2044747317 Initial ln Likelihood: -652.1691 optimizing: starting branch lengths, subset rates... pass 1:+ 155.944 (branch= 145.32 scale= 0.58 subset rates= 10.04) pass 2:+ 15.207 (branch= 10.68 scale= 0.00 subset rates= 4.52) pass 3:+ 3.710 (branch= 2.16 scale= 0.00 subset rates= 1.55) pass 4:+ 1.982 (branch= 1.40 scale= 0.00 subset rates= 0.58) pass 5:+ 0.365 (branch= 0.33 scale= 0.00 subset rates= 0.03) pass 6:+ 0.111 (branch= 0.11 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -474.8509 gen current_lnL precision last_tree_imp 0 -474.8509 0.010 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT 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: 0.60 2.01 2.86 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 5 branches were collapsed. NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 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. Results: Replicate 1 : -474.8623 Replicate 2 : -474.8505 Replicate 3 : -474.8833 Replicate 4 : -474.8495 (best) Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.474 0.599 2.020 2.815 rep 2: 4.516 0.599 2.014 2.838 rep 3: 4.460 0.600 2.010 2.837 rep 4: 4.504 0.598 2.009 2.859 Saving final trees from all search reps to out.p.mkvO.ssr.best.all.tre Saving final tree from best search rep (#4) to out.p.mkvO.ssr.best.tre ####################################################### >>>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 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=1380786643 Initial ln Likelihood: -628.4721 optimizing: starting branch lengths, subset rates... pass 1:+ 137.115 (branch= 125.84 scale= 0.86 subset rates= 10.41) pass 2:+ 12.972 (branch= 8.00 scale= 0.03 subset rates= 4.94) pass 3:+ 2.469 (branch= 0.79 scale= 0.00 subset rates= 1.68) pass 4:+ 0.826 (branch= 0.23 scale= 0.01 subset rates= 0.58) pass 5:+ 0.169 (branch= 0.13 scale= 0.00 subset rates= 0.04) pass 6:+ 0.011 (branch= 0.01 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -474.9108 gen current_lnL precision last_tree_imp 0 -474.9108 0.010 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT 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: 0.60 2.02 2.84 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 4 branches were collapsed. NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 5 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -474.8623 Replicate 2 : -474.8505 Replicate 3 : -474.8833 Replicate 4 : -474.8495 (best) Replicate 5 : -474.9075 Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.474 0.599 2.020 2.815 rep 2: 4.516 0.599 2.014 2.838 rep 3: 4.460 0.600 2.010 2.837 rep 4: 4.504 0.598 2.009 2.859 rep 5: 4.499 0.597 2.020 2.842 Saving final trees from all search reps to out.p.mkvO.ssr.best.all.tre Saving final tree from best search rep (#4) to out.p.mkvO.ssr.best.tre ####################################################### [Reading test.out.p.mkvO.ssr.nex ] Executing Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS storing read block: ASSUMPTIONS storing read block: TREES TREEFILES PASS ************************** Running checkpoint tests ... ************************** Running checkpoint test ./check/a.G3.conf Running checkpoint test ./check/a.G3.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./check/a.G3.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x30.stop.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data Warning: stop codon TAA found at codon site 11 (nuc site 31) in taxon MorNa6. Treating as missing data because ignorestopcodons = 1 is set in configuration file. Some sites treated as missing data for taxon MorNa6 due to ambiguity in translation. Aminoacids coded as missing for that taxon: 11 Warning: stop codon TAA found at codon site 11 (nuc site 31) in taxon ClownNa6. Treating as missing data because ignorestopcodons = 1 is set in configuration file. Some sites treated as missing data for taxon ClownNa6 due to ambiguity in translation. Aminoacids coded as missing for that taxon: 11 WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 11 sequences. 3 constant characters. 6 parsimony-informative characters. 1 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 10 total characters (11 before removing empty columns). 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 2 ####################################################### STARTING RUN Bootstrap reweighting... Subset 1: Random seed for bootstrap reweighting: 42 >>>Bootstrap rep 1 (of 1) <<< MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) 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 0.5000 with an invariant (invariable) site category, proportion estimated 0.0750 Substitution rate categories under this model: rate proportion 0.0000 0.0750 0.0603 0.3083 0.4894 0.3083 2.4503 0.3083 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.001 lnL Optimizing branchlengths... improved 0.178 lnL 7 8 9 10 11 Initial ln Likelihood: -94.5491 optimizing: starting branch lengths, alpha shape, prop. invar... pass 1:+ 1.029 (branch= 1.03 scale= 0.00 alpha= 0.00 pinv= 0.00) pass 2:+ 0.113 (branch= 0.11 scale= 0.00 alpha= 0.00 pinv= 0.00) lnL after optimization: -93.4068 gen current_lnL precision last_tree_imp 0 -93.4068 0.500 0 100 -93.0240 0.500 0 200 -91.3705 0.500 199 300 -90.7565 0.500 215 400 -90.4959 0.500 215 500 -90.3850 0.500 215 600 -90.2906 0.500 215 700 -90.2169 0.500 215 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 32-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/a.G3.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x30.stop.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data Warning: stop codon TAA found at codon site 11 (nuc site 31) in taxon MorNa6. Treating as missing data because ignorestopcodons = 1 is set in configuration file. Some sites treated as missing data for taxon MorNa6 due to ambiguity in translation. Aminoacids coded as missing for that taxon: 11 Warning: stop codon TAA found at codon site 11 (nuc site 31) in taxon ClownNa6. Treating as missing data because ignorestopcodons = 1 is set in configuration file. Some sites treated as missing data for taxon ClownNa6 due to ambiguity in translation. Aminoacids coded as missing for that taxon: 11 WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 11 sequences. 3 constant characters. 6 parsimony-informative characters. 1 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 10 total characters (11 before removing empty columns). 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 2 ####################################################### STARTING RUN Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... Bootstrap rep 1 (of 1) generation 742, seed 2077777172, best lnL -90.186 gen current_lnL precision last_tree_imp 742 -90.1864 0.500 215 800 -90.1648 0.500 215 Optimization precision reduced Optimizing parameters... improved 0.159 lnL Optimizing branchlengths... improved 0.317 lnL 900 -88.9507 0.010 879 1000 -88.8871 0.010 879 NOTE: ****Specified generation limit (1000) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT 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 0.9045 with an invariant (invariable) site category, proportion estimated 0.1355 Substitution rate categories under this model: rate proportion 0.0000 0.1355 0.1669 0.2882 0.6855 0.2882 2.1476 0.2882 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -88.8871 Parameter estimates: alpha pinv rep 1: 0.904 0.136 Treelengths: TL rep 1: 2.441 Saving best tree to bootstrap file ch.a.G3.boot.tre WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/a.G4.conf Running checkpoint test ./check/a.G4.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./check/a.G4.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.AA.fas as Fasta amino acid format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Amino acid data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 11 sequences. 3 constant characters. 6 parsimony-informative characters. 1 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 10 total characters (11 before removing empty columns). 10 unique patterns in compressed data matrix. ################################################### 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. 0.8 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 2 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) 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: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0750 Substitution rate categories under this model: rate proportion 0.0000 0.0750 0.0334 0.2313 0.2519 0.2313 0.8203 0.2313 2.8944 0.2313 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.001 lnL Optimizing branchlengths... improved 0.006 lnL 7 8 9 10 11 Initial ln Likelihood: -117.7431 optimizing: starting branch lengths, alpha shape, prop. invar... pass 1:+ 1.466 (branch= 1.13 scale= 0.33 alpha= 0.00 pinv= 0.00) pass 2:+ 0.134 (branch= 0.13 scale= 0.00 alpha= 0.00 pinv= 0.00) lnL after optimization: -116.1434 gen current_lnL precision last_tree_imp 0 -116.1434 0.500 0 100 -112.9555 0.500 84 200 -112.4964 0.500 84 300 -112.3224 0.500 84 400 -112.1061 0.500 84 500 -111.8129 0.500 84 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 32-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/a.G4.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.AA.fas as Fasta amino acid format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Amino acid data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 11 sequences. 3 constant characters. 6 parsimony-informative characters. 1 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 10 total characters (11 before removing empty columns). 10 unique patterns in compressed data matrix. ################################################### 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. 0.8 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 2 ####################################################### STARTING RUN Restarting from checkpoint... generation 554, seed 2134268789, best lnL -111.786 gen current_lnL precision last_tree_imp 554 -111.7863 0.500 84 600 -111.7788 0.500 84 Optimization precision reduced Optimizing parameters... improved 0.386 lnL Optimizing branchlengths... improved 0.390 lnL 700 -110.8142 0.010 615 800 -110.5642 0.010 707 900 -110.5555 0.010 707 1000 -110.5065 0.010 707 NOTE: ****Specified generation limit (1000) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT 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: 4 discrete gamma distributed rate categories, alpha param estimated 1.3049 with an invariant (invariable) site category, proportion estimated 0.0988 Substitution rate categories under this model: rate proportion 0.0000 0.0988 0.1936 0.2253 0.5525 0.2253 1.0366 0.2253 2.2174 0.2253 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. Saving site likelihoods to file ch.a.G4.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 : -110.5065 Parameter estimates: alpha pinv rep 1: 1.305 0.099 Treelengths: TL rep 1: 2.534 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 WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### TREEFILES PASS Running checkpoint test ./check/a.conf Running checkpoint test ./check/a.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./check/a.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 11 sequences. 3 constant characters. 6 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### 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. 0.2 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 2 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) 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: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 0.121 lnL 7 8 9 10 11 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -117.7533 optimizing: starting branch lengths... pass 1:+ 0.632 (branch= 0.63 scale= 0.00) pass 2:+ 0.134 (branch= 0.13 scale= 0.00) lnL after optimization: -116.9881 gen current_lnL precision last_tree_imp 0 -116.9881 0.500 0 100 -113.6842 0.500 91 200 -112.5462 0.500 160 300 -112.1250 0.500 160 400 -111.8851 0.500 160 500 -111.7755 0.500 160 600 -111.6975 0.500 563 700 -111.6876 0.500 563 800 -111.6844 0.500 563 900 -111.6835 0.500 563 1000 -111.6829 0.500 563 1100 -111.6827 0.500 563 Optimization precision reduced Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 0.000 lnL 1200 -111.6824 0.010 563 1300 -111.6822 0.010 563 1400 -111.6821 0.010 563 1500 -111.6819 0.010 563 1600 -111.6818 0.010 563 1700 -111.6818 0.010 563 1800 -111.6818 0.010 563 1900 -111.6818 0.010 563 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 32-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/a.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 11 sequences. 3 constant characters. 6 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### 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. 0.2 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 2 ####################################################### STARTING RUN Restarting from checkpoint... generation 1965, seed 702611603, best lnL -111.682 gen current_lnL precision last_tree_imp 1965 -111.6817 0.010 563 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: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. Saving site likelihoods to file ch.a.sitelikes.log ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -111.6817 Parameter estimates: Model contains no estimated parameters Treelengths: TL rep 1: 2.605 Saving final tree from best search rep (#1) to ch.a.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.internalstates.log ####################################################### TREEFILES PASS Running checkpoint test ./check/c.M3x2.conf Running checkpoint test ./check/c.M3x2.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./check/c.M3x2.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Codon data Base usage at codon positions: A C G T pos 1 0.27723 0.36634 0.21782 0.13861 pos 2 0.30693 0.20792 0.07921 0.40594 pos 3 0.10891 0.38614 0.26733 0.23762 all pos 0.23102 0.32013 0.18812 0.26073 Summary of data: 11 sequences. 0 constant characters. 9 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### 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. 1.3 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0094 0.0334 0.0231 0.0206 0.0064 0.0226 0.0157 0.0139 0.0024 0.0086 0.0060 0.0053 0.0125 0.0442 0.0306 0.0272 0.0125 0.0442 0.0306 0.0272 0.0084 0.0299 0.0207 0.0184 0.0032 0.0114 0.0079 0.0070 0.0165 0.0584 0.0405 0.0360 0.0074 0.0263 0.0182 0.0162 0.0050 0.0178 0.0123 0.0110 0.0019 0.0068 0.0047 0.0042 0.0098 0.0347 0.0241 0.0214 0.0167 0.0103 0.0032 0.0113 0.0078 0.0070 0.0043 0.0030 0.0027 0.0062 0.0221 0.0153 0.0136 Rate Heterogeneity Model: 2 nonsynonymous rate categories, rate and proportion of each estimated (this is effectively the M3 model of PAML) dN/dS Proportion 0.2500 0.5000 0.5000 0.5000 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 4.461 lnL Optimizing branchlengths... improved 0.701 lnL 7 8 9 10 11 Initial ln Likelihood: -215.8071 optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters... pass 1:+ 6.388 (branch= 0.00 scale= 0.44 omega= 0.01 rel rates= 5.93) pass 2:+ 0.434 (branch= 0.00 scale= 0.00 omega= 0.01 rel rates= 0.42) lnL after optimization: -208.9856 gen current_lnL precision last_tree_imp 0 -208.9856 0.500 0 10 -207.1401 0.500 10 20 -205.6892 0.500 18 30 -205.6499 0.500 18 40 -205.6371 0.500 18 50 -205.6175 0.500 18 60 -205.5990 0.500 53 NOTE: ****Specified time limit (10 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 32-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/c.M3x2.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Codon data Base usage at codon positions: A C G T pos 1 0.27723 0.36634 0.21782 0.13861 pos 2 0.30693 0.20792 0.07921 0.40594 pos 3 0.10891 0.38614 0.26733 0.23762 all pos 0.23102 0.32013 0.18812 0.26073 Summary of data: 11 sequences. 0 constant characters. 9 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### 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. 1.3 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN Restarting from checkpoint... generation 60, seed 1308822963, best lnL -205.599 gen current_lnL precision last_tree_imp 60 -205.5990 0.500 53 70 -205.5741 0.500 53 80 -205.4022 0.500 76 90 -205.3871 0.500 76 100 -205.3829 0.500 76 NOTE: ****Specified generation limit (100) reached... 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 = 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) 0.0094 0.0334 0.0231 0.0206 0.0064 0.0226 0.0157 0.0139 0.0024 0.0086 0.0060 0.0053 0.0125 0.0442 0.0306 0.0272 0.0125 0.0442 0.0306 0.0272 0.0084 0.0299 0.0207 0.0184 0.0032 0.0114 0.0079 0.0070 0.0165 0.0584 0.0405 0.0360 0.0074 0.0263 0.0182 0.0162 0.0050 0.0178 0.0123 0.0110 0.0019 0.0068 0.0047 0.0042 0.0098 0.0347 0.0241 0.0214 0.0167 0.0103 0.0032 0.0113 0.0078 0.0070 0.0043 0.0030 0.0027 0.0062 0.0221 0.0153 0.0136 Rate Heterogeneity Model: 2 nonsynonymous rate categories, rate and proportion of each estimated (this is effectively the M3 model of PAML) dN/dS Proportion 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 : -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: 0.049 0.521 0.499 0.479 1.586 3.999 0.04 2.453 3.968 1 Treelengths: TL 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 Running checkpoint test ./check/c.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./check/c.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Codon data Base usage at codon positions: A C G T pos 1 0.27723 0.36634 0.21782 0.13861 pos 2 0.30693 0.20792 0.07921 0.40594 pos 3 0.10891 0.38614 0.26733 0.23762 all pos 0.23102 0.32013 0.18812 0.26073 Summary of data: 11 sequences. 0 constant characters. 9 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 2 ####################################################### STARTING RUN Bootstrap reweighting... Subset 1: Random seed for bootstrap reweighting: 42 >>>Bootstrap rep 1 (of 1) <<< MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 61 (codon data, standard code) One estimated dN/dS ratio (aka omega) = 0.250000 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0094 0.0334 0.0231 0.0206 0.0064 0.0226 0.0157 0.0139 0.0024 0.0086 0.0060 0.0053 0.0125 0.0442 0.0306 0.0272 0.0125 0.0442 0.0306 0.0272 0.0084 0.0299 0.0207 0.0184 0.0032 0.0114 0.0079 0.0070 0.0165 0.0584 0.0405 0.0360 0.0074 0.0263 0.0182 0.0162 0.0050 0.0178 0.0123 0.0110 0.0019 0.0068 0.0047 0.0042 0.0098 0.0347 0.0241 0.0214 0.0167 0.0103 0.0032 0.0113 0.0078 0.0070 0.0043 0.0030 0.0027 0.0062 0.0221 0.0153 0.0136 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.353 lnL Optimizing branchlengths... improved 0.746 lnL 7 8 9 10 11 Initial ln Likelihood: -208.5106 optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters... pass 1:+ 10.487 (branch= 0.90 scale= 0.55 omega= 0.01 rel rates= 9.03) pass 2:+ 2.529 (branch= 2.19 scale= 0.00 omega= 0.00 rel rates= 0.34) pass 3:+ 0.095 (branch= 0.02 scale= 0.00 omega= 0.00 rel rates= 0.07) lnL after optimization: -195.3999 gen current_lnL precision last_tree_imp 0 -195.3999 0.500 0 10 -195.3553 0.500 0 20 -195.3340 0.500 0 30 -195.2776 0.500 0 40 -195.2555 0.500 0 50 -195.2137 0.500 0 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 32-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/c.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Codon data Base usage at codon positions: A C G T pos 1 0.27723 0.36634 0.21782 0.13861 pos 2 0.30693 0.20792 0.07921 0.40594 pos 3 0.10891 0.38614 0.26733 0.23762 all pos 0.23102 0.32013 0.18812 0.26073 Summary of data: 11 sequences. 0 constant characters. 9 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 2 ####################################################### STARTING RUN Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... Bootstrap rep 1 (of 1) generation 52, seed 754137322, best lnL -195.214 gen current_lnL precision last_tree_imp 52 -195.2137 0.500 0 60 -195.1629 0.500 0 70 -195.0043 0.500 0 80 -194.9478 0.500 0 90 -194.9092 0.500 0 100 -194.9092 0.500 0 NOTE: ****Specified generation limit (100) reached... 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 = 5.680, 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) 0.0094 0.0334 0.0231 0.0206 0.0064 0.0226 0.0157 0.0139 0.0024 0.0086 0.0060 0.0053 0.0125 0.0442 0.0306 0.0272 0.0125 0.0442 0.0306 0.0272 0.0084 0.0299 0.0207 0.0184 0.0032 0.0114 0.0079 0.0070 0.0165 0.0584 0.0405 0.0360 0.0074 0.0263 0.0182 0.0162 0.0050 0.0178 0.0123 0.0110 0.0019 0.0068 0.0047 0.0042 0.0098 0.0347 0.0241 0.0214 0.0167 0.0103 0.0032 0.0113 0.0078 0.0070 0.0043 0.0030 0.0027 0.0062 0.0221 0.0153 0.0136 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 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 : -194.9092 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 5.68 0.01146 4.174 2.324 1 Treelengths: TL rep 1: 9.255 Saving best tree to bootstrap file ch.c.boot.tre WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/g.dnaBnoZ.conf Running checkpoint test ./check/g.dnaBnoZ.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./check/g.dnaBnoZ.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/dnaGap.8x1K.nex ... Reading TAXA block...storing read block: TAXA successful Reading CHARACTERS block...storing read block: CHARACTERS found dna data... successful Reading CHARACTERS block...storing read block: CHARACTERS found standard data... successful Reading TREES block...storing read block: TREES successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1GapsAsMissing") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 8 sequences. 428 constant characters. 129 parsimony-informative characters. 100 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 239 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #2 ("Untitled DATA Block 1GapsAsBinary") Data read as Binary data, no constant state 0 chars, modeled as Binary data, no constant state 0 chars NOTE: entirely missing characters removed from matrix: 1 25 29-34 36 37 52-54 61 67-69 84 85 87 95 96 99 106 110-116 125 138-145 163-165 167 169-177 188 197-199 202-210 213 216-218 228-231 233-236 238-240 247 249 256 257 260 266-270 \ 2 271-277 281-285 290-294 298-300 311 312 322 325 331 332 336-338 344 359 369 373-378 397 404-406 413 416 417 420-426 439-442 450-454 \ 2 455-460 462 471 474-479 487-490 492 494 495 497 502-506 510 521-526 532 533 538-541 544 547 551-553 562 570-572 577 579 609 610 614 615 622 624-626 639 640 647-650 653 655-660 667 668 673-676 679 680 685 695 696 701-705 708-713 716 717 731 742-749 751-755 762 763 770 771 783 788 791-793 804 806-808 813 821-825 827 830-832 840 842 843 845 850 851 856-865 886-894 896 897 903-905 913 914 924 927 948-956 963-971 976-981 991-993 996 Subset of data with 2 states: chars 1-1000 Summary of data: 8 sequences. 502 constant characters. 39 parsimony-informative characters. 116 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 24 unique patterns in compressed data matrix. ################################################### 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 >= 2 MB good approx 2 MB to 2 MB low approx 2 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. 2.8 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN >>>Search rep 1 (of 2)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3220 0.2180 0.1602 0.2999 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.1629 Substitution rate categories under this model: rate proportion 0.0000 0.1629 0.0334 0.2093 0.2519 0.2093 0.8203 0.2093 2.8944 0.2093 Model 2 Number of states = 2 (binary data) Character change matrix: Binary, no all-zero columns (2-state symmetric one rate model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -4043.7391 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates... pass 1:+ 532.047 (branch= 438.84 scale= 6.77 alpha= 15.79 freqs= 3.30 rel rates= 8.48 pinv= 0.00 subset rates= 58.86) pass 2:+ 88.209 (branch= 42.39 scale= 0.83 alpha= 0.82 freqs= 0.72 rel rates= 0.01 pinv= 0.00 subset rates= 43.45) pass 3:+ 34.899 (branch= 0.70 scale= 2.02 alpha= 1.89 freqs= 0.04 rel rates= 0.72 pinv= 0.00 subset rates= 29.52) pass 4:+ 17.437 (branch= 4.66 scale= 2.38 alpha= 1.70 freqs= 0.05 rel rates= 0.01 pinv= 0.00 subset rates= 8.64) pass 5:+ 10.201 (branch= 4.19 scale= 1.64 alpha= 0.69 freqs= 0.05 rel rates= 2.14 pinv= 0.00 subset rates= 1.49) pass 6:+ 1.986 (branch= 0.00 scale= 1.92 alpha= 0.00 freqs= 0.06 rel rates= 0.01 pinv= 0.00 subset rates= 0.00) pass 7:+ 0.532 (branch= 0.47 scale= 0.00 alpha= 0.00 freqs= 0.06 rel rates= 0.01 pinv= 0.00 subset rates= 0.00) pass 8:+ 0.057 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.05 rel rates= 0.01 pinv= 0.00 subset rates= 0.00) lnL after optimization: -3358.3708 gen current_lnL precision last_tree_imp 0 -3358.3708 0.500 0 100 -3357.1202 0.500 0 200 -3356.8081 0.500 0 300 -3356.5911 0.500 0 400 -3355.9752 0.500 0 500 -3355.8101 0.500 0 Optimization precision reduced Optimizing parameters... improved 0.940 lnL Optimizing branchlengths... improved 0.000 lnL 600 -3354.6612 0.255 0 700 -3354.3974 0.255 0 800 -3354.0880 0.255 0 900 -3353.8938 0.255 0 1000 -3353.6942 0.255 0 Optimization precision reduced Optimizing parameters... improved 0.834 lnL Optimizing branchlengths... improved 0.084 lnL 1100 -3352.7219 0.010 0 1200 -3352.6779 0.010 0 1300 -3352.5564 0.010 0 1400 -3352.3174 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 32-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/g.dnaBnoZ.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/dnaGap.8x1K.nex ... Reading TAXA block...storing read block: TAXA successful Reading CHARACTERS block...storing read block: CHARACTERS found dna data... successful Reading CHARACTERS block...storing read block: CHARACTERS found standard data... successful Reading TREES block...storing read block: TREES successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1GapsAsMissing") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 8 sequences. 428 constant characters. 129 parsimony-informative characters. 100 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 239 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #2 ("Untitled DATA Block 1GapsAsBinary") Data read as Binary data, no constant state 0 chars, modeled as Binary data, no constant state 0 chars NOTE: entirely missing characters removed from matrix: 1 25 29-34 36 37 52-54 61 67-69 84 85 87 95 96 99 106 110-116 125 138-145 163-165 167 169-177 188 197-199 202-210 213 216-218 228-231 233-236 238-240 247 249 256 257 260 266-270 \ 2 271-277 281-285 290-294 298-300 311 312 322 325 331 332 336-338 344 359 369 373-378 397 404-406 413 416 417 420-426 439-442 450-454 \ 2 455-460 462 471 474-479 487-490 492 494 495 497 502-506 510 521-526 532 533 538-541 544 547 551-553 562 570-572 577 579 609 610 614 615 622 624-626 639 640 647-650 653 655-660 667 668 673-676 679 680 685 695 696 701-705 708-713 716 717 731 742-749 751-755 762 763 770 771 783 788 791-793 804 806-808 813 821-825 827 830-832 840 842 843 845 850 851 856-865 886-894 896 897 903-905 913 914 924 927 948-956 963-971 976-981 991-993 996 Subset of data with 2 states: chars 1-1000 Summary of data: 8 sequences. 502 constant characters. 39 parsimony-informative characters. 116 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 24 unique patterns in compressed data matrix. ################################################### 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 >= 2 MB good approx 2 MB to 2 MB low approx 2 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. 2.8 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN Restarting from checkpoint... Search rep 1 (of 2) generation 1408, seed 1138782053, best lnL -3352.317 gen current_lnL precision last_tree_imp 1408 -3352.3174 0.010 0 1500 -3352.2778 0.010 0 1600 -3352.1759 0.010 0 1700 -3352.1636 0.010 0 1800 -3352.0841 0.010 0 1900 -3351.7369 0.010 0 2000 -3351.6702 0.010 0 2100 -3351.4829 0.010 0 2200 -3351.2993 0.010 0 2300 -3351.2513 0.010 0 2400 -3351.2155 0.010 0 2500 -3351.1237 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... Current score = -3351.1237 Performing final optimizations... pass 1 : -3351.0219 (branch= 0.0000 alpha= 0.0000 pinv= 0.0230 eq freqs= 0.0150 rel rates= 0.0606 subset rates= 0.0032) pass 2 : -3350.9202 (branch= 0.0031 alpha= 0.0104 pinv= 0.0174 eq freqs= 0.0000 rel rates= 0.0709 subset rates= 0.0000) pass 3 : -3350.8301 (branch= 0.0090 alpha= 0.0165 pinv= 0.0154 eq freqs= 0.0014 rel rates= 0.0458 subset rates= 0.0020) pass 4 : -3350.7577 (branch= 0.0058 alpha= 0.0131 pinv= 0.0145 eq freqs= 0.0000 rel rates= 0.0378 subset rates= 0.0012) pass 5 : -3350.6916 (branch= 0.0065 alpha= 0.0131 pinv= 0.0135 eq freqs= 0.0000 rel rates= 0.0317 subset rates= 0.0013) pass 6 : -3350.6372 (branch= 0.0025 alpha= 0.0112 pinv= 0.0124 eq freqs= 0.0002 rel rates= 0.0281 subset rates= 0.0000) pass 7 : -3350.5870 (branch= 0.0006 alpha= 0.0116 pinv= 0.0112 eq freqs= 0.0000 rel rates= 0.0257 subset rates= 0.0011) pass 8 : -3350.5427 (branch= 0.0019 alpha= 0.0106 pinv= 0.0102 eq freqs= 0.0003 rel rates= 0.0213 subset rates= 0.0000) pass 9 : -3350.5047 (branch= 0.0004 alpha= 0.0096 pinv= 0.0093 eq freqs= 0.0001 rel rates= 0.0187 subset rates= 0.0000) pass 10: -3350.4688 (branch= 0.0001 alpha= 0.0091 pinv= 0.0089 eq freqs= 0.0000 rel rates= 0.0165 subset rates= 0.0012) pass 11: -3350.4392 (branch= 0.0007 alpha= 0.0080 pinv= 0.0075 eq freqs= 0.0000 rel rates= 0.0133 subset rates= 0.0000) pass 12: -3350.4134 (branch= 0.0001 alpha= 0.0071 pinv= 0.0068 eq freqs= 0.0000 rel rates= 0.0119 subset rates= 0.0000) pass 13: -3350.3903 (branch= 0.0000 alpha= 0.0067 pinv= 0.0060 eq freqs= 0.0000 rel rates= 0.0104 subset rates= 0.0000) pass 14: -3350.3699 (branch= 0.0000 alpha= 0.0060 pinv= 0.0054 eq freqs= 0.0000 rel rates= 0.0090 subset rates= 0.0000) pass 15: -3350.3520 (branch= 0.0000 alpha= 0.0054 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0077 subset rates= 0.0000) pass 16: -3350.3363 (branch= 0.0000 alpha= 0.0048 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0067 subset rates= 0.0000) pass 17: -3350.3226 (branch= 0.0000 alpha= 0.0042 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0057 subset rates= 0.0000) pass 18: -3350.3107 (branch= 0.0000 alpha= 0.0037 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0049 subset rates= 0.0000) pass 19: -3350.3003 (branch= 0.0000 alpha= 0.0033 pinv= 0.0029 eq freqs= 0.0000 rel rates= 0.0042 subset rates= 0.0000) pass 20: -3350.2912 (branch= 0.0000 alpha= 0.0029 pinv= 0.0026 eq freqs= 0.0000 rel rates= 0.0036 subset rates= 0.0000) optimization up to ... pass 30: -3350.2462 (branch= 0.0000 alpha= 0.0144 pinv= 0.0130 eq freqs= 0.0001 rel rates= 0.0175 subset rates= 0.0000) optimization up to ... pass 40: -3350.2361 (branch= 0.0000 alpha= 0.0031 pinv= 0.0029 eq freqs= 0.0000 rel rates= 0.0041 subset rates= 0.0000) optimization up to ... pass 50: -3350.2339 (branch= 0.0000 alpha= 0.0006 pinv= 0.0005 eq freqs= 0.0000 rel rates= 0.0011 subset rates= 0.0000) optimization up to ... pass 60: -3350.2335 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) optimization up to ... pass 70: -3350.2334 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) optimization up to ... pass 71: -3350.2334 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -3350.2334 Time used so far = 0 hours, 0 minutes and 13 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 3.116, AG = 10.417, AT = 2.691, CG = 0.001, CT = 21.902, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3329 0.2222 0.1567 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5789 with an invariant (invariable) site category, proportion estimated 0.3662 Substitution rate categories under this model: rate proportion 0.0000 0.3662 0.0488 0.1584 0.3003 0.1584 0.8702 0.1584 2.7807 0.1584 Model 2 Number of states = 2 (binary data) Character change matrix: Binary, no all-zero columns (2-state symmetric one rate model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.82 0.18 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. >>>Terminated Search rep 1 (of 2)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 2). Results: Replicate 1 : -3350.2334 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 3.116 10.42 2.691 0.001 21.9 1 0.333 0.222 0.157 0.288 0.579 0.366 Partition model subset 2: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) rep 1: 0.788 1.820 0.180 Saving final tree from best search rep (#1) to ch.g.dnaBnoZ.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/g.dnaMix.conf Running checkpoint test ./check/g.dnaMix.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./check/g.dnaMix.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/dnaGap.8x1K.nex ... Reading TAXA block...storing read block: TAXA successful Reading CHARACTERS block...storing read block: CHARACTERS found dna data... successful Reading CHARACTERS block...storing read block: CHARACTERS found standard data... successful Reading TREES block...storing read block: TREES successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1GapsAsMissing") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 8 sequences. 428 constant characters. 129 parsimony-informative characters. 100 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 239 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #2 ("Untitled DATA Block 1GapsAsBinary") Data read as Gap-coded data, oriented with respect to time, modeled as Gap-coded data, oriented with respect to time Summary of data: 8 sequences. 502 constant characters. 39 parsimony-informative characters. 116 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 24 unique patterns in compressed data matrix. ################################################### 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 >= 2 MB good approx 2 MB to 2 MB low approx 2 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. 3.2 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### WARNING - specified outgroup (1) being ignored due to inference of a rooted true ####################################################### STARTING RUN >>>Search rep 1 (of 2)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3220 0.2180 0.1602 0.2999 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.1629 Substitution rate categories under this model: rate proportion 0.0000 0.1629 0.0334 0.2093 0.2519 0.2093 0.8203 0.2093 2.8944 0.2093 Model 2 Number of states = 2 (0/1 coding of gaps) Character change matrix: irreversible matrix deletion rate parameter only estimated if using a partitioned model without subset rates deletion rate = 1.000 Equilibrium State Frequencies: proportion of inserted sites parameter insert proportion = 0.500 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 Initial ln Likelihood: -4257.0961 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, ins rate, del rate... pass 1:+ 640.405 (branch= 431.06 scale= 2.03 alpha= 9.92 freqs= 3.07 rel rates= 7.29 pinv= 0.00 ins/del=187.03) pass 2:+ 169.102 (branch= 75.12 scale= 1.32 alpha= 0.88 freqs= 0.65 rel rates= 0.01 pinv= 0.00 ins/del= 91.12) pass 3:+ 55.144 (branch= 7.14 scale= 1.85 alpha= 1.09 freqs= 0.05 rel rates= 0.90 pinv= 0.00 ins/del= 44.12) pass 4:+ 25.231 (branch= 7.02 scale= 1.52 alpha= 0.69 freqs= 0.06 rel rates= 0.01 pinv= 0.00 ins/del= 15.94) pass 5:+ 14.361 (branch= 7.97 scale= 1.87 alpha= 0.01 freqs= 0.05 rel rates= 2.45 pinv= 0.00 ins/del= 2.01) pass 6:+ 10.438 (branch= 7.36 scale= 2.34 alpha= 0.01 freqs= 0.07 rel rates= 0.00 pinv= 0.00 ins/del= 0.66) pass 7:+ 6.158 (branch= 5.23 scale= 0.83 alpha= 0.01 freqs= 0.06 rel rates= 0.00 pinv= 0.00 ins/del= 0.03) pass 8:+ 3.640 (branch= 2.31 scale= 0.00 alpha= 0.00 freqs= 0.05 rel rates= 0.60 pinv= 0.00 ins/del= 0.67) pass 9:+ 0.148 (branch= 0.08 scale= 0.00 alpha= 0.00 freqs= 0.06 rel rates= 0.00 pinv= 0.00 ins/del= 0.00) lnL after optimization: -3332.4700 gen current_lnL precision last_tree_imp 0 -3332.4700 0.500 0 100 -3324.9856 0.500 1 200 -3324.7543 0.500 1 300 -3324.3007 0.500 1 400 -3323.9848 0.500 1 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 32-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/g.dnaMix.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/dnaGap.8x1K.nex ... Reading TAXA block...storing read block: TAXA successful Reading CHARACTERS block...storing read block: CHARACTERS found dna data... successful Reading CHARACTERS block...storing read block: CHARACTERS found standard data... successful Reading TREES block...storing read block: TREES successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1GapsAsMissing") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 8 sequences. 428 constant characters. 129 parsimony-informative characters. 100 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 239 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #2 ("Untitled DATA Block 1GapsAsBinary") Data read as Gap-coded data, oriented with respect to time, modeled as Gap-coded data, oriented with respect to time Summary of data: 8 sequences. 502 constant characters. 39 parsimony-informative characters. 116 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 24 unique patterns in compressed data matrix. ################################################### 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 >= 2 MB good approx 2 MB to 2 MB low approx 2 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. 3.2 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### WARNING - specified outgroup (1) being ignored due to inference of a rooted true ####################################################### STARTING RUN Restarting from checkpoint... Search rep 1 (of 2) generation 493, seed 1330261031, best lnL -3323.682 gen current_lnL precision last_tree_imp 493 -3323.6818 0.500 1 500 -3323.6818 0.500 1 600 -3323.3459 0.500 1 Optimization precision reduced Optimizing parameters... improved 1.812 lnL Optimizing branchlengths... improved 0.023 lnL 700 -3321.3649 0.255 1 800 -3321.0294 0.255 1 900 -3321.0142 0.255 1 NOTE: ****Specified time limit (5 seconds) reached... Current score = -3320.9684 Performing final optimizations... pass 1 : -3320.2910 (branch= 0.0812 alpha= 0.0000 pinv= 0.0165 eq freqs= 0.0053 rel rates= 0.5492 ins/del rates= 0.0252) pass 2 : -3319.8331 (branch= 0.0649 alpha= 0.0065 pinv= 0.0163 eq freqs= 0.0000 rel rates= 0.3496 ins/del rates= 0.0205) pass 3 : -3319.4759 (branch= 0.0441 alpha= 0.0079 pinv= 0.0160 eq freqs= 0.0070 rel rates= 0.2671 ins/del rates= 0.0151) pass 4 : -3319.2077 (branch= 0.0229 alpha= 0.0107 pinv= 0.0153 eq freqs= 0.0013 rel rates= 0.2089 ins/del rates= 0.0091) pass 5 : -3318.9892 (branch= 0.0167 alpha= 0.0109 pinv= 0.0147 eq freqs= 0.0012 rel rates= 0.1686 ins/del rates= 0.0065) pass 6 : -3318.8024 (branch= 0.0125 alpha= 0.0097 pinv= 0.0138 eq freqs= 0.0011 rel rates= 0.1443 ins/del rates= 0.0054) pass 7 : -3318.6458 (branch= 0.0078 alpha= 0.0103 pinv= 0.0129 eq freqs= 0.0004 rel rates= 0.1220 ins/del rates= 0.0033) pass 8 : -3318.5189 (branch= 0.0049 alpha= 0.0104 pinv= 0.0121 eq freqs= 0.0002 rel rates= 0.0973 ins/del rates= 0.0021) pass 9 : -3318.4112 (branch= 0.0035 alpha= 0.0097 pinv= 0.0112 eq freqs= 0.0002 rel rates= 0.0816 ins/del rates= 0.0015) pass 10: -3318.3194 (branch= 0.0023 alpha= 0.0095 pinv= 0.0109 eq freqs= 0.0002 rel rates= 0.0678 ins/del rates= 0.0010) pass 11: -3318.2442 (branch= 0.0015 alpha= 0.0089 pinv= 0.0094 eq freqs= 0.0002 rel rates= 0.0545 ins/del rates= 0.0007) pass 12: -3318.1805 (branch= 0.0010 alpha= 0.0083 pinv= 0.0086 eq freqs= 0.0001 rel rates= 0.0453 ins/del rates= 0.0004) pass 13: -3318.1262 (branch= 0.0007 alpha= 0.0078 pinv= 0.0078 eq freqs= 0.0001 rel rates= 0.0376 ins/del rates= 0.0003) pass 14: -3318.0799 (branch= 0.0004 alpha= 0.0072 pinv= 0.0071 eq freqs= 0.0001 rel rates= 0.0314 ins/del rates= 0.0002) pass 15: -3318.0407 (branch= 0.0003 alpha= 0.0067 pinv= 0.0064 eq freqs= 0.0001 rel rates= 0.0257 ins/del rates= 0.0001) pass 16: -3318.0068 (branch= 0.0002 alpha= 0.0060 pinv= 0.0057 eq freqs= 0.0001 rel rates= 0.0218 ins/del rates= 0.0001) pass 17: -3317.9776 (branch= 0.0001 alpha= 0.0054 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0184 ins/del rates= 0.0000) pass 18: -3317.9523 (branch= 0.0001 alpha= 0.0049 pinv= 0.0046 eq freqs= 0.0000 rel rates= 0.0157 ins/del rates= 0.0000) pass 19: -3317.9303 (branch= 0.0000 alpha= 0.0044 pinv= 0.0041 eq freqs= 0.0000 rel rates= 0.0134 ins/del rates= 0.0000) pass 20: -3317.9112 (branch= 0.0000 alpha= 0.0039 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0114 ins/del rates= 0.0000) optimization up to ... pass 30: -3317.8162 (branch= 0.0001 alpha= 0.0212 pinv= 0.0195 eq freqs= 0.0001 rel rates= 0.0541 ins/del rates= 0.0000) optimization up to ... pass 40: -3317.7937 (branch= 0.0001 alpha= 0.0052 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0124 ins/del rates= 0.0000) optimization up to ... pass 50: -3317.7885 (branch= 0.0000 alpha= 0.0011 pinv= 0.0010 eq freqs= 0.0000 rel rates= 0.0030 ins/del rates= 0.0000) optimization up to ... pass 60: -3317.7873 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0007 ins/del rates= 0.0000) optimization up to ... pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 ins/del rates= 0.0000) optimization up to ... pass 73: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3317.7871 Time used so far = 0 hours, 0 minutes and 13 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 3.066, AG = 10.264, AT = 2.655, CG = 0.001, CT = 21.539, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3328 0.2223 0.1567 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5749 with an invariant (invariable) site category, proportion estimated 0.3614 Substitution rate categories under this model: rate proportion 0.0000 0.3614 0.0480 0.1597 0.2980 0.1597 0.8680 0.1597 2.7860 0.1597 Model 2 Number of states = 2 (0/1 coding of gaps) Character change matrix: irreversible matrix deletion rate parameter only estimated if using a partitioned model without subset rates deletion rate = 0.158 Equilibrium State Frequencies: proportion of inserted sites parameter insert proportion = 0.036 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. >>>Terminated Search rep 1 (of 2)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 2). Results: Replicate 1 : -3317.7871 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 3.066 10.26 2.655 0.001 21.54 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del rep 1: 0.036 0.158 **ins = proportion of columns that experienced an insertion **del = deletion rate relative to nucleotide substitution rate Treelengths: TL rep 1: 1.419 Saving final tree from best search rep (#1) to ch.g.dnaMix.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/n.G3.conf Running checkpoint test ./check/n.G3.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./check/n.G3.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### 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. 0.3 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0603 0.3028 0.4894 0.3028 2.4503 0.3028 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.004 lnL Optimizing branchlengths... improved 0.000 lnL 7 8 9 10 11 Initial ln Likelihood: -226.8217 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 3.951 (branch= 0.75 scale= 0.00 alpha= 0.00 freqs= 1.76 rel rates= 1.44 pinv= 0.00) pass 2:+ 0.586 (branch= 0.56 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.00) pass 3:+ 1.297 (branch= 0.66 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.61 pinv= 0.00) pass 4:+ 0.021 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.02 rel rates= 0.00 pinv= 0.00) lnL after optimization: -220.9660 gen current_lnL precision last_tree_imp 0 -220.9660 0.500 0 200 -214.6292 0.500 192 400 -213.8826 0.500 231 600 -213.2669 0.500 572 800 -213.0149 0.500 572 1000 -212.8168 0.500 572 Optimization precision reduced Optimizing parameters... improved 1.265 lnL Optimizing branchlengths... improved 0.275 lnL 1200 -211.1651 0.010 1104 1400 -211.1317 0.010 1104 1600 -211.0217 0.010 1104 1800 -210.9997 0.010 1104 2000 -210.9459 0.010 1104 2200 -210.8945 0.010 1104 2400 -210.8863 0.010 1104 2600 -210.8436 0.010 1104 2800 -210.8251 0.010 1104 3000 -210.8189 0.010 1104 3200 -210.7905 0.010 1104 3400 -210.7553 0.010 1104 3600 -210.7287 0.010 1104 3800 -210.7083 0.010 1104 4000 -210.6947 0.010 1104 4200 -210.6742 0.010 1104 4400 -210.6493 0.010 1104 4600 -210.6258 0.010 1104 4800 -210.5949 0.010 1104 5000 -210.5740 0.010 1104 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 32-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/n.G3.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### 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. 0.3 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN Restarting from checkpoint... generation 5151, seed 390961462, best lnL -210.570 gen current_lnL precision last_tree_imp 5151 -210.5697 0.010 1104 5200 -210.5694 0.010 1104 Reached termination condition! last topological improvement at gen 1104 Improvement over last 500 gen = 0.04047 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 2.798, AG = 5.231, AT = 0.196, CG = 4.937, CT = 7.821, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2331 0.3366 0.2107 0.2196 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 1.2338 with an invariant (invariable) site category, proportion estimated 0.1337 Substitution rate categories under this model: rate proportion 0.0000 0.1337 0.2378 0.2888 0.7622 0.2888 1.9999 0.2888 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. Saving site likelihoods to file ch.n.G3.sitelikes.log ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -210.5694 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 2.798 5.231 0.1964 4.937 7.821 1 0.233 0.337 0.211 0.220 1.234 0.134 Treelengths: TL rep 1: 2.254 Saving final tree from best search rep (#1) to ch.n.G3.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.G3.internalstates.log ####################################################### TREEFILES PASS Running checkpoint test ./check/n.G4.conf Running checkpoint test ./check/n.G4.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./check/n.G4.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### 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. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN Bootstrap reweighting... Subset 1: Random seed for bootstrap reweighting: 42 >>>Bootstrap rep 1 (of 1) <<< MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0334 0.2271 0.2519 0.2271 0.8203 0.2271 2.8944 0.2271 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.004 lnL Optimizing branchlengths... improved 0.786 lnL 7 8 9 10 11 Initial ln Likelihood: -178.2162 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 5.336 (branch= 0.56 scale= 1.69 alpha= 0.00 freqs= 1.38 rel rates= 1.70 pinv= 0.00) pass 2:+ 0.075 (branch= 0.04 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.00) lnL after optimization: -172.8046 gen current_lnL precision last_tree_imp 0 -172.8046 0.500 0 200 -171.4789 0.500 172 400 -170.7806 0.500 296 600 -170.2707 0.500 296 800 -169.9099 0.500 296 Optimization precision reduced Optimizing parameters... improved 2.192 lnL Optimizing branchlengths... improved 0.321 lnL 1000 -167.2062 0.010 843 1200 -167.1470 0.010 843 1400 -167.0481 0.010 843 1600 -166.9636 0.010 843 1800 -166.8217 0.010 843 2000 -166.6783 0.010 843 2200 -166.5883 0.010 843 2400 -166.4575 0.010 843 2600 -166.3858 0.010 843 2800 -166.3653 0.010 843 3000 -166.3065 0.010 843 3200 -166.2781 0.010 843 3400 -166.2093 0.010 843 3600 -166.0613 0.010 843 3800 -165.9516 0.010 843 4000 -165.8994 0.010 843 4200 -165.8521 0.010 843 4400 -165.7753 0.010 843 4600 -165.6384 0.010 843 4800 -165.6163 0.010 843 5000 -165.5786 0.010 843 5200 -165.5685 0.010 843 5400 -165.5324 0.010 843 5600 -165.3816 0.010 843 5800 -165.2859 0.010 843 6000 -165.2075 0.010 843 6200 -165.1217 0.010 843 6400 -164.9323 0.010 843 6600 -164.7902 0.010 843 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 32-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/n.G4.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### 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. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... Bootstrap rep 1 (of 1) generation 6705, seed 1902263460, best lnL -164.789 gen current_lnL precision last_tree_imp 6705 -164.7888 0.010 843 6800 -164.7536 0.010 843 6900 -164.5302 0.010 843 7000 -164.5192 0.010 843 7100 -164.4099 0.010 843 7200 -164.2828 0.010 843 7300 -164.2325 0.010 843 7400 -164.1755 0.010 843 7500 -164.1233 0.010 843 7600 -164.0834 0.010 843 7700 -163.9602 0.010 843 7800 -163.9585 0.010 843 7900 -163.9336 0.010 843 8000 -163.8260 0.010 843 8100 -163.7648 0.010 843 8200 -163.7640 0.010 843 8300 -163.6798 0.010 843 8400 -163.6065 0.010 843 8500 -163.6037 0.010 843 8600 -163.5241 0.010 843 8700 -163.4093 0.010 843 8800 -163.3973 0.010 843 8900 -163.3756 0.010 843 9000 -163.3331 0.010 843 9100 -163.3254 0.010 843 9200 -163.3200 0.010 843 9300 -163.2929 0.010 843 9400 -163.2860 0.010 843 9500 -163.2701 0.010 843 9600 -163.2585 0.010 843 9700 -163.2185 0.010 843 9800 -163.2174 0.010 843 9900 -163.2161 0.010 843 10000 -163.2061 0.010 843 Optimizing parameters... improved 1.203 lnL Optimizing branchlengths... improved 0.010 lnL NOTE: ****Specified generation limit (10000) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 0.840, AG = 12.212, AT = 2.930, CG = 4.820, CT = 55.192, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1330 0.4224 0.2438 0.2008 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 39.2376 with an invariant (invariable) site category, proportion estimated 0.3493 Substitution rate categories under this model: rate proportion 0.0000 0.3493 0.8050 0.1627 0.9411 0.1627 1.0443 0.1627 1.2095 0.1627 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 3 branches were collapsed. NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -161.9932 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 0.8397 12.21 2.93 4.82 55.19 1 0.133 0.422 0.244 0.201 39.238 0.349 Treelengths: TL rep 1: 3.542 Saving best tree to bootstrap file ch.n.G4.boot.tre WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/n.conf Running checkpoint test ./check/n.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./check/n.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### 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. 0.1 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 3.458 lnL 7 8 9 10 11 Initial ln Likelihood: -225.5327 optimizing: starting branch lengths, rel rates, eq freqs... pass 1:+ 7.466 (branch= 0.77 scale= 0.00 freqs= 0.02 rel rates= 6.68) pass 2:+ 0.468 (branch= 0.45 scale= 0.00 freqs= 0.02 rel rates= 0.00) lnL after optimization: -217.5990 gen current_lnL precision last_tree_imp 0 -217.5990 0.500 0 200 -215.8307 0.500 188 400 -214.8938 0.500 276 600 -214.3966 0.500 530 800 -214.1704 0.500 530 1000 -214.0528 0.500 530 Optimization precision reduced Optimizing parameters... improved 0.223 lnL Optimizing branchlengths... improved 0.080 lnL 1200 -213.6191 0.010 530 1400 -213.5801 0.010 530 1600 -213.5577 0.010 530 1800 -213.3952 0.010 530 2000 -213.3646 0.010 530 2200 -213.3319 0.010 530 2400 -213.2445 0.010 530 2600 -213.2282 0.010 530 2800 -213.2194 0.010 530 3000 -213.2002 0.010 530 3200 -213.1946 0.010 530 3400 -213.1682 0.010 530 3600 -213.1580 0.010 530 3800 -213.0251 0.010 3769 4000 -212.9704 0.010 3769 4200 -212.9481 0.010 3769 4400 -212.9232 0.010 3769 4600 -212.8794 0.010 3769 4800 -212.8766 0.010 3769 5000 -212.8761 0.010 3769 5200 -212.8556 0.010 3769 5400 -212.8533 0.010 3769 5600 -212.8186 0.010 3769 5800 -212.7686 0.010 3769 6000 -212.7263 0.010 3769 6200 -212.7248 0.010 3769 6400 -212.7244 0.010 3769 6600 -212.7154 0.010 3769 6800 -212.7057 0.010 3769 7000 -212.7024 0.010 3769 7200 -212.7024 0.010 3769 7400 -212.6754 0.010 3769 7600 -212.6692 0.010 3769 7800 -212.6655 0.010 3769 8000 -212.6638 0.010 3769 8200 -212.6580 0.010 3769 8400 -212.6570 0.010 3769 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 32-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/n.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### 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. 0.1 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN Restarting from checkpoint... generation 8468, seed 643910720, best lnL -212.650 gen current_lnL precision last_tree_imp 8468 -212.6501 0.010 3769 8500 -212.6501 0.010 3769 Reached termination condition! last topological improvement at gen 3769 Improvement over last 500 gen = 0.01375 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 5.648, AG = 10.889, AT = 0.436, CG = 10.683, CT = 7.058, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2206 0.2885 0.1829 0.3080 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. Saving site likelihoods to file ch.n.sitelikes.log ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -212.6501 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 5.648 10.89 0.4364 10.68 7.058 1 0.221 0.288 0.183 0.308 Treelengths: TL rep 1: 1.727 Saving final tree from best search rep (#1) to ch.n.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log ####################################################### TREEFILES PASS Running checkpoint test ./check/n.const.conf Running checkpoint test ./check/n.const.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./check/n.const.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### 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. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### Loading constraints from file data/z.pos.const.tre Found 6 positively constrained bipartition(s) Bipartition 1: (1,2,3,5,6,7,8,9,10) | (4,11) Bipartition 2: (1,3,5,6,7,8,9,10) | (2,4,11) Bipartition 3: (1,5,6,7,8,9,10) | (2,3,4,11) Bipartition 4: (1,2,3,4,5,8,9,10,11) | (6,7) Bipartition 5: (1,2,3,4,5,8,9,11) | (6,7,10) Bipartition 6: (1,5) | (2,3,4,6,7,8,9,10,11) STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0334 0.2271 0.2519 0.2271 0.8203 0.2271 2.8944 0.2271 Starting with seed=1 creating likelihood stepwise addition starting tree (compatible with constraints)... number of taxa added: 4 5 6 Optimizing parameters... improved 0.006 lnL Optimizing branchlengths... improved 11.173 lnL 7 8 9 10 11 Initial ln Likelihood: -225.0726 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 5.893 (branch= 2.29 scale= 0.89 alpha= 0.00 freqs= 1.20 rel rates= 1.50 pinv= 0.00) pass 2:+ 0.035 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.00) lnL after optimization: -219.1445 gen current_lnL precision last_tree_imp 0 -219.1445 0.500 0 200 -217.4629 0.500 32 400 -216.6525 0.500 363 600 -216.1293 0.500 474 800 -215.4112 0.500 669 1000 -215.0098 0.500 936 1200 -214.3654 0.500 936 1400 -214.0189 0.500 936 Optimization precision reduced Optimizing parameters... improved 1.908 lnL Optimizing branchlengths... improved 0.702 lnL 1600 -211.2008 0.010 1502 1800 -211.0870 0.010 1502 2000 -210.9689 0.010 1502 2200 -210.8961 0.010 1502 2400 -210.8906 0.010 1502 2600 -210.8174 0.010 1502 2800 -210.7848 0.010 1502 3000 -210.7511 0.010 2883 3200 -210.7244 0.010 2883 3400 -210.7007 0.010 2883 3600 -210.6994 0.010 2883 3800 -210.6779 0.010 2883 4000 -210.6776 0.010 2883 4200 -210.6762 0.010 2883 4400 -210.6528 0.010 2883 4600 -210.6398 0.010 2883 4800 -210.5994 0.010 4692 5000 -210.5910 0.010 4692 5200 -210.5711 0.010 4692 5400 -210.5437 0.010 4692 5600 -210.5248 0.010 4692 5800 -210.4688 0.010 4692 6000 -210.4351 0.010 4692 6200 -210.4278 0.010 4692 6400 -210.4185 0.010 4692 6600 -210.4167 0.010 4692 6800 -210.3984 0.010 4692 7000 -210.3950 0.010 4692 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## 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/n.const.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### 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. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### Loading constraints from file data/z.pos.const.tre Found 6 positively constrained bipartition(s) Bipartition 1: (1,2,3,5,6,7,8,9,10) | (4,11) Bipartition 2: (1,3,5,6,7,8,9,10) | (2,4,11) Bipartition 3: (1,5,6,7,8,9,10) | (2,3,4,11) Bipartition 4: (1,2,3,4,5,8,9,10,11) | (6,7) Bipartition 5: (1,2,3,4,5,8,9,11) | (6,7,10) Bipartition 6: (1,5) | (2,3,4,6,7,8,9,10,11) STARTING RUN Restarting from checkpoint... generation 7130, seed 1622107173, best lnL -210.395 gen current_lnL precision last_tree_imp 7130 -210.3950 0.010 4692 7200 -210.3950 0.010 4692 Reached termination condition! last topological improvement at gen 4692 Improvement over last 500 gen = 0.00995 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 2.134, AG = 4.038, AT = 0.190, CG = 3.824, CT = 6.948, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2403 0.3352 0.2122 0.2124 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 1.4069 with an invariant (invariable) site category, proportion estimated 0.1702 Substitution rate categories under this model: rate proportion 0.0000 0.1702 0.2106 0.2075 0.5723 0.2075 1.0445 0.2075 2.1727 0.2075 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with a positive constraint, it is possible for a constrained branch itself to be collapsed. If you care, be careful to check whether this has happened or turn off branch collapsing. Saving site likelihoods to file ch.n.const.sitelikes.log ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -210.3950 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 2.134 4.038 0.1902 3.824 6.948 1 0.240 0.335 0.212 0.212 1.407 0.170 Treelengths: TL rep 1: 2.398 Saving final tree from best search rep (#1) to ch.n.const.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.const.internalstates.log ####################################################### TREEFILES PASS Running checkpoint test ./check/p.3diff.conf Running checkpoint test ./check/p.3diff.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./check/p.3diff.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.byPos.11x2178.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful Reading SETS block...storing read block: SETS successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #1 ("1stpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 4 Summary of data: 11 sequences. 441 constant characters. 171 parsimony-informative characters. 113 uninformative variable characters. 725 total characters. 237 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #2 ("2ndpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 5 Summary of data: 11 sequences. 527 constant characters. 90 parsimony-informative characters. 108 uninformative variable characters. 725 total characters. 158 unique patterns in compressed data matrix. GARLI data subset 3 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #3 ("3rdpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 6 Summary of data: 11 sequences. 102 constant characters. 507 parsimony-informative characters. 116 uninformative variable characters. 725 total characters. 548 unique patterns in compressed data matrix. ################################################### 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 >= 11 MB good approx 10 MB to 9 MB low approx 8 MB to 5 MB very low approx 4 MB to 4 MB the minimum required availablememory is 4 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 16.0 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/p.3diff.start Reading TREES block...storing read block: TREES successful Reading GARLI block...storing read block: GARLI successful STARTING RUN Bootstrap reweighting... Subset 1: Random seed for bootstrap reweighting: 42 Subset 2: Random seed for bootstrap reweighting: 655766889 Subset 3: Random seed for bootstrap reweighting: 486988955 >>>Bootstrap rep 1 (of 1) <<< Obtained starting tree 1 from Nexus Obtained starting or fixed model parameter values from Nexus: MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) AC = 1.000, AG = 10.000, AT = 2.000, CG = 2.000, CT = 0.010, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3150 0.1749 0.3006 0.2095 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.6000 Substitution rate categories under this model: rate proportion 0.0531 0.2500 0.3123 0.2500 0.8813 0.2500 2.7533 0.2500 Model 2 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) AC = 4.000, AG = 4.000, AT = 1.000, CG = 4.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1000 0.2000 0.3000 0.4000 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.4000 Substitution rate categories under this model: rate proportion 0.0167 0.2500 0.1818 0.2500 0.7313 0.2500 3.0702 0.2500 Model 3 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) AC = 1.000, AG = 2.000, AT = 3.000, CG = 5.000, CT = 2.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.4000 0.2000 0.3000 0.1000 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0100 Substitution rate categories under this model: rate proportion 0.0000 0.0100 0.0334 0.2475 0.2519 0.2475 0.8203 0.2475 2.8944 0.2475 Subset rate multipliers: 0.54 0.30 2.16 Starting with seed=1 Initial ln Likelihood: -17331.1409 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates... pass 1:+ 3336.674 (branch=2061.91 scale= 45.13 alpha=125.85 freqs=435.78 rel rates=661.66 pinv= 0.00 subset rates= 6.34) pass 2:+ 338.355 (branch= 41.98 scale= 1.04 alpha= 22.50 freqs=192.29 rel rates= 77.24 pinv= 2.39 subset rates= 0.92) pass 3:+ 222.683 (branch= 0.46 scale= 0.67 alpha= 8.57 freqs= 98.23 rel rates=113.31 pinv= 0.80 subset rates= 0.64) pass 4:+ 44.580 (branch= 0.51 scale= 0.00 alpha= 1.57 freqs= 22.89 rel rates= 19.62 pinv= 0.00 subset rates= 0.00) pass 5:+ 8.682 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 4.12 rel rates= 4.53 pinv= 0.02 subset rates= 0.00) pass 6:+ 1.298 (branch= 0.59 scale= 0.00 alpha= 0.01 freqs= 0.65 rel rates= 0.01 pinv= 0.03 subset rates= 0.00) pass 7:+ 1.354 (branch= 0.00 scale= 0.49 alpha= 0.72 freqs= 0.12 rel rates= 0.02 pinv= 0.01 subset rates= 0.00) pass 8:+ 0.126 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.09 rel rates= 0.02 pinv= 0.01 subset rates= 0.00) lnL after optimization: -13377.3893 gen current_lnL precision last_tree_imp 0 -13377.3893 0.500 0 100 -13375.8793 0.500 0 200 -13373.8435 0.500 0 300 -13372.9677 0.500 0 400 -13371.8985 0.500 0 500 -13371.5864 0.500 0 Optimization precision reduced Optimizing parameters... improved 0.048 lnL Optimizing branchlengths... improved 0.000 lnL 600 -13371.2064 0.402 0 700 -13371.0754 0.402 0 800 -13370.9489 0.402 0 900 -13370.7802 0.402 0 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 32-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.3diff.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.byPos.11x2178.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful Reading SETS block...storing read block: SETS successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #1 ("1stpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 4 Summary of data: 11 sequences. 441 constant characters. 171 parsimony-informative characters. 113 uninformative variable characters. 725 total characters. 237 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #2 ("2ndpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 5 Summary of data: 11 sequences. 527 constant characters. 90 parsimony-informative characters. 108 uninformative variable characters. 725 total characters. 158 unique patterns in compressed data matrix. GARLI data subset 3 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #3 ("3rdpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 6 Summary of data: 11 sequences. 102 constant characters. 507 parsimony-informative characters. 116 uninformative variable characters. 725 total characters. 548 unique patterns in compressed data matrix. ################################################### 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 >= 11 MB good approx 10 MB to 9 MB low approx 8 MB to 5 MB very low approx 4 MB to 4 MB the minimum required availablememory is 4 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 16.0 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/p.3diff.start Reading TREES block...storing read block: TREES successful Reading GARLI block...storing read block: GARLI successful STARTING RUN Subset 1: Random seed for bootstrap reweighting: 42 Subset 2: Random seed for bootstrap reweighting: 655766889 Subset 3: Random seed for bootstrap reweighting: 486988955 Restarting from checkpoint... Bootstrap rep 1 (of 1) generation 904, seed 1520195435, best lnL -13370.780 gen current_lnL precision last_tree_imp 904 -13370.7802 0.402 0 1000 -13370.6791 0.402 0 Optimization precision reduced Optimizing parameters... improved 0.037 lnL Optimizing branchlengths... improved 0.000 lnL 1100 -13370.5869 0.304 0 NOTE: ****Specified time limit (1 seconds) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) AC = 1.598, AG = 2.495, AT = 1.210, CG = 1.210, CT = 4.135, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3116 0.1804 0.3067 0.2014 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.3640 Substitution rate categories under this model: rate proportion 0.0119 0.2500 0.1544 0.2500 0.6892 0.2500 3.1446 0.2500 Model 2 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) AC = 2.627, AG = 4.239, AT = 0.821, CG = 4.239, CT = 2.627, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2812 0.1772 0.1597 0.3819 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.2460 Substitution rate categories under this model: rate proportion 0.0019 0.2500 0.0638 0.2500 0.4929 0.2500 3.4413 0.2500 Model 3 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) AC = 1.000, AG = 5.347, AT = 4.290, CG = 0.632, CT = 5.347, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1555 0.3460 0.2769 0.2216 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 4.1101 with an invariant (invariable) site category, proportion estimated 0.0486 Substitution rate categories under this model: rate proportion 0.0000 0.0486 0.4603 0.2379 0.7789 0.2379 1.0844 0.2379 1.6764 0.2379 Subset rate multipliers: 0.53 0.29 2.18 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. >>>Terminated Bootstrap rep 1 (of 1) <<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -13370.5240 (TERMINATED PREMATURELY) Parameter estimates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha rep 1: 1.598 2.495 1.21 1.21 4.135 1 0.312 0.180 0.307 0.201 0.364 Partition model subset 2: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha rep 1: 2.627 4.239 0.8212 4.239 2.627 1 0.281 0.177 0.160 0.382 0.246 Partition model subset 3: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 1 5.347 4.29 0.6325 5.347 1 0.156 0.346 0.277 0.222 4.110 0.049 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 1.772 0.530 0.287 2.183 Saving best tree to bootstrap file ch.p.3diff.boot.tre WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mk.ssr.conf Running checkpoint test ./check/p.mk.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./check/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 >>>Search rep 1 (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 (standard data) Character change matrix: One rate (symmetric one rate Mk 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 Mk 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 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=1 Initial ln Likelihood: -609.1934 optimizing: starting branch lengths, subset rates... pass 1:+ 130.207 (branch= 124.97 scale= 0.94 subset rates= 4.29) pass 2:+ 9.056 (branch= 8.14 scale= 0.00 subset rates= 0.91) pass 3:+ 1.801 (branch= 1.66 scale= 0.02 subset rates= 0.12) pass 4:+ 0.302 (branch= 0.30 scale= 0.00 subset rates= 0.00) pass 5:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -467.8159 gen current_lnL precision last_tree_imp 0 -467.8159 0.010 0 100 -467.7859 0.010 76 200 -467.7773 0.010 76 300 -467.7656 0.010 76 400 -467.7624 0.010 76 500 -467.7571 0.010 76 600 -467.7514 0.010 76 700 -467.7504 0.010 76 800 -467.7491 0.010 76 900 -467.7479 0.010 76 1000 -467.7452 0.010 76 1100 -467.7392 0.010 76 1200 -467.7367 0.010 76 1300 -467.7363 0.010 76 1400 -467.7341 0.010 76 1500 -467.7316 0.010 76 1600 -467.7305 0.010 76 1700 -467.7283 0.010 76 1800 -467.7273 0.010 76 1900 -467.7270 0.010 76 2000 -467.7257 0.010 76 2100 -467.7254 0.010 76 2200 -467.7236 0.010 76 2300 -467.7230 0.010 76 2400 -467.7219 0.010 76 2500 -467.7214 0.010 76 2600 -467.7205 0.010 76 2700 -467.7204 0.010 76 2800 -467.7197 0.010 76 2900 -467.7193 0.010 76 3000 -467.7192 0.010 76 3100 -467.7187 0.010 76 3200 -467.7186 0.010 76 3300 -467.7184 0.010 76 3400 -467.7184 0.010 76 Reached termination condition! last topological improvement at gen 76 Improvement over last 500 gen = 0.00087 Current score = -467.7184 Performing final optimizations... pass 1 : -467.7136 (branch= 0.0000 subset rates= 0.0048) pass 2 : -467.6950 (branch= 0.0186 subset rates= 0.0000) pass 3 : -467.6931 (branch= 0.0019 subset rates= 0.0000) pass 4 : -467.6915 (branch= 0.0015 subset rates= 0.0000) pass 5 : -467.6847 (branch= 0.0020 subset rates= 0.0048) pass 6 : -467.6822 (branch= 0.0024 subset rates= 0.0000) pass 7 : -467.6815 (branch= 0.0008 subset rates= 0.0000) pass 8 : -467.6798 (branch= 0.0003 subset rates= 0.0013) pass 9 : -467.6793 (branch= 0.0006 subset rates= 0.0000) pass 10: -467.6791 (branch= 0.0002 subset rates= 0.0000) pass 11: -467.6786 (branch= 0.0001 subset rates= 0.0004) pass 12: -467.6783 (branch= 0.0003 subset rates= 0.0000) pass 13: -467.6782 (branch= 0.0001 subset rates= 0.0000) pass 14: -467.6782 (branch= 0.0000 subset rates= 0.0000) pass 15: -467.6782 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6782 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 Mk 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 Mk 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 Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.79 1.48 2.18 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. >>>Completed Search rep 1 (of 5)<<< >>>Search rep 2 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk 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 Mk 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 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=1713359200 Initial ln Likelihood: -593.3879 optimizing: starting branch lengths, subset rates... pass 1:+ 107.964 (branch= 101.79 scale= 1.42 subset rates= 4.75) pass 2:+ 11.667 (branch= 10.49 scale= 0.04 subset rates= 1.14) pass 3:+ 5.232 (branch= 5.12 scale= 0.00 subset rates= 0.11) pass 4:+ 0.672 (branch= 0.66 scale= 0.01 subset rates= 0.00) pass 5:+ 0.009 (branch= 0.01 scale= 0.00 subset rates= 0.00) lnL after optimization: -467.8445 gen current_lnL precision last_tree_imp 0 -467.8445 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 32-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 2 (of 5) generation 55, seed 1941991272, best lnL -467.826 gen current_lnL precision last_tree_imp 55 -467.8263 0.010 0 100 -467.8198 0.010 0 200 -467.8068 0.010 0 300 -467.7949 0.010 0 400 -467.7826 0.010 0 500 -467.7787 0.010 0 600 -467.7743 0.010 0 700 -467.7597 0.010 0 800 -467.7573 0.010 0 900 -467.7534 0.010 0 1000 -467.7459 0.010 0 1100 -467.7436 0.010 0 1200 -467.7413 0.010 0 1300 -467.7398 0.010 0 1400 -467.7386 0.010 0 1500 -467.7376 0.010 0 1600 -467.7371 0.010 0 1700 -467.7356 0.010 0 1800 -467.7354 0.010 0 1900 -467.7350 0.010 0 2000 -467.7349 0.010 0 2100 -467.7331 0.010 0 2200 -467.7314 0.010 0 2300 -467.7312 0.010 0 2400 -467.7305 0.010 0 2500 -467.7299 0.010 0 2600 -467.7299 0.010 0 2700 -467.7296 0.010 0 2800 -467.7292 0.010 0 2900 -467.7290 0.010 0 3000 -467.7290 0.010 0 Reached termination condition! last topological improvement at gen 0 Improvement over last 500 gen = 0.00098 Current score = -467.7290 Performing final optimizations... pass 1 : -467.7281 (branch= 0.0000 subset rates= 0.0008) pass 2 : -467.7069 (branch= 0.0195 subset rates= 0.0018) pass 3 : -467.6977 (branch= 0.0092 subset rates= 0.0000) pass 4 : -467.6916 (branch= 0.0061 subset rates= 0.0000) pass 5 : -467.6876 (branch= 0.0035 subset rates= 0.0005) pass 6 : -467.6835 (branch= 0.0041 subset rates= 0.0000) pass 7 : -467.6814 (branch= 0.0021 subset rates= 0.0000) pass 8 : -467.6799 (branch= 0.0016 subset rates= 0.0000) pass 9 : -467.6792 (branch= 0.0006 subset rates= 0.0000) pass 10: -467.6787 (branch= 0.0003 subset rates= 0.0003) pass 11: -467.6784 (branch= 0.0002 subset rates= 0.0000) pass 12: -467.6783 (branch= 0.0001 subset rates= 0.0001) pass 13: -467.6782 (branch= 0.0001 subset rates= 0.0000) pass 14: -467.6782 (branch= 0.0000 subset rates= 0.0000) pass 15: -467.6782 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6782 Time used so far = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk 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 Mk 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 Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.79 1.48 2.19 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. >>>Completed Search rep 2 (of 5)<<< >>>Search rep 3 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk 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 Mk 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 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=975681204 Initial ln Likelihood: -590.4310 optimizing: starting branch lengths, subset rates... pass 1:+ 111.273 (branch= 106.41 scale= 0.38 subset rates= 4.49) pass 2:+ 8.172 (branch= 7.22 scale= 0.00 subset rates= 0.95) pass 3:+ 2.417 (branch= 2.22 scale= 0.00 subset rates= 0.20) pass 4:+ 0.652 (branch= 0.62 scale= 0.01 subset rates= 0.01) pass 5:+ 0.055 (branch= 0.05 scale= 0.00 subset rates= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -467.8625 gen current_lnL precision last_tree_imp 0 -467.8625 0.010 0 100 -467.8011 0.010 75 200 -467.7933 0.010 75 300 -467.7853 0.010 75 400 -467.7712 0.010 75 500 -467.7598 0.010 75 600 -467.7543 0.010 75 700 -467.7490 0.010 75 NOTE: ****Specified time limit (5 seconds) reached... Current score = -467.7467 Performing final optimizations... pass 1 : -467.7454 (branch= 0.0000 subset rates= 0.0013) pass 2 : -467.7115 (branch= 0.0338 subset rates= 0.0001) pass 3 : -467.7005 (branch= 0.0107 subset rates= 0.0003) pass 4 : -467.6892 (branch= 0.0113 subset rates= 0.0000) pass 5 : -467.6833 (branch= 0.0058 subset rates= 0.0000) pass 6 : -467.6808 (branch= 0.0026 subset rates= 0.0000) pass 7 : -467.6795 (branch= 0.0012 subset rates= 0.0000) pass 8 : -467.6789 (branch= 0.0006 subset rates= 0.0000) pass 9 : -467.6786 (branch= 0.0003 subset rates= 0.0000) pass 10: -467.6785 (branch= 0.0001 subset rates= 0.0000) pass 11: -467.6784 (branch= 0.0001 subset rates= 0.0000) pass 12: -467.6784 (branch= 0.0000 subset rates= 0.0000) pass 13: -467.6784 (branch= 0.0000 subset rates= 0.0000) pass 14: -467.6783 (branch= 0.0000 subset rates= 0.0000) pass 15: -467.6783 (branch= 0.0000 subset rates= 0.0001) Looking for minimum length branches... Final score = -467.6783 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk 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 Mk 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 Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.79 1.48 2.18 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. >>>Terminated Search rep 3 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 3 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -467.6782 Replicate 2 : -467.6782 (best) (same topology as 1) Replicate 3 : -467.6783 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 3.843 0.786 1.480 2.181 rep 2: 3.843 0.786 1.477 2.187 rep 3: 3.841 0.787 1.475 2.183 Saving final tree from best search rep (#2) to ch.p.mk.ssr.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkO.ssr.conf Running checkpoint test ./check/p.mkO.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./check/p.mkO.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, modeled as Standard ordered k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN >>>Search rep 1 (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=1 Initial ln Likelihood: -641.9257 optimizing: starting branch lengths, subset rates... pass 1:+ 147.096 (branch= 136.58 scale= 0.83 subset rates= 9.68) pass 2:+ 12.451 (branch= 8.46 scale= 0.00 subset rates= 3.99) pass 3:+ 3.549 (branch= 2.32 scale= 0.03 subset rates= 1.20) pass 4:+ 0.759 (branch= 0.51 scale= 0.00 subset rates= 0.25) pass 5:+ 0.120 (branch= 0.11 scale= 0.00 subset rates= 0.01) pass 6:+ 0.011 (branch= 0.01 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -477.9403 gen current_lnL precision last_tree_imp 0 -477.9403 0.010 0 100 -477.8626 0.010 76 200 -477.8284 0.010 152 300 -477.7511 0.010 215 400 -477.5622 0.010 373 500 -477.5386 0.010 373 600 -477.5298 0.010 373 700 -477.5291 0.010 373 800 -477.5214 0.010 373 900 -477.5166 0.010 373 1000 -477.5163 0.010 373 1100 -477.5125 0.010 373 1200 -477.5109 0.010 373 1300 -477.5099 0.010 373 1400 -477.4981 0.010 373 1500 -477.4922 0.010 373 1600 -477.4850 0.010 373 1700 -477.4817 0.010 373 1800 -477.4773 0.010 373 1900 -477.4761 0.010 373 2000 -477.4748 0.010 373 2100 -477.4739 0.010 373 2200 -477.4732 0.010 373 2300 -477.4729 0.010 373 2400 -477.4726 0.010 373 2500 -477.4723 0.010 373 2600 -477.4711 0.010 373 2700 -477.4707 0.010 373 2800 -477.4705 0.010 373 2900 -477.4705 0.010 373 3000 -477.4702 0.010 373 3100 -477.4701 0.010 373 Reached termination condition! last topological improvement at gen 373 Improvement over last 500 gen = 0.00100 Current score = -477.4701 Performing final optimizations... pass 1 : -477.4701 (branch= 0.0000 subset rates= 0.0000) pass 2 : -477.4432 (branch= 0.0269 subset rates= 0.0000) pass 3 : -477.4393 (branch= 0.0039 subset rates= 0.0000) pass 4 : -477.4364 (branch= 0.0029 subset rates= 0.0000) pass 5 : -477.4351 (branch= 0.0012 subset rates= 0.0002) pass 6 : -477.4345 (branch= 0.0007 subset rates= 0.0000) pass 7 : -477.4333 (branch= 0.0012 subset rates= 0.0000) pass 8 : -477.4326 (branch= 0.0006 subset rates= 0.0000) pass 9 : -477.4323 (branch= 0.0004 subset rates= 0.0000) pass 10: -477.4319 (branch= 0.0002 subset rates= 0.0001) 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: -477.4317 (branch= 0.0000 subset rates= 0.0000) pass 16: -477.4317 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.4316 Time used so far = 0 hours, 0 minutes and 5 seconds 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 1.92 2.74 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. >>>Completed Search rep 1 (of 5)<<< >>>Search rep 2 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate 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=200420059 Initial ln Likelihood: -656.4902 optimizing: starting branch lengths, subset rates... pass 1:+ 148.906 (branch= 137.62 scale= 1.92 subset rates= 9.37) pass 2:+ 19.722 (branch= 15.83 scale= 0.00 subset rates= 3.89) pass 3:+ 3.560 (branch= 2.11 scale= 0.00 subset rates= 1.45) pass 4:+ 2.461 (branch= 2.02 scale= 0.00 subset rates= 0.44) pass 5:+ 3.226 (branch= 3.23 scale= 0.00 subset rates= 0.00) pass 6:+ 0.747 (branch= 0.71 scale= 0.01 subset rates= 0.02) pass 7:+ 0.016 (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: -477.8517 gen current_lnL precision last_tree_imp 0 -477.8517 0.010 0 100 -477.7860 0.010 74 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 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./restart/p.mkO.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, modeled as Standard ordered k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Restarting from checkpoint... Search rep 2 (of 5) generation 154, seed 1639935539, best lnL -477.776 gen current_lnL precision last_tree_imp 154 -477.7757 0.010 74 200 -477.7643 0.010 74 300 -477.7463 0.010 74 400 -477.7402 0.010 74 500 -477.7271 0.010 74 600 -477.7244 0.010 74 700 -477.7189 0.010 74 800 -477.7180 0.010 74 900 -477.7173 0.010 74 1000 -477.7111 0.010 74 1100 -477.7093 0.010 74 1200 -477.7091 0.010 74 1300 -477.7049 0.010 74 1400 -477.7022 0.010 74 1500 -477.6989 0.010 74 1600 -477.6967 0.010 74 1700 -477.6956 0.010 74 1800 -477.6946 0.010 74 1900 -477.6945 0.010 74 2000 -477.6902 0.010 74 2100 -477.6899 0.010 74 2200 -477.6898 0.010 74 2300 -477.6894 0.010 74 2400 -477.6889 0.010 74 2500 -477.6883 0.010 74 2600 -477.6879 0.010 74 2700 -477.6875 0.010 74 2800 -477.6865 0.010 74 2900 -477.6858 0.010 74 3000 -477.6851 0.010 74 3100 -477.6845 0.010 74 3200 -477.6839 0.010 74 3300 -477.6820 0.010 74 3400 -477.6806 0.010 74 3500 -477.6782 0.010 74 3600 -477.6776 0.010 74 NOTE: ****Specified time limit (5 seconds) reached... Current score = -477.5171 Performing final optimizations... pass 1 : -477.4999 (branch= 0.0103 subset rates= 0.0069) pass 2 : -477.4623 (branch= 0.0308 subset rates= 0.0067) pass 3 : -477.4441 (branch= 0.0171 subset rates= 0.0011) pass 4 : -477.4416 (branch= 0.0026 subset rates= 0.0000) pass 5 : -477.4375 (branch= 0.0040 subset rates= 0.0000) pass 6 : -477.4356 (branch= 0.0019 subset rates= 0.0001) pass 7 : -477.4343 (branch= 0.0012 subset rates= 0.0000) pass 8 : -477.4334 (branch= 0.0010 subset rates= 0.0000) pass 9 : -477.4327 (branch= 0.0007 subset rates= 0.0000) pass 10: -477.4324 (branch= 0.0003 subset rates= 0.0000) pass 11: -477.4322 (branch= 0.0002 subset rates= 0.0000) pass 12: -477.4321 (branch= 0.0001 subset rates= 0.0000) pass 13: -477.4320 (branch= 0.0001 subset rates= 0.0000) pass 14: -477.4320 (branch= 0.0000 subset rates= 0.0000) pass 15: -477.4320 (branch= 0.0000 subset rates= 0.0000) pass 16: -477.4320 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.4320 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT 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 2.75 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. >>>Terminated Search rep 2 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 2 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -477.4316 (best) Replicate 2 : -477.4320 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.930 0.631 1.918 2.736 rep 2: 4.926 0.633 1.906 2.747 Saving final tree from best search rep (#1) to ch.p.mkO.ssr.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkv.ssr.conf Running checkpoint test ./check/p.mkv.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./check/p.mkv.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, variable only, modeled as Standard k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Bootstrap reweighting... Subset 1: Random seed for bootstrap reweighting: 42 Subset 2: Random seed for bootstrap reweighting: 1339106791 Subset 3: Random seed for bootstrap reweighting: 974568031 >>>Bootstrap rep 1 (of 1) Search rep 1 (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 (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: 1.00 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -602.2288 optimizing: starting branch lengths, subset rates... pass 1:+ 152.798 (branch= 152.15 scale= 0.58 subset rates= 0.07) pass 2:+ 9.798 (branch= 9.64 scale= 0.00 subset rates= 0.16) pass 3:+ 0.369 (branch= 0.35 scale= 0.00 subset rates= 0.02) pass 4:+ 0.040 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 5:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -439.2245 gen current_lnL precision last_tree_imp 0 -439.2245 0.010 0 100 -430.2556 0.010 92 200 -427.7099 0.010 179 300 -426.9761 0.010 293 400 -425.6930 0.010 365 500 -425.6677 0.010 365 600 -425.6511 0.010 365 700 -425.6317 0.010 365 800 -425.6211 0.010 365 900 -425.6125 0.010 365 1000 -425.6094 0.010 365 1100 -425.6089 0.010 365 1200 -425.6082 0.010 365 1300 -425.6067 0.010 365 1400 -425.6057 0.010 365 1500 -425.6041 0.010 365 1600 -425.6021 0.010 365 1700 -425.5975 0.010 365 1800 -425.5971 0.010 365 1900 -425.5953 0.010 365 2000 -425.5949 0.010 365 2100 -425.5941 0.010 365 2200 -425.5912 0.010 365 2300 -425.5898 0.010 365 2400 -425.5892 0.010 365 2500 -425.5891 0.010 365 2600 -425.5889 0.010 365 2700 -425.5887 0.010 365 2800 -425.5883 0.010 365 2900 -425.5868 0.010 365 3000 -425.5867 0.010 365 3100 -425.5858 0.010 365 3200 -425.5857 0.010 365 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 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./restart/p.mkv.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, variable only, modeled as Standard k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Subset 1: Random seed for bootstrap reweighting: 42 Subset 2: Random seed for bootstrap reweighting: 1339106791 Subset 3: Random seed for bootstrap reweighting: 974568031 Restarting from checkpoint... Bootstrap rep 1 (of 1) Search rep 1 (of 5) generation 3273, seed 1700330852, best lnL -425.585 gen current_lnL precision last_tree_imp 3273 -425.5849 0.010 365 3300 -425.5849 0.010 365 3400 -425.5842 0.010 365 3500 -425.5842 0.010 365 3600 -425.5840 0.010 365 3700 -425.5839 0.010 365 3800 -425.5838 0.010 365 3900 -425.5838 0.010 365 Reached termination condition! last topological improvement at gen 365 Improvement over last 500 gen = 0.00044 Current score = -425.5838 Performing final optimizations... pass 1 : -425.5804 (branch= 0.0000 subset rates= 0.0033) pass 2 : -425.5633 (branch= 0.0144 subset rates= 0.0027) pass 3 : -425.5516 (branch= 0.0070 subset rates= 0.0047) pass 4 : -425.5509 (branch= 0.0007 subset rates= 0.0000) pass 5 : -425.5505 (branch= 0.0004 subset rates= 0.0000) pass 6 : -425.5498 (branch= 0.0007 subset rates= 0.0000) pass 7 : -425.5494 (branch= 0.0004 subset rates= 0.0000) pass 8 : -425.5490 (branch= 0.0004 subset rates= 0.0000) pass 9 : -425.5487 (branch= 0.0003 subset rates= 0.0000) pass 10: -425.5487 (branch= 0.0001 subset rates= 0.0000) pass 11: -425.5486 (branch= 0.0000 subset rates= 0.0000) pass 12: -425.5486 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.5486 Time used so far = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.87 1.53 1.12 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 10 branches were collapsed. >>>Completed Bootstrap rep 1 (of 1) Search rep 1 (of 5)<<< >>>Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< Obtained starting tree 1 from Nexus Starting with seed=222492842 Initial ln Likelihood: -586.0233 optimizing: starting branch lengths, subset rates... pass 1:+ 129.358 (branch= 127.50 scale= 1.82 subset rates= 0.04) pass 2:+ 11.580 (branch= 11.46 scale= 0.04 subset rates= 0.07) pass 3:+ 3.728 (branch= 3.71 scale= 0.00 subset rates= 0.02) pass 4:+ 1.685 (branch= 1.66 scale= 0.02 subset rates= 0.01) pass 5:+ 0.130 (branch= 0.13 scale= 0.00 subset rates= 0.00) pass 6:+ 0.037 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 7:+ 0.031 (branch= 0.03 scale= 0.00 subset rates= 0.00) pass 8:+ 0.037 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 9:+ 0.043 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass10:+ 0.052 (branch= 0.05 scale= 0.00 subset rates= 0.00) pass11:+ 0.061 (branch= 0.06 scale= 0.00 subset rates= 0.00) pass12:+ 0.042 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass13:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) pass14:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -439.2273 gen current_lnL precision last_tree_imp 0 -439.2273 0.010 0 100 -428.8676 0.010 98 200 -428.0498 0.010 164 300 -427.6002 0.010 249 400 -427.5648 0.010 249 500 -427.4910 0.010 499 600 -427.3863 0.010 511 700 -425.7187 0.010 668 800 -425.6950 0.010 722 900 -425.6794 0.010 722 1000 -425.6689 0.010 722 1100 -425.6640 0.010 722 1200 -425.6430 0.010 722 1300 -425.6381 0.010 722 1400 -425.6345 0.010 722 1500 -425.6342 0.010 722 1600 -425.6274 0.010 722 1700 -425.6240 0.010 722 1800 -425.6236 0.010 722 1900 -425.6226 0.010 722 2000 -425.6202 0.010 722 2100 -425.6197 0.010 722 2200 -425.6174 0.010 722 2300 -425.6146 0.010 722 2400 -425.6135 0.010 722 2500 -425.6104 0.010 722 NOTE: ****Specified time limit (5 seconds) reached... Current score = -425.6103 Performing final optimizations... pass 1 : -425.5974 (branch= 0.0000 subset rates= 0.0129) pass 2 : -425.5619 (branch= 0.0206 subset rates= 0.0150) pass 3 : -425.5565 (branch= 0.0042 subset rates= 0.0012) pass 4 : -425.5537 (branch= 0.0028 subset rates= 0.0000) pass 5 : -425.5520 (branch= 0.0017 subset rates= 0.0000) pass 6 : -425.5503 (branch= 0.0017 subset rates= 0.0000) pass 7 : -425.5496 (branch= 0.0007 subset rates= 0.0000) pass 8 : -425.5493 (branch= 0.0004 subset rates= 0.0000) pass 9 : -425.5490 (branch= 0.0002 subset rates= 0.0000) pass 10: -425.5489 (branch= 0.0001 subset rates= 0.0000) pass 11: -425.5489 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.5489 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.87 1.53 1.13 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 9 branches were collapsed. >>>Terminated Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 2 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -425.5486 (best) Replicate 2 : -425.5489 (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 3.038 0.868 1.529 1.123 rep 2: 3.036 0.868 1.527 1.132 Saving tree from best search rep (#1) to bootstrap file ch.p.mkv.ssr.boot.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkvO.ssr.conf Running checkpoint test ./check/p.mkvO.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-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 ./check/p.mkvO.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, variable only, modeled as Standard ordered k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN >>>Search rep 1 (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=1 Initial ln Likelihood: -637.9212 optimizing: starting branch lengths, subset rates... pass 1:+ 144.867 (branch= 134.40 scale= 0.48 subset rates= 9.98) pass 2:+ 12.967 (branch= 8.30 scale= 0.00 subset rates= 4.67) pass 3:+ 3.847 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.162 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.156 (branch= 0.12 scale= 0.00 subset rates= 0.03) pass 6:+ 0.044 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 7:+ 0.015 (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: -474.8631 gen current_lnL precision last_tree_imp 0 -474.8631 0.010 0 100 -474.7513 0.010 68 200 -474.7185 0.010 68 300 -474.6982 0.010 68 400 -474.6394 0.010 329 500 -474.1548 0.010 455 600 -474.1344 0.010 560 700 -474.0336 0.010 653 800 -474.0224 0.010 653 900 -474.0130 0.010 653 1000 -474.0072 0.010 653 1100 -474.0048 0.010 653 1200 -474.0017 0.010 653 1300 -473.9998 0.010 653 1400 -473.9960 0.010 653 1500 -473.9930 0.010 653 1600 -473.9888 0.010 653 1700 -473.9875 0.010 653 1800 -473.9857 0.010 653 1900 -473.9846 0.010 653 2000 -473.9839 0.010 653 2100 -473.9834 0.010 653 2200 -473.9820 0.010 653 2300 -473.9814 0.010 653 2400 -473.9804 0.010 653 2500 -473.9804 0.010 653 2600 -473.9801 0.010 653 2700 -473.9793 0.010 653 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 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./restart/p.mkvO.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, variable only, modeled as Standard ordered k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Restarting from checkpoint... Search rep 1 (of 5) generation 2754, seed 1747510246, best lnL -473.979 gen current_lnL precision last_tree_imp 2754 -473.9791 0.010 653 2800 -473.9779 0.010 653 2900 -473.9777 0.010 653 3000 -473.9777 0.010 653 3100 -473.9773 0.010 653 3200 -473.9772 0.010 653 3300 -473.9771 0.010 653 Reached termination condition! last topological improvement at gen 653 Improvement over last 500 gen = 0.00088 Current score = -473.9771 Performing final optimizations... pass 1 : -473.9742 (branch= 0.0000 subset rates= 0.0029) pass 2 : -473.9558 (branch= 0.0183 subset rates= 0.0000) pass 3 : -473.9558 (branch= 0.0000 subset rates= 0.0000) pass 4 : -473.9548 (branch= 0.0011 subset rates= 0.0000) pass 5 : -473.9529 (branch= 0.0018 subset rates= 0.0000) pass 6 : -473.9525 (branch= 0.0004 subset rates= 0.0000) pass 7 : -473.9517 (branch= 0.0008 subset rates= 0.0000) pass 8 : -473.9513 (branch= 0.0004 subset rates= 0.0000) pass 9 : -473.9511 (branch= 0.0003 subset rates= 0.0000) pass 10: -473.9510 (branch= 0.0001 subset rates= 0.0000) pass 11: -473.9510 (branch= 0.0000 subset rates= 0.0000) pass 12: -473.9509 (branch= 0.0000 subset rates= 0.0000) pass 13: -473.9509 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -473.9509 Time used so far = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.59 2.07 2.82 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. >>>Completed Search rep 1 (of 5)<<< >>>Search rep 2 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=2125680066 Initial ln Likelihood: -649.8224 optimizing: starting branch lengths, subset rates... pass 1:+ 148.288 (branch= 136.88 scale= 0.96 subset rates= 10.45) pass 2:+ 18.126 (branch= 13.41 scale= 0.03 subset rates= 4.69) pass 3:+ 5.650 (branch= 3.93 scale= 0.00 subset rates= 1.72) pass 4:+ 2.344 (branch= 1.67 scale= 0.00 subset rates= 0.67) pass 5:+ 0.473 (branch= 0.43 scale= 0.01 subset rates= 0.03) pass 6:+ 0.135 (branch= 0.13 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -474.8070 gen current_lnL precision last_tree_imp 0 -474.8070 0.010 0 100 -474.7912 0.010 0 200 -474.7022 0.010 123 300 -474.5643 0.010 272 400 -474.5191 0.010 272 500 -474.5075 0.010 272 600 -474.5034 0.010 272 700 -474.4997 0.010 272 800 -474.4937 0.010 272 900 -474.4914 0.010 272 1000 -474.4880 0.010 272 1100 -474.4855 0.010 272 1200 -474.4848 0.010 272 1300 -474.4839 0.010 272 1400 -474.4822 0.010 272 1500 -474.4805 0.010 272 1600 -474.4799 0.010 272 1700 -474.4796 0.010 272 1800 -474.4791 0.010 272 1900 -474.4787 0.010 272 2000 -474.4786 0.010 272 2100 -474.4782 0.010 272 2200 -474.4775 0.010 272 2300 -474.4768 0.010 272 2400 -474.4765 0.010 272 2500 -474.4765 0.010 272 NOTE: ****Specified time limit (5 seconds) reached... Current score = -474.4752 Performing final optimizations... pass 1 : -474.4686 (branch= 0.0066 subset rates= 0.0000) pass 2 : -474.4452 (branch= 0.0234 subset rates= 0.0000) pass 3 : -474.4368 (branch= 0.0083 subset rates= 0.0000) pass 4 : -474.4353 (branch= 0.0015 subset rates= 0.0000) pass 5 : -474.4334 (branch= 0.0019 subset rates= 0.0000) pass 6 : -474.4309 (branch= 0.0020 subset rates= 0.0006) pass 7 : -474.4295 (branch= 0.0014 subset rates= 0.0000) pass 8 : -474.4287 (branch= 0.0008 subset rates= 0.0000) pass 9 : -474.4285 (branch= 0.0002 subset rates= 0.0000) pass 10: -474.4284 (branch= 0.0001 subset rates= 0.0000) pass 11: -474.4282 (branch= 0.0001 subset rates= 0.0000) pass 12: -474.4282 (branch= 0.0000 subset rates= 0.0000) pass 13: -474.4282 (branch= 0.0000 subset rates= 0.0000) pass 14: -474.4282 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -474.4282 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT 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 2.03 2.92 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. >>>Terminated Search rep 2 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 2 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -473.9509 (best) Replicate 2 : -474.4282 (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.351 0.587 2.065 2.818 rep 2: 4.599 0.588 2.031 2.920 Saving final tree from best search rep (#1) to ch.p.mkvO.ssr.best.tre ####################################################### TREEFILES PASS ALL TESTS COMPLETED SUCCESSFULLY make[4]: Leaving directory '/build/reproducible-path/garli-2.1/tests' make[3]: Leaving directory '/build/reproducible-path/garli-2.1/tests' make[3]: Entering directory '/build/reproducible-path/garli-2.1' make[3]: Leaving directory '/build/reproducible-path/garli-2.1' make[2]: Leaving directory '/build/reproducible-path/garli-2.1' # restore original test dir rm -rf tests mv tests.bak tests make[1]: Leaving directory '/build/reproducible-path/garli-2.1' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j11 install DESTDIR=/build/reproducible-path/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/garli-2.1' Making install in src make[2]: Entering directory '/build/reproducible-path/garli-2.1/src' make[3]: Entering directory '/build/reproducible-path/garli-2.1/src' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/garli-2.1/debian/tmp/usr/bin' /usr/bin/install -c Garli '/build/reproducible-path/garli-2.1/debian/tmp/usr/bin' make install-exec-hook make[4]: Entering directory '/build/reproducible-path/garli-2.1/src' cd /build/reproducible-path/garli-2.1/debian/tmp/usr/bin && \ mv -f Garli Garli-2.1 && \ ln -s Garli-2.1 Garli make[4]: Leaving directory '/build/reproducible-path/garli-2.1/src' make[3]: Leaving directory '/build/reproducible-path/garli-2.1/src' make[2]: Leaving directory '/build/reproducible-path/garli-2.1/src' Making install in tests make[2]: Entering directory '/build/reproducible-path/garli-2.1/tests' make[3]: Entering directory '/build/reproducible-path/garli-2.1/tests' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/garli-2.1/tests' make[2]: Leaving directory '/build/reproducible-path/garli-2.1/tests' make[2]: Entering directory '/build/reproducible-path/garli-2.1' make[3]: Entering directory '/build/reproducible-path/garli-2.1' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/garli-2.1' make[2]: Leaving directory '/build/reproducible-path/garli-2.1' make[1]: Leaving directory '/build/reproducible-path/garli-2.1' dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'garli' in '../garli_2.1-9_i386.deb'. dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-9_i386.deb'. dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-9_i386.deb'. dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-9_all.deb'. dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-9_i386.deb'. dpkg-genbuildinfo --build=binary -O../garli_2.1-9_i386.buildinfo dpkg-genchanges --build=binary -O../garli_2.1-9_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/34980 and its subdirectories I: Current time: Fri Dec 20 11:38:15 -12 2024 I: pbuilder-time-stamp: 1734737895 Fri Dec 20 23:38:16 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos6-i386.debian.net. Fri Dec 20 23:38:16 UTC 2024 I: Preparing to do remote build '2' on ionos6-i386.debian.net. Fri Dec 20 23:43:39 UTC 2024 I: Deleting $TMPDIR on ionos6-i386.debian.net. Fri Dec 20 23:43:40 UTC 2024 I: garli_2.1-9_i386.changes: Format: 1.8 Date: Thu, 19 Dec 2024 20:44:33 +0100 Source: garli Binary: garli garli-dbgsym garli-examples garli-mpi garli-mpi-dbgsym Architecture: i386 all Version: 2.1-9 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: garli - phylogenetic analysis of molecular sequence data using maximum-li garli-examples - phylogenetic analysis of molecular sequence data (examples) garli-mpi - phylogenetic analysis of molecular sequence data using maximum-li Changes: garli (2.1-9) unstable; urgency=medium . * Team upload. * d/rules: skip tests on armel: too heavy. * d/t/control: skip autopkgtest on armel: too heavy. Checksums-Sha1: d980601f538f64f3c23197bf6a1f8f444c34ba92 9141968 garli-dbgsym_2.1-9_i386.deb 9190fdad700fcdc0fc9fe53c5c92c112dc23d533 103464 garli-examples_2.1-9_all.deb f91a1a290e0b3c3a28300fec41e3a16e0dc224b8 9524196 garli-mpi-dbgsym_2.1-9_i386.deb 94819acad3c939226d39a2332cb17e3f4baa67f8 569384 garli-mpi_2.1-9_i386.deb 7dc55af6f96d5639f2c29030d25e5c757e81efd8 6385 garli_2.1-9_i386.buildinfo a8b0e547758906179df90d8700bce53ef749ed77 589928 garli_2.1-9_i386.deb Checksums-Sha256: acb0947adca3fcd206bf2d4d7f03b242121144ee17b22d5af09827ba75c30ea0 9141968 garli-dbgsym_2.1-9_i386.deb 932b8ad8935349f05f0abbf62fbba0c7f312a7d912d9bc30ec9287833081b095 103464 garli-examples_2.1-9_all.deb aa67e7691a1565126d21d9ea634dc09487b5547ee4a0d7302d7ecb1086b28750 9524196 garli-mpi-dbgsym_2.1-9_i386.deb dd716f76e7aa12993408a525c94d5761ee96aecaa3a23ac93d5f337031745fc9 569384 garli-mpi_2.1-9_i386.deb dc74665c83401da202b91fec1795962099456407269e9164242ae6cc3fec56fb 6385 garli_2.1-9_i386.buildinfo 22d1a649a5d4b5665ed46176eb11208ec463f7627eaea3334d64ad1220cb36e0 589928 garli_2.1-9_i386.deb Files: 86067e9d8b66a1ce2059ef7f95722a51 9141968 debug optional garli-dbgsym_2.1-9_i386.deb d7e71d1f8908fce11e935020473b4b15 103464 science optional garli-examples_2.1-9_all.deb ad1d7d4a7d6839d82433744dc2c91440 9524196 debug optional garli-mpi-dbgsym_2.1-9_i386.deb b5fa8d0b916472a07fcfdc3ea05cd7da 569384 science optional garli-mpi_2.1-9_i386.deb 80682ffc3661e212900626c76292a5cd 6385 science optional garli_2.1-9_i386.buildinfo 79a2c1d9b7d3b89be731d519b9ce6dee 589928 science optional garli_2.1-9_i386.deb Fri Dec 20 23:43:41 UTC 2024 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_5-44276.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.L6wO1cWn/garli_2.1-9.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.L6wO1cWn/garli_2.1-9.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.L6wO1cWn/garli_2.1-9.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.L6wO1cWn/b1/garli_2.1-9_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.L6wO1cWn/b2/garli_2.1-9_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.510s) 0.510s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.187s) 0.187s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 816ms CPU time consumed: 817ms Fri Dec 20 23:43:42 UTC 2024 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists. Fri Dec 20 23:43:42 UTC 2024 I: garli from unstable built successfully and reproducibly on i386. Fri Dec 20 23:43:43 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Dec 20 23:43:43 UTC 2024 I: Submitting 8.0K b1/garli_2.1-9_i386.buildinfo.asc Fri Dec 20 23:43:45 UTC 2024 I: Submitting 8.0K b2/garli_2.1-9_i386.buildinfo.asc Fri Dec 20 23:43:46 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Dec 20 23:43:46 UTC 2024 I: Done submitting .buildinfo files. Fri Dec 20 23:43:46 UTC 2024 I: Removing signed garli_2.1-9_i386.buildinfo.asc files: removed './b1/garli_2.1-9_i386.buildinfo.asc' removed './b2/garli_2.1-9_i386.buildinfo.asc'