Running as unit: rb-build-amd64_25-54238.service; invocation ID: b0ce7ce57719413f8b6f1d7447f30743 ==================================================================================== Thu Sep 18 07:29:06 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_25) on jenkins, called using "ionos1-amd64 ionos5-amd64" as arguments. Thu Sep 18 07:29:06 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-y8Nflwfw" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Sep 18 07:29:06 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Thu Sep 18 07:29:06 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-x640c4' Thu Sep 18 07:29:06 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Thu Sep 18 07:29:06 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-1aoDLE' ok, let's check if garli is building anywhere yet… ok, garli is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of garli in forky on amd64 on jenkins now. 1st build will be done on ionos1-amd64.debian.net. 2nd build will be done on ionos5-amd64.debian.net. ============================================================================= Thu Sep 18 07:29:12 UTC 2025 I: starting to build garli/forky/amd64 on jenkins on '2025-09-18 07:29' Thu Sep 18 07:29:12 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_25/54238/console.log 1758180552 amd64 forky garli Thu Sep 18 07:29:12 UTC 2025 I: Downloading source for forky/garli=2.1-9 --2025-09-18 07:29:13-- 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% 21.4M=0s 2025-09-18 07:29:13 (21.4 MB/s) - ‘garli_2.1-9.dsc’ saved [2186/2186] --2025-09-18 07:29:13-- 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% 21.4M=0s 2025-09-18 07:29:13 (21.4 MB/s) - ‘garli_2.1-9.dsc’ saved [2186/2186] Thu Sep 18 07:29:13 UTC 2025 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----- Thu Sep 18 07:29:13 UTC 2025 I: Checking whether the package is not for us Thu Sep 18 07:29:13 UTC 2025 I: Starting 1st build on remote node ionos1-amd64.debian.net. Thu Sep 18 07:29:13 UTC 2025 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Thu Sep 18 07:29:13 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Thu Sep 18 07:29:13 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-faWkjj' ==================================================================================== Thu Sep 18 07:29:13 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos1-amd64, called using "1 garli forky /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w 2.1-9" as arguments. Thu Sep 18 07:29:13 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-ddBeef1p" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Sep 18 07:29:13 UTC 2025 I: Downloading source for forky/garli=2.1-9 Reading package lists... NOTICE: 'garli' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/garli.git Please use: git clone https://salsa.debian.org/med-team/garli.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1256 kB of source archives. Get:1 http://deb.debian.org/debian forky/main garli 2.1-9 (dsc) [2186 B] Get:2 http://deb.debian.org/debian forky/main garli 2.1-9 (tar) [1249 kB] Get:3 http://deb.debian.org/debian forky/main garli 2.1-9 (diff) [5072 B] Fetched 1256 kB in 0s (15.1 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'garli' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/garli.git Please use: git clone https://salsa.debian.org/med-team/garli.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1256 kB of source archives. Get:1 http://deb.debian.org/debian forky/main garli 2.1-9 (dsc) [2186 B] Get:2 http://deb.debian.org/debian forky/main garli 2.1-9 (tar) [1249 kB] Get:3 http://deb.debian.org/debian forky/main garli 2.1-9 (diff) [5072 B] Fetched 1256 kB in 0s (15.1 MB/s) Download complete and in download only mode ============================================================================= Building garli in forky on amd64 on ionos1-amd64 now. Date: Thu Sep 18 07:29:14 UTC 2025 Date UTC: Thu Sep 18 07:29:14 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 17 19:29:14 -12 2025 I: pbuilder-time-stamp: 1758180554 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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: 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 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/4082616/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='fcede2e9c9734edeb0817bb04baae1cf' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='4082616' 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.sP9jpE6w/pbuilderrc_CBRI --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/b1 --logfile b1/build.log garli_2.1-9.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' 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 ionos1-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4082616/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: amd64 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 ... 19917 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-15{a} gfortran-15-x86-64-linux-gnu{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libcbor0.10{a} libcom-err2{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libfabric1{a} libffi8{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-15-dev{a} libgfortran5{a} libgssapi-krb5-2{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{a} libibverbs-dev{a} libibverbs1{a} libjs-jquery{a} libjs-jquery-ui{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libllvm17t64{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libncl-dev{a} libncl2{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi40{a} libpciaccess0{a} libpipeline1{a} libpsm2-2{a} librdmacm1t64{a} libreadline8t64{a} libtool{a} libuchardet0{a} libucx0{a} libunistring5{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2-16{a} libxnvctrl0{a} libz3-4{a} libze1{a} m4{a} man-db{a} mpi-default-dev{a} ncl-tools{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} po-debconf{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libmail-sendmail-perl lynx wget xauth 0 packages upgraded, 103 newly installed, 0 to remove and 0 not upgraded. Need to get 164 MB of archives. After unpacking 694 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 libfido2-1 amd64 1.16.0-2 [78.8 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 19 http://deb.debian.org/debian forky/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 openssh-client amd64 1:10.0p1-8 [986 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 bc amd64 1.07.1-4 [103 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 35 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 36 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 38 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 40 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 libgfortran-15-dev amd64 15.2.0-4 [886 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-4 [78.8 MB] Get: 46 http://deb.debian.org/debian forky/main amd64 gfortran-15 amd64 15.2.0-4 [17.9 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 libnl-3-200 amd64 3.11.0-2 [67.1 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 libnl-route-3-200 amd64 3.11.0-2 [211 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 libibverbs1 amd64 56.1-1 [62.4 kB] Get: 50 http://deb.debian.org/debian forky/main amd64 ibverbs-providers amd64 56.1-1 [357 kB] Get: 51 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 libllvm17t64 amd64 1:17.0.6-22+b3 [23.6 MB] Get: 54 http://deb.debian.org/debian forky/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get: 55 http://deb.debian.org/debian forky/main amd64 libdrm-common all 2.4.125-2 [8576 B] Get: 56 http://deb.debian.org/debian forky/main amd64 libdrm2 amd64 2.4.125-2 [39.1 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 libdrm-amdgpu1 amd64 2.4.125-2 [23.2 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 libnuma1 amd64 2.0.19-1 [22.2 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 libhsakmt1 amd64 6.2.4+ds-1 [61.1 kB] Get: 60 http://deb.debian.org/debian forky/main amd64 libhsa-runtime64-1 amd64 6.1.2-3 [535 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 libamdhip64-5 amd64 5.7.1-6 [8924 kB] Get: 62 http://deb.debian.org/debian forky/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 63 http://deb.debian.org/debian forky/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get: 64 http://deb.debian.org/debian forky/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b1 [108 kB] Get: 65 http://deb.debian.org/debian forky/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get: 66 http://deb.debian.org/debian forky/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b1 [61.1 kB] Get: 67 http://deb.debian.org/debian forky/main amd64 libevent-dev amd64 2.1.12-stable-10+b1 [305 kB] Get: 68 http://deb.debian.org/debian forky/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get: 69 http://deb.debian.org/debian forky/main amd64 librdmacm1t64 amd64 56.1-1 [70.4 kB] Get: 70 http://deb.debian.org/debian forky/main amd64 libfabric1 amd64 2.1.0-1.1 [706 kB] Get: 71 http://deb.debian.org/debian forky/main amd64 libhwloc15 amd64 2.12.2-1 [164 kB] Get: 72 http://deb.debian.org/debian forky/main amd64 libnuma-dev amd64 2.0.19-1 [36.5 kB] Get: 73 http://deb.debian.org/debian forky/main amd64 libltdl7 amd64 2.5.4-5 [416 kB] Get: 74 http://deb.debian.org/debian forky/main amd64 libltdl-dev amd64 2.5.4-5 [168 kB] Get: 75 http://deb.debian.org/debian forky/main amd64 libhwloc-dev amd64 2.12.2-1 [257 kB] Get: 76 http://deb.debian.org/debian forky/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 77 http://deb.debian.org/debian forky/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 78 http://deb.debian.org/debian forky/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 79 http://deb.debian.org/debian forky/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 80 http://deb.debian.org/debian forky/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 81 http://deb.debian.org/debian forky/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 82 http://deb.debian.org/debian forky/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 83 http://deb.debian.org/debian forky/main amd64 libxnvctrl0 amd64 535.171.04-1+b2 [14.2 kB] Get: 84 http://deb.debian.org/debian forky/main amd64 libze1 amd64 1.24.1-2 [514 kB] Get: 85 http://deb.debian.org/debian forky/main amd64 ocl-icd-libopencl1 amd64 2.3.3-1 [42.9 kB] Get: 86 http://deb.debian.org/debian forky/main amd64 libhwloc-plugins amd64 2.12.2-1 [23.5 kB] Get: 87 http://deb.debian.org/debian forky/main amd64 libibumad3 amd64 56.1-1 [30.0 kB] Get: 88 http://deb.debian.org/debian forky/main amd64 libibmad5 amd64 56.1-1 [44.5 kB] Get: 89 http://deb.debian.org/debian forky/main amd64 libnl-3-dev amd64 3.11.0-2 [110 kB] Get: 90 http://deb.debian.org/debian forky/main amd64 libnl-route-3-dev amd64 3.11.0-2 [235 kB] Get: 91 http://deb.debian.org/debian forky/main amd64 libibverbs-dev amd64 56.1-1 [654 kB] Get: 92 http://deb.debian.org/debian forky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 93 http://deb.debian.org/debian forky/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 94 http://deb.debian.org/debian forky/main amd64 libncl2 amd64 2.1.21+git20210811.b1213a7-6 [383 kB] Get: 95 http://deb.debian.org/debian forky/main amd64 libncl-dev amd64 2.1.21+git20210811.b1213a7-6 [599 kB] Get: 96 http://deb.debian.org/debian forky/main amd64 libucx0 amd64 1.19.0+ds-1 [1336 kB] Get: 97 http://deb.debian.org/debian forky/main amd64 libopenmpi40 amd64 5.0.8-9 [3258 kB] Get: 98 http://deb.debian.org/debian forky/main amd64 openmpi-common all 5.0.8-9 [107 kB] Get: 99 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 100 http://deb.debian.org/debian forky/main amd64 openmpi-bin amd64 5.0.8-9 [203 kB] Get: 101 http://deb.debian.org/debian forky/main amd64 libopenmpi-dev amd64 5.0.8-9 [1228 kB] Get: 102 http://deb.debian.org/debian forky/main amd64 mpi-default-dev amd64 1.18 [3372 B] Get: 103 http://deb.debian.org/debian forky/main amd64 ncl-tools amd64 2.1.21+git20210811.b1213a7-6 [190 kB] Fetched 164 MB in 26s (6364 kB/s) Preconfiguring packages ... Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../000-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../003-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../006-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../007-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../008-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../009-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../010-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../011-libedit2_3.1-20250104-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20250104-1) ... Selecting previously unselected package libcbor0.10:amd64. Preparing to unpack .../012-libcbor0.10_0.10.2-2_amd64.deb ... Unpacking libcbor0.10:amd64 (0.10.2-2) ... Selecting previously unselected package libfido2-1:amd64. Preparing to unpack .../013-libfido2-1_1.16.0-2_amd64.deb ... Unpacking libfido2-1:amd64 (1.16.0-2) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../014-libkrb5support0_1.21.3-5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-5) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../015-libcom-err2_1.47.2-3+b3_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-3+b3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../016-libk5crypto3_1.21.3-5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../017-libkeyutils1_1.6.3-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../018-libkrb5-3_1.21.3-5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../019-libgssapi-krb5-2_1.21.3-5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-5) ... Selecting previously unselected package openssh-client. Preparing to unpack .../020-openssh-client_1%3a10.0p1-8_amd64.deb ... Unpacking openssh-client (1:10.0p1-8) ... Selecting previously unselected package m4. Preparing to unpack .../021-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../022-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../023-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../024-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../025-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../026-libreadline8t64_8.3-3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package bc. Preparing to unpack .../027-bc_1.07.1-4_amd64.deb ... Unpacking bc (1.07.1-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../028-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../029-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../030-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../031-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 .../032-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../033-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../034-libelf1t64_0.193-3_amd64.deb ... Unpacking libelf1t64:amd64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../035-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../036-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../037-libxml2-16_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../038-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../039-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../040-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../041-debhelper_13.26_all.deb ... Unpacking debhelper (13.26) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../042-libgfortran5_15.2.0-4_amd64.deb ... Unpacking libgfortran5:amd64 (15.2.0-4) ... Selecting previously unselected package libgfortran-15-dev:amd64. Preparing to unpack .../043-libgfortran-15-dev_15.2.0-4_amd64.deb ... Unpacking libgfortran-15-dev:amd64 (15.2.0-4) ... Selecting previously unselected package gfortran-15-x86-64-linux-gnu. Preparing to unpack .../044-gfortran-15-x86-64-linux-gnu_15.2.0-4_amd64.deb ... Unpacking gfortran-15-x86-64-linux-gnu (15.2.0-4) ... Selecting previously unselected package gfortran-15. Preparing to unpack .../045-gfortran-15_15.2.0-4_amd64.deb ... Unpacking gfortran-15 (15.2.0-4) ... Selecting previously unselected package libnl-3-200:amd64. Preparing to unpack .../046-libnl-3-200_3.11.0-2_amd64.deb ... Unpacking libnl-3-200:amd64 (3.11.0-2) ... Selecting previously unselected package libnl-route-3-200:amd64. Preparing to unpack .../047-libnl-route-3-200_3.11.0-2_amd64.deb ... Unpacking libnl-route-3-200:amd64 (3.11.0-2) ... Selecting previously unselected package libibverbs1:amd64. Preparing to unpack .../048-libibverbs1_56.1-1_amd64.deb ... Unpacking libibverbs1:amd64 (56.1-1) ... Selecting previously unselected package ibverbs-providers:amd64. Preparing to unpack .../049-ibverbs-providers_56.1-1_amd64.deb ... Unpacking ibverbs-providers:amd64 (56.1-1) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../050-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package libz3-4:amd64. Preparing to unpack .../051-libz3-4_4.13.3-1_amd64.deb ... Unpacking libz3-4:amd64 (4.13.3-1) ... Selecting previously unselected package libllvm17t64:amd64. Preparing to unpack .../052-libllvm17t64_1%3a17.0.6-22+b3_amd64.deb ... Unpacking libllvm17t64:amd64 (1:17.0.6-22+b3) ... Selecting previously unselected package libamd-comgr2:amd64. Preparing to unpack .../053-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3+b2_amd64.deb ... Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Selecting previously unselected package libdrm-common. Preparing to unpack .../054-libdrm-common_2.4.125-2_all.deb ... Unpacking libdrm-common (2.4.125-2) ... Selecting previously unselected package libdrm2:amd64. Preparing to unpack .../055-libdrm2_2.4.125-2_amd64.deb ... Unpacking libdrm2:amd64 (2.4.125-2) ... Selecting previously unselected package libdrm-amdgpu1:amd64. Preparing to unpack .../056-libdrm-amdgpu1_2.4.125-2_amd64.deb ... Unpacking libdrm-amdgpu1:amd64 (2.4.125-2) ... Selecting previously unselected package libnuma1:amd64. Preparing to unpack .../057-libnuma1_2.0.19-1_amd64.deb ... Unpacking libnuma1:amd64 (2.0.19-1) ... Selecting previously unselected package libhsakmt1:amd64. Preparing to unpack .../058-libhsakmt1_6.2.4+ds-1_amd64.deb ... Unpacking libhsakmt1:amd64 (6.2.4+ds-1) ... Selecting previously unselected package libhsa-runtime64-1:amd64. Preparing to unpack .../059-libhsa-runtime64-1_6.1.2-3_amd64.deb ... Unpacking libhsa-runtime64-1:amd64 (6.1.2-3) ... Selecting previously unselected package libamdhip64-5:amd64. Preparing to unpack .../060-libamdhip64-5_5.7.1-6_amd64.deb ... Unpacking libamdhip64-5:amd64 (5.7.1-6) ... Selecting previously unselected package libevent-2.1-7t64:amd64. Preparing to unpack .../061-libevent-2.1-7t64_2.1.12-stable-10+b1_amd64.deb ... Unpacking libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libevent-core-2.1-7t64:amd64. Preparing to unpack .../062-libevent-core-2.1-7t64_2.1.12-stable-10+b1_amd64.deb ... Unpacking libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libevent-extra-2.1-7t64:amd64. Preparing to unpack .../063-libevent-extra-2.1-7t64_2.1.12-stable-10+b1_amd64.deb ... Unpacking libevent-extra-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64. Preparing to unpack .../064-libevent-pthreads-2.1-7t64_2.1.12-stable-10+b1_amd64.deb ... Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libevent-openssl-2.1-7t64:amd64. Preparing to unpack .../065-libevent-openssl-2.1-7t64_2.1.12-stable-10+b1_amd64.deb ... Unpacking libevent-openssl-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libevent-dev. Preparing to unpack .../066-libevent-dev_2.1.12-stable-10+b1_amd64.deb ... Unpacking libevent-dev (2.1.12-stable-10+b1) ... Selecting previously unselected package libpsm2-2. Preparing to unpack .../067-libpsm2-2_11.2.185-2.1_amd64.deb ... Unpacking libpsm2-2 (11.2.185-2.1) ... Selecting previously unselected package librdmacm1t64:amd64. Preparing to unpack .../068-librdmacm1t64_56.1-1_amd64.deb ... Unpacking librdmacm1t64:amd64 (56.1-1) ... Selecting previously unselected package libfabric1:amd64. Preparing to unpack .../069-libfabric1_2.1.0-1.1_amd64.deb ... Unpacking libfabric1:amd64 (2.1.0-1.1) ... Selecting previously unselected package libhwloc15:amd64. Preparing to unpack .../070-libhwloc15_2.12.2-1_amd64.deb ... Unpacking libhwloc15:amd64 (2.12.2-1) ... Selecting previously unselected package libnuma-dev:amd64. Preparing to unpack .../071-libnuma-dev_2.0.19-1_amd64.deb ... Unpacking libnuma-dev:amd64 (2.0.19-1) ... Selecting previously unselected package libltdl7:amd64. Preparing to unpack .../072-libltdl7_2.5.4-5_amd64.deb ... Unpacking libltdl7:amd64 (2.5.4-5) ... Selecting previously unselected package libltdl-dev:amd64. Preparing to unpack .../073-libltdl-dev_2.5.4-5_amd64.deb ... Unpacking libltdl-dev:amd64 (2.5.4-5) ... Selecting previously unselected package libhwloc-dev:amd64. Preparing to unpack .../074-libhwloc-dev_2.12.2-1_amd64.deb ... Unpacking libhwloc-dev:amd64 (2.12.2-1) ... Selecting previously unselected package libpciaccess0:amd64. Preparing to unpack .../075-libpciaccess0_0.17-3+b3_amd64.deb ... Unpacking libpciaccess0:amd64 (0.17-3+b3) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../076-libxau6_1%3a1.0.11-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../077-libxdmcp6_1%3a1.1.5-1_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.5-1) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../078-libxcb1_1.17.0-2+b1_amd64.deb ... Unpacking libxcb1:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../079-libx11-data_2%3a1.8.12-1_all.deb ... Unpacking libx11-data (2:1.8.12-1) ... 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Setting up libcom-err2:amd64 (1.47.2-3+b3) ... Setting up file (1:5.46-5) ... Setting up libncl2:amd64 (2.1.21+git20210811.b1213a7-6) ... Setting up libze1:amd64 (1.24.1-2) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up libncl-dev:amd64 (2.1.21+git20210811.b1213a7-6) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up autotools-dev (20240727.1) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libx11-data (2:1.8.12-1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up libhwloc15:amd64 (2.12.2-1) ... Setting up autopoint (0.23.1-2) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libltdl7:amd64 (2.5.4-5) ... Setting up libgfortran5:amd64 (15.2.0-4) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up libnuma1:amd64 (2.0.19-1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up ocl-icd-libopencl1:amd64 (2.3.3-1) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up libnl-3-200:amd64 (3.11.0-2) ... Setting up libpsm2-2 (11.2.185-2.1) ... Setting up openmpi-common (5.0.8-9) ... Setting up libx11-6:amd64 (2:1.8.12-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:amd64 (1.16.0-2) ... Setting up libdrm-common (2.4.125-2) ... Setting up readline-common (8.3-3) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libevent-openssl-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up ncl-tools (2.1.21+git20210811.b1213a7-6) ... 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Setting up openmpi-bin (5.0.8-9) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:amd64 (5.0.8-9) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up mpi-default-dev (1.18) ... Processing triggers for libc-bin (2.41-12) ... 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 amd64 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=x86_64-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/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-ncl=/usr --enable-mpi checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 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 xargs -n works... yes checking whether UID '1111' is supported by ustar format... yes checking whether GID '1111' is supported by ustar format... yes checking 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 -j40 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from configoptions.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] 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++/15/string:51, from bipartition.h:23, from bipartition.cpp:19: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from garlimain.cpp:40: 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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from population.h:23: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from model.cpp:17: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/refwrap.h:41, from /usr/include/c++/15/vector:70, from tree.h:24: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from adaptation.cpp:18: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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 configreader.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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from configreader.cpp:21: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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; | ~~~~~~~^~~~~~~~~~~~~~~~~~ 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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from population.h:23: /usr/include/c++/15/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++/15/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++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, from 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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from mpitrick.cpp:21: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/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++/15/bits/refwrap.h:41, from /usr/include/c++/15/vector:70, from tree.cpp:21: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/bits/refwrap.h:41, from /usr/include/c++/15/vector:70, from population.cpp:23: /usr/include/c++/15/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++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, from individual.cpp:28: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/iomanip:47, from individual.cpp:21: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from population.cpp:49: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;idlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6845:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6845 | fread(&dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6849:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6849 | fread(&dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6855:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6855 | fread(&dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6858:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6858 | fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6862:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6862 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6865:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6865 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6868:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6868 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6872:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6872 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6878:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6878 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6881 | fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ reconnode.h: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)': reconnode.h:388:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 388 | fread(&unique, scalarSize, 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ reconnode.h: In constructor 'Swap::Swap(FILE*&)': reconnode.h:264:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 264 | fread(&count, scalarSize, 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from treenode.h:30, from tree.h:31: bipartition.h: In member function 'void Bipartition::BinaryInput(FILE*&)': bipartition.h:518:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 518 | fread((char*) rep, sizeof(unsigned int), nBlocks, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ population.cpp: In member function 'void Population::ReadPopulationCheckpoint()': population.cpp:1880:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1880 | fread((char *) &seed, sizeof(seed), 1, pin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ population.cpp:1887:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1887 | fread((char *) &t, sizeof(t), 1, pin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ population.cpp:1896:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(this, scalarSize, 1, pin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, 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/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from model.h:25, from clamanager.h:25, from condlike.cpp:22: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from rng.h:36, from tree.h:30: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from configreader.cpp:18: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from treenode.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, 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/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/ncl/ncl.h:27, from garlireader.cpp:41: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] /usr/include/x86_64-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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from datamatr.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from population.cpp:25: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] garlimain.cpp: In function 'int SubGarliMain(int)': garlimain.cpp:323:49: warning: '%d' directive writing between 2 and 10 bytes into a region of size 6 [-Wformat-overflow=] 323 | else sprintf(temp, ".run%d", rank); | ^~ garlimain.cpp:323:44: note: directive argument in the range [10, 2147483647] 323 | else sprintf(temp, ".run%d", rank); | ^~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int SubGarliMain(int)' at garlimain.cpp:323:16: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 15 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 ()); | ~~~~~~~~~~~~~~~~~ garlimain.cpp: In function 'int SubGarliMain(int)': garlimain.cpp:322:59: warning: '%d' directive writing between 1 and 11 bytes into a region of size 5 [-Wformat-overflow=] 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); | ^~ garlimain.cpp:322:53: note: directive argument in the range [-2147483648, 9] 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int SubGarliMain(int)' at garlimain.cpp:322:25: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 17 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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, 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/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': population.cpp:3066:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~ population.cpp:3066:47: note: directive argument in the range [1, 2147483647] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mpic++ -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -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[4]: Leaving directory '/build/reproducible-path/garli-2.1/src' Making all in tests make[4]: Entering directory '/build/reproducible-path/garli-2.1/tests' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/garli-2.1/tests' make[4]: Entering directory '/build/reproducible-path/garli-2.1' make[4]: Leaving 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' mkdir -p debian/mpi mv src/Garli debian/mpi/Garli-mpi make distclean make[2]: Entering directory '/build/reproducible-path/garli-2.1' Making distclean in src make[3]: Entering directory '/build/reproducible-path/garli-2.1/src' rm -f Garli rm -f *.o rm -f *.tab.c rm -f test . = "." || rm -f rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags rm -f ./.deps/adaptation.Po rm -f ./.deps/bipartition.Po rm -f ./.deps/condlike.Po rm -f ./.deps/configoptions.Po rm -f ./.deps/configreader.Po rm -f ./.deps/datamatr.Po rm -f ./.deps/funcs.Po rm -f ./.deps/garlimain.Po rm -f ./.deps/garlireader.Po rm -f ./.deps/individual.Po rm -f ./.deps/linalg.Po rm -f ./.deps/model.Po rm -f ./.deps/mpitrick.Po rm -f ./.deps/optimization.Po rm -f ./.deps/population.Po rm -f ./.deps/rng.Po rm -f ./.deps/sequencedata.Po rm -f ./.deps/set.Po rm -f ./.deps/translatetable.Po rm -f ./.deps/tree.Po rm -f ./.deps/treenode.Po rm -f Makefile make[3]: Leaving directory '/build/reproducible-path/garli-2.1/src' Making distclean in tests make[3]: Entering directory '/build/reproducible-path/garli-2.1/tests' rm -f test . = "." || rm -f rm -f Makefile make[3]: Leaving directory '/build/reproducible-path/garli-2.1/tests' make[3]: Entering directory '/build/reproducible-path/garli-2.1' rm -f test . = "." || rm -f rm -f config.h stamp-h1 rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags rm -f cscope.out cscope.in.out cscope.po.out cscope.files make[3]: Leaving directory '/build/reproducible-path/garli-2.1' rm -f config.status config.cache config.log configure.lineno config.status.lineno rm -f Makefile make[2]: Leaving directory '/build/reproducible-path/garli-2.1' # Now build single processor binary dh_auto_configure -- --with-ncl=/usr ./configure --build=x86_64-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/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-ncl=/usr checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 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 xargs -n works... yes checking whether UID '1111' is supported by ustar format... yes checking whether GID '1111' is supported by ustar format... yes checking 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 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 make[1]: Leaving directory '/build/reproducible-path/garli-2.1' dh_auto_build make -j40 make[1]: Entering directory '/build/reproducible-path/garli-2.1' make all-recursive make[2]: Entering directory '/build/reproducible-path/garli-2.1' Making all in src make[3]: Entering directory '/build/reproducible-path/garli-2.1/src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o adaptation.o adaptation.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o bipartition.o bipartition.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o condlike.o condlike.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configoptions.o configoptions.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configreader.o configreader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o datamatr.o datamatr.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o funcs.o funcs.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlimain.o garlimain.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlireader.o garlireader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o individual.o individual.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.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 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++/15/string:51, from bipartition.h:23, from bipartition.cpp:19: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from configoptions.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] 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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/iomanip:47, from individual.cpp:21: /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from garlimain.cpp:40: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public 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++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from population.h:23: /usr/include/c++/15/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++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/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++/15/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from adaptation.cpp:18: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/refwrap.h:41, from /usr/include/c++/15/vector:70, from population.cpp:23: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from model.cpp:17: /usr/include/c++/15/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++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from configreader.cpp:21: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/refwrap.h:41, from /usr/include/c++/15/vector:70, from tree.h:24: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/refwrap.h:41, from /usr/include/c++/15/vector:70, from tree.cpp:21: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from population.h:23: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)': adaptation.cpp:271:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 271 | fread((char *) this, 1, scalarSize, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:278:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 278 | fread((char *) improvetotal, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:280:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 280 | fread((char *) randNNI, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:281:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 281 | fread((char *) randNNInum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:283:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 283 | fread((char *) exNNI, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:284:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 284 | fread((char *) exNNInum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:286:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 286 | fread((char *) randSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:287:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 287 | fread((char *) randSPRnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:289:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 289 | fread((char *) limSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:290:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 290 | fread((char *) limSPRnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:292:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 292 | fread((char *) exlimSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:293:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 293 | fread((char *) exlimSPRnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:295:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 295 | fread((char *) randRecom, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:296:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 296 | fread((char *) randRecomnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:298:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 298 | fread((char *) bipartRecom, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:299:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | fread((char *) bipartRecomnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:301:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 301 | fread((char *) onlyBrlen, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:302:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 302 | fread((char *) onlyBrlennum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:304:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 304 | fread((char *) anyModel, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:305:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 305 | fread((char *) anyModelnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from model.h:25, from clamanager.h:25, from condlike.cpp:22: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, 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/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, 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/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from configreader.cpp:18: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from datamatr.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from treenode.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from rng.h:36, from tree.h:30: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/ncl/ncl.h:27, from garlireader.cpp:41: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from population.cpp:25: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, 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/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': population.cpp:3066:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~ population.cpp:3066:47: note: directive argument in the range [1, 2147483647] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -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 -j40 check "TESTSUITEFLAGS=-j40 --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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 0.925 (branch= 0.64 scale= 0.00 omega= 0.28 rel rates= 0.00) pass 3:+ 0.733 (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: -213.0379 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 77.066 (branch= 2.27 scale= 0.00 alpha= 4.14 freqs= 10.82 rel rates= 3.11 pinv= 0.78 subset rates= 55.95) pass 3:+ 49.994 (branch= 6.88 scale= 0.78 alpha= 5.67 freqs= 1.20 rel rates= 1.34 pinv= 0.01 subset rates= 34.11) pass 4:+ 15.059 (branch= 0.00 scale= 0.72 alpha= 0.64 freqs= 1.21 rel rates= 0.50 pinv= 0.00 subset rates= 12.00) pass 5:+ 5.778 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.10 rel rates= 0.77 pinv= 0.00 subset rates= 4.91) pass 6:+ 0.115 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.09 rel rates= 0.01 pinv= 0.00 subset rates= 0.00) lnL after optimization: -13342.2046 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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= 4.30) pass 2:+ 9.055 (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:+ 0.303 (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: -467.8152 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 12.450 (branch= 8.46 scale= 0.00 subset rates= 3.99) pass 3:+ 3.552 (branch= 2.32 scale= 0.03 subset rates= 1.21) pass 4:+ 0.758 (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: -477.9401 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 129.564 (branch= 123.99 scale= 0.59 subset rates= 4.98) pass 2:+ 9.273 (branch= 7.97 scale= 0.00 subset rates= 1.30) pass 3:+ 1.739 (branch= 1.57 scale= 0.00 subset rates= 0.17) pass 4:+ 0.312 (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: -464.7107 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 3.846 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.161 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.158 (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: -474.8622 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 1 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 10 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 7 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 : -3355.4806 (branch= 0.9931 alpha= 0.0078 pinv= 0.0071 eq freqs= 0.1960 rel rates= 1.3003 subset rates= 0.3859) pass 2 : -3354.0831 (branch= 0.5204 alpha= 0.0089 pinv= 0.0117 eq freqs= 0.0202 rel rates= 0.6677 subset rates= 0.1686) pass 3 : -3353.2198 (branch= 0.2864 alpha= 0.0000 pinv= 0.0086 eq freqs= 0.0160 rel rates= 0.4622 subset rates= 0.0901) pass 4 : -3352.6255 (branch= 0.1646 alpha= 0.0037 pinv= 0.0159 eq freqs= 0.0035 rel rates= 0.3594 subset rates= 0.0473) pass 5 : -3352.1694 (branch= 0.0978 alpha= 0.0045 pinv= 0.0165 eq freqs= 0.0021 rel rates= 0.3101 subset rates= 0.0251) pass 6 : -3351.8162 (branch= 0.0577 alpha= 0.0065 pinv= 0.0165 eq freqs= 0.0009 rel rates= 0.2567 subset rates= 0.0148) pass 7 : -3351.5408 (branch= 0.0284 alpha= 0.0087 pinv= 0.0158 eq freqs= 0.0010 rel rates= 0.2101 subset rates= 0.0114) pass 8 : -3351.3231 (branch= 0.0191 alpha= 0.0100 pinv= 0.0149 eq freqs= 0.0007 rel rates= 0.1668 subset rates= 0.0062) pass 9 : -3351.1479 (branch= 0.0117 alpha= 0.0106 pinv= 0.0140 eq freqs= 0.0005 rel rates= 0.1344 subset rates= 0.0041) pass 10: -3351.0053 (branch= 0.0070 alpha= 0.0105 pinv= 0.0138 eq freqs= 0.0004 rel rates= 0.1083 subset rates= 0.0026) pass 11: -3350.8878 (branch= 0.0043 alpha= 0.0103 pinv= 0.0127 eq freqs= 0.0003 rel rates= 0.0881 subset rates= 0.0018) pass 12: -3350.7912 (branch= 0.0033 alpha= 0.0098 pinv= 0.0116 eq freqs= 0.0002 rel rates= 0.0716 subset rates= 0.0000) pass 13: -3350.7078 (branch= 0.0008 alpha= 0.0096 pinv= 0.0105 eq freqs= 0.0002 rel rates= 0.0606 subset rates= 0.0018) pass 14: -3350.6403 (branch= 0.0012 alpha= 0.0090 pinv= 0.0095 eq freqs= 0.0002 rel rates= 0.0475 subset rates= 0.0000) pass 15: -3350.5832 (branch= 0.0003 alpha= 0.0082 pinv= 0.0081 eq freqs= 0.0001 rel rates= 0.0404 subset rates= 0.0000) pass 16: -3350.5328 (branch= 0.0001 alpha= 0.0079 pinv= 0.0073 eq freqs= 0.0001 rel rates= 0.0339 subset rates= 0.0012) pass 17: -3350.4923 (branch= 0.0008 alpha= 0.0069 pinv= 0.0066 eq freqs= 0.0001 rel rates= 0.0262 subset rates= 0.0000) pass 18: -3350.4574 (branch= 0.0002 alpha= 0.0060 pinv= 0.0059 eq freqs= 0.0000 rel rates= 0.0227 subset rates= 0.0000) pass 19: -3350.4270 (branch= 0.0000 alpha= 0.0056 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0195 subset rates= 0.0000) pass 20: -3350.4005 (branch= 0.0000 alpha= 0.0051 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0167 subset rates= 0.0000) optimization up to ... pass 30: -3350.2715 (branch= 0.0001 alpha= 0.0273 pinv= 0.0248 eq freqs= 0.0002 rel rates= 0.0767 subset rates= 0.0000) optimization up to ... pass 40: -3350.2419 (branch= 0.0000 alpha= 0.0064 pinv= 0.0060 eq freqs= 0.0000 rel rates= 0.0171 subset rates= 0.0000) optimization up to ... pass 50: -3350.2353 (branch= 0.0000 alpha= 0.0013 pinv= 0.0012 eq freqs= 0.0000 rel rates= 0.0042 subset rates= 0.0000) optimization up to ... pass 60: -3350.2337 (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: -3350.2334 (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: -3350.2333 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) Looking for minimum length branches... Final score = -3350.2333 Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -3350.2333 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: 3.113 10.41 2.688 0.001 21.89 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 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 3350.23331 ***Expected is 3350.2345 ***SCORE DIFFERENCE IS -.00119 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 : -3329.9920 (branch= 1.3745 alpha= 0.0217 pinv= 0.0099 eq freqs= 0.2403 rel rates= 0.7561 ins/del rates= 0.0754) pass 2 : -3329.0411 (branch= 0.3511 alpha= 0.0000 pinv= 0.0096 eq freqs= 0.0000 rel rates= 0.5271 ins/del rates= 0.0631) pass 3 : -3328.4283 (branch= 0.1466 alpha= 0.0039 pinv= 0.0146 eq freqs= 0.0187 rel rates= 0.3867 ins/del rates= 0.0424) pass 4 : -3327.9685 (branch= 0.0855 alpha= 0.0067 pinv= 0.0148 eq freqs= 0.0031 rel rates= 0.3207 ins/del rates= 0.0290) pass 5 : -3327.6169 (branch= 0.0530 alpha= 0.0080 pinv= 0.0147 eq freqs= 0.0017 rel rates= 0.2561 ins/del rates= 0.0181) pass 6 : -3327.3365 (branch= 0.0344 alpha= 0.0079 pinv= 0.0146 eq freqs= 0.0008 rel rates= 0.2111 ins/del rates= 0.0115) pass 7 : -3327.1138 (branch= 0.0219 alpha= 0.0094 pinv= 0.0140 eq freqs= 0.0007 rel rates= 0.1690 ins/del rates= 0.0077) pass 8 : -3326.9319 (branch= 0.0143 alpha= 0.0098 pinv= 0.0133 eq freqs= 0.0006 rel rates= 0.1388 ins/del rates= 0.0051) pass 9 : -3326.7851 (branch= 0.0094 alpha= 0.0099 pinv= 0.0125 eq freqs= 0.0004 rel rates= 0.1113 ins/del rates= 0.0034) pass 10: -3326.6639 (branch= 0.0063 alpha= 0.0097 pinv= 0.0123 eq freqs= 0.0003 rel rates= 0.0903 ins/del rates= 0.0023) pass 11: -3326.5636 (branch= 0.0042 alpha= 0.0095 pinv= 0.0114 eq freqs= 0.0002 rel rates= 0.0735 ins/del rates= 0.0015) pass 12: -3326.4810 (branch= 0.0028 alpha= 0.0090 pinv= 0.0099 eq freqs= 0.0002 rel rates= 0.0596 ins/del rates= 0.0010) pass 13: -3326.4117 (branch= 0.0019 alpha= 0.0085 pinv= 0.0091 eq freqs= 0.0001 rel rates= 0.0490 ins/del rates= 0.0007) pass 14: -3326.3528 (branch= 0.0013 alpha= 0.0080 pinv= 0.0083 eq freqs= 0.0001 rel rates= 0.0408 ins/del rates= 0.0005) pass 15: -3326.3023 (branch= 0.0009 alpha= 0.0074 pinv= 0.0076 eq freqs= 0.0001 rel rates= 0.0342 ins/del rates= 0.0003) pass 16: -3326.2594 (branch= 0.0006 alpha= 0.0069 pinv= 0.0068 eq freqs= 0.0001 rel rates= 0.0283 ins/del rates= 0.0002) pass 17: -3326.2227 (branch= 0.0004 alpha= 0.0064 pinv= 0.0062 eq freqs= 0.0001 rel rates= 0.0235 ins/del rates= 0.0001) pass 18: -3326.1910 (branch= 0.0002 alpha= 0.0057 pinv= 0.0056 eq freqs= 0.0001 rel rates= 0.0201 ins/del rates= 0.0001) pass 19: -3326.1634 (branch= 0.0001 alpha= 0.0052 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0171 ins/del rates= 0.0000) pass 20: -3326.1395 (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= 0.0001 rel rates= 0.0688 ins/del rates= 0.0001) optimization up to ... pass 40: -3325.9908 (branch= 0.0000 alpha= 0.0068 pinv= 0.0064 eq freqs= 0.0000 rel rates= 0.0157 ins/del rates= 0.0000) optimization up to ... pass 50: -3325.9841 (branch= 0.0000 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 76: -3325.9822 (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 = -3325.9822 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 : -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: 3.062 10.26 2.656 0.001 21.52 1 0.333 0.222 0.157 0.288 0.574 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 3325.98220 ***Expected is 3325.98222 ***SCORE DIFFERENCE IS -.00002 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 2061.640 (branch=1982.89 scale= 74.28 freqs= 0.89 rel rates= 3.59) pass 2:+ 221.898 (branch= 220.63 scale= 0.00 freqs= 0.84 rel rates= 0.43) pass 3:+ 4.926 (branch= 4.77 scale= 0.00 freqs= 0.07 rel rates= 0.09) pass 4:+ 0.328 (branch= 0.31 scale= 0.00 freqs= 0.00 rel rates= 0.02) pass 5:+ 0.069 (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: -16071.0881 gen current_lnL precision last_tree_imp 0 -16071.0881 0.010 0 100 -14502.1424 0.010 73 200 -14502.1082 0.010 73 300 -14501.0360 0.010 73 400 -14500.4215 0.010 73 500 -14500.0792 0.010 73 600 -14499.5615 0.010 73 700 -14499.2365 0.010 73 800 -14499.1060 0.010 73 900 -14499.1049 0.010 73 1000 -14499.1049 0.010 73 1100 -14498.9970 0.010 73 1200 -14498.9970 0.010 73 1300 -14498.9879 0.010 73 1400 -14498.9879 0.010 73 1500 -14498.9852 0.010 73 1600 -14498.9678 0.010 73 Reached termination condition! last topological improvement at gen 73 Improvement over last 500 gen = 0.02921 Current score = -14498.9678 Performing final optimizations... pass 1 : -14498.9160 (branch= 0.0243 eq freqs= 0.0185 rel rates= 0.0090) pass 2 : -14498.8971 (branch= 0.0099 eq freqs= 0.0002 rel rates= 0.0089) pass 3 : -14498.8909 (branch= 0.0037 eq freqs= 0.0001 rel rates= 0.0023) pass 4 : -14498.8878 (branch= 0.0010 eq freqs= 0.0019 rel rates= 0.0002) pass 5 : -14498.8866 (branch= 0.0006 eq freqs= 0.0004 rel rates= 0.0002) pass 6 : -14498.8859 (branch= 0.0004 eq freqs= 0.0000 rel rates= 0.0002) pass 7 : -14498.8857 (branch= 0.0002 eq freqs= 0.0000 rel rates= 0.0001) pass 8 : -14498.8855 (branch= 0.0002 eq freqs= 0.0000 rel rates= 0.0000) pass 9 : -14498.8854 (branch= 0.0001 eq freqs= 0.0000 rel rates= 0.0000) pass 10: -14498.8853 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 11: -14498.8853 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 12: -14498.8853 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -14498.8853 Time used = 0 hours, 0 minutes and 3 seconds MODEL REPORT - Parameter values are FINAL 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 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 : -14498.8853 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 1.869 3.671 1.221 1.853 4.414 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 14486.03850 ***Expected is 14486.03829 ***SCORE DIFFERENCE IS .00021 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 36.660 (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: -13315.7939 Current score = -13315.7939 Performing final optimizations... pass 1 : -13309.3700 (branch= 2.8300 alpha= 0.8831 pinv= 0.0158 eq freqs= 0.2323 rel rates= 1.8454 subset rates= 0.6173) pass 2 : -13307.8842 (branch= 0.4328 alpha= 0.2019 pinv= 0.0134 eq freqs= 0.1232 rel rates= 0.6633 subset rates= 0.0513) pass 3 : -13307.2657 (branch= 0.1095 alpha= 0.0595 pinv= 0.0031 eq freqs= 0.0081 rel rates= 0.4287 subset rates= 0.0096) pass 4 : -13306.9109 (branch= 0.0241 alpha= 0.0171 pinv= 0.0026 eq freqs= 0.0085 rel rates= 0.2993 subset rates= 0.0032) pass 5 : -13306.6767 (branch= 0.0088 alpha= 0.0057 pinv= 0.0013 eq freqs= 0.0072 rel rates= 0.2110 subset rates= 0.0002) pass 6 : -13306.5232 (branch= 0.0036 alpha= 0.0020 pinv= 0.0004 eq freqs= 0.0043 rel rates= 0.1433 subset rates= 0.0000) pass 7 : -13306.4217 (branch= 0.0011 alpha= 0.0004 pinv= 0.0001 eq freqs= 0.0035 rel rates= 0.0964 subset rates= 0.0000) pass 8 : -13306.3532 (branch= 0.0006 alpha= 0.0002 pinv= 0.0001 eq freqs= 0.0020 rel rates= 0.0656 subset rates= 0.0000) pass 9 : -13306.3069 (branch= 0.0003 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0015 rel rates= 0.0444 subset rates= 0.0000) pass 10: -13306.2750 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0012 rel rates= 0.0306 subset rates= 0.0000) pass 11: -13306.2534 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0206 subset rates= 0.0002) pass 12: -13306.2381 (branch= 0.0001 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0142 subset rates= 0.0005) pass 13: -13306.2280 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0097 subset rates= 0.0000) pass 14: -13306.2211 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0067 subset rates= 0.0000) pass 15: -13306.2164 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0045 subset rates= 0.0000) pass 16: -13306.2134 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0030 subset rates= 0.0000) pass 17: -13306.2112 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0021 subset rates= 0.0000) pass 18: -13306.2097 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014 subset rates= 0.0000) pass 19: -13306.2087 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010 subset rates= 0.0000) pass 20: -13306.2080 (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: -13306.2065 (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: -13306.2063 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0001) Looking for minimum length branches... Final score = -13306.2063 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 : -13306.2063 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 1.413 1.413 3.72 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: 4.369 7.051 1.608 7.051 4.369 1 0.270 0.164 0.161 0.406 0.361 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 4.034 0.033 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 1.694 0.540 0.300 2.160 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 13306.20634 ***Expected is 13306.20608 ***SCORE DIFFERENCE IS .00026 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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= 4.30) pass 2:+ 9.055 (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:+ 0.303 (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: -467.8152 Current score = -467.8152 Performing final optimizations... pass 1 : -467.7873 (branch= 0.0213 subset rates= 0.0066) pass 2 : -467.7197 (branch= 0.0649 subset rates= 0.0027) pass 3 : -467.6968 (branch= 0.0229 subset rates= 0.0000) pass 4 : -467.6869 (branch= 0.0099 subset rates= 0.0000) pass 5 : -467.6823 (branch= 0.0046 subset rates= 0.0000) pass 6 : -467.6802 (branch= 0.0020 subset rates= 0.0000) pass 7 : -467.6793 (branch= 0.0009 subset rates= 0.0000) pass 8 : -467.6788 (branch= 0.0005 subset rates= 0.0000) pass 9 : -467.6785 (branch= 0.0003 subset rates= 0.0000) pass 10: -467.6784 (branch= 0.0001 subset rates= 0.0000) pass 11: -467.6783 (branch= 0.0000 subset rates= 0.0000) pass 12: -467.6783 (branch= 0.0000 subset rates= 0.0000) pass 13: -467.6783 (branch= 0.0000 subset rates= 0.0000) pass 14: -467.6783 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6783 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -467.6783 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: 3.842 0.786 1.480 2.177 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 467.67829 ***Expected is 467.6783 ***SCORE DIFFERENCE IS -.00001 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 12.450 (branch= 8.46 scale= 0.00 subset rates= 3.99) pass 3:+ 3.552 (branch= 2.32 scale= 0.03 subset rates= 1.21) pass 4:+ 0.758 (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: -477.9401 Current score = -477.9401 Performing final optimizations... pass 1 : -477.8535 (branch= 0.0858 subset rates= 0.0008) pass 2 : -477.7572 (branch= 0.0963 subset rates= 0.0000) pass 3 : -477.7255 (branch= 0.0301 subset rates= 0.0016) pass 4 : -477.7048 (branch= 0.0207 subset rates= 0.0000) pass 5 : -477.6964 (branch= 0.0085 subset rates= 0.0000) pass 6 : -477.6921 (branch= 0.0043 subset rates= 0.0000) pass 7 : -477.6900 (branch= 0.0021 subset rates= 0.0000) pass 8 : -477.6888 (branch= 0.0011 subset rates= 0.0000) pass 9 : -477.6882 (branch= 0.0007 subset rates= 0.0000) pass 10: -477.6861 (branch= 0.0004 subset rates= 0.0016) pass 11: -477.6854 (branch= 0.0008 subset rates= 0.0000) pass 12: -477.6850 (branch= 0.0003 subset rates= 0.0000) pass 13: -477.6849 (branch= 0.0002 subset rates= 0.0000) pass 14: -477.6847 (branch= 0.0001 subset rates= 0.0000) pass 15: -477.6847 (branch= 0.0000 subset rates= 0.0000) pass 16: -477.6847 (branch= 0.0000 subset rates= 0.0000) pass 17: -477.6847 (branch= 0.0000 subset rates= 0.0000) pass 18: -477.6846 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.6846 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 : -477.6846 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: 4.914 0.631 1.899 2.807 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 477.68463 ***Expected is 477.6848 ***SCORE DIFFERENCE IS -.00017 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 129.564 (branch= 123.99 scale= 0.59 subset rates= 4.98) pass 2:+ 9.273 (branch= 7.97 scale= 0.00 subset rates= 1.30) pass 3:+ 1.739 (branch= 1.57 scale= 0.00 subset rates= 0.17) pass 4:+ 0.312 (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: -464.7107 Current score = -464.7107 Performing final optimizations... pass 1 : -464.6735 (branch= 0.0277 subset rates= 0.0095) pass 2 : -464.5879 (branch= 0.0823 subset rates= 0.0033) pass 3 : -464.5682 (branch= 0.0185 subset rates= 0.0012) pass 4 : -464.5557 (branch= 0.0125 subset rates= 0.0000) pass 5 : -464.5526 (branch= 0.0031 subset rates= 0.0000) pass 6 : -464.5498 (branch= 0.0022 subset rates= 0.0006) pass 7 : -464.5490 (branch= 0.0007 subset rates= 0.0000) pass 8 : -464.5482 (branch= 0.0008 subset rates= 0.0000) pass 9 : -464.5478 (branch= 0.0004 subset rates= 0.0000) pass 10: -464.5477 (branch= 0.0001 subset rates= 0.0000) pass 11: -464.5476 (branch= 0.0001 subset rates= 0.0000) pass 12: -464.5476 (branch= 0.0000 subset rates= 0.0000) pass 13: -464.5476 (branch= 0.0000 subset rates= 0.0000) pass 14: -464.5476 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -464.5476 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 : -464.5476 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 0.772 1.641 2.452 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 464.54756 ***Expected is 464.5473 ***SCORE DIFFERENCE IS .00026 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 3.846 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.161 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.158 (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: -474.8622 Current score = -474.8622 Performing final optimizations... pass 1 : -474.7981 (branch= 0.0576 subset rates= 0.0066) pass 2 : -474.6999 (branch= 0.0911 subset rates= 0.0071) pass 3 : -474.6746 (branch= 0.0233 subset rates= 0.0020) pass 4 : -474.6609 (branch= 0.0137 subset rates= 0.0000) pass 5 : -474.6539 (branch= 0.0070 subset rates= 0.0000) pass 6 : -474.6510 (branch= 0.0029 subset rates= 0.0000) pass 7 : -474.6490 (branch= 0.0011 subset rates= 0.0009) pass 8 : -474.6470 (branch= 0.0012 subset rates= 0.0008) pass 9 : -474.6464 (branch= 0.0007 subset rates= 0.0000) pass 10: -474.6460 (branch= 0.0004 subset rates= 0.0000) pass 11: -474.6458 (branch= 0.0002 subset rates= 0.0000) pass 12: -474.6457 (branch= 0.0001 subset rates= 0.0001) pass 13: -474.6456 (branch= 0.0001 subset rates= 0.0000) pass 14: -474.6455 (branch= 0.0000 subset rates= 0.0000) pass 15: -474.6455 (branch= 0.0000 subset rates= 0.0000) pass 16: -474.6455 (branch= 0.0000 subset rates= 0.0000) pass 17: -474.6455 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -474.6455 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 : -474.6455 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: 4.585 0.585 2.017 2.998 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 474.64547 ***Expected is 474.6455633 ***SCORE DIFFERENCE IS -.0000933 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 -210.8784 0.010 1215 2000 -210.6679 0.010 1215 2500 -210.6042 0.010 1215 3000 -210.5103 0.010 1215 3500 -210.4074 0.010 1215 Reached termination condition! last topological improvement at gen 1215 Improvement over last 500 gen = 0.04856 Current score = -210.3682 Performing final optimizations... pass 1 : -210.0050 (branch= 0.0000 alpha= 0.0802 pinv= 0.2366 eq freqs= 0.0000 rel rates= 0.0463) pass 2 : -209.4569 (branch= 0.0070 alpha= 0.3208 pinv= 0.2046 eq freqs= 0.0043 rel rates= 0.0115) pass 3 : -209.3004 (branch= 0.0331 alpha= 0.0941 pinv= 0.0091 eq freqs= 0.0085 rel rates= 0.0117) pass 4 : -209.2399 (branch= 0.0368 alpha= 0.0184 pinv= 0.0014 eq freqs= 0.0008 rel rates= 0.0031) pass 5 : -209.1932 (branch= 0.0307 alpha= 0.0102 pinv= 0.0005 eq freqs= 0.0000 rel rates= 0.0052) pass 6 : -209.1657 (branch= 0.0133 alpha= 0.0051 pinv= 0.0005 eq freqs= 0.0009 rel rates= 0.0076) pass 7 : -209.1439 (branch= 0.0077 alpha= 0.0024 pinv= 0.0002 eq freqs= 0.0005 rel rates= 0.0110) pass 8 : -209.1281 (branch= 0.0045 alpha= 0.0005 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0104) pass 9 : -209.1165 (branch= 0.0016 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0095) pass 10: -209.1072 (branch= 0.0007 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0082) pass 11: -209.0991 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0074) pass 12: -209.0921 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0067) pass 13: -209.0857 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0061) pass 14: -209.0798 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0057) pass 15: -209.0744 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0053) pass 16: -209.0691 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0051) pass 17: -209.0644 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 18: -209.0596 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 19: -209.0547 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 20: -209.0495 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) optimization up to ... pass 30: -208.9548 (branch= 0.0159 alpha= 0.0000 pinv= 0.0005 eq freqs= 0.0028 rel rates= 0.0755) optimization up to ... pass 40: -208.7782 (branch= 0.0289 alpha= 0.0000 pinv= 0.0019 eq freqs= 0.0089 rel rates= 0.1370) optimization up to ... pass 50: -208.6671 (branch= 0.0060 alpha= 0.0000 pinv= 0.0008 eq freqs= 0.0032 rel rates= 0.1009) optimization up to ... pass 60: -208.6038 (branch= 0.0007 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0623) optimization up to ... pass 70: -208.5599 (branch= 0.0002 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0434) optimization up to ... pass 80: -208.5276 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0321) optimization up to ... pass 90: -208.5027 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0247) optimization up to ... pass 100: -208.4832 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0194) optimization up to ... pass 110: -208.4674 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0156) optimization up to ... pass 120: -208.4545 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0129) optimization up to ... pass 130: -208.4437 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0107) optimization up to ... pass 140: -208.4345 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0091) optimization up to ... pass 150: -208.4266 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0078) optimization up to ... pass 160: -208.4199 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) optimization up to ... pass 170: -208.4141 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) optimization up to ... pass 180: -208.4090 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0051) optimization up to ... pass 190: -208.4044 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0045) optimization up to ... pass 200: -208.4004 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) optimization up to ... pass 210: -208.3969 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0036) optimization up to ... pass 220: -208.3936 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... pass 230: -208.3907 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) optimization up to ... pass 240: -208.3880 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0027) optimization up to ... pass 250: -208.3856 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0025) optimization up to ... pass 260: -208.3833 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... pass 270: -208.3813 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) optimization up to ... pass 280: -208.3794 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 290: -208.3776 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) optimization up to ... pass 300: -208.3760 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 310: -208.3744 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... pass 320: -208.3730 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 330: -208.3716 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 340: -208.3704 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 350: -208.3692 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 360: -208.3681 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 370: -208.3671 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 380: -208.3661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 390: -208.3652 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 400: -208.3644 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 410: -208.3635 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 420: -208.3627 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 430: -208.3620 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 440: -208.3613 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 450: -208.3606 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 460: -208.3600 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 470: -208.3594 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 480: -208.3590 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0004) optimization up to ... pass 490: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) optimization up to ... pass 492: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.3587 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 = 121.128, AG = 186.935, AT = 6.902, CG = 202.957, CT = 193.125, 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. ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -208.3587 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: 121.1 186.9 6.902 203 193.1 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 -212.3288 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 = 0.03824 Current score = -211.2855 Performing final optimizations... pass 1 : -208.9608 (branch= 0.0000 alpha= 0.7627 pinv= 1.4695 eq freqs= 0.0065 rel rates= 0.0860) pass 2 : -208.5654 (branch= 0.0411 alpha= 0.3048 pinv= 0.0095 eq freqs= 0.0118 rel rates= 0.0282) pass 3 : -208.5084 (branch= 0.0299 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0018 rel rates= 0.0253) pass 4 : -208.4811 (branch= 0.0032 alpha= 0.0022 pinv= 0.0017 eq freqs= 0.0000 rel rates= 0.0202) pass 5 : -208.4608 (branch= 0.0022 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0176) pass 6 : -208.4423 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0177) pass 7 : -208.4250 (branch= 0.0009 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0160) pass 8 : -208.4103 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0144) pass 9 : -208.3965 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0135) pass 10: -208.3839 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0124) pass 11: -208.3723 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0115) pass 12: -208.3618 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0104) pass 13: -208.3520 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0098) pass 14: -208.3430 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0090) pass 15: -208.3347 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0083) pass 16: -208.3272 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0075) pass 17: -208.3199 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0072) pass 18: -208.3133 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) pass 19: -208.3068 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0064) pass 20: -208.3010 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) optimization up to ... pass 30: -208.2568 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0440) optimization up to ... pass 40: -208.2293 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0274) optimization up to ... pass 50: -208.2106 (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: -208.1865 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0104) optimization up to ... pass 80: -208.1782 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0082) optimization up to ... pass 90: -208.1716 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) optimization up to ... pass 100: -208.1661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0055) optimization up to ... pass 110: -208.1615 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) 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: -208.1260 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 350: -208.1254 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... 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 8 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 22.242, AG = 32.319, AT = 0.001, CG = 36.406, CT = 80.314, 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 80.31 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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: -219.1444 gen current_lnL precision last_tree_imp 0 -219.1444 0.500 0 500 -216.3490 0.500 474 1000 -215.0097 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 -210.9688 0.010 1502 2500 -210.8711 0.010 1502 3000 -210.7510 0.010 2883 3500 -210.7005 0.010 2883 4000 -210.6775 0.010 2883 4500 -210.6277 0.010 2883 5000 -210.5646 0.010 2883 5500 -210.5008 0.010 2883 6000 -210.3538 0.010 2883 Reached termination condition! last topological improvement at gen 2883 Improvement over last 500 gen = 0.04187 Current score = -210.3452 Performing final optimizations... pass 1 : -209.7259 (branch= 0.0025 alpha= 0.1839 pinv= 0.3304 eq freqs= 0.0000 rel rates= 0.1026) pass 2 : -209.3742 (branch= 0.0078 alpha= 0.2626 pinv= 0.0730 eq freqs= 0.0000 rel rates= 0.0083) pass 3 : -209.2734 (branch= 0.0558 alpha= 0.0257 pinv= 0.0046 eq freqs= 0.0058 rel rates= 0.0088) pass 4 : -209.2185 (branch= 0.0250 alpha= 0.0158 pinv= 0.0000 eq freqs= 0.0049 rel rates= 0.0093) pass 5 : -209.1816 (branch= 0.0224 alpha= 0.0077 pinv= 0.0012 eq freqs= 0.0004 rel rates= 0.0052) pass 6 : -209.1540 (branch= 0.0130 alpha= 0.0052 pinv= 0.0002 eq freqs= 0.0012 rel rates= 0.0080) pass 7 : -209.1308 (branch= 0.0091 alpha= 0.0028 pinv= 0.0001 eq freqs= 0.0006 rel rates= 0.0106) pass 8 : -209.1164 (branch= 0.0042 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0094) pass 9 : -209.1063 (branch= 0.0014 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0082) pass 10: -209.0981 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0073) pass 11: -209.0910 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0065) pass 12: -209.0847 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0059) pass 13: -209.0791 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0054) pass 14: -209.0738 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0051) pass 15: -209.0686 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) pass 16: -209.0634 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) pass 17: -209.0579 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0051) pass 18: -209.0519 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0052) pass 19: -209.0454 (branch= 0.0009 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0056) pass 20: -209.0380 (branch= 0.0012 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0061) optimization up to ... pass 30: -208.9100 (branch= 0.0260 alpha= 0.0000 pinv= 0.0009 eq freqs= 0.0049 rel rates= 0.0963) optimization up to ... pass 40: -208.7402 (branch= 0.0229 alpha= 0.0000 pinv= 0.0019 eq freqs= 0.0080 rel rates= 0.1371) optimization up to ... pass 50: -208.6479 (branch= 0.0029 alpha= 0.0000 pinv= 0.0004 eq freqs= 0.0017 rel rates= 0.0873) optimization up to ... pass 60: -208.5911 (branch= 0.0005 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0560) optimization up to ... pass 70: -208.5508 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0399) optimization up to ... pass 80: -208.5205 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0301) optimization up to ... pass 90: -208.4972 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0231) optimization up to ... pass 100: -208.4788 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0182) optimization up to ... pass 110: -208.4638 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0149) optimization up to ... pass 120: -208.4514 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0123) optimization up to ... pass 130: -208.4411 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0103) optimization up to ... pass 140: -208.4322 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0088) optimization up to ... pass 150: -208.4247 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0075) optimization up to ... pass 160: -208.4183 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0064) optimization up to ... pass 170: -208.4127 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0056) optimization up to ... pass 180: -208.4077 (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= 0.0044) optimization up to ... pass 200: -208.3995 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0039) optimization up to ... pass 210: -208.3960 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0035) optimization up to ... pass 220: -208.3929 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... pass 230: -208.3900 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0028) optimization up to ... pass 240: -208.3874 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) optimization up to ... pass 250: -208.3850 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... pass 260: -208.3828 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... pass 270: -208.3808 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... pass 280: -208.3789 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 290: -208.3772 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 300: -208.3756 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 310: -208.3741 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... pass 320: -208.3727 (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: -208.3701 (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: -208.3679 (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= 0.0010) 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: -208.3626 (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: -208.3605 (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 488: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... Final score = -208.3586 Time used = 0 hours, 0 minutes and 5 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 121.794, AG = 187.954, AT = 6.949, CG = 204.067, CT = 194.168, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2225 0.2905 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 : -208.3586 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: 121.8 188 6.949 204.1 194.2 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 -210.6026 0.010 1230 Reached termination condition! last topological improvement at gen 1230 Improvement over last 500 gen = 0.04161 Current score = -210.5932 Performing final optimizations... pass 1 : -210.1850 (branch= 0.0000 alpha= 0.1339 pinv= 0.2110 eq freqs= 0.0000 rel rates= 0.0632) pass 2 : -209.5580 (branch= 0.0093 alpha= 0.3569 pinv= 0.2371 eq freqs= 0.0050 rel rates= 0.0187) pass 3 : -209.3359 (branch= 0.0380 alpha= 0.1430 pinv= 0.0187 eq freqs= 0.0077 rel rates= 0.0147) pass 4 : -209.2571 (branch= 0.0476 alpha= 0.0199 pinv= 0.0030 eq freqs= 0.0034 rel rates= 0.0049) pass 5 : -209.2088 (branch= 0.0334 alpha= 0.0098 pinv= 0.0009 eq freqs= 0.0000 rel rates= 0.0043) pass 6 : -209.1769 (branch= 0.0177 alpha= 0.0054 pinv= 0.0005 eq freqs= 0.0014 rel rates= 0.0069) pass 7 : -209.1511 (branch= 0.0101 alpha= 0.0036 pinv= 0.0002 eq freqs= 0.0009 rel rates= 0.0110) pass 8 : -209.1300 (branch= 0.0071 alpha= 0.0017 pinv= 0.0000 eq freqs= 0.0009 rel rates= 0.0115) pass 9 : -209.1160 (branch= 0.0031 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0008 rel rates= 0.0100) pass 10: -209.1057 (branch= 0.0011 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0087) pass 11: -209.0970 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0078) pass 12: -209.0897 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0068) pass 13: -209.0833 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0061) pass 14: -209.0775 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0056) pass 15: -209.0720 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0053) pass 16: -209.0670 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0049) pass 17: -209.0621 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 18: -209.0573 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 19: -209.0525 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) pass 20: -209.0471 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) optimization up to ... pass 30: -208.9462 (branch= 0.0176 alpha= 0.0000 pinv= 0.0006 eq freqs= 0.0033 rel rates= 0.0793) optimization up to ... pass 40: -208.7696 (branch= 0.0280 alpha= 0.0000 pinv= 0.0020 eq freqs= 0.0088 rel rates= 0.1378) optimization up to ... pass 50: -208.6633 (branch= 0.0052 alpha= 0.0000 pinv= 0.0007 eq freqs= 0.0028 rel rates= 0.0976) optimization up to ... pass 60: -208.6013 (branch= 0.0006 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0609) optimization up to ... pass 70: -208.5582 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0427) optimization up to ... pass 80: -208.5262 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0317) optimization up to ... pass 90: -208.5016 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0244) optimization up to ... pass 100: -208.4824 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0192) optimization up to ... pass 110: -208.4668 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0155) optimization up to ... pass 120: -208.4539 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0128) optimization up to ... pass 130: -208.4432 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0107) optimization up to ... pass 140: -208.4341 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0090) optimization up to ... pass 150: -208.4263 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0078) optimization up to ... pass 160: -208.4196 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) optimization up to ... pass 170: -208.4138 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) optimization up to ... pass 180: -208.4087 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) optimization up to ... pass 190: -208.4043 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0044) optimization up to ... pass 200: -208.4003 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) optimization up to ... pass 210: -208.3967 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0036) optimization up to ... pass 220: -208.3935 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... pass 230: -208.3906 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) optimization up to ... pass 240: -208.3879 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0027) optimization up to ... pass 250: -208.3854 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... pass 260: -208.3832 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... pass 270: -208.3812 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... pass 280: -208.3792 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 290: -208.3775 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 300: -208.3758 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 310: -208.3743 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... pass 320: -208.3729 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 330: -208.3716 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... pass 340: -208.3703 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 350: -208.3692 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 360: -208.3681 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 370: -208.3671 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 380: -208.3661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 390: -208.3652 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 400: -208.3643 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 410: -208.3635 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 420: -208.3627 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 430: -208.3620 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 440: -208.3613 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 450: -208.3606 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 460: -208.3600 (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: -208.3588 (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= 0.0003) optimization up to ... pass 493: -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 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 122.551, AG = 189.112, AT = 6.991, CG = 205.325, CT = 195.363, 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: 122.6 189.1 6.991 205.3 195.4 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 0.925 (branch= 0.64 scale= 0.00 omega= 0.28 rel rates= 0.00) pass 3:+ 0.733 (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: -213.0379 gen current_lnL precision last_tree_imp 0 -213.0379 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) = 0.130445 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 : -210.2321 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 77.066 (branch= 2.27 scale= 0.00 alpha= 4.14 freqs= 10.82 rel rates= 3.11 pinv= 0.78 subset rates= 55.95) pass 3:+ 49.994 (branch= 6.88 scale= 0.78 alpha= 5.67 freqs= 1.20 rel rates= 1.34 pinv= 0.01 subset rates= 34.11) pass 4:+ 15.059 (branch= 0.00 scale= 0.72 alpha= 0.64 freqs= 1.21 rel rates= 0.50 pinv= 0.00 subset rates= 12.00) pass 5:+ 5.778 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.10 rel rates= 0.77 pinv= 0.00 subset rates= 4.91) pass 6:+ 0.115 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.09 rel rates= 0.01 pinv= 0.00 subset rates= 0.00) lnL after optimization: -13342.2046 gen current_lnL precision last_tree_imp 0 -13342.2046 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 = 1.337, CG = 1.337, CT = 3.999, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3134 0.1755 0.2988 0.2122 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 = 6.057, AT = 1.217, CG = 6.057, CT = 3.969, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2816 0.1661 0.1574 0.3949 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.3385 Substitution rate categories under this model: rate proportion 0.0089 0.2500 0.1346 0.2500 0.6551 0.2500 3.2014 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 = 4.110, AT = 2.501, CG = 0.382, CT = 4.110, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1597 0.3517 0.2835 0.2051 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 4.3250 with an invariant (invariable) site category, proportion estimated 0.0388 Substitution rate categories under this model: rate proportion 0.0000 0.0388 0.4714 0.2403 0.7857 0.2403 1.0842 0.2403 1.6587 0.2403 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 : -13323.9616 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 1.337 1.337 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 6.057 1.217 6.057 3.969 1 0.282 0.166 0.157 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 4.11 2.501 0.3821 4.11 1 0.160 0.352 0.284 0.205 4.325 0.039 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 1.695 0.539 0.326 2.136 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 3.846 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.161 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.158 (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: -474.8622 gen current_lnL precision last_tree_imp 0 -474.8622 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 : -474.8614 (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 2.019 2.820 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:+ 5.106 (branch= 3.29 scale= 0.00 subset rates= 1.82) pass 4:+ 0.827 (branch= 0.20 scale= 0.00 subset rates= 0.62) pass 5:+ 0.064 (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 : -474.8614 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 2.019 2.820 rep 2: 4.516 0.599 2.014 2.839 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:+ 0.939 (branch= 0.38 scale= 0.00 subset rates= 0.56) pass 5:+ 0.207 (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: -474.8925 gen current_lnL precision last_tree_imp 0 -474.8925 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 : -474.8614 Replicate 2 : -474.8505 (best) Replicate 3 : -474.8831 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 2.019 2.820 rep 2: 4.516 0.599 2.014 2.839 rep 3: 4.460 0.600 2.010 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 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:+ 3.711 (branch= 2.16 scale= 0.00 subset rates= 1.55) pass 4:+ 1.981 (branch= 1.40 scale= 0.00 subset rates= 0.58) pass 5:+ 0.364 (branch= 0.33 scale= 0.00 subset rates= 0.03) pass 6:+ 0.110 (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: -474.8512 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 2.85 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 : -474.8614 Replicate 2 : -474.8505 Replicate 3 : -474.8831 Replicate 4 : -474.8498 (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 2.019 2.820 rep 2: 4.516 0.599 2.014 2.839 rep 3: 4.460 0.600 2.010 2.838 rep 4: 4.504 0.598 2.010 2.854 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:+ 0.168 (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: -474.9109 gen current_lnL precision last_tree_imp 0 -474.9109 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 : -474.8614 Replicate 2 : -474.8505 Replicate 3 : -474.8831 Replicate 4 : -474.8498 (best) Replicate 5 : -474.9076 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 2.019 2.820 rep 2: 4.516 0.599 2.014 2.839 rep 3: 4.460 0.600 2.010 2.838 rep 4: 4.504 0.598 2.010 2.854 rep 5: 4.499 0.597 2.021 2.840 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 0.500 215 800 -90.1648 0.500 215 Optimization precision reduced Optimizing parameters... improved 0.159 lnL Optimizing branchlengths... improved 0.317 lnL NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 879, seed 1680541178, best lnL -88.955 gen current_lnL precision last_tree_imp 879 -88.9552 0.010 879 900 -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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 84 600 -111.7788 0.500 84 Optimization precision reduced Optimizing parameters... improved 0.386 lnL Optimizing branchlengths... improved 0.390 lnL 700 -110.8142 0.010 615 800 -110.5642 0.010 707 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 800, seed 1245259246, best lnL -110.564 gen current_lnL precision last_tree_imp 800 -110.5642 0.010 707 900 -110.5555 0.010 707 1000 -110.5066 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 0.1935 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 : -110.5066 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 2000 -111.6817 0.010 563 2100 -111.6817 0.010 563 2200 -111.6817 0.010 563 2300 -111.6817 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 2300, seed 1579946663, best lnL -111.682 gen current_lnL precision last_tree_imp 2300 -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) No branches were short enough to be 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 70 -205.5741 0.500 53 80 -205.4022 0.500 76 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 80, seed 1732378755, best lnL -205.402 gen current_lnL precision last_tree_imp 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 -195.2554 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 51, seed 1784766670, best lnL -195.214 gen current_lnL precision last_tree_imp 51 -195.2137 0.500 0 60 -195.1629 0.500 0 70 -195.0042 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) = 0.120507 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 0.831 lnL Optimizing branchlengths... improved 0.085 lnL 1100 -3352.7180 0.010 0 1200 -3352.6366 0.010 0 1300 -3352.5137 0.010 0 1400 -3352.4036 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 1431, seed 2054937967, best lnL -3352.404 gen current_lnL precision last_tree_imp 1431 -3352.4036 0.010 0 1500 -3352.3987 0.010 0 1600 -3352.2919 0.010 0 1700 -3352.2843 0.010 0 1800 -3352.2036 0.010 0 1900 -3351.8476 0.010 0 2000 -3351.7698 0.010 0 2100 -3351.6181 0.010 0 2200 -3351.3750 0.010 0 2300 -3351.3499 0.010 0 2400 -3351.3426 0.010 0 2500 -3351.2398 0.010 0 2600 -3351.1737 0.010 0 2700 -3351.1734 0.010 0 2800 -3351.1196 0.010 0 2900 -3351.1184 0.010 0 3000 -3351.1143 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... Current score = -3351.1019 Performing final optimizations... pass 1 : -3351.0533 (branch= 0.0000 alpha= 0.0000 pinv= 0.0100 eq freqs= 0.0001 rel rates= 0.0384 subset rates= 0.0000) pass 2 : -3350.9538 (branch= 0.0000 alpha= 0.0117 pinv= 0.0197 eq freqs= 0.0100 rel rates= 0.0582 subset rates= 0.0000) pass 3 : -3350.8653 (branch= 0.0034 alpha= 0.0189 pinv= 0.0170 eq freqs= 0.0020 rel rates= 0.0471 subset rates= 0.0000) pass 4 : -3350.7873 (branch= 0.0049 alpha= 0.0175 pinv= 0.0160 eq freqs= 0.0000 rel rates= 0.0369 subset rates= 0.0026) pass 5 : -3350.7205 (branch= 0.0049 alpha= 0.0139 pinv= 0.0149 eq freqs= 0.0009 rel rates= 0.0310 subset rates= 0.0012) pass 6 : -3350.6609 (branch= 0.0041 alpha= 0.0133 pinv= 0.0137 eq freqs= 0.0002 rel rates= 0.0272 subset rates= 0.0010) pass 7 : -3350.6103 (branch= 0.0024 alpha= 0.0123 pinv= 0.0126 eq freqs= 0.0002 rel rates= 0.0231 subset rates= 0.0000) pass 8 : -3350.5641 (branch= 0.0003 alpha= 0.0116 pinv= 0.0114 eq freqs= 0.0000 rel rates= 0.0213 subset rates= 0.0015) pass 9 : -3350.5239 (branch= 0.0013 alpha= 0.0108 pinv= 0.0104 eq freqs= 0.0001 rel rates= 0.0176 subset rates= 0.0000) pass 10: -3350.4880 (branch= 0.0002 alpha= 0.0098 pinv= 0.0100 eq freqs= 0.0000 rel rates= 0.0159 subset rates= 0.0000) pass 11: -3350.4557 (branch= 0.0000 alpha= 0.0094 pinv= 0.0090 eq freqs= 0.0000 rel rates= 0.0139 subset rates= 0.0000) pass 12: -3350.4266 (branch= 0.0000 alpha= 0.0085 pinv= 0.0075 eq freqs= 0.0000 rel rates= 0.0120 subset rates= 0.0011) pass 13: -3350.4023 (branch= 0.0007 alpha= 0.0072 pinv= 0.0068 eq freqs= 0.0000 rel rates= 0.0096 subset rates= 0.0000) pass 14: -3350.3812 (branch= 0.0001 alpha= 0.0063 pinv= 0.0061 eq freqs= 0.0000 rel rates= 0.0086 subset rates= 0.0000) pass 15: -3350.3622 (branch= 0.0000 alpha= 0.0060 pinv= 0.0054 eq freqs= 0.0000 rel rates= 0.0075 subset rates= 0.0000) pass 16: -3350.3453 (branch= 0.0000 alpha= 0.0054 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0067 subset rates= 0.0000) pass 17: -3350.3306 (branch= 0.0000 alpha= 0.0048 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0057 subset rates= 0.0000) pass 18: -3350.3177 (branch= 0.0000 alpha= 0.0042 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0049 subset rates= 0.0000) pass 19: -3350.3063 (branch= 0.0000 alpha= 0.0037 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0042 subset rates= 0.0000) pass 20: -3350.2965 (branch= 0.0000 alpha= 0.0033 pinv= 0.0029 eq freqs= 0.0000 rel rates= 0.0036 subset rates= 0.0000) optimization up to ... pass 30: -3350.2472 (branch= 0.0000 alpha= 0.0166 pinv= 0.0150 eq freqs= 0.0000 rel rates= 0.0176 subset rates= 0.0000) optimization up to ... pass 40: -3350.2360 (branch= 0.0000 alpha= 0.0037 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0041 subset rates= 0.0000) optimization up to ... pass 50: -3350.2337 (branch= 0.0000 alpha= 0.0007 pinv= 0.0006 eq freqs= 0.0000 rel rates= 0.0010 subset rates= 0.0000) optimization up to ... pass 60: -3350.2332 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) optimization up to ... pass 68: -3350.2331 (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 = -3350.2331 Time used so far = 0 hours, 0 minutes and 15 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 3.115, AG = 10.420, AT = 2.692, CG = 0.001, CT = 21.928, 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 0.5773 with an invariant (invariable) site category, proportion estimated 0.3656 Substitution rate categories under this model: rate proportion 0.0000 0.3656 0.0485 0.1586 0.2994 0.1586 0.8693 0.1586 2.7828 0.1586 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 : -3350.2331 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 3.115 10.42 2.692 0.001 21.93 1 0.333 0.222 0.157 0.288 0.577 0.366 Partition model subset 2: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) rep 1: 0.789 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 400, seed 198833985, best lnL -3323.985 gen current_lnL precision last_tree_imp 400 -3323.9848 0.500 1 500 -3323.6818 0.500 1 600 -3323.3459 0.500 1 Optimization precision reduced Optimizing parameters... improved 1.812 lnL Optimizing branchlengths... improved 0.023 lnL 700 -3321.3650 0.255 1 800 -3321.0295 0.255 1 900 -3321.0142 0.255 1 1000 -3320.9667 0.255 1 NOTE: ****Specified time limit (5 seconds) reached... Current score = -3320.8988 Performing final optimizations... pass 1 : -3320.2605 (branch= 0.0468 alpha= 0.0000 pinv= 0.0155 eq freqs= 0.0001 rel rates= 0.5593 ins/del rates= 0.0166) pass 2 : -3319.8108 (branch= 0.0687 alpha= 0.0065 pinv= 0.0159 eq freqs= 0.0000 rel rates= 0.3405 ins/del rates= 0.0180) pass 3 : -3319.4666 (branch= 0.0455 alpha= 0.0079 pinv= 0.0157 eq freqs= 0.0000 rel rates= 0.2549 ins/del rates= 0.0201) pass 4 : -3319.2019 (branch= 0.0263 alpha= 0.0102 pinv= 0.0153 eq freqs= 0.0024 rel rates= 0.2005 ins/del rates= 0.0101) pass 5 : -3318.9818 (branch= 0.0182 alpha= 0.0103 pinv= 0.0147 eq freqs= 0.0011 rel rates= 0.1683 ins/del rates= 0.0075) pass 6 : -3318.8010 (branch= 0.0120 alpha= 0.0105 pinv= 0.0139 eq freqs= 0.0012 rel rates= 0.1381 ins/del rates= 0.0051) pass 7 : -3318.6466 (branch= 0.0085 alpha= 0.0099 pinv= 0.0130 eq freqs= 0.0004 rel rates= 0.1192 ins/del rates= 0.0035) pass 8 : -3318.5179 (branch= 0.0056 alpha= 0.0099 pinv= 0.0121 eq freqs= 0.0003 rel rates= 0.0983 ins/del rates= 0.0024) pass 9 : -3318.4100 (branch= 0.0037 alpha= 0.0099 pinv= 0.0112 eq freqs= 0.0003 rel rates= 0.0812 ins/del rates= 0.0016) pass 10: -3318.3186 (branch= 0.0024 alpha= 0.0095 pinv= 0.0109 eq freqs= 0.0002 rel rates= 0.0673 ins/del rates= 0.0011) pass 11: -3318.2438 (branch= 0.0016 alpha= 0.0089 pinv= 0.0094 eq freqs= 0.0002 rel rates= 0.0540 ins/del rates= 0.0007) pass 12: -3318.1803 (branch= 0.0011 alpha= 0.0083 pinv= 0.0086 eq freqs= 0.0001 rel rates= 0.0449 ins/del rates= 0.0005) pass 13: -3318.1262 (branch= 0.0007 alpha= 0.0078 pinv= 0.0078 eq freqs= 0.0001 rel rates= 0.0374 ins/del rates= 0.0003) pass 14: -3318.0801 (branch= 0.0004 alpha= 0.0073 pinv= 0.0071 eq freqs= 0.0001 rel rates= 0.0309 ins/del rates= 0.0002) pass 15: -3318.0410 (branch= 0.0003 alpha= 0.0066 pinv= 0.0064 eq freqs= 0.0001 rel rates= 0.0256 ins/del rates= 0.0001) pass 16: -3318.0073 (branch= 0.0002 alpha= 0.0060 pinv= 0.0058 eq freqs= 0.0001 rel rates= 0.0216 ins/del rates= 0.0001) pass 17: -3317.9780 (branch= 0.0001 alpha= 0.0054 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0184 ins/del rates= 0.0000) pass 18: -3317.9527 (branch= 0.0001 alpha= 0.0049 pinv= 0.0046 eq freqs= 0.0000 rel rates= 0.0157 ins/del rates= 0.0000) pass 19: -3317.9307 (branch= 0.0000 alpha= 0.0044 pinv= 0.0041 eq freqs= 0.0000 rel rates= 0.0134 ins/del rates= 0.0000) pass 20: -3317.9115 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0114 ins/del rates= 0.0000) optimization up to ... pass 30: -3317.8163 (branch= 0.0001 alpha= 0.0212 pinv= 0.0196 eq freqs= 0.0001 rel rates= 0.0542 ins/del rates= 0.0000) optimization up to ... pass 40: -3317.7937 (branch= 0.0001 alpha= 0.0053 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: -3317.7874 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0007 ins/del rates= 0.0000) optimization up to ... pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) optimization up to ... pass 74: -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 = 3.064, AG = 10.260, AT = 2.655, CG = 0.001, CT = 21.528, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3328 0.2223 0.1566 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5750 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 0.2981 0.1597 0.8680 0.1597 2.7859 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: 3.064 10.26 2.655 0.001 21.53 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del 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: 1.418 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 1.264 lnL Optimizing branchlengths... improved 0.275 lnL 1200 -211.1652 0.010 1104 1400 -211.1318 0.010 1104 1600 -211.0218 0.010 1104 1800 -210.9997 0.010 1104 2000 -210.9460 0.010 1104 2200 -210.8946 0.010 1104 2400 -210.8864 0.010 1104 2600 -210.8436 0.010 1104 2800 -210.8249 0.010 1104 3000 -210.8188 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 -210.6946 0.010 1104 4200 -210.6740 0.010 1104 4400 -210.6493 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 4420, seed 2050063237, best lnL -210.649 gen current_lnL precision last_tree_imp 4420 -210.6493 0.010 1104 4500 -210.6477 0.010 1104 Reached termination condition! last topological improvement at gen 1104 Improvement over last 500 gen = 0.04686 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 2.570, AG = 4.891, AT = 0.202, CG = 4.460, CT = 7.252, 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 1.1902 with an invariant (invariable) site category, proportion estimated 0.1208 Substitution rate categories under this model: rate proportion 0.0000 0.1208 0.2293 0.2931 0.7543 0.2931 2.0165 0.2931 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 : -210.6477 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: 2.57 4.891 0.2023 4.46 7.252 1 0.233 0.337 0.211 0.220 1.190 0.121 Treelengths: TL rep 1: 2.247 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 0.319 lnL 1000 -167.2082 0.010 843 1200 -167.1487 0.010 843 1400 -167.0497 0.010 843 1600 -166.9651 0.010 843 1800 -166.8256 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 1800, seed 174826483, best lnL -166.826 gen current_lnL precision last_tree_imp 1800 -166.8256 0.010 843 1900 -166.7180 0.010 843 2000 -166.7014 0.010 843 2100 -166.6757 0.010 843 2200 -166.6037 0.010 843 2300 -166.5465 0.010 843 2400 -166.5437 0.010 843 2500 -166.5375 0.010 843 2600 -166.4761 0.010 843 2700 -166.4664 0.010 843 2800 -166.4631 0.010 843 2900 -166.4514 0.010 843 3000 -166.4054 0.010 843 3100 -166.3571 0.010 843 3200 -166.3555 0.010 843 3300 -166.3530 0.010 843 3400 -166.2985 0.010 843 3500 -166.2534 0.010 843 3600 -166.2506 0.010 843 3700 -166.1918 0.010 843 3800 -166.1403 0.010 843 3900 -166.1393 0.010 843 4000 -166.1354 0.010 843 4100 -166.1094 0.010 843 4200 -166.0869 0.010 843 4300 -166.0372 0.010 843 4400 -166.0244 0.010 843 4500 -165.9962 0.010 843 4600 -165.9672 0.010 843 4700 -165.9608 0.010 843 4800 -165.9475 0.010 843 4900 -165.8872 0.010 843 5000 -165.8859 0.010 843 5100 -165.8706 0.010 843 5200 -165.8689 0.010 843 5300 -165.8440 0.010 843 5400 -165.8337 0.010 843 5500 -165.7368 0.010 843 5600 -165.6916 0.010 843 5700 -165.6356 0.010 843 5800 -165.5811 0.010 843 5900 -165.5485 0.010 843 6000 -165.5435 0.010 843 6100 -165.5044 0.010 843 6200 -165.4997 0.010 843 6300 -165.4047 0.010 843 6400 -165.3822 0.010 843 6500 -165.3294 0.010 843 6600 -165.3045 0.010 843 6700 -165.2908 0.010 843 6800 -165.1802 0.010 6750 6900 -165.1514 0.010 6750 7000 -165.1486 0.010 6750 7100 -165.1452 0.010 6750 7200 -165.1326 0.010 6750 7300 -165.0450 0.010 6750 7400 -164.9712 0.010 6750 7500 -164.9350 0.010 6750 7600 -164.9063 0.010 7540 7700 -164.7982 0.010 7540 7800 -164.7723 0.010 7540 7900 -164.7470 0.010 7540 8000 -164.6934 0.010 7540 8100 -164.5821 0.010 7540 8200 -164.5487 0.010 7540 NOTE: ****Specified time limit (5 seconds) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 0.743, AG = 9.547, AT = 1.586, CG = 3.762, CT = 20.251, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1288 0.4051 0.2333 0.2328 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 2.9470 with an invariant (invariable) site category, proportion estimated 0.3098 Substitution rate categories under this model: rate proportion 0.0000 0.3098 0.3851 0.1725 0.7286 0.1725 1.0822 0.1725 1.8041 0.1725 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 2 branches were 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 : -164.4785 (TERMINATED PREMATURELY) 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: 0.7427 9.547 1.586 3.762 20.25 1 0.129 0.405 0.233 0.233 2.947 0.310 Treelengths: TL rep 1: 2.446 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 -213.6190 0.010 530 1400 -213.5800 0.010 530 1600 -213.5576 0.010 530 1800 -213.3951 0.010 530 2000 -213.3646 0.010 530 2200 -213.3318 0.010 530 2400 -213.2445 0.010 530 2600 -213.2282 0.010 530 2800 -213.2193 0.010 530 3000 -213.2001 0.010 530 3200 -213.1945 0.010 530 3400 -213.1682 0.010 530 3600 -213.1580 0.010 530 3800 -213.0250 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 -212.8760 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 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 6400, seed 300440726, best lnL -212.724 gen current_lnL precision last_tree_imp 6400 -212.7244 0.010 3769 6500 -212.7244 0.010 3769 Reached termination condition! last topological improvement at gen 3769 Improvement over last 500 gen = 0.00190 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 4.839, AG = 9.614, AT = 0.397, CG = 9.744, CT = 6.243, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2222 0.2881 0.1826 0.3071 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 : -212.7244 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 4.839 9.614 0.397 9.744 6.243 1 0.222 0.288 0.183 0.307 Treelengths: TL rep 1: 1.732 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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: -219.1444 gen current_lnL precision last_tree_imp 0 -219.1444 0.500 0 200 -217.4629 0.500 32 400 -216.6525 0.500 363 600 -216.1292 0.500 474 800 -215.4112 0.500 669 1000 -215.0097 0.500 936 1200 -214.3653 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 -210.9688 0.010 1502 2200 -210.8960 0.010 1502 2400 -210.8906 0.010 1502 2600 -210.8172 0.010 1502 2800 -210.7847 0.010 1502 3000 -210.7510 0.010 2883 3200 -210.7243 0.010 2883 3400 -210.7006 0.010 2883 3600 -210.6993 0.010 2883 3800 -210.6778 0.010 2883 4000 -210.6775 0.010 2883 4200 -210.6505 0.010 2883 4400 -210.6306 0.010 2883 4600 -210.6208 0.010 2883 4800 -210.5769 0.010 2883 5000 -210.5646 0.010 2883 5200 -210.5368 0.010 2883 5400 -210.5093 0.010 2883 5600 -210.5005 0.010 2883 5800 -210.3871 0.010 2883 6000 -210.3538 0.010 2883 6200 -210.3498 0.010 2883 6400 -210.3399 0.010 2883 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 6420, seed 1385520058, best lnL -210.339 gen current_lnL precision last_tree_imp 6420 -210.3390 0.010 2883 6500 -210.3384 0.010 2883 Reached termination condition! last topological improvement at gen 2883 Improvement over last 500 gen = 0.01539 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 2.043, AG = 4.107, AT = 0.207, CG = 3.870, CT = 7.237, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2409 0.3408 0.2110 0.2074 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 1.4302 with an invariant (invariable) site category, proportion estimated 0.1961 Substitution rate categories under this model: rate proportion 0.0000 0.1961 0.2143 0.2010 0.5765 0.2010 1.0460 0.2010 2.1631 0.2010 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with a positive constraint, it is possible for a constrained branch itself to be collapsed. If you care, be careful to check whether this has happened or turn off branch collapsing. Saving site likelihoods to file ch.n.const.sitelikes.log ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -210.3384 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: 2.043 4.107 0.2071 3.87 7.237 1 0.241 0.341 0.211 0.207 1.430 0.196 Treelengths: TL rep 1: 2.440 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 222.682 (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 -13375.8794 0.500 0 200 -13373.8436 0.500 0 300 -13372.9678 0.500 0 400 -13371.8986 0.500 0 500 -13371.5865 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 -13371.0755 0.402 0 800 -13370.9489 0.402 0 900 -13370.7802 0.402 0 1000 -13370.6791 0.402 0 Optimization precision reduced Optimizing parameters... improved 0.037 lnL Optimizing branchlengths... improved 0.000 lnL NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 1000, seed 355230265, best lnL -13370.642 gen current_lnL precision last_tree_imp 1000 -13370.6422 0.304 0 1100 -13370.5869 0.304 0 1200 -13370.5241 0.304 0 1300 -13370.5104 0.304 0 1400 -13370.5063 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 = 1.208, CG = 1.208, CT = 4.135, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3079 0.1814 0.3083 0.2024 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 0.2768 0.2217 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 : -13370.5063 (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 1.208 1.208 4.135 1 0.308 0.181 0.308 0.202 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 0.155 0.346 0.277 0.222 4.110 0.049 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 1.763 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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= 4.30) pass 2:+ 9.055 (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:+ 0.303 (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: -467.8152 gen current_lnL precision last_tree_imp 0 -467.8152 0.010 0 100 -467.7854 0.010 76 200 -467.7768 0.010 76 300 -467.7654 0.010 76 400 -467.7615 0.010 76 500 -467.7562 0.010 76 600 -467.7505 0.010 76 700 -467.7495 0.010 76 800 -467.7483 0.010 76 900 -467.7471 0.010 76 1000 -467.7427 0.010 76 1100 -467.7372 0.010 76 1200 -467.7330 0.010 76 1300 -467.7317 0.010 76 1400 -467.7307 0.010 76 1500 -467.7301 0.010 76 1600 -467.7294 0.010 76 1700 -467.7252 0.010 76 1800 -467.7239 0.010 76 1900 -467.7239 0.010 76 2000 -467.7234 0.010 76 2100 -467.7228 0.010 76 2200 -467.7218 0.010 76 2300 -467.7216 0.010 76 2400 -467.7209 0.010 76 2500 -467.7205 0.010 76 2600 -467.7205 0.010 76 2700 -467.7197 0.010 76 2800 -467.7190 0.010 76 2900 -467.7186 0.010 76 3000 -467.7184 0.010 76 3100 -467.7181 0.010 76 3200 -467.7180 0.010 76 3300 -467.7179 0.010 76 3400 -467.7178 0.010 76 Reached termination condition! last topological improvement at gen 76 Improvement over last 500 gen = 0.00072 Current score = -467.7178 Performing final optimizations... pass 1 : -467.7126 (branch= 0.0000 subset rates= 0.0052) pass 2 : -467.6927 (branch= 0.0182 subset rates= 0.0018) pass 3 : -467.6906 (branch= 0.0018 subset rates= 0.0003) pass 4 : -467.6866 (branch= 0.0040 subset rates= 0.0000) pass 5 : -467.6836 (branch= 0.0018 subset rates= 0.0011) pass 6 : -467.6820 (branch= 0.0017 subset rates= 0.0000) pass 7 : -467.6809 (branch= 0.0010 subset rates= 0.0000) pass 8 : -467.6803 (branch= 0.0006 subset rates= 0.0000) pass 9 : -467.6800 (branch= 0.0003 subset rates= 0.0000) pass 10: -467.6799 (branch= 0.0001 subset rates= 0.0000) pass 11: -467.6798 (branch= 0.0001 subset rates= 0.0000) pass 12: -467.6798 (branch= 0.0000 subset rates= 0.0000) pass 13: -467.6798 (branch= 0.0000 subset rates= 0.0000) pass 14: -467.6798 (branch= 0.0000 subset rates= 0.0000) pass 15: -467.6797 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6797 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 2.15 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=864977241 Initial ln Likelihood: -614.0831 optimizing: starting branch lengths, subset rates... pass 1:+ 127.392 (branch= 121.24 scale= 1.98 subset rates= 4.16) pass 2:+ 15.987 (branch= 15.02 scale= 0.02 subset rates= 0.96) pass 3:+ 2.694 (branch= 2.46 scale= 0.04 subset rates= 0.20) pass 4:+ 0.135 (branch= 0.13 scale= 0.00 subset rates= 0.00) pass 5:+ 0.039 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -467.8359 gen current_lnL precision last_tree_imp 0 -467.8359 0.010 0 100 -467.8013 0.010 0 200 -467.7836 0.010 0 300 -467.7721 0.010 0 400 -467.7470 0.010 0 500 -467.7426 0.010 0 600 -467.7398 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 634, seed 34875524, best lnL -467.739 gen current_lnL precision last_tree_imp 634 -467.7393 0.010 0 700 -467.7362 0.010 0 800 -467.7332 0.010 0 900 -467.7319 0.010 0 1000 -467.7290 0.010 0 1100 -467.7275 0.010 0 1200 -467.7204 0.010 0 1300 -467.7192 0.010 0 1400 -467.7176 0.010 0 1500 -467.7150 0.010 0 1600 -467.7149 0.010 0 1700 -467.7133 0.010 0 1800 -467.7124 0.010 0 1900 -467.7123 0.010 0 2000 -467.7121 0.010 0 2100 -467.7105 0.010 0 2200 -467.7090 0.010 0 2300 -467.7089 0.010 0 2400 -467.7088 0.010 0 2500 -467.7081 0.010 0 2600 -467.7078 0.010 0 2700 -467.7077 0.010 0 2800 -467.7071 0.010 0 2900 -467.7069 0.010 0 3000 -467.7067 0.010 0 3100 -467.7060 0.010 0 3200 -467.7054 0.010 0 3300 -467.7038 0.010 0 3400 -467.7033 0.010 0 3500 -467.7031 0.010 0 3600 -467.7029 0.010 0 3700 -467.7027 0.010 0 3800 -467.7026 0.010 0 3900 -467.7019 0.010 0 4000 -467.7013 0.010 0 4100 -467.7011 0.010 0 4200 -467.7011 0.010 0 4300 -467.7006 0.010 0 4400 -467.7005 0.010 0 4500 -467.7004 0.010 0 Reached termination condition! last topological improvement at gen 0 Improvement over last 500 gen = 0.00086 Current score = -467.7004 Performing final optimizations... pass 1 : -467.7004 (branch= 0.0000 subset rates= 0.0000) pass 2 : -467.6882 (branch= 0.0122 subset rates= 0.0000) pass 3 : -467.6834 (branch= 0.0048 subset rates= 0.0000) pass 4 : -467.6825 (branch= 0.0009 subset rates= 0.0000) pass 5 : -467.6814 (branch= 0.0011 subset rates= 0.0000) pass 6 : -467.6800 (branch= 0.0014 subset rates= 0.0000) pass 7 : -467.6790 (branch= 0.0010 subset rates= 0.0000) pass 8 : -467.6787 (branch= 0.0002 subset rates= 0.0000) pass 9 : -467.6785 (branch= 0.0002 subset rates= 0.0000) pass 10: -467.6784 (branch= 0.0002 subset rates= 0.0000) pass 11: -467.6783 (branch= 0.0000 subset rates= 0.0000) pass 12: -467.6783 (branch= 0.0000 subset rates= 0.0000) pass 13: -467.6783 (branch= 0.0000 subset rates= 0.0000) pass 14: -467.6783 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6783 Time used so far = 0 hours, 0 minutes and 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 2.18 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=1668858692 Initial ln Likelihood: -630.9240 optimizing: starting branch lengths, subset rates... pass 1:+ 146.354 (branch= 140.50 scale= 1.37 subset rates= 4.49) pass 2:+ 13.171 (branch= 11.99 scale= 0.01 subset rates= 1.17) pass 3:+ 3.302 (branch= 3.17 scale= 0.00 subset rates= 0.13) pass 4:+ 0.252 (branch= 0.25 scale= 0.00 subset rates= 0.00) pass 5:+ 0.024 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -467.8203 gen current_lnL precision last_tree_imp 0 -467.8203 0.010 0 100 -467.7944 0.010 0 200 -467.7835 0.010 0 300 -467.7680 0.010 0 400 -467.7552 0.010 0 500 -467.7483 0.010 0 600 -467.7437 0.010 0 700 -467.7409 0.010 0 800 -467.7404 0.010 0 900 -467.7397 0.010 0 1000 -467.7346 0.010 0 1100 -467.7325 0.010 0 1200 -467.7292 0.010 0 1300 -467.7278 0.010 0 1400 -467.7254 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... Current score = -467.7254 Performing final optimizations... pass 1 : -467.7254 (branch= 0.0000 subset rates= 0.0000) pass 2 : -467.7070 (branch= 0.0183 subset rates= 0.0000) pass 3 : -467.6961 (branch= 0.0109 subset rates= 0.0000) pass 4 : -467.6901 (branch= 0.0060 subset rates= 0.0000) pass 5 : -467.6843 (branch= 0.0058 subset rates= 0.0000) pass 6 : -467.6824 (branch= 0.0019 subset rates= 0.0000) pass 7 : -467.6809 (branch= 0.0014 subset rates= 0.0000) pass 8 : -467.6803 (branch= 0.0006 subset rates= 0.0000) pass 9 : -467.6799 (branch= 0.0004 subset rates= 0.0000) pass 10: -467.6797 (branch= 0.0002 subset rates= 0.0000) pass 11: -467.6796 (branch= 0.0001 subset rates= 0.0000) pass 12: -467.6792 (branch= 0.0000 subset rates= 0.0003) pass 13: -467.6792 (branch= 0.0000 subset rates= 0.0000) pass 14: -467.6789 (branch= 0.0000 subset rates= 0.0003) pass 15: -467.6788 (branch= 0.0001 subset rates= 0.0000) pass 16: -467.6788 (branch= 0.0000 subset rates= 0.0000) pass 17: -467.6788 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6788 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: 0.78 1.49 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 : -467.6797 Replicate 2 : -467.6783 (best) (same topology as 1) Replicate 3 : -467.6788 (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: 3.838 0.789 1.477 2.150 rep 2: 3.841 0.787 1.478 2.178 rep 3: 3.845 0.784 1.486 2.184 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 12.450 (branch= 8.46 scale= 0.00 subset rates= 3.99) pass 3:+ 3.552 (branch= 2.32 scale= 0.03 subset rates= 1.21) pass 4:+ 0.758 (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: -477.9401 gen current_lnL precision last_tree_imp 0 -477.9401 0.010 0 100 -477.8632 0.010 76 200 -477.8299 0.010 152 300 -477.7567 0.010 215 400 -477.5628 0.010 373 500 -477.5393 0.010 373 600 -477.5302 0.010 373 700 -477.5293 0.010 373 800 -477.5220 0.010 373 900 -477.5163 0.010 373 1000 -477.5148 0.010 373 1100 -477.5133 0.010 373 1200 -477.5083 0.010 373 1300 -477.5075 0.010 373 1400 -477.4995 0.010 373 1500 -477.4940 0.010 373 1600 -477.4867 0.010 373 1700 -477.4839 0.010 373 1800 -477.4824 0.010 373 1900 -477.4794 0.010 373 2000 -477.4782 0.010 373 2100 -477.4777 0.010 373 2200 -477.4766 0.010 373 2300 -477.4758 0.010 373 2400 -477.4754 0.010 373 2500 -477.4753 0.010 373 2600 -477.4749 0.010 373 2700 -477.4738 0.010 373 2800 -477.4737 0.010 373 2900 -477.4725 0.010 373 3000 -477.4725 0.010 373 3100 -477.4725 0.010 373 3200 -477.4718 0.010 373 3300 -477.4718 0.010 373 3400 -477.4717 0.010 373 Reached termination condition! last topological improvement at gen 373 Improvement over last 500 gen = 0.00083 Current score = -477.4717 Performing final optimizations... pass 1 : -477.4695 (branch= 0.0000 subset rates= 0.0022) pass 2 : -477.4423 (branch= 0.0272 subset rates= 0.0000) pass 3 : -477.4395 (branch= 0.0028 subset rates= 0.0000) pass 4 : -477.4388 (branch= 0.0007 subset rates= 0.0000) pass 5 : -477.4372 (branch= 0.0016 subset rates= 0.0000) pass 6 : -477.4355 (branch= 0.0016 subset rates= 0.0000) pass 7 : -477.4339 (branch= 0.0009 subset rates= 0.0007) pass 8 : -477.4330 (branch= 0.0010 subset rates= 0.0000) pass 9 : -477.4322 (branch= 0.0006 subset rates= 0.0001) pass 10: -477.4320 (branch= 0.0003 subset rates= 0.0000) pass 11: -477.4319 (branch= 0.0001 subset rates= 0.0000) pass 12: -477.4318 (branch= 0.0001 subset rates= 0.0000) pass 13: -477.4318 (branch= 0.0000 subset rates= 0.0000) pass 14: -477.4318 (branch= 0.0000 subset rates= 0.0000) pass 15: -477.4318 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.4318 Time used so far = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate 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 2.72 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=425957087 Initial ln Likelihood: -636.0761 optimizing: starting branch lengths, subset rates... pass 1:+ 138.672 (branch= 128.04 scale= 0.72 subset rates= 9.91) pass 2:+ 13.747 (branch= 9.73 scale= 0.00 subset rates= 4.02) pass 3:+ 3.414 (branch= 2.10 scale= 0.00 subset rates= 1.31) pass 4:+ 1.365 (branch= 1.09 scale= 0.00 subset rates= 0.27) pass 5:+ 0.834 (branch= 0.80 scale= 0.01 subset rates= 0.02) pass 6:+ 0.191 (branch= 0.19 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -477.8544 gen current_lnL precision last_tree_imp 0 -477.8544 0.010 0 100 -477.7502 0.010 36 200 -477.7249 0.010 149 300 -477.4594 0.010 203 400 -477.3874 0.010 366 500 -477.3748 0.010 366 600 -477.3633 0.010 366 700 -477.3569 0.010 366 800 -477.3520 0.010 366 900 -477.3483 0.010 366 1000 -477.3445 0.010 366 1100 -477.3365 0.010 366 1200 -477.3113 0.010 1197 1300 -477.2903 0.010 1197 1400 -477.2877 0.010 1197 1500 -477.2841 0.010 1197 1600 -477.2783 0.010 1197 1700 -477.2762 0.010 1197 1800 -477.2729 0.010 1197 1900 -477.2723 0.010 1197 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 1949, seed 894358758, best lnL -477.272 gen current_lnL precision last_tree_imp 1949 -477.2722 0.010 1197 2000 -477.2721 0.010 1197 2100 -477.2715 0.010 1197 2200 -477.2703 0.010 1197 2300 -477.2696 0.010 1197 2400 -477.2695 0.010 1197 2500 -477.2686 0.010 1197 2600 -477.2680 0.010 1197 2700 -477.2670 0.010 1197 2800 -477.2662 0.010 1197 2900 -477.2654 0.010 1197 3000 -477.2649 0.010 1197 3100 -477.2645 0.010 1197 3200 -477.2631 0.010 1197 3300 -477.2630 0.010 1197 3400 -477.2630 0.010 1197 3500 -477.2625 0.010 1197 3600 -477.2619 0.010 1197 3700 -477.2618 0.010 1197 3800 -477.2615 0.010 1197 3900 -477.2611 0.010 1197 4000 -477.2611 0.010 1197 4100 -477.2609 0.010 1197 4200 -477.2609 0.010 1197 Reached termination condition! last topological improvement at gen 1197 Improvement over last 500 gen = 0.00088 Current score = -477.2609 Performing final optimizations... pass 1 : -477.2399 (branch= 0.0055 subset rates= 0.0155) pass 2 : -477.2268 (branch= 0.0069 subset rates= 0.0062) pass 3 : -477.2118 (branch= 0.0143 subset rates= 0.0007) pass 4 : -477.2095 (branch= 0.0022 subset rates= 0.0000) pass 5 : -477.2078 (branch= 0.0018 subset rates= 0.0000) pass 6 : -477.2070 (branch= 0.0008 subset rates= 0.0000) pass 7 : -477.2060 (branch= 0.0010 subset rates= 0.0000) pass 8 : -477.2054 (branch= 0.0006 subset rates= 0.0000) pass 9 : -477.2052 (branch= 0.0002 subset rates= 0.0000) pass 10: -477.2051 (branch= 0.0001 subset rates= 0.0000) pass 11: -477.2051 (branch= 0.0000 subset rates= 0.0000) pass 12: -477.2050 (branch= 0.0000 subset rates= 0.0000) pass 13: -477.2050 (branch= 0.0000 subset rates= 0.0000) pass 14: -477.2050 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.2050 Time used so far = 0 hours, 0 minutes and 9 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 1.94 2.64 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 (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=792142821 Initial ln Likelihood: -607.1513 optimizing: starting branch lengths, subset rates... pass 1:+ 108.828 (branch= 98.09 scale= 0.82 subset rates= 9.92) pass 2:+ 14.908 (branch= 10.91 scale= 0.01 subset rates= 3.98) pass 3:+ 3.027 (branch= 1.70 scale= 0.00 subset rates= 1.32) pass 4:+ 1.411 (branch= 1.08 scale= 0.00 subset rates= 0.33) pass 5:+ 0.976 (branch= 0.95 scale= 0.00 subset rates= 0.03) pass 6:+ 0.207 (branch= 0.19 scale= 0.01 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -477.7945 gen current_lnL precision last_tree_imp 0 -477.7945 0.010 0 100 -477.7794 0.010 0 200 -477.7563 0.010 0 300 -477.7529 0.010 0 400 -477.7432 0.010 0 500 -477.7418 0.010 0 600 -477.3413 0.010 537 700 -477.3275 0.010 537 800 -477.3202 0.010 537 900 -477.3116 0.010 537 1000 -477.3054 0.010 537 1100 -477.3026 0.010 537 1200 -477.3003 0.010 537 1300 -477.2955 0.010 537 1400 -477.2902 0.010 537 1500 -477.2883 0.010 537 1600 -477.2865 0.010 537 1700 -477.2852 0.010 537 1800 -477.2835 0.010 537 1900 -477.2826 0.010 537 2000 -477.2805 0.010 537 NOTE: ****Specified time limit (5 seconds) reached... Current score = -477.2805 Performing final optimizations... pass 1 : -477.2425 (branch= 0.0000 subset rates= 0.0379) pass 2 : -477.2286 (branch= 0.0103 subset rates= 0.0036) pass 3 : -477.2191 (branch= 0.0092 subset rates= 0.0004) pass 4 : -477.2155 (branch= 0.0034 subset rates= 0.0002) pass 5 : -477.2088 (branch= 0.0066 subset rates= 0.0000) pass 6 : -477.2059 (branch= 0.0030 subset rates= 0.0000) pass 7 : -477.2056 (branch= 0.0003 subset rates= 0.0000) pass 8 : -477.2054 (branch= 0.0002 subset rates= 0.0000) pass 9 : -477.2046 (branch= 0.0003 subset rates= 0.0005) pass 10: -477.2043 (branch= 0.0002 subset rates= 0.0000) pass 11: -477.2043 (branch= 0.0000 subset rates= 0.0000) pass 12: -477.2043 (branch= 0.0000 subset rates= 0.0000) pass 13: -477.2043 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.2043 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 1.94 2.63 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 : -477.4318 Replicate 2 : -477.2050 Replicate 3 : -477.2043 (best) (same topology as 2) (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: 4.927 0.632 1.917 2.725 rep 2: 4.703 0.632 1.943 2.641 rep 3: 4.696 0.635 1.935 2.629 Saving final tree from best search rep (#3) to ch.p.mkO.ssr.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkv.ssr.conf Running checkpoint test ./check/p.mkv.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 0.368 (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 -430.2565 0.010 92 200 -427.7102 0.010 179 300 -426.9763 0.010 293 400 -425.6930 0.010 365 500 -425.6677 0.010 365 600 -425.6512 0.010 365 700 -425.6318 0.010 365 800 -425.6212 0.010 365 900 -425.6126 0.010 365 1000 -425.6095 0.010 365 1100 -425.6090 0.010 365 1200 -425.6083 0.010 365 1300 -425.6068 0.010 365 1400 -425.6058 0.010 365 1500 -425.6042 0.010 365 1600 -425.6022 0.010 365 1700 -425.5976 0.010 365 1800 -425.5972 0.010 365 1900 -425.5954 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 1933, seed 413780019, best lnL -425.595 gen current_lnL precision last_tree_imp 1933 -425.5950 0.010 365 2000 -425.5950 0.010 365 2100 -425.5942 0.010 365 2200 -425.5913 0.010 365 2300 -425.5899 0.010 365 2400 -425.5893 0.010 365 2500 -425.5891 0.010 365 2600 -425.5890 0.010 365 2700 -425.5888 0.010 365 2800 -425.5883 0.010 365 2900 -425.5869 0.010 365 3000 -425.5868 0.010 365 3100 -425.5859 0.010 365 3200 -425.5858 0.010 365 3300 -425.5850 0.010 365 3400 -425.5843 0.010 365 3500 -425.5843 0.010 365 3600 -425.5841 0.010 365 3700 -425.5839 0.010 365 3800 -425.5839 0.010 365 3900 -425.5839 0.010 365 Reached termination condition! last topological improvement at gen 365 Improvement over last 500 gen = 0.00044 Current score = -425.5839 Performing final optimizations... pass 1 : -425.5730 (branch= 0.0000 subset rates= 0.0109) pass 2 : -425.5586 (branch= 0.0144 subset rates= 0.0000) pass 3 : -425.5516 (branch= 0.0070 subset rates= 0.0000) 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 : -425.5488 (branch= 0.0005 subset rates= 0.0000) pass 9 : -425.5487 (branch= 0.0001 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 9 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:+ 1.686 (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: -439.2276 gen current_lnL precision last_tree_imp 0 -439.2276 0.010 0 100 -428.8676 0.010 98 200 -428.0499 0.010 164 300 -427.6003 0.010 249 400 -427.5649 0.010 249 500 -427.4911 0.010 499 600 -427.3864 0.010 511 700 -425.7188 0.010 668 800 -425.6951 0.010 722 900 -425.6795 0.010 722 1000 -425.6689 0.010 722 1100 -425.6640 0.010 722 NOTE: ****Specified time limit (5 seconds) reached... Current score = -425.6509 Performing final optimizations... pass 1 : -425.6081 (branch= 0.0136 subset rates= 0.0292) pass 2 : -425.5757 (branch= 0.0324 subset rates= 0.0000) pass 3 : -425.5588 (branch= 0.0169 subset rates= 0.0000) pass 4 : -425.5546 (branch= 0.0041 subset rates= 0.0000) pass 5 : -425.5523 (branch= 0.0024 subset rates= 0.0000) pass 6 : -425.5501 (branch= 0.0022 subset rates= 0.0000) pass 7 : -425.5495 (branch= 0.0006 subset rates= 0.0000) pass 8 : -425.5491 (branch= 0.0003 subset rates= 0.0000) pass 9 : -425.5490 (branch= 0.0001 subset rates= 0.0000) pass 10: -425.5490 (branch= 0.0001 subset rates= 0.0000) pass 11: -425.5489 (branch= 0.0001 subset rates= 0.0000) pass 12: -425.5489 (branch= 0.0000 subset rates= 0.0000) pass 13: -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 1.52 1.13 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 10 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 (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: 3.038 0.868 1.530 1.121 rep 2: 3.038 0.869 1.525 1.128 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 3.846 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.161 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.158 (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: -474.8622 gen current_lnL precision last_tree_imp 0 -474.8622 0.010 0 100 -474.7511 0.010 68 200 -474.7181 0.010 68 300 -474.6977 0.010 68 400 -474.6394 0.010 329 500 -474.1564 0.010 455 600 -474.1360 0.010 560 700 -474.0348 0.010 653 800 -474.0229 0.010 653 900 -474.0144 0.010 653 1000 -474.0143 0.010 653 1100 -474.0135 0.010 653 1200 -474.0077 0.010 653 1300 -474.0014 0.010 653 1400 -473.9965 0.010 653 1500 -473.9958 0.010 653 1600 -473.9945 0.010 653 1700 -473.9894 0.010 653 1800 -473.9877 0.010 653 1900 -473.9867 0.010 653 2000 -473.9852 0.010 653 2100 -473.9830 0.010 653 2200 -473.9824 0.010 653 2300 -473.9816 0.010 653 2400 -473.9807 0.010 653 2500 -473.9801 0.010 653 2600 -473.9795 0.010 653 2700 -473.9790 0.010 653 2800 -473.9779 0.010 653 2900 -473.9776 0.010 653 3000 -473.9775 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 3050, seed 1821801759, best lnL -473.977 gen current_lnL precision last_tree_imp 3050 -473.9772 0.010 653 3100 -473.9771 0.010 653 3200 -473.9769 0.010 653 3300 -473.9766 0.010 653 3400 -473.9762 0.010 653 3500 -473.9761 0.010 653 3600 -473.9761 0.010 653 3700 -473.9759 0.010 653 Reached termination condition! last topological improvement at gen 653 Improvement over last 500 gen = 0.00096 Current score = -473.9759 Performing final optimizations... pass 1 : -473.9758 (branch= 0.0001 subset rates= 0.0000) pass 2 : -473.9558 (branch= 0.0183 subset rates= 0.0016) pass 3 : -473.9558 (branch= 0.0000 subset rates= 0.0000) pass 4 : -473.9550 (branch= 0.0009 subset rates= 0.0000) pass 5 : -473.9525 (branch= 0.0007 subset rates= 0.0018) pass 6 : -473.9521 (branch= 0.0004 subset rates= 0.0000) pass 7 : -473.9516 (branch= 0.0004 subset rates= 0.0000) pass 8 : -473.9512 (branch= 0.0004 subset rates= 0.0000) pass 9 : -473.9510 (branch= 0.0002 subset rates= 0.0000) pass 10: -473.9509 (branch= 0.0001 subset rates= 0.0000) pass 11: -473.9508 (branch= 0.0001 subset rates= 0.0000) pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) pass 13: -473.9508 (branch= 0.0000 subset rates= 0.0000) pass 14: -473.9508 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -473.9508 Time used so far = 0 hours, 0 minutes and 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 2.81 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=74284197 Initial ln Likelihood: -646.1143 optimizing: starting branch lengths, subset rates... pass 1:+ 146.023 (branch= 135.13 scale= 0.95 subset rates= 9.94) pass 2:+ 17.326 (branch= 12.98 scale= 0.01 subset rates= 4.33) pass 3:+ 4.642 (branch= 3.12 scale= 0.00 subset rates= 1.52) pass 4:+ 2.490 (branch= 1.89 scale= 0.00 subset rates= 0.60) pass 5:+ 0.684 (branch= 0.61 scale= 0.02 subset rates= 0.05) pass 6:+ 0.130 (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: -474.8185 gen current_lnL precision last_tree_imp 0 -474.8185 0.010 0 100 -474.7244 0.010 55 200 -474.7128 0.010 55 300 -474.7037 0.010 55 400 -474.6654 0.010 339 500 -474.5695 0.010 496 600 -474.0703 0.010 585 700 -474.0481 0.010 585 800 -474.0412 0.010 585 900 -474.0316 0.010 585 1000 -474.0282 0.010 585 1100 -474.0225 0.010 585 1200 -474.0142 0.010 585 1300 -474.0116 0.010 585 1400 -474.0080 0.010 585 1500 -474.0041 0.010 585 1600 -474.0016 0.010 585 1700 -474.0010 0.010 585 1800 -473.9994 0.010 585 1900 -473.9983 0.010 585 NOTE: ****Specified time limit (5 seconds) reached... Current score = -473.9971 Performing final optimizations... pass 1 : -473.9874 (branch= 0.0000 subset rates= 0.0097) pass 2 : -473.9638 (branch= 0.0207 subset rates= 0.0030) pass 3 : -473.9574 (branch= 0.0063 subset rates= 0.0000) pass 4 : -473.9566 (branch= 0.0009 subset rates= 0.0000) pass 5 : -473.9545 (branch= 0.0021 subset rates= 0.0000) pass 6 : -473.9532 (branch= 0.0013 subset rates= 0.0000) pass 7 : -473.9520 (branch= 0.0012 subset rates= 0.0000) pass 8 : -473.9515 (branch= 0.0005 subset rates= 0.0000) pass 9 : -473.9513 (branch= 0.0002 subset rates= 0.0000) pass 10: -473.9512 (branch= 0.0001 subset rates= 0.0000) pass 11: -473.9512 (branch= 0.0001 subset rates= 0.0000) pass 12: -473.9511 (branch= 0.0000 subset rates= 0.0000) pass 13: -473.9511 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -473.9511 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 2.06 2.81 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 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 : -473.9508 (best) Replicate 2 : -473.9511 (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: 4.351 0.587 2.066 2.813 rep 2: 4.347 0.590 2.059 2.806 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 -j40 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' /usr/bin/mkdir -p '/build/reproducible-path/garli-2.1/debian/tmp/usr/bin' make[3]: Nothing to be done for 'install-data-am'. /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-mpi' in '../garli-mpi_2.1-9_amd64.deb'. dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-9_all.deb'. dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-9_amd64.deb'. dpkg-deb: building package 'garli' in '../garli_2.1-9_amd64.deb'. dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-9_amd64.deb'. dpkg-genbuildinfo --build=binary -O../garli_2.1-9_amd64.buildinfo dpkg-genchanges --build=binary -O../garli_2.1-9_amd64.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/4082616 and its subdirectories I: Current time: Wed Sep 17 19:43:56 -12 2025 I: pbuilder-time-stamp: 1758181436 Thu Sep 18 07:43:56 UTC 2025 I: Signing ./b1/garli_2.1-9_amd64.buildinfo as garli_2.1-9_amd64.buildinfo.asc Thu Sep 18 07:43:56 UTC 2025 I: Signed ./b1/garli_2.1-9_amd64.buildinfo as ./b1/garli_2.1-9_amd64.buildinfo.asc Thu Sep 18 07:43:56 UTC 2025 - build #1 for garli/forky/amd64 on ionos1-amd64 done. Starting cleanup. All cleanup done. Thu Sep 18 07:43:56 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-ddBeef1p, removing. /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 07:43 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 07:29 b2 -rw-rw-r-- 1 jenkins jenkins 2186 Dec 19 2024 garli_2.1-9.dsc -rw------- 1 jenkins jenkins 3257 Sep 18 07:29 rbuildlog.IszsNDe /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/b1: total 21300 -rw-r--r-- 1 jenkins jenkins 885211 Sep 18 07:43 build.log -rw-r--r-- 1 jenkins jenkins 9531080 Sep 18 07:43 garli-dbgsym_2.1-9_amd64.deb -rw-r--r-- 1 jenkins jenkins 103464 Sep 18 07:43 garli-examples_2.1-9_all.deb -rw-r--r-- 1 jenkins jenkins 9915936 Sep 18 07:43 garli-mpi-dbgsym_2.1-9_amd64.deb -rw-r--r-- 1 jenkins jenkins 650548 Sep 18 07:43 garli-mpi_2.1-9_amd64.deb -rw-r--r-- 1 jenkins jenkins 5072 Sep 18 07:43 garli_2.1-9.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2186 Sep 18 07:43 garli_2.1-9.dsc -rw-r--r-- 1 jenkins jenkins 8131 Sep 18 07:43 garli_2.1-9_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 9013 Sep 18 07:43 garli_2.1-9_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2388 Sep 18 07:43 garli_2.1-9_amd64.changes -rw-r--r-- 1 jenkins jenkins 673680 Sep 18 07:43 garli_2.1-9_amd64.deb -rw-r--r-- 1 jenkins jenkins 1220 Sep 18 07:43 garli_2.1-9_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/b2: total 0 Thu Sep 18 07:43:57 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 17 19:29:14 -12 2025 I: pbuilder-time-stamp: 1758180554 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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: 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 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/4082616/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='fcede2e9c9734edeb0817bb04baae1cf' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='4082616' 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.sP9jpE6w/pbuilderrc_CBRI --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/b1 --logfile b1/build.log garli_2.1-9.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' 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 ionos1-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4082616/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: amd64 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 ... 19917 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-15{a} gfortran-15-x86-64-linux-gnu{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libcbor0.10{a} libcom-err2{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libfabric1{a} libffi8{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-15-dev{a} libgfortran5{a} libgssapi-krb5-2{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{a} libibverbs-dev{a} libibverbs1{a} libjs-jquery{a} libjs-jquery-ui{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libllvm17t64{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libncl-dev{a} libncl2{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi40{a} libpciaccess0{a} libpipeline1{a} libpsm2-2{a} librdmacm1t64{a} libreadline8t64{a} libtool{a} libuchardet0{a} libucx0{a} libunistring5{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2-16{a} libxnvctrl0{a} libz3-4{a} libze1{a} m4{a} man-db{a} mpi-default-dev{a} ncl-tools{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} po-debconf{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libmail-sendmail-perl lynx wget xauth 0 packages upgraded, 103 newly installed, 0 to remove and 0 not upgraded. Need to get 164 MB of archives. After unpacking 694 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 libfido2-1 amd64 1.16.0-2 [78.8 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 19 http://deb.debian.org/debian forky/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 openssh-client amd64 1:10.0p1-8 [986 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 bc amd64 1.07.1-4 [103 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 35 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 36 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 38 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 40 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 libgfortran-15-dev amd64 15.2.0-4 [886 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-4 [78.8 MB] Get: 46 http://deb.debian.org/debian forky/main amd64 gfortran-15 amd64 15.2.0-4 [17.9 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 libnl-3-200 amd64 3.11.0-2 [67.1 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 libnl-route-3-200 amd64 3.11.0-2 [211 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 libibverbs1 amd64 56.1-1 [62.4 kB] Get: 50 http://deb.debian.org/debian forky/main amd64 ibverbs-providers amd64 56.1-1 [357 kB] Get: 51 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 libllvm17t64 amd64 1:17.0.6-22+b3 [23.6 MB] Get: 54 http://deb.debian.org/debian forky/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get: 55 http://deb.debian.org/debian forky/main amd64 libdrm-common all 2.4.125-2 [8576 B] Get: 56 http://deb.debian.org/debian forky/main amd64 libdrm2 amd64 2.4.125-2 [39.1 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 libdrm-amdgpu1 amd64 2.4.125-2 [23.2 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 libnuma1 amd64 2.0.19-1 [22.2 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 libhsakmt1 amd64 6.2.4+ds-1 [61.1 kB] Get: 60 http://deb.debian.org/debian forky/main amd64 libhsa-runtime64-1 amd64 6.1.2-3 [535 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 libamdhip64-5 amd64 5.7.1-6 [8924 kB] Get: 62 http://deb.debian.org/debian forky/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 63 http://deb.debian.org/debian forky/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get: 64 http://deb.debian.org/debian forky/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b1 [108 kB] Get: 65 http://deb.debian.org/debian forky/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get: 66 http://deb.debian.org/debian forky/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b1 [61.1 kB] Get: 67 http://deb.debian.org/debian forky/main amd64 libevent-dev amd64 2.1.12-stable-10+b1 [305 kB] Get: 68 http://deb.debian.org/debian forky/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get: 69 http://deb.debian.org/debian forky/main amd64 librdmacm1t64 amd64 56.1-1 [70.4 kB] Get: 70 http://deb.debian.org/debian forky/main amd64 libfabric1 amd64 2.1.0-1.1 [706 kB] Get: 71 http://deb.debian.org/debian forky/main amd64 libhwloc15 amd64 2.12.2-1 [164 kB] Get: 72 http://deb.debian.org/debian forky/main amd64 libnuma-dev amd64 2.0.19-1 [36.5 kB] Get: 73 http://deb.debian.org/debian forky/main amd64 libltdl7 amd64 2.5.4-5 [416 kB] Get: 74 http://deb.debian.org/debian forky/main amd64 libltdl-dev amd64 2.5.4-5 [168 kB] Get: 75 http://deb.debian.org/debian forky/main amd64 libhwloc-dev amd64 2.12.2-1 [257 kB] Get: 76 http://deb.debian.org/debian forky/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 77 http://deb.debian.org/debian forky/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 78 http://deb.debian.org/debian forky/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 79 http://deb.debian.org/debian forky/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 80 http://deb.debian.org/debian forky/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 81 http://deb.debian.org/debian forky/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 82 http://deb.debian.org/debian forky/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 83 http://deb.debian.org/debian forky/main amd64 libxnvctrl0 amd64 535.171.04-1+b2 [14.2 kB] Get: 84 http://deb.debian.org/debian forky/main amd64 libze1 amd64 1.24.1-2 [514 kB] Get: 85 http://deb.debian.org/debian forky/main amd64 ocl-icd-libopencl1 amd64 2.3.3-1 [42.9 kB] Get: 86 http://deb.debian.org/debian forky/main amd64 libhwloc-plugins amd64 2.12.2-1 [23.5 kB] Get: 87 http://deb.debian.org/debian forky/main amd64 libibumad3 amd64 56.1-1 [30.0 kB] Get: 88 http://deb.debian.org/debian forky/main amd64 libibmad5 amd64 56.1-1 [44.5 kB] Get: 89 http://deb.debian.org/debian forky/main amd64 libnl-3-dev amd64 3.11.0-2 [110 kB] Get: 90 http://deb.debian.org/debian forky/main amd64 libnl-route-3-dev amd64 3.11.0-2 [235 kB] Get: 91 http://deb.debian.org/debian forky/main amd64 libibverbs-dev amd64 56.1-1 [654 kB] Get: 92 http://deb.debian.org/debian forky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 93 http://deb.debian.org/debian forky/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 94 http://deb.debian.org/debian forky/main amd64 libncl2 amd64 2.1.21+git20210811.b1213a7-6 [383 kB] Get: 95 http://deb.debian.org/debian forky/main amd64 libncl-dev amd64 2.1.21+git20210811.b1213a7-6 [599 kB] Get: 96 http://deb.debian.org/debian forky/main amd64 libucx0 amd64 1.19.0+ds-1 [1336 kB] Get: 97 http://deb.debian.org/debian forky/main amd64 libopenmpi40 amd64 5.0.8-9 [3258 kB] Get: 98 http://deb.debian.org/debian forky/main amd64 openmpi-common all 5.0.8-9 [107 kB] Get: 99 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 100 http://deb.debian.org/debian forky/main amd64 openmpi-bin amd64 5.0.8-9 [203 kB] Get: 101 http://deb.debian.org/debian forky/main amd64 libopenmpi-dev amd64 5.0.8-9 [1228 kB] Get: 102 http://deb.debian.org/debian forky/main amd64 mpi-default-dev amd64 1.18 [3372 B] Get: 103 http://deb.debian.org/debian forky/main amd64 ncl-tools amd64 2.1.21+git20210811.b1213a7-6 [190 kB] Fetched 164 MB in 26s (6364 kB/s) Preconfiguring packages ... Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../000-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../003-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../006-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../007-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../008-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../009-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../010-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../011-libedit2_3.1-20250104-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20250104-1) ... Selecting previously unselected package libcbor0.10:amd64. Preparing to unpack .../012-libcbor0.10_0.10.2-2_amd64.deb ... Unpacking libcbor0.10:amd64 (0.10.2-2) ... Selecting previously unselected package libfido2-1:amd64. Preparing to unpack .../013-libfido2-1_1.16.0-2_amd64.deb ... Unpacking libfido2-1:amd64 (1.16.0-2) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../014-libkrb5support0_1.21.3-5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-5) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../015-libcom-err2_1.47.2-3+b3_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-3+b3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../016-libk5crypto3_1.21.3-5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../017-libkeyutils1_1.6.3-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../018-libkrb5-3_1.21.3-5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../019-libgssapi-krb5-2_1.21.3-5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-5) ... Selecting previously unselected package openssh-client. Preparing to unpack .../020-openssh-client_1%3a10.0p1-8_amd64.deb ... Unpacking openssh-client (1:10.0p1-8) ... Selecting previously unselected package m4. Preparing to unpack .../021-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../022-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../023-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../024-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../025-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../026-libreadline8t64_8.3-3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package bc. Preparing to unpack .../027-bc_1.07.1-4_amd64.deb ... Unpacking bc (1.07.1-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../028-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../029-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../030-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../031-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 .../032-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../033-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../034-libelf1t64_0.193-3_amd64.deb ... Unpacking libelf1t64:amd64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../035-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../036-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../037-libxml2-16_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../038-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../039-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../040-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../041-debhelper_13.26_all.deb ... Unpacking debhelper (13.26) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../042-libgfortran5_15.2.0-4_amd64.deb ... Unpacking libgfortran5:amd64 (15.2.0-4) ... Selecting previously unselected package libgfortran-15-dev:amd64. Preparing to unpack .../043-libgfortran-15-dev_15.2.0-4_amd64.deb ... Unpacking libgfortran-15-dev:amd64 (15.2.0-4) ... Selecting previously unselected package gfortran-15-x86-64-linux-gnu. Preparing to unpack .../044-gfortran-15-x86-64-linux-gnu_15.2.0-4_amd64.deb ... Unpacking gfortran-15-x86-64-linux-gnu (15.2.0-4) ... Selecting previously unselected package gfortran-15. Preparing to unpack .../045-gfortran-15_15.2.0-4_amd64.deb ... Unpacking gfortran-15 (15.2.0-4) ... Selecting previously unselected package libnl-3-200:amd64. Preparing to unpack .../046-libnl-3-200_3.11.0-2_amd64.deb ... Unpacking libnl-3-200:amd64 (3.11.0-2) ... Selecting previously unselected package libnl-route-3-200:amd64. Preparing to unpack .../047-libnl-route-3-200_3.11.0-2_amd64.deb ... Unpacking libnl-route-3-200:amd64 (3.11.0-2) ... Selecting previously unselected package libibverbs1:amd64. Preparing to unpack .../048-libibverbs1_56.1-1_amd64.deb ... Unpacking libibverbs1:amd64 (56.1-1) ... Selecting previously unselected package ibverbs-providers:amd64. Preparing to unpack .../049-ibverbs-providers_56.1-1_amd64.deb ... Unpacking ibverbs-providers:amd64 (56.1-1) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../050-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package libz3-4:amd64. Preparing to unpack .../051-libz3-4_4.13.3-1_amd64.deb ... Unpacking libz3-4:amd64 (4.13.3-1) ... Selecting previously unselected package libllvm17t64:amd64. Preparing to unpack .../052-libllvm17t64_1%3a17.0.6-22+b3_amd64.deb ... Unpacking libllvm17t64:amd64 (1:17.0.6-22+b3) ... Selecting previously unselected package libamd-comgr2:amd64. Preparing to unpack .../053-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3+b2_amd64.deb ... Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Selecting previously unselected package libdrm-common. Preparing to unpack .../054-libdrm-common_2.4.125-2_all.deb ... Unpacking libdrm-common (2.4.125-2) ... Selecting previously unselected package libdrm2:amd64. Preparing to unpack .../055-libdrm2_2.4.125-2_amd64.deb ... Unpacking libdrm2:amd64 (2.4.125-2) ... Selecting previously unselected package libdrm-amdgpu1:amd64. Preparing to unpack .../056-libdrm-amdgpu1_2.4.125-2_amd64.deb ... Unpacking libdrm-amdgpu1:amd64 (2.4.125-2) ... Selecting previously unselected package libnuma1:amd64. Preparing to unpack .../057-libnuma1_2.0.19-1_amd64.deb ... Unpacking libnuma1:amd64 (2.0.19-1) ... Selecting previously unselected package libhsakmt1:amd64. 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Setting up libgfortran-15-dev:amd64 (15.2.0-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:amd64 (2.0.19-1) ... Setting up libnl-route-3-200:amd64 (3.11.0-2) ... Setting up libxnvctrl0:amd64 (535.171.04-1+b2) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:amd64 (2.5.4-5) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libllvm17t64:amd64 (1:17.0.6-22+b3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libevent-extra-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libreadline8t64:amd64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up libdrm2:amd64 (2.4.125-2) ... Setting up libnl-3-dev:amd64 (3.11.0-2) ... Setting up groff-base (1.23.0-9) ... Setting up libhwloc-dev:amd64 (2.12.2-1) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Setting up libdrm-amdgpu1:amd64 (2.4.125-2) ... Setting up gfortran-15-x86-64-linux-gnu (15.2.0-4) ... Setting up libibverbs1:amd64 (56.1-1) ... Setting up ibverbs-providers:amd64 (56.1-1) ... Setting up openssh-client (1:10.0p1-8) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up bc (1.07.1-4) ... Setting up libhwloc-plugins:amd64 (2.12.2-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnl-route-3-dev:amd64 (3.11.0-2) ... Setting up libevent-dev (2.1.12-stable-10+b1) ... Setting up librdmacm1t64:amd64 (56.1-1) ... Setting up libhsakmt1:amd64 (6.2.4+ds-1) ... Setting up gfortran-15 (15.2.0-4) ... Setting up libfabric1:amd64 (2.1.0-1.1) ... Setting up debhelper (13.26) ... Setting up libibverbs-dev:amd64 (56.1-1) ... Setting up libhsa-runtime64-1:amd64 (6.1.2-3) ... Setting up libamdhip64-5:amd64 (5.7.1-6) ... Setting up libucx0:amd64 (1.19.0+ds-1) ... Setting up libopenmpi40:amd64 (5.0.8-9) ... Setting up openmpi-bin (5.0.8-9) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:amd64 (5.0.8-9) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up mpi-default-dev (1.18) ... Processing triggers for libc-bin (2.41-12) ... 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 amd64 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=x86_64-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/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-ncl=/usr --enable-mpi checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 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 xargs -n works... yes checking whether UID '1111' is supported by ustar format... yes checking whether GID '1111' is supported by ustar format... yes checking 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 -j40 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from configoptions.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] 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++/15/string:51, from bipartition.h:23, from bipartition.cpp:19: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from garlimain.cpp:40: 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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from population.h:23: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from model.cpp:17: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/refwrap.h:41, from /usr/include/c++/15/vector:70, from tree.h:24: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from adaptation.cpp:18: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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 configreader.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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from configreader.cpp:21: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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; | ~~~~~~~^~~~~~~~~~~~~~~~~~ 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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from population.h:23: /usr/include/c++/15/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++/15/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++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, from 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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from mpitrick.cpp:21: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/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++/15/bits/refwrap.h:41, from /usr/include/c++/15/vector:70, from tree.cpp:21: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/bits/refwrap.h:41, from /usr/include/c++/15/vector:70, from population.cpp:23: /usr/include/c++/15/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++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, from individual.cpp:28: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/iomanip:47, from individual.cpp:21: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from population.cpp:49: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;idlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6845:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6845 | fread(&dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6849:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6849 | fread(&dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6855:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6855 | fread(&dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6858:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6858 | fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6862:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6862 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6865:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6865 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6868:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6868 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6872:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6872 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6878:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6878 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6881 | fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ reconnode.h: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)': reconnode.h:388:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 388 | fread(&unique, scalarSize, 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ reconnode.h: In constructor 'Swap::Swap(FILE*&)': reconnode.h:264:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 264 | fread(&count, scalarSize, 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from treenode.h:30, from tree.h:31: bipartition.h: In member function 'void Bipartition::BinaryInput(FILE*&)': bipartition.h:518:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 518 | fread((char*) rep, sizeof(unsigned int), nBlocks, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ population.cpp: In member function 'void Population::ReadPopulationCheckpoint()': population.cpp:1880:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1880 | fread((char *) &seed, sizeof(seed), 1, pin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ population.cpp:1887:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1887 | fread((char *) &t, sizeof(t), 1, pin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ population.cpp:1896:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(this, scalarSize, 1, pin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, 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/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from model.h:25, from clamanager.h:25, from condlike.cpp:22: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from rng.h:36, from tree.h:30: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from configreader.cpp:18: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from treenode.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, 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/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/ncl/ncl.h:27, from garlireader.cpp:41: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] /usr/include/x86_64-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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from datamatr.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from population.cpp:25: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] garlimain.cpp: In function 'int SubGarliMain(int)': garlimain.cpp:323:49: warning: '%d' directive writing between 2 and 10 bytes into a region of size 6 [-Wformat-overflow=] 323 | else sprintf(temp, ".run%d", rank); | ^~ garlimain.cpp:323:44: note: directive argument in the range [10, 2147483647] 323 | else sprintf(temp, ".run%d", rank); | ^~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int SubGarliMain(int)' at garlimain.cpp:323:16: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 15 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 ()); | ~~~~~~~~~~~~~~~~~ garlimain.cpp: In function 'int SubGarliMain(int)': garlimain.cpp:322:59: warning: '%d' directive writing between 1 and 11 bytes into a region of size 5 [-Wformat-overflow=] 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); | ^~ garlimain.cpp:322:53: note: directive argument in the range [-2147483648, 9] 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int SubGarliMain(int)' at garlimain.cpp:322:25: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 17 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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, 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/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': population.cpp:3066:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~ population.cpp:3066:47: note: directive argument in the range [1, 2147483647] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mpic++ -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -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[4]: Leaving directory '/build/reproducible-path/garli-2.1/src' Making all in tests make[4]: Entering directory '/build/reproducible-path/garli-2.1/tests' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/garli-2.1/tests' make[4]: Entering directory '/build/reproducible-path/garli-2.1' make[4]: Leaving 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' mkdir -p debian/mpi mv src/Garli debian/mpi/Garli-mpi make distclean make[2]: Entering directory '/build/reproducible-path/garli-2.1' Making distclean in src make[3]: Entering directory '/build/reproducible-path/garli-2.1/src' rm -f Garli rm -f *.o rm -f *.tab.c rm -f test . = "." || rm -f rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags rm -f ./.deps/adaptation.Po rm -f ./.deps/bipartition.Po rm -f ./.deps/condlike.Po rm -f ./.deps/configoptions.Po rm -f ./.deps/configreader.Po rm -f ./.deps/datamatr.Po rm -f ./.deps/funcs.Po rm -f ./.deps/garlimain.Po rm -f ./.deps/garlireader.Po rm -f ./.deps/individual.Po rm -f ./.deps/linalg.Po rm -f ./.deps/model.Po rm -f ./.deps/mpitrick.Po rm -f ./.deps/optimization.Po rm -f ./.deps/population.Po rm -f ./.deps/rng.Po rm -f ./.deps/sequencedata.Po rm -f ./.deps/set.Po rm -f ./.deps/translatetable.Po rm -f ./.deps/tree.Po rm -f ./.deps/treenode.Po rm -f Makefile make[3]: Leaving directory '/build/reproducible-path/garli-2.1/src' Making distclean in tests make[3]: Entering directory '/build/reproducible-path/garli-2.1/tests' rm -f test . = "." || rm -f rm -f Makefile make[3]: Leaving directory '/build/reproducible-path/garli-2.1/tests' make[3]: Entering directory '/build/reproducible-path/garli-2.1' rm -f test . = "." || rm -f rm -f config.h stamp-h1 rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags rm -f cscope.out cscope.in.out cscope.po.out cscope.files make[3]: Leaving directory '/build/reproducible-path/garli-2.1' rm -f config.status config.cache config.log configure.lineno config.status.lineno rm -f Makefile make[2]: Leaving directory '/build/reproducible-path/garli-2.1' # Now build single processor binary dh_auto_configure -- --with-ncl=/usr ./configure --build=x86_64-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/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-ncl=/usr checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 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 xargs -n works... yes checking whether UID '1111' is supported by ustar format... yes checking whether GID '1111' is supported by ustar format... yes checking 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 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 make[1]: Leaving directory '/build/reproducible-path/garli-2.1' dh_auto_build make -j40 make[1]: Entering directory '/build/reproducible-path/garli-2.1' make all-recursive make[2]: Entering directory '/build/reproducible-path/garli-2.1' Making all in src make[3]: Entering directory '/build/reproducible-path/garli-2.1/src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o adaptation.o adaptation.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o bipartition.o bipartition.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o condlike.o condlike.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configoptions.o configoptions.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configreader.o configreader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o datamatr.o datamatr.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o funcs.o funcs.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlimain.o garlimain.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlireader.o garlireader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o individual.o individual.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.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 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++/15/string:51, from bipartition.h:23, from bipartition.cpp:19: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from configoptions.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] 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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/iomanip:47, from individual.cpp:21: /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from garlimain.cpp:40: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public 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++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from population.h:23: /usr/include/c++/15/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++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/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++/15/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from adaptation.cpp:18: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/refwrap.h:41, from /usr/include/c++/15/vector:70, from population.cpp:23: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from model.cpp:17: /usr/include/c++/15/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++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from configreader.cpp:21: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/refwrap.h:41, from /usr/include/c++/15/vector:70, from tree.h:24: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/refwrap.h:41, from /usr/include/c++/15/vector:70, from tree.cpp:21: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from population.h:23: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)': adaptation.cpp:271:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 271 | fread((char *) this, 1, scalarSize, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:278:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 278 | fread((char *) improvetotal, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:280:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 280 | fread((char *) randNNI, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:281:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 281 | fread((char *) randNNInum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:283:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 283 | fread((char *) exNNI, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:284:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 284 | fread((char *) exNNInum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:286:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 286 | fread((char *) randSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:287:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 287 | fread((char *) randSPRnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:289:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 289 | fread((char *) limSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:290:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 290 | fread((char *) limSPRnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:292:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 292 | fread((char *) exlimSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:293:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 293 | fread((char *) exlimSPRnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:295:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 295 | fread((char *) randRecom, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:296:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 296 | fread((char *) randRecomnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:298:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 298 | fread((char *) bipartRecom, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:299:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | fread((char *) bipartRecomnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:301:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 301 | fread((char *) onlyBrlen, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:302:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 302 | fread((char *) onlyBrlennum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:304:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 304 | fread((char *) anyModel, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:305:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 305 | fread((char *) anyModelnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from model.h:25, from clamanager.h:25, from condlike.cpp:22: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, 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/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, 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/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from configreader.cpp:18: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from datamatr.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from treenode.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from rng.h:36, from tree.h:30: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/ncl/ncl.h:27, from garlireader.cpp:41: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from population.cpp:25: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, 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/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': population.cpp:3066:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~ population.cpp:3066:47: note: directive argument in the range [1, 2147483647] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -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 -j40 check "TESTSUITEFLAGS=-j40 --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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 0.925 (branch= 0.64 scale= 0.00 omega= 0.28 rel rates= 0.00) pass 3:+ 0.733 (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: -213.0379 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 77.066 (branch= 2.27 scale= 0.00 alpha= 4.14 freqs= 10.82 rel rates= 3.11 pinv= 0.78 subset rates= 55.95) pass 3:+ 49.994 (branch= 6.88 scale= 0.78 alpha= 5.67 freqs= 1.20 rel rates= 1.34 pinv= 0.01 subset rates= 34.11) pass 4:+ 15.059 (branch= 0.00 scale= 0.72 alpha= 0.64 freqs= 1.21 rel rates= 0.50 pinv= 0.00 subset rates= 12.00) pass 5:+ 5.778 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.10 rel rates= 0.77 pinv= 0.00 subset rates= 4.91) pass 6:+ 0.115 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.09 rel rates= 0.01 pinv= 0.00 subset rates= 0.00) lnL after optimization: -13342.2046 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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= 4.30) pass 2:+ 9.055 (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:+ 0.303 (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: -467.8152 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 12.450 (branch= 8.46 scale= 0.00 subset rates= 3.99) pass 3:+ 3.552 (branch= 2.32 scale= 0.03 subset rates= 1.21) pass 4:+ 0.758 (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: -477.9401 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 129.564 (branch= 123.99 scale= 0.59 subset rates= 4.98) pass 2:+ 9.273 (branch= 7.97 scale= 0.00 subset rates= 1.30) pass 3:+ 1.739 (branch= 1.57 scale= 0.00 subset rates= 0.17) pass 4:+ 0.312 (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: -464.7107 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 3.846 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.161 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.158 (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: -474.8622 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 1 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 10 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 7 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 : -3355.4806 (branch= 0.9931 alpha= 0.0078 pinv= 0.0071 eq freqs= 0.1960 rel rates= 1.3003 subset rates= 0.3859) pass 2 : -3354.0831 (branch= 0.5204 alpha= 0.0089 pinv= 0.0117 eq freqs= 0.0202 rel rates= 0.6677 subset rates= 0.1686) pass 3 : -3353.2198 (branch= 0.2864 alpha= 0.0000 pinv= 0.0086 eq freqs= 0.0160 rel rates= 0.4622 subset rates= 0.0901) pass 4 : -3352.6255 (branch= 0.1646 alpha= 0.0037 pinv= 0.0159 eq freqs= 0.0035 rel rates= 0.3594 subset rates= 0.0473) pass 5 : -3352.1694 (branch= 0.0978 alpha= 0.0045 pinv= 0.0165 eq freqs= 0.0021 rel rates= 0.3101 subset rates= 0.0251) pass 6 : -3351.8162 (branch= 0.0577 alpha= 0.0065 pinv= 0.0165 eq freqs= 0.0009 rel rates= 0.2567 subset rates= 0.0148) pass 7 : -3351.5408 (branch= 0.0284 alpha= 0.0087 pinv= 0.0158 eq freqs= 0.0010 rel rates= 0.2101 subset rates= 0.0114) pass 8 : -3351.3231 (branch= 0.0191 alpha= 0.0100 pinv= 0.0149 eq freqs= 0.0007 rel rates= 0.1668 subset rates= 0.0062) pass 9 : -3351.1479 (branch= 0.0117 alpha= 0.0106 pinv= 0.0140 eq freqs= 0.0005 rel rates= 0.1344 subset rates= 0.0041) pass 10: -3351.0053 (branch= 0.0070 alpha= 0.0105 pinv= 0.0138 eq freqs= 0.0004 rel rates= 0.1083 subset rates= 0.0026) pass 11: -3350.8878 (branch= 0.0043 alpha= 0.0103 pinv= 0.0127 eq freqs= 0.0003 rel rates= 0.0881 subset rates= 0.0018) pass 12: -3350.7912 (branch= 0.0033 alpha= 0.0098 pinv= 0.0116 eq freqs= 0.0002 rel rates= 0.0716 subset rates= 0.0000) pass 13: -3350.7078 (branch= 0.0008 alpha= 0.0096 pinv= 0.0105 eq freqs= 0.0002 rel rates= 0.0606 subset rates= 0.0018) pass 14: -3350.6403 (branch= 0.0012 alpha= 0.0090 pinv= 0.0095 eq freqs= 0.0002 rel rates= 0.0475 subset rates= 0.0000) pass 15: -3350.5832 (branch= 0.0003 alpha= 0.0082 pinv= 0.0081 eq freqs= 0.0001 rel rates= 0.0404 subset rates= 0.0000) pass 16: -3350.5328 (branch= 0.0001 alpha= 0.0079 pinv= 0.0073 eq freqs= 0.0001 rel rates= 0.0339 subset rates= 0.0012) pass 17: -3350.4923 (branch= 0.0008 alpha= 0.0069 pinv= 0.0066 eq freqs= 0.0001 rel rates= 0.0262 subset rates= 0.0000) pass 18: -3350.4574 (branch= 0.0002 alpha= 0.0060 pinv= 0.0059 eq freqs= 0.0000 rel rates= 0.0227 subset rates= 0.0000) pass 19: -3350.4270 (branch= 0.0000 alpha= 0.0056 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0195 subset rates= 0.0000) pass 20: -3350.4005 (branch= 0.0000 alpha= 0.0051 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0167 subset rates= 0.0000) optimization up to ... pass 30: -3350.2715 (branch= 0.0001 alpha= 0.0273 pinv= 0.0248 eq freqs= 0.0002 rel rates= 0.0767 subset rates= 0.0000) optimization up to ... pass 40: -3350.2419 (branch= 0.0000 alpha= 0.0064 pinv= 0.0060 eq freqs= 0.0000 rel rates= 0.0171 subset rates= 0.0000) optimization up to ... pass 50: -3350.2353 (branch= 0.0000 alpha= 0.0013 pinv= 0.0012 eq freqs= 0.0000 rel rates= 0.0042 subset rates= 0.0000) optimization up to ... pass 60: -3350.2337 (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: -3350.2334 (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: -3350.2333 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) Looking for minimum length branches... Final score = -3350.2333 Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -3350.2333 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: 3.113 10.41 2.688 0.001 21.89 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 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 3350.23331 ***Expected is 3350.2345 ***SCORE DIFFERENCE IS -.00119 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 : -3329.9920 (branch= 1.3745 alpha= 0.0217 pinv= 0.0099 eq freqs= 0.2403 rel rates= 0.7561 ins/del rates= 0.0754) pass 2 : -3329.0411 (branch= 0.3511 alpha= 0.0000 pinv= 0.0096 eq freqs= 0.0000 rel rates= 0.5271 ins/del rates= 0.0631) pass 3 : -3328.4283 (branch= 0.1466 alpha= 0.0039 pinv= 0.0146 eq freqs= 0.0187 rel rates= 0.3867 ins/del rates= 0.0424) pass 4 : -3327.9685 (branch= 0.0855 alpha= 0.0067 pinv= 0.0148 eq freqs= 0.0031 rel rates= 0.3207 ins/del rates= 0.0290) pass 5 : -3327.6169 (branch= 0.0530 alpha= 0.0080 pinv= 0.0147 eq freqs= 0.0017 rel rates= 0.2561 ins/del rates= 0.0181) pass 6 : -3327.3365 (branch= 0.0344 alpha= 0.0079 pinv= 0.0146 eq freqs= 0.0008 rel rates= 0.2111 ins/del rates= 0.0115) pass 7 : -3327.1138 (branch= 0.0219 alpha= 0.0094 pinv= 0.0140 eq freqs= 0.0007 rel rates= 0.1690 ins/del rates= 0.0077) pass 8 : -3326.9319 (branch= 0.0143 alpha= 0.0098 pinv= 0.0133 eq freqs= 0.0006 rel rates= 0.1388 ins/del rates= 0.0051) pass 9 : -3326.7851 (branch= 0.0094 alpha= 0.0099 pinv= 0.0125 eq freqs= 0.0004 rel rates= 0.1113 ins/del rates= 0.0034) pass 10: -3326.6639 (branch= 0.0063 alpha= 0.0097 pinv= 0.0123 eq freqs= 0.0003 rel rates= 0.0903 ins/del rates= 0.0023) pass 11: -3326.5636 (branch= 0.0042 alpha= 0.0095 pinv= 0.0114 eq freqs= 0.0002 rel rates= 0.0735 ins/del rates= 0.0015) pass 12: -3326.4810 (branch= 0.0028 alpha= 0.0090 pinv= 0.0099 eq freqs= 0.0002 rel rates= 0.0596 ins/del rates= 0.0010) pass 13: -3326.4117 (branch= 0.0019 alpha= 0.0085 pinv= 0.0091 eq freqs= 0.0001 rel rates= 0.0490 ins/del rates= 0.0007) pass 14: -3326.3528 (branch= 0.0013 alpha= 0.0080 pinv= 0.0083 eq freqs= 0.0001 rel rates= 0.0408 ins/del rates= 0.0005) pass 15: -3326.3023 (branch= 0.0009 alpha= 0.0074 pinv= 0.0076 eq freqs= 0.0001 rel rates= 0.0342 ins/del rates= 0.0003) pass 16: -3326.2594 (branch= 0.0006 alpha= 0.0069 pinv= 0.0068 eq freqs= 0.0001 rel rates= 0.0283 ins/del rates= 0.0002) pass 17: -3326.2227 (branch= 0.0004 alpha= 0.0064 pinv= 0.0062 eq freqs= 0.0001 rel rates= 0.0235 ins/del rates= 0.0001) pass 18: -3326.1910 (branch= 0.0002 alpha= 0.0057 pinv= 0.0056 eq freqs= 0.0001 rel rates= 0.0201 ins/del rates= 0.0001) pass 19: -3326.1634 (branch= 0.0001 alpha= 0.0052 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0171 ins/del rates= 0.0000) pass 20: -3326.1395 (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= 0.0001 rel rates= 0.0688 ins/del rates= 0.0001) optimization up to ... pass 40: -3325.9908 (branch= 0.0000 alpha= 0.0068 pinv= 0.0064 eq freqs= 0.0000 rel rates= 0.0157 ins/del rates= 0.0000) optimization up to ... pass 50: -3325.9841 (branch= 0.0000 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 76: -3325.9822 (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 = -3325.9822 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 : -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: 3.062 10.26 2.656 0.001 21.52 1 0.333 0.222 0.157 0.288 0.574 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 3325.98220 ***Expected is 3325.98222 ***SCORE DIFFERENCE IS -.00002 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 2061.640 (branch=1982.89 scale= 74.28 freqs= 0.89 rel rates= 3.59) pass 2:+ 221.898 (branch= 220.63 scale= 0.00 freqs= 0.84 rel rates= 0.43) pass 3:+ 4.926 (branch= 4.77 scale= 0.00 freqs= 0.07 rel rates= 0.09) pass 4:+ 0.328 (branch= 0.31 scale= 0.00 freqs= 0.00 rel rates= 0.02) pass 5:+ 0.069 (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: -16071.0881 gen current_lnL precision last_tree_imp 0 -16071.0881 0.010 0 100 -14502.1424 0.010 73 200 -14502.1082 0.010 73 300 -14501.0360 0.010 73 400 -14500.4215 0.010 73 500 -14500.0792 0.010 73 600 -14499.5615 0.010 73 700 -14499.2365 0.010 73 800 -14499.1060 0.010 73 900 -14499.1049 0.010 73 1000 -14499.1049 0.010 73 1100 -14498.9970 0.010 73 1200 -14498.9970 0.010 73 1300 -14498.9879 0.010 73 1400 -14498.9879 0.010 73 1500 -14498.9852 0.010 73 1600 -14498.9678 0.010 73 Reached termination condition! last topological improvement at gen 73 Improvement over last 500 gen = 0.02921 Current score = -14498.9678 Performing final optimizations... pass 1 : -14498.9160 (branch= 0.0243 eq freqs= 0.0185 rel rates= 0.0090) pass 2 : -14498.8971 (branch= 0.0099 eq freqs= 0.0002 rel rates= 0.0089) pass 3 : -14498.8909 (branch= 0.0037 eq freqs= 0.0001 rel rates= 0.0023) pass 4 : -14498.8878 (branch= 0.0010 eq freqs= 0.0019 rel rates= 0.0002) pass 5 : -14498.8866 (branch= 0.0006 eq freqs= 0.0004 rel rates= 0.0002) pass 6 : -14498.8859 (branch= 0.0004 eq freqs= 0.0000 rel rates= 0.0002) pass 7 : -14498.8857 (branch= 0.0002 eq freqs= 0.0000 rel rates= 0.0001) pass 8 : -14498.8855 (branch= 0.0002 eq freqs= 0.0000 rel rates= 0.0000) pass 9 : -14498.8854 (branch= 0.0001 eq freqs= 0.0000 rel rates= 0.0000) pass 10: -14498.8853 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 11: -14498.8853 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 12: -14498.8853 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -14498.8853 Time used = 0 hours, 0 minutes and 3 seconds MODEL REPORT - Parameter values are FINAL 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 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 : -14498.8853 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 1.869 3.671 1.221 1.853 4.414 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 14486.03850 ***Expected is 14486.03829 ***SCORE DIFFERENCE IS .00021 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 36.660 (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: -13315.7939 Current score = -13315.7939 Performing final optimizations... pass 1 : -13309.3700 (branch= 2.8300 alpha= 0.8831 pinv= 0.0158 eq freqs= 0.2323 rel rates= 1.8454 subset rates= 0.6173) pass 2 : -13307.8842 (branch= 0.4328 alpha= 0.2019 pinv= 0.0134 eq freqs= 0.1232 rel rates= 0.6633 subset rates= 0.0513) pass 3 : -13307.2657 (branch= 0.1095 alpha= 0.0595 pinv= 0.0031 eq freqs= 0.0081 rel rates= 0.4287 subset rates= 0.0096) pass 4 : -13306.9109 (branch= 0.0241 alpha= 0.0171 pinv= 0.0026 eq freqs= 0.0085 rel rates= 0.2993 subset rates= 0.0032) pass 5 : -13306.6767 (branch= 0.0088 alpha= 0.0057 pinv= 0.0013 eq freqs= 0.0072 rel rates= 0.2110 subset rates= 0.0002) pass 6 : -13306.5232 (branch= 0.0036 alpha= 0.0020 pinv= 0.0004 eq freqs= 0.0043 rel rates= 0.1433 subset rates= 0.0000) pass 7 : -13306.4217 (branch= 0.0011 alpha= 0.0004 pinv= 0.0001 eq freqs= 0.0035 rel rates= 0.0964 subset rates= 0.0000) pass 8 : -13306.3532 (branch= 0.0006 alpha= 0.0002 pinv= 0.0001 eq freqs= 0.0020 rel rates= 0.0656 subset rates= 0.0000) pass 9 : -13306.3069 (branch= 0.0003 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0015 rel rates= 0.0444 subset rates= 0.0000) pass 10: -13306.2750 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0012 rel rates= 0.0306 subset rates= 0.0000) pass 11: -13306.2534 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0206 subset rates= 0.0002) pass 12: -13306.2381 (branch= 0.0001 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0142 subset rates= 0.0005) pass 13: -13306.2280 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0097 subset rates= 0.0000) pass 14: -13306.2211 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0067 subset rates= 0.0000) pass 15: -13306.2164 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0045 subset rates= 0.0000) pass 16: -13306.2134 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0030 subset rates= 0.0000) pass 17: -13306.2112 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0021 subset rates= 0.0000) pass 18: -13306.2097 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014 subset rates= 0.0000) pass 19: -13306.2087 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010 subset rates= 0.0000) pass 20: -13306.2080 (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: -13306.2065 (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: -13306.2063 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0001) Looking for minimum length branches... Final score = -13306.2063 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 : -13306.2063 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 1.413 1.413 3.72 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: 4.369 7.051 1.608 7.051 4.369 1 0.270 0.164 0.161 0.406 0.361 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 4.034 0.033 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 1.694 0.540 0.300 2.160 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 13306.20634 ***Expected is 13306.20608 ***SCORE DIFFERENCE IS .00026 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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= 4.30) pass 2:+ 9.055 (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:+ 0.303 (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: -467.8152 Current score = -467.8152 Performing final optimizations... pass 1 : -467.7873 (branch= 0.0213 subset rates= 0.0066) pass 2 : -467.7197 (branch= 0.0649 subset rates= 0.0027) pass 3 : -467.6968 (branch= 0.0229 subset rates= 0.0000) pass 4 : -467.6869 (branch= 0.0099 subset rates= 0.0000) pass 5 : -467.6823 (branch= 0.0046 subset rates= 0.0000) pass 6 : -467.6802 (branch= 0.0020 subset rates= 0.0000) pass 7 : -467.6793 (branch= 0.0009 subset rates= 0.0000) pass 8 : -467.6788 (branch= 0.0005 subset rates= 0.0000) pass 9 : -467.6785 (branch= 0.0003 subset rates= 0.0000) pass 10: -467.6784 (branch= 0.0001 subset rates= 0.0000) pass 11: -467.6783 (branch= 0.0000 subset rates= 0.0000) pass 12: -467.6783 (branch= 0.0000 subset rates= 0.0000) pass 13: -467.6783 (branch= 0.0000 subset rates= 0.0000) pass 14: -467.6783 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6783 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -467.6783 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: 3.842 0.786 1.480 2.177 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 467.67829 ***Expected is 467.6783 ***SCORE DIFFERENCE IS -.00001 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 12.450 (branch= 8.46 scale= 0.00 subset rates= 3.99) pass 3:+ 3.552 (branch= 2.32 scale= 0.03 subset rates= 1.21) pass 4:+ 0.758 (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: -477.9401 Current score = -477.9401 Performing final optimizations... pass 1 : -477.8535 (branch= 0.0858 subset rates= 0.0008) pass 2 : -477.7572 (branch= 0.0963 subset rates= 0.0000) pass 3 : -477.7255 (branch= 0.0301 subset rates= 0.0016) pass 4 : -477.7048 (branch= 0.0207 subset rates= 0.0000) pass 5 : -477.6964 (branch= 0.0085 subset rates= 0.0000) pass 6 : -477.6921 (branch= 0.0043 subset rates= 0.0000) pass 7 : -477.6900 (branch= 0.0021 subset rates= 0.0000) pass 8 : -477.6888 (branch= 0.0011 subset rates= 0.0000) pass 9 : -477.6882 (branch= 0.0007 subset rates= 0.0000) pass 10: -477.6861 (branch= 0.0004 subset rates= 0.0016) pass 11: -477.6854 (branch= 0.0008 subset rates= 0.0000) pass 12: -477.6850 (branch= 0.0003 subset rates= 0.0000) pass 13: -477.6849 (branch= 0.0002 subset rates= 0.0000) pass 14: -477.6847 (branch= 0.0001 subset rates= 0.0000) pass 15: -477.6847 (branch= 0.0000 subset rates= 0.0000) pass 16: -477.6847 (branch= 0.0000 subset rates= 0.0000) pass 17: -477.6847 (branch= 0.0000 subset rates= 0.0000) pass 18: -477.6846 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.6846 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 : -477.6846 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: 4.914 0.631 1.899 2.807 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 477.68463 ***Expected is 477.6848 ***SCORE DIFFERENCE IS -.00017 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 129.564 (branch= 123.99 scale= 0.59 subset rates= 4.98) pass 2:+ 9.273 (branch= 7.97 scale= 0.00 subset rates= 1.30) pass 3:+ 1.739 (branch= 1.57 scale= 0.00 subset rates= 0.17) pass 4:+ 0.312 (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: -464.7107 Current score = -464.7107 Performing final optimizations... pass 1 : -464.6735 (branch= 0.0277 subset rates= 0.0095) pass 2 : -464.5879 (branch= 0.0823 subset rates= 0.0033) pass 3 : -464.5682 (branch= 0.0185 subset rates= 0.0012) pass 4 : -464.5557 (branch= 0.0125 subset rates= 0.0000) pass 5 : -464.5526 (branch= 0.0031 subset rates= 0.0000) pass 6 : -464.5498 (branch= 0.0022 subset rates= 0.0006) pass 7 : -464.5490 (branch= 0.0007 subset rates= 0.0000) pass 8 : -464.5482 (branch= 0.0008 subset rates= 0.0000) pass 9 : -464.5478 (branch= 0.0004 subset rates= 0.0000) pass 10: -464.5477 (branch= 0.0001 subset rates= 0.0000) pass 11: -464.5476 (branch= 0.0001 subset rates= 0.0000) pass 12: -464.5476 (branch= 0.0000 subset rates= 0.0000) pass 13: -464.5476 (branch= 0.0000 subset rates= 0.0000) pass 14: -464.5476 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -464.5476 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 : -464.5476 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 0.772 1.641 2.452 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 464.54756 ***Expected is 464.5473 ***SCORE DIFFERENCE IS .00026 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 3.846 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.161 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.158 (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: -474.8622 Current score = -474.8622 Performing final optimizations... pass 1 : -474.7981 (branch= 0.0576 subset rates= 0.0066) pass 2 : -474.6999 (branch= 0.0911 subset rates= 0.0071) pass 3 : -474.6746 (branch= 0.0233 subset rates= 0.0020) pass 4 : -474.6609 (branch= 0.0137 subset rates= 0.0000) pass 5 : -474.6539 (branch= 0.0070 subset rates= 0.0000) pass 6 : -474.6510 (branch= 0.0029 subset rates= 0.0000) pass 7 : -474.6490 (branch= 0.0011 subset rates= 0.0009) pass 8 : -474.6470 (branch= 0.0012 subset rates= 0.0008) pass 9 : -474.6464 (branch= 0.0007 subset rates= 0.0000) pass 10: -474.6460 (branch= 0.0004 subset rates= 0.0000) pass 11: -474.6458 (branch= 0.0002 subset rates= 0.0000) pass 12: -474.6457 (branch= 0.0001 subset rates= 0.0001) pass 13: -474.6456 (branch= 0.0001 subset rates= 0.0000) pass 14: -474.6455 (branch= 0.0000 subset rates= 0.0000) pass 15: -474.6455 (branch= 0.0000 subset rates= 0.0000) pass 16: -474.6455 (branch= 0.0000 subset rates= 0.0000) pass 17: -474.6455 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -474.6455 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 : -474.6455 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: 4.585 0.585 2.017 2.998 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 474.64547 ***Expected is 474.6455633 ***SCORE DIFFERENCE IS -.0000933 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 -210.8784 0.010 1215 2000 -210.6679 0.010 1215 2500 -210.6042 0.010 1215 3000 -210.5103 0.010 1215 3500 -210.4074 0.010 1215 Reached termination condition! last topological improvement at gen 1215 Improvement over last 500 gen = 0.04856 Current score = -210.3682 Performing final optimizations... pass 1 : -210.0050 (branch= 0.0000 alpha= 0.0802 pinv= 0.2366 eq freqs= 0.0000 rel rates= 0.0463) pass 2 : -209.4569 (branch= 0.0070 alpha= 0.3208 pinv= 0.2046 eq freqs= 0.0043 rel rates= 0.0115) pass 3 : -209.3004 (branch= 0.0331 alpha= 0.0941 pinv= 0.0091 eq freqs= 0.0085 rel rates= 0.0117) pass 4 : -209.2399 (branch= 0.0368 alpha= 0.0184 pinv= 0.0014 eq freqs= 0.0008 rel rates= 0.0031) pass 5 : -209.1932 (branch= 0.0307 alpha= 0.0102 pinv= 0.0005 eq freqs= 0.0000 rel rates= 0.0052) pass 6 : -209.1657 (branch= 0.0133 alpha= 0.0051 pinv= 0.0005 eq freqs= 0.0009 rel rates= 0.0076) pass 7 : -209.1439 (branch= 0.0077 alpha= 0.0024 pinv= 0.0002 eq freqs= 0.0005 rel rates= 0.0110) pass 8 : -209.1281 (branch= 0.0045 alpha= 0.0005 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0104) pass 9 : -209.1165 (branch= 0.0016 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0095) pass 10: -209.1072 (branch= 0.0007 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0082) pass 11: -209.0991 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0074) pass 12: -209.0921 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0067) pass 13: -209.0857 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0061) pass 14: -209.0798 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0057) pass 15: -209.0744 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0053) pass 16: -209.0691 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0051) pass 17: -209.0644 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 18: -209.0596 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 19: -209.0547 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 20: -209.0495 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) optimization up to ... pass 30: -208.9548 (branch= 0.0159 alpha= 0.0000 pinv= 0.0005 eq freqs= 0.0028 rel rates= 0.0755) optimization up to ... pass 40: -208.7782 (branch= 0.0289 alpha= 0.0000 pinv= 0.0019 eq freqs= 0.0089 rel rates= 0.1370) optimization up to ... pass 50: -208.6671 (branch= 0.0060 alpha= 0.0000 pinv= 0.0008 eq freqs= 0.0032 rel rates= 0.1009) optimization up to ... pass 60: -208.6038 (branch= 0.0007 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0623) optimization up to ... pass 70: -208.5599 (branch= 0.0002 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0434) optimization up to ... pass 80: -208.5276 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0321) optimization up to ... pass 90: -208.5027 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0247) optimization up to ... pass 100: -208.4832 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0194) optimization up to ... pass 110: -208.4674 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0156) optimization up to ... pass 120: -208.4545 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0129) optimization up to ... pass 130: -208.4437 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0107) optimization up to ... pass 140: -208.4345 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0091) optimization up to ... pass 150: -208.4266 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0078) optimization up to ... pass 160: -208.4199 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) optimization up to ... pass 170: -208.4141 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) optimization up to ... pass 180: -208.4090 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0051) optimization up to ... pass 190: -208.4044 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0045) optimization up to ... pass 200: -208.4004 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) optimization up to ... pass 210: -208.3969 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0036) optimization up to ... pass 220: -208.3936 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... pass 230: -208.3907 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) optimization up to ... pass 240: -208.3880 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0027) optimization up to ... pass 250: -208.3856 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0025) optimization up to ... pass 260: -208.3833 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... pass 270: -208.3813 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) optimization up to ... pass 280: -208.3794 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 290: -208.3776 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) optimization up to ... pass 300: -208.3760 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 310: -208.3744 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... pass 320: -208.3730 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 330: -208.3716 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 340: -208.3704 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 350: -208.3692 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 360: -208.3681 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 370: -208.3671 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 380: -208.3661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 390: -208.3652 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 400: -208.3644 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 410: -208.3635 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 420: -208.3627 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 430: -208.3620 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 440: -208.3613 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 450: -208.3606 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 460: -208.3600 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 470: -208.3594 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 480: -208.3590 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0004) optimization up to ... pass 490: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) optimization up to ... pass 492: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.3587 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 = 121.128, AG = 186.935, AT = 6.902, CG = 202.957, CT = 193.125, 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. ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -208.3587 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: 121.1 186.9 6.902 203 193.1 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 -212.3288 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 = 0.03824 Current score = -211.2855 Performing final optimizations... pass 1 : -208.9608 (branch= 0.0000 alpha= 0.7627 pinv= 1.4695 eq freqs= 0.0065 rel rates= 0.0860) pass 2 : -208.5654 (branch= 0.0411 alpha= 0.3048 pinv= 0.0095 eq freqs= 0.0118 rel rates= 0.0282) pass 3 : -208.5084 (branch= 0.0299 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0018 rel rates= 0.0253) pass 4 : -208.4811 (branch= 0.0032 alpha= 0.0022 pinv= 0.0017 eq freqs= 0.0000 rel rates= 0.0202) pass 5 : -208.4608 (branch= 0.0022 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0176) pass 6 : -208.4423 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0177) pass 7 : -208.4250 (branch= 0.0009 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0160) pass 8 : -208.4103 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0144) pass 9 : -208.3965 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0135) pass 10: -208.3839 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0124) pass 11: -208.3723 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0115) pass 12: -208.3618 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0104) pass 13: -208.3520 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0098) pass 14: -208.3430 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0090) pass 15: -208.3347 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0083) pass 16: -208.3272 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0075) pass 17: -208.3199 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0072) pass 18: -208.3133 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) pass 19: -208.3068 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0064) pass 20: -208.3010 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) optimization up to ... pass 30: -208.2568 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0440) optimization up to ... pass 40: -208.2293 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0274) optimization up to ... pass 50: -208.2106 (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: -208.1865 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0104) optimization up to ... pass 80: -208.1782 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0082) optimization up to ... pass 90: -208.1716 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) optimization up to ... pass 100: -208.1661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0055) optimization up to ... pass 110: -208.1615 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) 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: -208.1260 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 350: -208.1254 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... 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 8 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 22.242, AG = 32.319, AT = 0.001, CG = 36.406, CT = 80.314, 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 80.31 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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: -219.1444 gen current_lnL precision last_tree_imp 0 -219.1444 0.500 0 500 -216.3490 0.500 474 1000 -215.0097 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 -210.9688 0.010 1502 2500 -210.8711 0.010 1502 3000 -210.7510 0.010 2883 3500 -210.7005 0.010 2883 4000 -210.6775 0.010 2883 4500 -210.6277 0.010 2883 5000 -210.5646 0.010 2883 5500 -210.5008 0.010 2883 6000 -210.3538 0.010 2883 Reached termination condition! last topological improvement at gen 2883 Improvement over last 500 gen = 0.04187 Current score = -210.3452 Performing final optimizations... pass 1 : -209.7259 (branch= 0.0025 alpha= 0.1839 pinv= 0.3304 eq freqs= 0.0000 rel rates= 0.1026) pass 2 : -209.3742 (branch= 0.0078 alpha= 0.2626 pinv= 0.0730 eq freqs= 0.0000 rel rates= 0.0083) pass 3 : -209.2734 (branch= 0.0558 alpha= 0.0257 pinv= 0.0046 eq freqs= 0.0058 rel rates= 0.0088) pass 4 : -209.2185 (branch= 0.0250 alpha= 0.0158 pinv= 0.0000 eq freqs= 0.0049 rel rates= 0.0093) pass 5 : -209.1816 (branch= 0.0224 alpha= 0.0077 pinv= 0.0012 eq freqs= 0.0004 rel rates= 0.0052) pass 6 : -209.1540 (branch= 0.0130 alpha= 0.0052 pinv= 0.0002 eq freqs= 0.0012 rel rates= 0.0080) pass 7 : -209.1308 (branch= 0.0091 alpha= 0.0028 pinv= 0.0001 eq freqs= 0.0006 rel rates= 0.0106) pass 8 : -209.1164 (branch= 0.0042 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0094) pass 9 : -209.1063 (branch= 0.0014 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0082) pass 10: -209.0981 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0073) pass 11: -209.0910 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0065) pass 12: -209.0847 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0059) pass 13: -209.0791 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0054) pass 14: -209.0738 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0051) pass 15: -209.0686 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) pass 16: -209.0634 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) pass 17: -209.0579 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0051) pass 18: -209.0519 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0052) pass 19: -209.0454 (branch= 0.0009 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0056) pass 20: -209.0380 (branch= 0.0012 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0061) optimization up to ... pass 30: -208.9100 (branch= 0.0260 alpha= 0.0000 pinv= 0.0009 eq freqs= 0.0049 rel rates= 0.0963) optimization up to ... pass 40: -208.7402 (branch= 0.0229 alpha= 0.0000 pinv= 0.0019 eq freqs= 0.0080 rel rates= 0.1371) optimization up to ... pass 50: -208.6479 (branch= 0.0029 alpha= 0.0000 pinv= 0.0004 eq freqs= 0.0017 rel rates= 0.0873) optimization up to ... pass 60: -208.5911 (branch= 0.0005 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0560) optimization up to ... pass 70: -208.5508 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0399) optimization up to ... pass 80: -208.5205 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0301) optimization up to ... pass 90: -208.4972 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0231) optimization up to ... pass 100: -208.4788 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0182) optimization up to ... pass 110: -208.4638 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0149) optimization up to ... pass 120: -208.4514 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0123) optimization up to ... pass 130: -208.4411 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0103) optimization up to ... pass 140: -208.4322 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0088) optimization up to ... pass 150: -208.4247 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0075) optimization up to ... pass 160: -208.4183 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0064) optimization up to ... pass 170: -208.4127 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0056) optimization up to ... pass 180: -208.4077 (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= 0.0044) optimization up to ... pass 200: -208.3995 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0039) optimization up to ... pass 210: -208.3960 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0035) optimization up to ... pass 220: -208.3929 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... pass 230: -208.3900 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0028) optimization up to ... pass 240: -208.3874 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) optimization up to ... pass 250: -208.3850 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... pass 260: -208.3828 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... pass 270: -208.3808 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... pass 280: -208.3789 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 290: -208.3772 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 300: -208.3756 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 310: -208.3741 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... pass 320: -208.3727 (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: -208.3701 (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: -208.3679 (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= 0.0010) 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: -208.3626 (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: -208.3605 (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 488: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... Final score = -208.3586 Time used = 0 hours, 0 minutes and 5 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 121.794, AG = 187.954, AT = 6.949, CG = 204.067, CT = 194.168, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2225 0.2905 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 : -208.3586 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: 121.8 188 6.949 204.1 194.2 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 -210.6026 0.010 1230 Reached termination condition! last topological improvement at gen 1230 Improvement over last 500 gen = 0.04161 Current score = -210.5932 Performing final optimizations... pass 1 : -210.1850 (branch= 0.0000 alpha= 0.1339 pinv= 0.2110 eq freqs= 0.0000 rel rates= 0.0632) pass 2 : -209.5580 (branch= 0.0093 alpha= 0.3569 pinv= 0.2371 eq freqs= 0.0050 rel rates= 0.0187) pass 3 : -209.3359 (branch= 0.0380 alpha= 0.1430 pinv= 0.0187 eq freqs= 0.0077 rel rates= 0.0147) pass 4 : -209.2571 (branch= 0.0476 alpha= 0.0199 pinv= 0.0030 eq freqs= 0.0034 rel rates= 0.0049) pass 5 : -209.2088 (branch= 0.0334 alpha= 0.0098 pinv= 0.0009 eq freqs= 0.0000 rel rates= 0.0043) pass 6 : -209.1769 (branch= 0.0177 alpha= 0.0054 pinv= 0.0005 eq freqs= 0.0014 rel rates= 0.0069) pass 7 : -209.1511 (branch= 0.0101 alpha= 0.0036 pinv= 0.0002 eq freqs= 0.0009 rel rates= 0.0110) pass 8 : -209.1300 (branch= 0.0071 alpha= 0.0017 pinv= 0.0000 eq freqs= 0.0009 rel rates= 0.0115) pass 9 : -209.1160 (branch= 0.0031 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0008 rel rates= 0.0100) pass 10: -209.1057 (branch= 0.0011 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0087) pass 11: -209.0970 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0078) pass 12: -209.0897 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0068) pass 13: -209.0833 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0061) pass 14: -209.0775 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0056) pass 15: -209.0720 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0053) pass 16: -209.0670 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0049) pass 17: -209.0621 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 18: -209.0573 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 19: -209.0525 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) pass 20: -209.0471 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) optimization up to ... pass 30: -208.9462 (branch= 0.0176 alpha= 0.0000 pinv= 0.0006 eq freqs= 0.0033 rel rates= 0.0793) optimization up to ... pass 40: -208.7696 (branch= 0.0280 alpha= 0.0000 pinv= 0.0020 eq freqs= 0.0088 rel rates= 0.1378) optimization up to ... pass 50: -208.6633 (branch= 0.0052 alpha= 0.0000 pinv= 0.0007 eq freqs= 0.0028 rel rates= 0.0976) optimization up to ... pass 60: -208.6013 (branch= 0.0006 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0609) optimization up to ... pass 70: -208.5582 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0427) optimization up to ... pass 80: -208.5262 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0317) optimization up to ... pass 90: -208.5016 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0244) optimization up to ... pass 100: -208.4824 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0192) optimization up to ... pass 110: -208.4668 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0155) optimization up to ... pass 120: -208.4539 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0128) optimization up to ... pass 130: -208.4432 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0107) optimization up to ... pass 140: -208.4341 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0090) optimization up to ... pass 150: -208.4263 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0078) optimization up to ... pass 160: -208.4196 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) optimization up to ... pass 170: -208.4138 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) optimization up to ... pass 180: -208.4087 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) optimization up to ... pass 190: -208.4043 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0044) optimization up to ... pass 200: -208.4003 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) optimization up to ... pass 210: -208.3967 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0036) optimization up to ... pass 220: -208.3935 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... pass 230: -208.3906 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) optimization up to ... pass 240: -208.3879 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0027) optimization up to ... pass 250: -208.3854 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... pass 260: -208.3832 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... pass 270: -208.3812 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... pass 280: -208.3792 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 290: -208.3775 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 300: -208.3758 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 310: -208.3743 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... pass 320: -208.3729 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 330: -208.3716 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... pass 340: -208.3703 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 350: -208.3692 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 360: -208.3681 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 370: -208.3671 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 380: -208.3661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 390: -208.3652 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 400: -208.3643 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 410: -208.3635 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 420: -208.3627 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 430: -208.3620 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 440: -208.3613 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 450: -208.3606 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 460: -208.3600 (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: -208.3588 (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= 0.0003) optimization up to ... pass 493: -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 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 122.551, AG = 189.112, AT = 6.991, CG = 205.325, CT = 195.363, 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: 122.6 189.1 6.991 205.3 195.4 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 0.925 (branch= 0.64 scale= 0.00 omega= 0.28 rel rates= 0.00) pass 3:+ 0.733 (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: -213.0379 gen current_lnL precision last_tree_imp 0 -213.0379 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) = 0.130445 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 : -210.2321 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 77.066 (branch= 2.27 scale= 0.00 alpha= 4.14 freqs= 10.82 rel rates= 3.11 pinv= 0.78 subset rates= 55.95) pass 3:+ 49.994 (branch= 6.88 scale= 0.78 alpha= 5.67 freqs= 1.20 rel rates= 1.34 pinv= 0.01 subset rates= 34.11) pass 4:+ 15.059 (branch= 0.00 scale= 0.72 alpha= 0.64 freqs= 1.21 rel rates= 0.50 pinv= 0.00 subset rates= 12.00) pass 5:+ 5.778 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.10 rel rates= 0.77 pinv= 0.00 subset rates= 4.91) pass 6:+ 0.115 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.09 rel rates= 0.01 pinv= 0.00 subset rates= 0.00) lnL after optimization: -13342.2046 gen current_lnL precision last_tree_imp 0 -13342.2046 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 = 1.337, CG = 1.337, CT = 3.999, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3134 0.1755 0.2988 0.2122 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 = 6.057, AT = 1.217, CG = 6.057, CT = 3.969, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2816 0.1661 0.1574 0.3949 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.3385 Substitution rate categories under this model: rate proportion 0.0089 0.2500 0.1346 0.2500 0.6551 0.2500 3.2014 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 = 4.110, AT = 2.501, CG = 0.382, CT = 4.110, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1597 0.3517 0.2835 0.2051 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 4.3250 with an invariant (invariable) site category, proportion estimated 0.0388 Substitution rate categories under this model: rate proportion 0.0000 0.0388 0.4714 0.2403 0.7857 0.2403 1.0842 0.2403 1.6587 0.2403 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 : -13323.9616 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 1.337 1.337 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 6.057 1.217 6.057 3.969 1 0.282 0.166 0.157 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 4.11 2.501 0.3821 4.11 1 0.160 0.352 0.284 0.205 4.325 0.039 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 1.695 0.539 0.326 2.136 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 3.846 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.161 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.158 (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: -474.8622 gen current_lnL precision last_tree_imp 0 -474.8622 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 : -474.8614 (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 2.019 2.820 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:+ 5.106 (branch= 3.29 scale= 0.00 subset rates= 1.82) pass 4:+ 0.827 (branch= 0.20 scale= 0.00 subset rates= 0.62) pass 5:+ 0.064 (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 : -474.8614 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 2.019 2.820 rep 2: 4.516 0.599 2.014 2.839 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:+ 0.939 (branch= 0.38 scale= 0.00 subset rates= 0.56) pass 5:+ 0.207 (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: -474.8925 gen current_lnL precision last_tree_imp 0 -474.8925 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 : -474.8614 Replicate 2 : -474.8505 (best) Replicate 3 : -474.8831 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 2.019 2.820 rep 2: 4.516 0.599 2.014 2.839 rep 3: 4.460 0.600 2.010 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 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:+ 3.711 (branch= 2.16 scale= 0.00 subset rates= 1.55) pass 4:+ 1.981 (branch= 1.40 scale= 0.00 subset rates= 0.58) pass 5:+ 0.364 (branch= 0.33 scale= 0.00 subset rates= 0.03) pass 6:+ 0.110 (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: -474.8512 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 2.85 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 : -474.8614 Replicate 2 : -474.8505 Replicate 3 : -474.8831 Replicate 4 : -474.8498 (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 2.019 2.820 rep 2: 4.516 0.599 2.014 2.839 rep 3: 4.460 0.600 2.010 2.838 rep 4: 4.504 0.598 2.010 2.854 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:+ 0.168 (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: -474.9109 gen current_lnL precision last_tree_imp 0 -474.9109 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 : -474.8614 Replicate 2 : -474.8505 Replicate 3 : -474.8831 Replicate 4 : -474.8498 (best) Replicate 5 : -474.9076 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 2.019 2.820 rep 2: 4.516 0.599 2.014 2.839 rep 3: 4.460 0.600 2.010 2.838 rep 4: 4.504 0.598 2.010 2.854 rep 5: 4.499 0.597 2.021 2.840 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 0.500 215 800 -90.1648 0.500 215 Optimization precision reduced Optimizing parameters... improved 0.159 lnL Optimizing branchlengths... improved 0.317 lnL NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 879, seed 1680541178, best lnL -88.955 gen current_lnL precision last_tree_imp 879 -88.9552 0.010 879 900 -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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 84 600 -111.7788 0.500 84 Optimization precision reduced Optimizing parameters... improved 0.386 lnL Optimizing branchlengths... improved 0.390 lnL 700 -110.8142 0.010 615 800 -110.5642 0.010 707 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 800, seed 1245259246, best lnL -110.564 gen current_lnL precision last_tree_imp 800 -110.5642 0.010 707 900 -110.5555 0.010 707 1000 -110.5066 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 0.1935 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 : -110.5066 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 2000 -111.6817 0.010 563 2100 -111.6817 0.010 563 2200 -111.6817 0.010 563 2300 -111.6817 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 2300, seed 1579946663, best lnL -111.682 gen current_lnL precision last_tree_imp 2300 -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) No branches were short enough to be 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 70 -205.5741 0.500 53 80 -205.4022 0.500 76 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 80, seed 1732378755, best lnL -205.402 gen current_lnL precision last_tree_imp 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 -195.2554 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 51, seed 1784766670, best lnL -195.214 gen current_lnL precision last_tree_imp 51 -195.2137 0.500 0 60 -195.1629 0.500 0 70 -195.0042 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) = 0.120507 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 0.831 lnL Optimizing branchlengths... improved 0.085 lnL 1100 -3352.7180 0.010 0 1200 -3352.6366 0.010 0 1300 -3352.5137 0.010 0 1400 -3352.4036 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 1431, seed 2054937967, best lnL -3352.404 gen current_lnL precision last_tree_imp 1431 -3352.4036 0.010 0 1500 -3352.3987 0.010 0 1600 -3352.2919 0.010 0 1700 -3352.2843 0.010 0 1800 -3352.2036 0.010 0 1900 -3351.8476 0.010 0 2000 -3351.7698 0.010 0 2100 -3351.6181 0.010 0 2200 -3351.3750 0.010 0 2300 -3351.3499 0.010 0 2400 -3351.3426 0.010 0 2500 -3351.2398 0.010 0 2600 -3351.1737 0.010 0 2700 -3351.1734 0.010 0 2800 -3351.1196 0.010 0 2900 -3351.1184 0.010 0 3000 -3351.1143 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... Current score = -3351.1019 Performing final optimizations... pass 1 : -3351.0533 (branch= 0.0000 alpha= 0.0000 pinv= 0.0100 eq freqs= 0.0001 rel rates= 0.0384 subset rates= 0.0000) pass 2 : -3350.9538 (branch= 0.0000 alpha= 0.0117 pinv= 0.0197 eq freqs= 0.0100 rel rates= 0.0582 subset rates= 0.0000) pass 3 : -3350.8653 (branch= 0.0034 alpha= 0.0189 pinv= 0.0170 eq freqs= 0.0020 rel rates= 0.0471 subset rates= 0.0000) pass 4 : -3350.7873 (branch= 0.0049 alpha= 0.0175 pinv= 0.0160 eq freqs= 0.0000 rel rates= 0.0369 subset rates= 0.0026) pass 5 : -3350.7205 (branch= 0.0049 alpha= 0.0139 pinv= 0.0149 eq freqs= 0.0009 rel rates= 0.0310 subset rates= 0.0012) pass 6 : -3350.6609 (branch= 0.0041 alpha= 0.0133 pinv= 0.0137 eq freqs= 0.0002 rel rates= 0.0272 subset rates= 0.0010) pass 7 : -3350.6103 (branch= 0.0024 alpha= 0.0123 pinv= 0.0126 eq freqs= 0.0002 rel rates= 0.0231 subset rates= 0.0000) pass 8 : -3350.5641 (branch= 0.0003 alpha= 0.0116 pinv= 0.0114 eq freqs= 0.0000 rel rates= 0.0213 subset rates= 0.0015) pass 9 : -3350.5239 (branch= 0.0013 alpha= 0.0108 pinv= 0.0104 eq freqs= 0.0001 rel rates= 0.0176 subset rates= 0.0000) pass 10: -3350.4880 (branch= 0.0002 alpha= 0.0098 pinv= 0.0100 eq freqs= 0.0000 rel rates= 0.0159 subset rates= 0.0000) pass 11: -3350.4557 (branch= 0.0000 alpha= 0.0094 pinv= 0.0090 eq freqs= 0.0000 rel rates= 0.0139 subset rates= 0.0000) pass 12: -3350.4266 (branch= 0.0000 alpha= 0.0085 pinv= 0.0075 eq freqs= 0.0000 rel rates= 0.0120 subset rates= 0.0011) pass 13: -3350.4023 (branch= 0.0007 alpha= 0.0072 pinv= 0.0068 eq freqs= 0.0000 rel rates= 0.0096 subset rates= 0.0000) pass 14: -3350.3812 (branch= 0.0001 alpha= 0.0063 pinv= 0.0061 eq freqs= 0.0000 rel rates= 0.0086 subset rates= 0.0000) pass 15: -3350.3622 (branch= 0.0000 alpha= 0.0060 pinv= 0.0054 eq freqs= 0.0000 rel rates= 0.0075 subset rates= 0.0000) pass 16: -3350.3453 (branch= 0.0000 alpha= 0.0054 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0067 subset rates= 0.0000) pass 17: -3350.3306 (branch= 0.0000 alpha= 0.0048 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0057 subset rates= 0.0000) pass 18: -3350.3177 (branch= 0.0000 alpha= 0.0042 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0049 subset rates= 0.0000) pass 19: -3350.3063 (branch= 0.0000 alpha= 0.0037 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0042 subset rates= 0.0000) pass 20: -3350.2965 (branch= 0.0000 alpha= 0.0033 pinv= 0.0029 eq freqs= 0.0000 rel rates= 0.0036 subset rates= 0.0000) optimization up to ... pass 30: -3350.2472 (branch= 0.0000 alpha= 0.0166 pinv= 0.0150 eq freqs= 0.0000 rel rates= 0.0176 subset rates= 0.0000) optimization up to ... pass 40: -3350.2360 (branch= 0.0000 alpha= 0.0037 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0041 subset rates= 0.0000) optimization up to ... pass 50: -3350.2337 (branch= 0.0000 alpha= 0.0007 pinv= 0.0006 eq freqs= 0.0000 rel rates= 0.0010 subset rates= 0.0000) optimization up to ... pass 60: -3350.2332 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) optimization up to ... pass 68: -3350.2331 (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 = -3350.2331 Time used so far = 0 hours, 0 minutes and 15 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 3.115, AG = 10.420, AT = 2.692, CG = 0.001, CT = 21.928, 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 0.5773 with an invariant (invariable) site category, proportion estimated 0.3656 Substitution rate categories under this model: rate proportion 0.0000 0.3656 0.0485 0.1586 0.2994 0.1586 0.8693 0.1586 2.7828 0.1586 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 : -3350.2331 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 3.115 10.42 2.692 0.001 21.93 1 0.333 0.222 0.157 0.288 0.577 0.366 Partition model subset 2: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) rep 1: 0.789 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 400, seed 198833985, best lnL -3323.985 gen current_lnL precision last_tree_imp 400 -3323.9848 0.500 1 500 -3323.6818 0.500 1 600 -3323.3459 0.500 1 Optimization precision reduced Optimizing parameters... improved 1.812 lnL Optimizing branchlengths... improved 0.023 lnL 700 -3321.3650 0.255 1 800 -3321.0295 0.255 1 900 -3321.0142 0.255 1 1000 -3320.9667 0.255 1 NOTE: ****Specified time limit (5 seconds) reached... Current score = -3320.8988 Performing final optimizations... pass 1 : -3320.2605 (branch= 0.0468 alpha= 0.0000 pinv= 0.0155 eq freqs= 0.0001 rel rates= 0.5593 ins/del rates= 0.0166) pass 2 : -3319.8108 (branch= 0.0687 alpha= 0.0065 pinv= 0.0159 eq freqs= 0.0000 rel rates= 0.3405 ins/del rates= 0.0180) pass 3 : -3319.4666 (branch= 0.0455 alpha= 0.0079 pinv= 0.0157 eq freqs= 0.0000 rel rates= 0.2549 ins/del rates= 0.0201) pass 4 : -3319.2019 (branch= 0.0263 alpha= 0.0102 pinv= 0.0153 eq freqs= 0.0024 rel rates= 0.2005 ins/del rates= 0.0101) pass 5 : -3318.9818 (branch= 0.0182 alpha= 0.0103 pinv= 0.0147 eq freqs= 0.0011 rel rates= 0.1683 ins/del rates= 0.0075) pass 6 : -3318.8010 (branch= 0.0120 alpha= 0.0105 pinv= 0.0139 eq freqs= 0.0012 rel rates= 0.1381 ins/del rates= 0.0051) pass 7 : -3318.6466 (branch= 0.0085 alpha= 0.0099 pinv= 0.0130 eq freqs= 0.0004 rel rates= 0.1192 ins/del rates= 0.0035) pass 8 : -3318.5179 (branch= 0.0056 alpha= 0.0099 pinv= 0.0121 eq freqs= 0.0003 rel rates= 0.0983 ins/del rates= 0.0024) pass 9 : -3318.4100 (branch= 0.0037 alpha= 0.0099 pinv= 0.0112 eq freqs= 0.0003 rel rates= 0.0812 ins/del rates= 0.0016) pass 10: -3318.3186 (branch= 0.0024 alpha= 0.0095 pinv= 0.0109 eq freqs= 0.0002 rel rates= 0.0673 ins/del rates= 0.0011) pass 11: -3318.2438 (branch= 0.0016 alpha= 0.0089 pinv= 0.0094 eq freqs= 0.0002 rel rates= 0.0540 ins/del rates= 0.0007) pass 12: -3318.1803 (branch= 0.0011 alpha= 0.0083 pinv= 0.0086 eq freqs= 0.0001 rel rates= 0.0449 ins/del rates= 0.0005) pass 13: -3318.1262 (branch= 0.0007 alpha= 0.0078 pinv= 0.0078 eq freqs= 0.0001 rel rates= 0.0374 ins/del rates= 0.0003) pass 14: -3318.0801 (branch= 0.0004 alpha= 0.0073 pinv= 0.0071 eq freqs= 0.0001 rel rates= 0.0309 ins/del rates= 0.0002) pass 15: -3318.0410 (branch= 0.0003 alpha= 0.0066 pinv= 0.0064 eq freqs= 0.0001 rel rates= 0.0256 ins/del rates= 0.0001) pass 16: -3318.0073 (branch= 0.0002 alpha= 0.0060 pinv= 0.0058 eq freqs= 0.0001 rel rates= 0.0216 ins/del rates= 0.0001) pass 17: -3317.9780 (branch= 0.0001 alpha= 0.0054 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0184 ins/del rates= 0.0000) pass 18: -3317.9527 (branch= 0.0001 alpha= 0.0049 pinv= 0.0046 eq freqs= 0.0000 rel rates= 0.0157 ins/del rates= 0.0000) pass 19: -3317.9307 (branch= 0.0000 alpha= 0.0044 pinv= 0.0041 eq freqs= 0.0000 rel rates= 0.0134 ins/del rates= 0.0000) pass 20: -3317.9115 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0114 ins/del rates= 0.0000) optimization up to ... pass 30: -3317.8163 (branch= 0.0001 alpha= 0.0212 pinv= 0.0196 eq freqs= 0.0001 rel rates= 0.0542 ins/del rates= 0.0000) optimization up to ... pass 40: -3317.7937 (branch= 0.0001 alpha= 0.0053 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: -3317.7874 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0007 ins/del rates= 0.0000) optimization up to ... pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) optimization up to ... pass 74: -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 = 3.064, AG = 10.260, AT = 2.655, CG = 0.001, CT = 21.528, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3328 0.2223 0.1566 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5750 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 0.2981 0.1597 0.8680 0.1597 2.7859 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: 3.064 10.26 2.655 0.001 21.53 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del 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: 1.418 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 1.264 lnL Optimizing branchlengths... improved 0.275 lnL 1200 -211.1652 0.010 1104 1400 -211.1318 0.010 1104 1600 -211.0218 0.010 1104 1800 -210.9997 0.010 1104 2000 -210.9460 0.010 1104 2200 -210.8946 0.010 1104 2400 -210.8864 0.010 1104 2600 -210.8436 0.010 1104 2800 -210.8249 0.010 1104 3000 -210.8188 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 -210.6946 0.010 1104 4200 -210.6740 0.010 1104 4400 -210.6493 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 4420, seed 2050063237, best lnL -210.649 gen current_lnL precision last_tree_imp 4420 -210.6493 0.010 1104 4500 -210.6477 0.010 1104 Reached termination condition! last topological improvement at gen 1104 Improvement over last 500 gen = 0.04686 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 2.570, AG = 4.891, AT = 0.202, CG = 4.460, CT = 7.252, 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 1.1902 with an invariant (invariable) site category, proportion estimated 0.1208 Substitution rate categories under this model: rate proportion 0.0000 0.1208 0.2293 0.2931 0.7543 0.2931 2.0165 0.2931 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 : -210.6477 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: 2.57 4.891 0.2023 4.46 7.252 1 0.233 0.337 0.211 0.220 1.190 0.121 Treelengths: TL rep 1: 2.247 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 0.319 lnL 1000 -167.2082 0.010 843 1200 -167.1487 0.010 843 1400 -167.0497 0.010 843 1600 -166.9651 0.010 843 1800 -166.8256 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 1800, seed 174826483, best lnL -166.826 gen current_lnL precision last_tree_imp 1800 -166.8256 0.010 843 1900 -166.7180 0.010 843 2000 -166.7014 0.010 843 2100 -166.6757 0.010 843 2200 -166.6037 0.010 843 2300 -166.5465 0.010 843 2400 -166.5437 0.010 843 2500 -166.5375 0.010 843 2600 -166.4761 0.010 843 2700 -166.4664 0.010 843 2800 -166.4631 0.010 843 2900 -166.4514 0.010 843 3000 -166.4054 0.010 843 3100 -166.3571 0.010 843 3200 -166.3555 0.010 843 3300 -166.3530 0.010 843 3400 -166.2985 0.010 843 3500 -166.2534 0.010 843 3600 -166.2506 0.010 843 3700 -166.1918 0.010 843 3800 -166.1403 0.010 843 3900 -166.1393 0.010 843 4000 -166.1354 0.010 843 4100 -166.1094 0.010 843 4200 -166.0869 0.010 843 4300 -166.0372 0.010 843 4400 -166.0244 0.010 843 4500 -165.9962 0.010 843 4600 -165.9672 0.010 843 4700 -165.9608 0.010 843 4800 -165.9475 0.010 843 4900 -165.8872 0.010 843 5000 -165.8859 0.010 843 5100 -165.8706 0.010 843 5200 -165.8689 0.010 843 5300 -165.8440 0.010 843 5400 -165.8337 0.010 843 5500 -165.7368 0.010 843 5600 -165.6916 0.010 843 5700 -165.6356 0.010 843 5800 -165.5811 0.010 843 5900 -165.5485 0.010 843 6000 -165.5435 0.010 843 6100 -165.5044 0.010 843 6200 -165.4997 0.010 843 6300 -165.4047 0.010 843 6400 -165.3822 0.010 843 6500 -165.3294 0.010 843 6600 -165.3045 0.010 843 6700 -165.2908 0.010 843 6800 -165.1802 0.010 6750 6900 -165.1514 0.010 6750 7000 -165.1486 0.010 6750 7100 -165.1452 0.010 6750 7200 -165.1326 0.010 6750 7300 -165.0450 0.010 6750 7400 -164.9712 0.010 6750 7500 -164.9350 0.010 6750 7600 -164.9063 0.010 7540 7700 -164.7982 0.010 7540 7800 -164.7723 0.010 7540 7900 -164.7470 0.010 7540 8000 -164.6934 0.010 7540 8100 -164.5821 0.010 7540 8200 -164.5487 0.010 7540 NOTE: ****Specified time limit (5 seconds) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 0.743, AG = 9.547, AT = 1.586, CG = 3.762, CT = 20.251, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1288 0.4051 0.2333 0.2328 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 2.9470 with an invariant (invariable) site category, proportion estimated 0.3098 Substitution rate categories under this model: rate proportion 0.0000 0.3098 0.3851 0.1725 0.7286 0.1725 1.0822 0.1725 1.8041 0.1725 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 2 branches were 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 : -164.4785 (TERMINATED PREMATURELY) 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: 0.7427 9.547 1.586 3.762 20.25 1 0.129 0.405 0.233 0.233 2.947 0.310 Treelengths: TL rep 1: 2.446 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 -213.6190 0.010 530 1400 -213.5800 0.010 530 1600 -213.5576 0.010 530 1800 -213.3951 0.010 530 2000 -213.3646 0.010 530 2200 -213.3318 0.010 530 2400 -213.2445 0.010 530 2600 -213.2282 0.010 530 2800 -213.2193 0.010 530 3000 -213.2001 0.010 530 3200 -213.1945 0.010 530 3400 -213.1682 0.010 530 3600 -213.1580 0.010 530 3800 -213.0250 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 -212.8760 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 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 6400, seed 300440726, best lnL -212.724 gen current_lnL precision last_tree_imp 6400 -212.7244 0.010 3769 6500 -212.7244 0.010 3769 Reached termination condition! last topological improvement at gen 3769 Improvement over last 500 gen = 0.00190 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 4.839, AG = 9.614, AT = 0.397, CG = 9.744, CT = 6.243, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2222 0.2881 0.1826 0.3071 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 : -212.7244 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 4.839 9.614 0.397 9.744 6.243 1 0.222 0.288 0.183 0.307 Treelengths: TL rep 1: 1.732 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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: -219.1444 gen current_lnL precision last_tree_imp 0 -219.1444 0.500 0 200 -217.4629 0.500 32 400 -216.6525 0.500 363 600 -216.1292 0.500 474 800 -215.4112 0.500 669 1000 -215.0097 0.500 936 1200 -214.3653 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 -210.9688 0.010 1502 2200 -210.8960 0.010 1502 2400 -210.8906 0.010 1502 2600 -210.8172 0.010 1502 2800 -210.7847 0.010 1502 3000 -210.7510 0.010 2883 3200 -210.7243 0.010 2883 3400 -210.7006 0.010 2883 3600 -210.6993 0.010 2883 3800 -210.6778 0.010 2883 4000 -210.6775 0.010 2883 4200 -210.6505 0.010 2883 4400 -210.6306 0.010 2883 4600 -210.6208 0.010 2883 4800 -210.5769 0.010 2883 5000 -210.5646 0.010 2883 5200 -210.5368 0.010 2883 5400 -210.5093 0.010 2883 5600 -210.5005 0.010 2883 5800 -210.3871 0.010 2883 6000 -210.3538 0.010 2883 6200 -210.3498 0.010 2883 6400 -210.3399 0.010 2883 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 6420, seed 1385520058, best lnL -210.339 gen current_lnL precision last_tree_imp 6420 -210.3390 0.010 2883 6500 -210.3384 0.010 2883 Reached termination condition! last topological improvement at gen 2883 Improvement over last 500 gen = 0.01539 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 2.043, AG = 4.107, AT = 0.207, CG = 3.870, CT = 7.237, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2409 0.3408 0.2110 0.2074 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 1.4302 with an invariant (invariable) site category, proportion estimated 0.1961 Substitution rate categories under this model: rate proportion 0.0000 0.1961 0.2143 0.2010 0.5765 0.2010 1.0460 0.2010 2.1631 0.2010 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with a positive constraint, it is possible for a constrained branch itself to be collapsed. If you care, be careful to check whether this has happened or turn off branch collapsing. Saving site likelihoods to file ch.n.const.sitelikes.log ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -210.3384 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: 2.043 4.107 0.2071 3.87 7.237 1 0.241 0.341 0.211 0.207 1.430 0.196 Treelengths: TL rep 1: 2.440 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 222.682 (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 -13375.8794 0.500 0 200 -13373.8436 0.500 0 300 -13372.9678 0.500 0 400 -13371.8986 0.500 0 500 -13371.5865 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 -13371.0755 0.402 0 800 -13370.9489 0.402 0 900 -13370.7802 0.402 0 1000 -13370.6791 0.402 0 Optimization precision reduced Optimizing parameters... improved 0.037 lnL Optimizing branchlengths... improved 0.000 lnL NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 1000, seed 355230265, best lnL -13370.642 gen current_lnL precision last_tree_imp 1000 -13370.6422 0.304 0 1100 -13370.5869 0.304 0 1200 -13370.5241 0.304 0 1300 -13370.5104 0.304 0 1400 -13370.5063 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 = 1.208, CG = 1.208, CT = 4.135, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3079 0.1814 0.3083 0.2024 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 0.2768 0.2217 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 : -13370.5063 (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 1.208 1.208 4.135 1 0.308 0.181 0.308 0.202 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 0.155 0.346 0.277 0.222 4.110 0.049 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 1.763 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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= 4.30) pass 2:+ 9.055 (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:+ 0.303 (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: -467.8152 gen current_lnL precision last_tree_imp 0 -467.8152 0.010 0 100 -467.7854 0.010 76 200 -467.7768 0.010 76 300 -467.7654 0.010 76 400 -467.7615 0.010 76 500 -467.7562 0.010 76 600 -467.7505 0.010 76 700 -467.7495 0.010 76 800 -467.7483 0.010 76 900 -467.7471 0.010 76 1000 -467.7427 0.010 76 1100 -467.7372 0.010 76 1200 -467.7330 0.010 76 1300 -467.7317 0.010 76 1400 -467.7307 0.010 76 1500 -467.7301 0.010 76 1600 -467.7294 0.010 76 1700 -467.7252 0.010 76 1800 -467.7239 0.010 76 1900 -467.7239 0.010 76 2000 -467.7234 0.010 76 2100 -467.7228 0.010 76 2200 -467.7218 0.010 76 2300 -467.7216 0.010 76 2400 -467.7209 0.010 76 2500 -467.7205 0.010 76 2600 -467.7205 0.010 76 2700 -467.7197 0.010 76 2800 -467.7190 0.010 76 2900 -467.7186 0.010 76 3000 -467.7184 0.010 76 3100 -467.7181 0.010 76 3200 -467.7180 0.010 76 3300 -467.7179 0.010 76 3400 -467.7178 0.010 76 Reached termination condition! last topological improvement at gen 76 Improvement over last 500 gen = 0.00072 Current score = -467.7178 Performing final optimizations... pass 1 : -467.7126 (branch= 0.0000 subset rates= 0.0052) pass 2 : -467.6927 (branch= 0.0182 subset rates= 0.0018) pass 3 : -467.6906 (branch= 0.0018 subset rates= 0.0003) pass 4 : -467.6866 (branch= 0.0040 subset rates= 0.0000) pass 5 : -467.6836 (branch= 0.0018 subset rates= 0.0011) pass 6 : -467.6820 (branch= 0.0017 subset rates= 0.0000) pass 7 : -467.6809 (branch= 0.0010 subset rates= 0.0000) pass 8 : -467.6803 (branch= 0.0006 subset rates= 0.0000) pass 9 : -467.6800 (branch= 0.0003 subset rates= 0.0000) pass 10: -467.6799 (branch= 0.0001 subset rates= 0.0000) pass 11: -467.6798 (branch= 0.0001 subset rates= 0.0000) pass 12: -467.6798 (branch= 0.0000 subset rates= 0.0000) pass 13: -467.6798 (branch= 0.0000 subset rates= 0.0000) pass 14: -467.6798 (branch= 0.0000 subset rates= 0.0000) pass 15: -467.6797 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6797 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 2.15 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=864977241 Initial ln Likelihood: -614.0831 optimizing: starting branch lengths, subset rates... pass 1:+ 127.392 (branch= 121.24 scale= 1.98 subset rates= 4.16) pass 2:+ 15.987 (branch= 15.02 scale= 0.02 subset rates= 0.96) pass 3:+ 2.694 (branch= 2.46 scale= 0.04 subset rates= 0.20) pass 4:+ 0.135 (branch= 0.13 scale= 0.00 subset rates= 0.00) pass 5:+ 0.039 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -467.8359 gen current_lnL precision last_tree_imp 0 -467.8359 0.010 0 100 -467.8013 0.010 0 200 -467.7836 0.010 0 300 -467.7721 0.010 0 400 -467.7470 0.010 0 500 -467.7426 0.010 0 600 -467.7398 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 634, seed 34875524, best lnL -467.739 gen current_lnL precision last_tree_imp 634 -467.7393 0.010 0 700 -467.7362 0.010 0 800 -467.7332 0.010 0 900 -467.7319 0.010 0 1000 -467.7290 0.010 0 1100 -467.7275 0.010 0 1200 -467.7204 0.010 0 1300 -467.7192 0.010 0 1400 -467.7176 0.010 0 1500 -467.7150 0.010 0 1600 -467.7149 0.010 0 1700 -467.7133 0.010 0 1800 -467.7124 0.010 0 1900 -467.7123 0.010 0 2000 -467.7121 0.010 0 2100 -467.7105 0.010 0 2200 -467.7090 0.010 0 2300 -467.7089 0.010 0 2400 -467.7088 0.010 0 2500 -467.7081 0.010 0 2600 -467.7078 0.010 0 2700 -467.7077 0.010 0 2800 -467.7071 0.010 0 2900 -467.7069 0.010 0 3000 -467.7067 0.010 0 3100 -467.7060 0.010 0 3200 -467.7054 0.010 0 3300 -467.7038 0.010 0 3400 -467.7033 0.010 0 3500 -467.7031 0.010 0 3600 -467.7029 0.010 0 3700 -467.7027 0.010 0 3800 -467.7026 0.010 0 3900 -467.7019 0.010 0 4000 -467.7013 0.010 0 4100 -467.7011 0.010 0 4200 -467.7011 0.010 0 4300 -467.7006 0.010 0 4400 -467.7005 0.010 0 4500 -467.7004 0.010 0 Reached termination condition! last topological improvement at gen 0 Improvement over last 500 gen = 0.00086 Current score = -467.7004 Performing final optimizations... pass 1 : -467.7004 (branch= 0.0000 subset rates= 0.0000) pass 2 : -467.6882 (branch= 0.0122 subset rates= 0.0000) pass 3 : -467.6834 (branch= 0.0048 subset rates= 0.0000) pass 4 : -467.6825 (branch= 0.0009 subset rates= 0.0000) pass 5 : -467.6814 (branch= 0.0011 subset rates= 0.0000) pass 6 : -467.6800 (branch= 0.0014 subset rates= 0.0000) pass 7 : -467.6790 (branch= 0.0010 subset rates= 0.0000) pass 8 : -467.6787 (branch= 0.0002 subset rates= 0.0000) pass 9 : -467.6785 (branch= 0.0002 subset rates= 0.0000) pass 10: -467.6784 (branch= 0.0002 subset rates= 0.0000) pass 11: -467.6783 (branch= 0.0000 subset rates= 0.0000) pass 12: -467.6783 (branch= 0.0000 subset rates= 0.0000) pass 13: -467.6783 (branch= 0.0000 subset rates= 0.0000) pass 14: -467.6783 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6783 Time used so far = 0 hours, 0 minutes and 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 2.18 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=1668858692 Initial ln Likelihood: -630.9240 optimizing: starting branch lengths, subset rates... pass 1:+ 146.354 (branch= 140.50 scale= 1.37 subset rates= 4.49) pass 2:+ 13.171 (branch= 11.99 scale= 0.01 subset rates= 1.17) pass 3:+ 3.302 (branch= 3.17 scale= 0.00 subset rates= 0.13) pass 4:+ 0.252 (branch= 0.25 scale= 0.00 subset rates= 0.00) pass 5:+ 0.024 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -467.8203 gen current_lnL precision last_tree_imp 0 -467.8203 0.010 0 100 -467.7944 0.010 0 200 -467.7835 0.010 0 300 -467.7680 0.010 0 400 -467.7552 0.010 0 500 -467.7483 0.010 0 600 -467.7437 0.010 0 700 -467.7409 0.010 0 800 -467.7404 0.010 0 900 -467.7397 0.010 0 1000 -467.7346 0.010 0 1100 -467.7325 0.010 0 1200 -467.7292 0.010 0 1300 -467.7278 0.010 0 1400 -467.7254 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... Current score = -467.7254 Performing final optimizations... pass 1 : -467.7254 (branch= 0.0000 subset rates= 0.0000) pass 2 : -467.7070 (branch= 0.0183 subset rates= 0.0000) pass 3 : -467.6961 (branch= 0.0109 subset rates= 0.0000) pass 4 : -467.6901 (branch= 0.0060 subset rates= 0.0000) pass 5 : -467.6843 (branch= 0.0058 subset rates= 0.0000) pass 6 : -467.6824 (branch= 0.0019 subset rates= 0.0000) pass 7 : -467.6809 (branch= 0.0014 subset rates= 0.0000) pass 8 : -467.6803 (branch= 0.0006 subset rates= 0.0000) pass 9 : -467.6799 (branch= 0.0004 subset rates= 0.0000) pass 10: -467.6797 (branch= 0.0002 subset rates= 0.0000) pass 11: -467.6796 (branch= 0.0001 subset rates= 0.0000) pass 12: -467.6792 (branch= 0.0000 subset rates= 0.0003) pass 13: -467.6792 (branch= 0.0000 subset rates= 0.0000) pass 14: -467.6789 (branch= 0.0000 subset rates= 0.0003) pass 15: -467.6788 (branch= 0.0001 subset rates= 0.0000) pass 16: -467.6788 (branch= 0.0000 subset rates= 0.0000) pass 17: -467.6788 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6788 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: 0.78 1.49 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 : -467.6797 Replicate 2 : -467.6783 (best) (same topology as 1) Replicate 3 : -467.6788 (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: 3.838 0.789 1.477 2.150 rep 2: 3.841 0.787 1.478 2.178 rep 3: 3.845 0.784 1.486 2.184 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 12.450 (branch= 8.46 scale= 0.00 subset rates= 3.99) pass 3:+ 3.552 (branch= 2.32 scale= 0.03 subset rates= 1.21) pass 4:+ 0.758 (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: -477.9401 gen current_lnL precision last_tree_imp 0 -477.9401 0.010 0 100 -477.8632 0.010 76 200 -477.8299 0.010 152 300 -477.7567 0.010 215 400 -477.5628 0.010 373 500 -477.5393 0.010 373 600 -477.5302 0.010 373 700 -477.5293 0.010 373 800 -477.5220 0.010 373 900 -477.5163 0.010 373 1000 -477.5148 0.010 373 1100 -477.5133 0.010 373 1200 -477.5083 0.010 373 1300 -477.5075 0.010 373 1400 -477.4995 0.010 373 1500 -477.4940 0.010 373 1600 -477.4867 0.010 373 1700 -477.4839 0.010 373 1800 -477.4824 0.010 373 1900 -477.4794 0.010 373 2000 -477.4782 0.010 373 2100 -477.4777 0.010 373 2200 -477.4766 0.010 373 2300 -477.4758 0.010 373 2400 -477.4754 0.010 373 2500 -477.4753 0.010 373 2600 -477.4749 0.010 373 2700 -477.4738 0.010 373 2800 -477.4737 0.010 373 2900 -477.4725 0.010 373 3000 -477.4725 0.010 373 3100 -477.4725 0.010 373 3200 -477.4718 0.010 373 3300 -477.4718 0.010 373 3400 -477.4717 0.010 373 Reached termination condition! last topological improvement at gen 373 Improvement over last 500 gen = 0.00083 Current score = -477.4717 Performing final optimizations... pass 1 : -477.4695 (branch= 0.0000 subset rates= 0.0022) pass 2 : -477.4423 (branch= 0.0272 subset rates= 0.0000) pass 3 : -477.4395 (branch= 0.0028 subset rates= 0.0000) pass 4 : -477.4388 (branch= 0.0007 subset rates= 0.0000) pass 5 : -477.4372 (branch= 0.0016 subset rates= 0.0000) pass 6 : -477.4355 (branch= 0.0016 subset rates= 0.0000) pass 7 : -477.4339 (branch= 0.0009 subset rates= 0.0007) pass 8 : -477.4330 (branch= 0.0010 subset rates= 0.0000) pass 9 : -477.4322 (branch= 0.0006 subset rates= 0.0001) pass 10: -477.4320 (branch= 0.0003 subset rates= 0.0000) pass 11: -477.4319 (branch= 0.0001 subset rates= 0.0000) pass 12: -477.4318 (branch= 0.0001 subset rates= 0.0000) pass 13: -477.4318 (branch= 0.0000 subset rates= 0.0000) pass 14: -477.4318 (branch= 0.0000 subset rates= 0.0000) pass 15: -477.4318 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.4318 Time used so far = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate 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 2.72 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=425957087 Initial ln Likelihood: -636.0761 optimizing: starting branch lengths, subset rates... pass 1:+ 138.672 (branch= 128.04 scale= 0.72 subset rates= 9.91) pass 2:+ 13.747 (branch= 9.73 scale= 0.00 subset rates= 4.02) pass 3:+ 3.414 (branch= 2.10 scale= 0.00 subset rates= 1.31) pass 4:+ 1.365 (branch= 1.09 scale= 0.00 subset rates= 0.27) pass 5:+ 0.834 (branch= 0.80 scale= 0.01 subset rates= 0.02) pass 6:+ 0.191 (branch= 0.19 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -477.8544 gen current_lnL precision last_tree_imp 0 -477.8544 0.010 0 100 -477.7502 0.010 36 200 -477.7249 0.010 149 300 -477.4594 0.010 203 400 -477.3874 0.010 366 500 -477.3748 0.010 366 600 -477.3633 0.010 366 700 -477.3569 0.010 366 800 -477.3520 0.010 366 900 -477.3483 0.010 366 1000 -477.3445 0.010 366 1100 -477.3365 0.010 366 1200 -477.3113 0.010 1197 1300 -477.2903 0.010 1197 1400 -477.2877 0.010 1197 1500 -477.2841 0.010 1197 1600 -477.2783 0.010 1197 1700 -477.2762 0.010 1197 1800 -477.2729 0.010 1197 1900 -477.2723 0.010 1197 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 1949, seed 894358758, best lnL -477.272 gen current_lnL precision last_tree_imp 1949 -477.2722 0.010 1197 2000 -477.2721 0.010 1197 2100 -477.2715 0.010 1197 2200 -477.2703 0.010 1197 2300 -477.2696 0.010 1197 2400 -477.2695 0.010 1197 2500 -477.2686 0.010 1197 2600 -477.2680 0.010 1197 2700 -477.2670 0.010 1197 2800 -477.2662 0.010 1197 2900 -477.2654 0.010 1197 3000 -477.2649 0.010 1197 3100 -477.2645 0.010 1197 3200 -477.2631 0.010 1197 3300 -477.2630 0.010 1197 3400 -477.2630 0.010 1197 3500 -477.2625 0.010 1197 3600 -477.2619 0.010 1197 3700 -477.2618 0.010 1197 3800 -477.2615 0.010 1197 3900 -477.2611 0.010 1197 4000 -477.2611 0.010 1197 4100 -477.2609 0.010 1197 4200 -477.2609 0.010 1197 Reached termination condition! last topological improvement at gen 1197 Improvement over last 500 gen = 0.00088 Current score = -477.2609 Performing final optimizations... pass 1 : -477.2399 (branch= 0.0055 subset rates= 0.0155) pass 2 : -477.2268 (branch= 0.0069 subset rates= 0.0062) pass 3 : -477.2118 (branch= 0.0143 subset rates= 0.0007) pass 4 : -477.2095 (branch= 0.0022 subset rates= 0.0000) pass 5 : -477.2078 (branch= 0.0018 subset rates= 0.0000) pass 6 : -477.2070 (branch= 0.0008 subset rates= 0.0000) pass 7 : -477.2060 (branch= 0.0010 subset rates= 0.0000) pass 8 : -477.2054 (branch= 0.0006 subset rates= 0.0000) pass 9 : -477.2052 (branch= 0.0002 subset rates= 0.0000) pass 10: -477.2051 (branch= 0.0001 subset rates= 0.0000) pass 11: -477.2051 (branch= 0.0000 subset rates= 0.0000) pass 12: -477.2050 (branch= 0.0000 subset rates= 0.0000) pass 13: -477.2050 (branch= 0.0000 subset rates= 0.0000) pass 14: -477.2050 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.2050 Time used so far = 0 hours, 0 minutes and 9 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 1.94 2.64 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 (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=792142821 Initial ln Likelihood: -607.1513 optimizing: starting branch lengths, subset rates... pass 1:+ 108.828 (branch= 98.09 scale= 0.82 subset rates= 9.92) pass 2:+ 14.908 (branch= 10.91 scale= 0.01 subset rates= 3.98) pass 3:+ 3.027 (branch= 1.70 scale= 0.00 subset rates= 1.32) pass 4:+ 1.411 (branch= 1.08 scale= 0.00 subset rates= 0.33) pass 5:+ 0.976 (branch= 0.95 scale= 0.00 subset rates= 0.03) pass 6:+ 0.207 (branch= 0.19 scale= 0.01 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -477.7945 gen current_lnL precision last_tree_imp 0 -477.7945 0.010 0 100 -477.7794 0.010 0 200 -477.7563 0.010 0 300 -477.7529 0.010 0 400 -477.7432 0.010 0 500 -477.7418 0.010 0 600 -477.3413 0.010 537 700 -477.3275 0.010 537 800 -477.3202 0.010 537 900 -477.3116 0.010 537 1000 -477.3054 0.010 537 1100 -477.3026 0.010 537 1200 -477.3003 0.010 537 1300 -477.2955 0.010 537 1400 -477.2902 0.010 537 1500 -477.2883 0.010 537 1600 -477.2865 0.010 537 1700 -477.2852 0.010 537 1800 -477.2835 0.010 537 1900 -477.2826 0.010 537 2000 -477.2805 0.010 537 NOTE: ****Specified time limit (5 seconds) reached... Current score = -477.2805 Performing final optimizations... pass 1 : -477.2425 (branch= 0.0000 subset rates= 0.0379) pass 2 : -477.2286 (branch= 0.0103 subset rates= 0.0036) pass 3 : -477.2191 (branch= 0.0092 subset rates= 0.0004) pass 4 : -477.2155 (branch= 0.0034 subset rates= 0.0002) pass 5 : -477.2088 (branch= 0.0066 subset rates= 0.0000) pass 6 : -477.2059 (branch= 0.0030 subset rates= 0.0000) pass 7 : -477.2056 (branch= 0.0003 subset rates= 0.0000) pass 8 : -477.2054 (branch= 0.0002 subset rates= 0.0000) pass 9 : -477.2046 (branch= 0.0003 subset rates= 0.0005) pass 10: -477.2043 (branch= 0.0002 subset rates= 0.0000) pass 11: -477.2043 (branch= 0.0000 subset rates= 0.0000) pass 12: -477.2043 (branch= 0.0000 subset rates= 0.0000) pass 13: -477.2043 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.2043 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 1.94 2.63 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 : -477.4318 Replicate 2 : -477.2050 Replicate 3 : -477.2043 (best) (same topology as 2) (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: 4.927 0.632 1.917 2.725 rep 2: 4.703 0.632 1.943 2.641 rep 3: 4.696 0.635 1.935 2.629 Saving final tree from best search rep (#3) to ch.p.mkO.ssr.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkv.ssr.conf Running checkpoint test ./check/p.mkv.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 0.368 (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 -430.2565 0.010 92 200 -427.7102 0.010 179 300 -426.9763 0.010 293 400 -425.6930 0.010 365 500 -425.6677 0.010 365 600 -425.6512 0.010 365 700 -425.6318 0.010 365 800 -425.6212 0.010 365 900 -425.6126 0.010 365 1000 -425.6095 0.010 365 1100 -425.6090 0.010 365 1200 -425.6083 0.010 365 1300 -425.6068 0.010 365 1400 -425.6058 0.010 365 1500 -425.6042 0.010 365 1600 -425.6022 0.010 365 1700 -425.5976 0.010 365 1800 -425.5972 0.010 365 1900 -425.5954 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 1933, seed 413780019, best lnL -425.595 gen current_lnL precision last_tree_imp 1933 -425.5950 0.010 365 2000 -425.5950 0.010 365 2100 -425.5942 0.010 365 2200 -425.5913 0.010 365 2300 -425.5899 0.010 365 2400 -425.5893 0.010 365 2500 -425.5891 0.010 365 2600 -425.5890 0.010 365 2700 -425.5888 0.010 365 2800 -425.5883 0.010 365 2900 -425.5869 0.010 365 3000 -425.5868 0.010 365 3100 -425.5859 0.010 365 3200 -425.5858 0.010 365 3300 -425.5850 0.010 365 3400 -425.5843 0.010 365 3500 -425.5843 0.010 365 3600 -425.5841 0.010 365 3700 -425.5839 0.010 365 3800 -425.5839 0.010 365 3900 -425.5839 0.010 365 Reached termination condition! last topological improvement at gen 365 Improvement over last 500 gen = 0.00044 Current score = -425.5839 Performing final optimizations... pass 1 : -425.5730 (branch= 0.0000 subset rates= 0.0109) pass 2 : -425.5586 (branch= 0.0144 subset rates= 0.0000) pass 3 : -425.5516 (branch= 0.0070 subset rates= 0.0000) 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 : -425.5488 (branch= 0.0005 subset rates= 0.0000) pass 9 : -425.5487 (branch= 0.0001 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 9 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:+ 1.686 (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: -439.2276 gen current_lnL precision last_tree_imp 0 -439.2276 0.010 0 100 -428.8676 0.010 98 200 -428.0499 0.010 164 300 -427.6003 0.010 249 400 -427.5649 0.010 249 500 -427.4911 0.010 499 600 -427.3864 0.010 511 700 -425.7188 0.010 668 800 -425.6951 0.010 722 900 -425.6795 0.010 722 1000 -425.6689 0.010 722 1100 -425.6640 0.010 722 NOTE: ****Specified time limit (5 seconds) reached... Current score = -425.6509 Performing final optimizations... pass 1 : -425.6081 (branch= 0.0136 subset rates= 0.0292) pass 2 : -425.5757 (branch= 0.0324 subset rates= 0.0000) pass 3 : -425.5588 (branch= 0.0169 subset rates= 0.0000) pass 4 : -425.5546 (branch= 0.0041 subset rates= 0.0000) pass 5 : -425.5523 (branch= 0.0024 subset rates= 0.0000) pass 6 : -425.5501 (branch= 0.0022 subset rates= 0.0000) pass 7 : -425.5495 (branch= 0.0006 subset rates= 0.0000) pass 8 : -425.5491 (branch= 0.0003 subset rates= 0.0000) pass 9 : -425.5490 (branch= 0.0001 subset rates= 0.0000) pass 10: -425.5490 (branch= 0.0001 subset rates= 0.0000) pass 11: -425.5489 (branch= 0.0001 subset rates= 0.0000) pass 12: -425.5489 (branch= 0.0000 subset rates= 0.0000) pass 13: -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 1.52 1.13 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 10 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 (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: 3.038 0.868 1.530 1.121 rep 2: 3.038 0.869 1.525 1.128 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 3.846 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.161 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.158 (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: -474.8622 gen current_lnL precision last_tree_imp 0 -474.8622 0.010 0 100 -474.7511 0.010 68 200 -474.7181 0.010 68 300 -474.6977 0.010 68 400 -474.6394 0.010 329 500 -474.1564 0.010 455 600 -474.1360 0.010 560 700 -474.0348 0.010 653 800 -474.0229 0.010 653 900 -474.0144 0.010 653 1000 -474.0143 0.010 653 1100 -474.0135 0.010 653 1200 -474.0077 0.010 653 1300 -474.0014 0.010 653 1400 -473.9965 0.010 653 1500 -473.9958 0.010 653 1600 -473.9945 0.010 653 1700 -473.9894 0.010 653 1800 -473.9877 0.010 653 1900 -473.9867 0.010 653 2000 -473.9852 0.010 653 2100 -473.9830 0.010 653 2200 -473.9824 0.010 653 2300 -473.9816 0.010 653 2400 -473.9807 0.010 653 2500 -473.9801 0.010 653 2600 -473.9795 0.010 653 2700 -473.9790 0.010 653 2800 -473.9779 0.010 653 2900 -473.9776 0.010 653 3000 -473.9775 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 3050, seed 1821801759, best lnL -473.977 gen current_lnL precision last_tree_imp 3050 -473.9772 0.010 653 3100 -473.9771 0.010 653 3200 -473.9769 0.010 653 3300 -473.9766 0.010 653 3400 -473.9762 0.010 653 3500 -473.9761 0.010 653 3600 -473.9761 0.010 653 3700 -473.9759 0.010 653 Reached termination condition! last topological improvement at gen 653 Improvement over last 500 gen = 0.00096 Current score = -473.9759 Performing final optimizations... pass 1 : -473.9758 (branch= 0.0001 subset rates= 0.0000) pass 2 : -473.9558 (branch= 0.0183 subset rates= 0.0016) pass 3 : -473.9558 (branch= 0.0000 subset rates= 0.0000) pass 4 : -473.9550 (branch= 0.0009 subset rates= 0.0000) pass 5 : -473.9525 (branch= 0.0007 subset rates= 0.0018) pass 6 : -473.9521 (branch= 0.0004 subset rates= 0.0000) pass 7 : -473.9516 (branch= 0.0004 subset rates= 0.0000) pass 8 : -473.9512 (branch= 0.0004 subset rates= 0.0000) pass 9 : -473.9510 (branch= 0.0002 subset rates= 0.0000) pass 10: -473.9509 (branch= 0.0001 subset rates= 0.0000) pass 11: -473.9508 (branch= 0.0001 subset rates= 0.0000) pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) pass 13: -473.9508 (branch= 0.0000 subset rates= 0.0000) pass 14: -473.9508 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -473.9508 Time used so far = 0 hours, 0 minutes and 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 2.81 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=74284197 Initial ln Likelihood: -646.1143 optimizing: starting branch lengths, subset rates... pass 1:+ 146.023 (branch= 135.13 scale= 0.95 subset rates= 9.94) pass 2:+ 17.326 (branch= 12.98 scale= 0.01 subset rates= 4.33) pass 3:+ 4.642 (branch= 3.12 scale= 0.00 subset rates= 1.52) pass 4:+ 2.490 (branch= 1.89 scale= 0.00 subset rates= 0.60) pass 5:+ 0.684 (branch= 0.61 scale= 0.02 subset rates= 0.05) pass 6:+ 0.130 (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: -474.8185 gen current_lnL precision last_tree_imp 0 -474.8185 0.010 0 100 -474.7244 0.010 55 200 -474.7128 0.010 55 300 -474.7037 0.010 55 400 -474.6654 0.010 339 500 -474.5695 0.010 496 600 -474.0703 0.010 585 700 -474.0481 0.010 585 800 -474.0412 0.010 585 900 -474.0316 0.010 585 1000 -474.0282 0.010 585 1100 -474.0225 0.010 585 1200 -474.0142 0.010 585 1300 -474.0116 0.010 585 1400 -474.0080 0.010 585 1500 -474.0041 0.010 585 1600 -474.0016 0.010 585 1700 -474.0010 0.010 585 1800 -473.9994 0.010 585 1900 -473.9983 0.010 585 NOTE: ****Specified time limit (5 seconds) reached... Current score = -473.9971 Performing final optimizations... pass 1 : -473.9874 (branch= 0.0000 subset rates= 0.0097) pass 2 : -473.9638 (branch= 0.0207 subset rates= 0.0030) pass 3 : -473.9574 (branch= 0.0063 subset rates= 0.0000) pass 4 : -473.9566 (branch= 0.0009 subset rates= 0.0000) pass 5 : -473.9545 (branch= 0.0021 subset rates= 0.0000) pass 6 : -473.9532 (branch= 0.0013 subset rates= 0.0000) pass 7 : -473.9520 (branch= 0.0012 subset rates= 0.0000) pass 8 : -473.9515 (branch= 0.0005 subset rates= 0.0000) pass 9 : -473.9513 (branch= 0.0002 subset rates= 0.0000) pass 10: -473.9512 (branch= 0.0001 subset rates= 0.0000) pass 11: -473.9512 (branch= 0.0001 subset rates= 0.0000) pass 12: -473.9511 (branch= 0.0000 subset rates= 0.0000) pass 13: -473.9511 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -473.9511 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 2.06 2.81 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 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 : -473.9508 (best) Replicate 2 : -473.9511 (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: 4.351 0.587 2.066 2.813 rep 2: 4.347 0.590 2.059 2.806 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 -j40 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' /usr/bin/mkdir -p '/build/reproducible-path/garli-2.1/debian/tmp/usr/bin' make[3]: Nothing to be done for 'install-data-am'. /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-mpi' in '../garli-mpi_2.1-9_amd64.deb'. dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-9_all.deb'. dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-9_amd64.deb'. dpkg-deb: building package 'garli' in '../garli_2.1-9_amd64.deb'. dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-9_amd64.deb'. dpkg-genbuildinfo --build=binary -O../garli_2.1-9_amd64.buildinfo dpkg-genchanges --build=binary -O../garli_2.1-9_amd64.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/4082616 and its subdirectories I: Current time: Wed Sep 17 19:43:56 -12 2025 I: pbuilder-time-stamp: 1758181436 Thu Sep 18 07:43:57 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Thu Sep 18 07:43:57 UTC 2025 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Thu Sep 18 07:43:57 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Thu Sep 18 07:43:57 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-5EilBD' ==================================================================================== Wed Oct 21 14:06:57 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos5-amd64, called using "2 garli forky /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w 2.1-9" as arguments. Wed Oct 21 14:06:57 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-7bqFSjWH" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Oct 21 14:06:57 UTC 2026 I: Downloading source for forky/garli=2.1-9 Reading package lists... NOTICE: 'garli' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/garli.git Please use: git clone https://salsa.debian.org/med-team/garli.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1256 kB of source archives. Get:1 http://deb.debian.org/debian forky/main garli 2.1-9 (dsc) [2186 B] Get:2 http://deb.debian.org/debian forky/main garli 2.1-9 (tar) [1249 kB] Get:3 http://deb.debian.org/debian forky/main garli 2.1-9 (diff) [5072 B] Fetched 1256 kB in 0s (11.3 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'garli' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/garli.git Please use: git clone https://salsa.debian.org/med-team/garli.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1256 kB of source archives. Get:1 http://deb.debian.org/debian forky/main garli 2.1-9 (dsc) [2186 B] Get:2 http://deb.debian.org/debian forky/main garli 2.1-9 (tar) [1249 kB] Get:3 http://deb.debian.org/debian forky/main garli 2.1-9 (diff) [5072 B] Fetched 1256 kB in 0s (11.3 MB/s) Download complete and in download only mode ============================================================================= Re-Building garli in forky on amd64 on ionos5-amd64 now. Date: Wed Oct 21 14:06:58 UTC 2026 Date UTC: Wed Oct 21 14:06:58 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/pbuilderrc_iBiM + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' garli = debian-installer -o garli = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' garli = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/pbuilderrc_iBiM --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/b2 --logfile b2/build.log garli_2.1-9.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Oct 22 04:06:58 +14 2026 I: pbuilder-time-stamp: 1792591618 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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: 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 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/1872835/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Oct 21 14:07 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1872835/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1872835/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.3.3(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=forky EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=3d335d2935234f7e87ed5379c3129348 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1872835 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/pbuilderrc_iBiM --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/b2 --logfile b2/build.log garli_2.1-9.dsc' SUDO_GID=110 SUDO_HOME=/var/lib/jenkins SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1872835/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: amd64 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 ... 19917 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-15{a} gfortran-15-x86-64-linux-gnu{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libcbor0.10{a} libcom-err2{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libfabric1{a} libffi8{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-15-dev{a} libgfortran5{a} libgssapi-krb5-2{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{a} libibverbs-dev{a} libibverbs1{a} libjs-jquery{a} libjs-jquery-ui{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libllvm17t64{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libncl-dev{a} libncl2{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi40{a} libpciaccess0{a} libpipeline1{a} libpsm2-2{a} librdmacm1t64{a} libreadline8t64{a} libtool{a} libuchardet0{a} libucx0{a} libunistring5{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2-16{a} libxnvctrl0{a} libz3-4{a} libze1{a} m4{a} man-db{a} mpi-default-dev{a} ncl-tools{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} po-debconf{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libmail-sendmail-perl lynx wget xauth 0 packages upgraded, 103 newly installed, 0 to remove and 0 not upgraded. Need to get 164 MB of archives. After unpacking 694 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 libfido2-1 amd64 1.16.0-2 [78.8 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 19 http://deb.debian.org/debian forky/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 openssh-client amd64 1:10.0p1-8 [986 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 bc amd64 1.07.1-4 [103 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 35 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 36 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 38 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 40 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 libgfortran-15-dev amd64 15.2.0-4 [886 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-4 [78.8 MB] Get: 46 http://deb.debian.org/debian forky/main amd64 gfortran-15 amd64 15.2.0-4 [17.9 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 libnl-3-200 amd64 3.11.0-2 [67.1 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 libnl-route-3-200 amd64 3.11.0-2 [211 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 libibverbs1 amd64 56.1-1 [62.4 kB] Get: 50 http://deb.debian.org/debian forky/main amd64 ibverbs-providers amd64 56.1-1 [357 kB] Get: 51 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 libllvm17t64 amd64 1:17.0.6-22+b3 [23.6 MB] Get: 54 http://deb.debian.org/debian forky/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get: 55 http://deb.debian.org/debian forky/main amd64 libdrm-common all 2.4.125-2 [8576 B] Get: 56 http://deb.debian.org/debian forky/main amd64 libdrm2 amd64 2.4.125-2 [39.1 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 libdrm-amdgpu1 amd64 2.4.125-2 [23.2 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 libnuma1 amd64 2.0.19-1 [22.2 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 libhsakmt1 amd64 6.2.4+ds-1 [61.1 kB] Get: 60 http://deb.debian.org/debian forky/main amd64 libhsa-runtime64-1 amd64 6.1.2-3 [535 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 libamdhip64-5 amd64 5.7.1-6 [8924 kB] Get: 62 http://deb.debian.org/debian forky/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 63 http://deb.debian.org/debian forky/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get: 64 http://deb.debian.org/debian forky/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b1 [108 kB] Get: 65 http://deb.debian.org/debian forky/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get: 66 http://deb.debian.org/debian forky/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b1 [61.1 kB] Get: 67 http://deb.debian.org/debian forky/main amd64 libevent-dev amd64 2.1.12-stable-10+b1 [305 kB] Get: 68 http://deb.debian.org/debian forky/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get: 69 http://deb.debian.org/debian forky/main amd64 librdmacm1t64 amd64 56.1-1 [70.4 kB] Get: 70 http://deb.debian.org/debian forky/main amd64 libfabric1 amd64 2.1.0-1.1 [706 kB] Get: 71 http://deb.debian.org/debian forky/main amd64 libhwloc15 amd64 2.12.2-1 [164 kB] Get: 72 http://deb.debian.org/debian forky/main amd64 libnuma-dev amd64 2.0.19-1 [36.5 kB] Get: 73 http://deb.debian.org/debian forky/main amd64 libltdl7 amd64 2.5.4-5 [416 kB] Get: 74 http://deb.debian.org/debian forky/main amd64 libltdl-dev amd64 2.5.4-5 [168 kB] Get: 75 http://deb.debian.org/debian forky/main amd64 libhwloc-dev amd64 2.12.2-1 [257 kB] Get: 76 http://deb.debian.org/debian forky/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 77 http://deb.debian.org/debian forky/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 78 http://deb.debian.org/debian forky/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 79 http://deb.debian.org/debian forky/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 80 http://deb.debian.org/debian forky/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 81 http://deb.debian.org/debian forky/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 82 http://deb.debian.org/debian forky/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 83 http://deb.debian.org/debian forky/main amd64 libxnvctrl0 amd64 535.171.04-1+b2 [14.2 kB] Get: 84 http://deb.debian.org/debian forky/main amd64 libze1 amd64 1.24.1-2 [514 kB] Get: 85 http://deb.debian.org/debian forky/main amd64 ocl-icd-libopencl1 amd64 2.3.3-1 [42.9 kB] Get: 86 http://deb.debian.org/debian forky/main amd64 libhwloc-plugins amd64 2.12.2-1 [23.5 kB] Get: 87 http://deb.debian.org/debian forky/main amd64 libibumad3 amd64 56.1-1 [30.0 kB] Get: 88 http://deb.debian.org/debian forky/main amd64 libibmad5 amd64 56.1-1 [44.5 kB] Get: 89 http://deb.debian.org/debian forky/main amd64 libnl-3-dev amd64 3.11.0-2 [110 kB] Get: 90 http://deb.debian.org/debian forky/main amd64 libnl-route-3-dev amd64 3.11.0-2 [235 kB] Get: 91 http://deb.debian.org/debian forky/main amd64 libibverbs-dev amd64 56.1-1 [654 kB] Get: 92 http://deb.debian.org/debian forky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 93 http://deb.debian.org/debian forky/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 94 http://deb.debian.org/debian forky/main amd64 libncl2 amd64 2.1.21+git20210811.b1213a7-6 [383 kB] Get: 95 http://deb.debian.org/debian forky/main amd64 libncl-dev amd64 2.1.21+git20210811.b1213a7-6 [599 kB] Get: 96 http://deb.debian.org/debian forky/main amd64 libucx0 amd64 1.19.0+ds-1 [1336 kB] Get: 97 http://deb.debian.org/debian forky/main amd64 libopenmpi40 amd64 5.0.8-9 [3258 kB] Get: 98 http://deb.debian.org/debian forky/main amd64 openmpi-common all 5.0.8-9 [107 kB] Get: 99 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 100 http://deb.debian.org/debian forky/main amd64 openmpi-bin amd64 5.0.8-9 [203 kB] Get: 101 http://deb.debian.org/debian forky/main amd64 libopenmpi-dev amd64 5.0.8-9 [1228 kB] Get: 102 http://deb.debian.org/debian forky/main amd64 mpi-default-dev amd64 1.18 [3372 B] Get: 103 http://deb.debian.org/debian forky/main amd64 ncl-tools amd64 2.1.21+git20210811.b1213a7-6 [190 kB] Fetched 164 MB in 21s (7894 kB/s) Preconfiguring packages ... Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../000-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. 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Setting up openmpi-bin (5.0.8-9) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:amd64 (5.0.8-9) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up mpi-default-dev (1.18) ... Processing triggers for libc-bin (2.41-12) ... 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: user script /srv/workspace/pbuilder/1872835/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for forky I: user script /srv/workspace/pbuilder/1872835/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/garli-2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../garli_2.1-9_source.changes dpkg-buildpackage: info: source package garli dpkg-buildpackage: info: source version 2.1-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 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=x86_64-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/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-ncl=/usr --enable-mpi checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 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 xargs -n works... yes checking whether UID '2222' is supported by ustar format... yes checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking for gcc... gcc 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 -j42 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)': linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1322 | register int nsq = n * n; | ^~~ garlimain.cpp:434:66: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ garlimain.cpp:434:76: warning: macro '__TIME__' might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ 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++/15/string:51, from bipartition.h:23, from bipartition.cpp:19: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from configoptions.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] 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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from model.cpp:17: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from population.h:23: /usr/include/c++/15/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++/15/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++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, from 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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from adaptation.cpp:18: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, from individual.cpp:28: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/iomanip:47, from individual.cpp:21: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/refwrap.h:41, from /usr/include/c++/15/vector:70, from population.cpp:23: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/refwrap.h:41, from /usr/include/c++/15/vector:70, from tree.h:24: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from mpitrick.cpp:21: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from configreader.cpp:21: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from garlimain.cpp:40: 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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from population.h:23: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/refwrap.h:41, from /usr/include/c++/15/vector:70, from tree.cpp:21: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, 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/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from treenode.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, 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/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from rng.h:36, from tree.h:30: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from model.h:25, from clamanager.h:25, from condlike.cpp:22: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/ncl/ncl.h:27, from garlireader.cpp:41: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' In file included from /usr/include/stdio.h:970, from configreader.cpp:18: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] /usr/include/x86_64-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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from datamatr.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from population.cpp:25: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, 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/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] garlimain.cpp: In function 'int SubGarliMain(int)': garlimain.cpp:323:49: warning: '%d' directive writing between 2 and 10 bytes into a region of size 6 [-Wformat-overflow=] 323 | else sprintf(temp, ".run%d", rank); | ^~ garlimain.cpp:323:44: note: directive argument in the range [10, 2147483647] 323 | else sprintf(temp, ".run%d", rank); | ^~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int SubGarliMain(int)' at garlimain.cpp:323:16: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 15 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 ()); | ~~~~~~~~~~~~~~~~~ garlimain.cpp: In function 'int SubGarliMain(int)': garlimain.cpp:322:59: warning: '%d' directive writing between 1 and 11 bytes into a region of size 5 [-Wformat-overflow=] 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); | ^~ garlimain.cpp:322:53: note: directive argument in the range [-2147483648, 9] 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int SubGarliMain(int)' at garlimain.cpp:322:25: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 17 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 ()); | ~~~~~~~~~~~~~~~~~ population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': population.cpp:3066:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~ population.cpp:3066:47: note: directive argument in the range [1, 2147483647] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mpic++ -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -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[4]: Leaving directory '/build/reproducible-path/garli-2.1/src' Making all in tests make[4]: Entering directory '/build/reproducible-path/garli-2.1/tests' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/garli-2.1/tests' make[4]: Entering directory '/build/reproducible-path/garli-2.1' make[4]: Leaving 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' mkdir -p debian/mpi mv src/Garli debian/mpi/Garli-mpi make distclean make[2]: Entering directory '/build/reproducible-path/garli-2.1' Making distclean in src make[3]: Entering directory '/build/reproducible-path/garli-2.1/src' rm -f Garli rm -f *.o rm -f *.tab.c rm -f test . = "." || rm -f rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags rm -f ./.deps/adaptation.Po rm -f ./.deps/bipartition.Po rm -f ./.deps/condlike.Po rm -f ./.deps/configoptions.Po rm -f ./.deps/configreader.Po rm -f ./.deps/datamatr.Po rm -f ./.deps/funcs.Po rm -f ./.deps/garlimain.Po rm -f ./.deps/garlireader.Po rm -f ./.deps/individual.Po rm -f ./.deps/linalg.Po rm -f ./.deps/model.Po rm -f ./.deps/mpitrick.Po rm -f ./.deps/optimization.Po rm -f ./.deps/population.Po rm -f ./.deps/rng.Po rm -f ./.deps/sequencedata.Po rm -f ./.deps/set.Po rm -f ./.deps/translatetable.Po rm -f ./.deps/tree.Po rm -f ./.deps/treenode.Po rm -f Makefile make[3]: Leaving directory '/build/reproducible-path/garli-2.1/src' Making distclean in tests make[3]: Entering directory '/build/reproducible-path/garli-2.1/tests' rm -f test . = "." || rm -f rm -f Makefile make[3]: Leaving directory '/build/reproducible-path/garli-2.1/tests' make[3]: Entering directory '/build/reproducible-path/garli-2.1' rm -f test . = "." || rm -f rm -f config.h stamp-h1 rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags rm -f cscope.out cscope.in.out cscope.po.out cscope.files make[3]: Leaving directory '/build/reproducible-path/garli-2.1' rm -f config.status config.cache config.log configure.lineno config.status.lineno rm -f Makefile make[2]: Leaving directory '/build/reproducible-path/garli-2.1' # Now build single processor binary dh_auto_configure -- --with-ncl=/usr ./configure --build=x86_64-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/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-ncl=/usr checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 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 xargs -n works... yes checking whether UID '2222' is supported by ustar format... yes checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking for gcc... gcc 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 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 make[1]: Leaving directory '/build/reproducible-path/garli-2.1' dh_auto_build make -j42 make[1]: Entering directory '/build/reproducible-path/garli-2.1' make all-recursive make[2]: Entering directory '/build/reproducible-path/garli-2.1' Making all in src make[3]: Entering directory '/build/reproducible-path/garli-2.1/src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o adaptation.o adaptation.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o bipartition.o bipartition.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o condlike.o condlike.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configoptions.o configoptions.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configreader.o configreader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o datamatr.o datamatr.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o funcs.o funcs.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlimain.o garlimain.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlireader.o garlireader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o individual.o individual.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)': linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1322 | register int nsq = n * n; | ^~~ garlimain.cpp:434:66: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ garlimain.cpp:434:76: warning: macro '__TIME__' might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from configoptions.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] 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++/15/string:51, from bipartition.h:23, from bipartition.cpp:19: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from 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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from population.h:23: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from adaptation.cpp:18: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from garlimain.cpp:40: 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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from population.h:23: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from model.cpp:17: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/refwrap.h:41, from /usr/include/c++/15/vector:70, from tree.h:24: /usr/include/c++/15/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++/15/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++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from garlimain.cpp:46: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i std::bind2nd(const _Operation&, const _Tp&) [with _Operation = 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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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 configreader.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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from configreader.cpp:21: /usr/include/c++/15/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++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, from individual.cpp:28: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/iomanip:47, from individual.cpp:21: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/refwrap.h:41, from /usr/include/c++/15/vector:70, from population.cpp:23: /usr/include/c++/15/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++/15/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++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i 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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/refwrap.h:41, from /usr/include/c++/15/vector:70, from tree.cpp:21: /usr/include/c++/15/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++/15/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++/15/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++/15/bits/stl_function.h:1441: /usr/include/c++/15/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++/15/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 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++/15/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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, 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/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from rng.h:36, from tree.h:30: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from model.h:25, from clamanager.h:25, from condlike.cpp:22: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, 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/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from treenode.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from configreader.cpp:18: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/ncl/ncl.h:27, from garlireader.cpp:41: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from datamatr.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from population.cpp:25: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, 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/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': population.cpp:3066:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~ population.cpp:3066:47: note: directive argument in the range [1, 2147483647] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -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 -j42 check "TESTSUITEFLAGS=-j42 --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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 0.925 (branch= 0.64 scale= 0.00 omega= 0.28 rel rates= 0.00) pass 3:+ 0.733 (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: -213.0379 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 77.066 (branch= 2.27 scale= 0.00 alpha= 4.14 freqs= 10.82 rel rates= 3.11 pinv= 0.78 subset rates= 55.95) pass 3:+ 49.994 (branch= 6.88 scale= 0.78 alpha= 5.67 freqs= 1.20 rel rates= 1.34 pinv= 0.01 subset rates= 34.11) pass 4:+ 15.059 (branch= 0.00 scale= 0.72 alpha= 0.64 freqs= 1.21 rel rates= 0.50 pinv= 0.00 subset rates= 12.00) pass 5:+ 5.778 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.10 rel rates= 0.77 pinv= 0.00 subset rates= 4.91) pass 6:+ 0.115 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.09 rel rates= 0.01 pinv= 0.00 subset rates= 0.00) lnL after optimization: -13342.2046 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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= 4.30) pass 2:+ 9.055 (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:+ 0.303 (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: -467.8152 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 12.450 (branch= 8.46 scale= 0.00 subset rates= 3.99) pass 3:+ 3.552 (branch= 2.32 scale= 0.03 subset rates= 1.21) pass 4:+ 0.758 (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: -477.9401 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 129.564 (branch= 123.99 scale= 0.59 subset rates= 4.98) pass 2:+ 9.273 (branch= 7.97 scale= 0.00 subset rates= 1.30) pass 3:+ 1.739 (branch= 1.57 scale= 0.00 subset rates= 0.17) pass 4:+ 0.312 (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: -464.7107 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 3.846 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.161 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.158 (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: -474.8622 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 9 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 6 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 : -3355.4806 (branch= 0.9931 alpha= 0.0078 pinv= 0.0071 eq freqs= 0.1960 rel rates= 1.3003 subset rates= 0.3859) pass 2 : -3354.0831 (branch= 0.5204 alpha= 0.0089 pinv= 0.0117 eq freqs= 0.0202 rel rates= 0.6677 subset rates= 0.1686) pass 3 : -3353.2198 (branch= 0.2864 alpha= 0.0000 pinv= 0.0086 eq freqs= 0.0160 rel rates= 0.4622 subset rates= 0.0901) pass 4 : -3352.6255 (branch= 0.1646 alpha= 0.0037 pinv= 0.0159 eq freqs= 0.0035 rel rates= 0.3594 subset rates= 0.0473) pass 5 : -3352.1694 (branch= 0.0978 alpha= 0.0045 pinv= 0.0165 eq freqs= 0.0021 rel rates= 0.3101 subset rates= 0.0251) pass 6 : -3351.8162 (branch= 0.0577 alpha= 0.0065 pinv= 0.0165 eq freqs= 0.0009 rel rates= 0.2567 subset rates= 0.0148) pass 7 : -3351.5408 (branch= 0.0284 alpha= 0.0087 pinv= 0.0158 eq freqs= 0.0010 rel rates= 0.2101 subset rates= 0.0114) pass 8 : -3351.3231 (branch= 0.0191 alpha= 0.0100 pinv= 0.0149 eq freqs= 0.0007 rel rates= 0.1668 subset rates= 0.0062) pass 9 : -3351.1479 (branch= 0.0117 alpha= 0.0106 pinv= 0.0140 eq freqs= 0.0005 rel rates= 0.1344 subset rates= 0.0041) pass 10: -3351.0053 (branch= 0.0070 alpha= 0.0105 pinv= 0.0138 eq freqs= 0.0004 rel rates= 0.1083 subset rates= 0.0026) pass 11: -3350.8878 (branch= 0.0043 alpha= 0.0103 pinv= 0.0127 eq freqs= 0.0003 rel rates= 0.0881 subset rates= 0.0018) pass 12: -3350.7912 (branch= 0.0033 alpha= 0.0098 pinv= 0.0116 eq freqs= 0.0002 rel rates= 0.0716 subset rates= 0.0000) pass 13: -3350.7078 (branch= 0.0008 alpha= 0.0096 pinv= 0.0105 eq freqs= 0.0002 rel rates= 0.0606 subset rates= 0.0018) pass 14: -3350.6403 (branch= 0.0012 alpha= 0.0090 pinv= 0.0095 eq freqs= 0.0002 rel rates= 0.0475 subset rates= 0.0000) pass 15: -3350.5832 (branch= 0.0003 alpha= 0.0082 pinv= 0.0081 eq freqs= 0.0001 rel rates= 0.0404 subset rates= 0.0000) pass 16: -3350.5328 (branch= 0.0001 alpha= 0.0079 pinv= 0.0073 eq freqs= 0.0001 rel rates= 0.0339 subset rates= 0.0012) pass 17: -3350.4923 (branch= 0.0008 alpha= 0.0069 pinv= 0.0066 eq freqs= 0.0001 rel rates= 0.0262 subset rates= 0.0000) pass 18: -3350.4574 (branch= 0.0002 alpha= 0.0060 pinv= 0.0059 eq freqs= 0.0000 rel rates= 0.0227 subset rates= 0.0000) pass 19: -3350.4270 (branch= 0.0000 alpha= 0.0056 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0195 subset rates= 0.0000) pass 20: -3350.4005 (branch= 0.0000 alpha= 0.0051 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0167 subset rates= 0.0000) optimization up to ... pass 30: -3350.2715 (branch= 0.0001 alpha= 0.0273 pinv= 0.0248 eq freqs= 0.0002 rel rates= 0.0767 subset rates= 0.0000) optimization up to ... pass 40: -3350.2419 (branch= 0.0000 alpha= 0.0064 pinv= 0.0060 eq freqs= 0.0000 rel rates= 0.0171 subset rates= 0.0000) optimization up to ... pass 50: -3350.2353 (branch= 0.0000 alpha= 0.0013 pinv= 0.0012 eq freqs= 0.0000 rel rates= 0.0042 subset rates= 0.0000) optimization up to ... pass 60: -3350.2337 (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: -3350.2334 (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: -3350.2333 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) Looking for minimum length branches... Final score = -3350.2333 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -3350.2333 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: 3.113 10.41 2.688 0.001 21.89 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 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 3350.23331 ***Expected is 3350.2345 ***SCORE DIFFERENCE IS -.00119 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 : -3329.9920 (branch= 1.3745 alpha= 0.0217 pinv= 0.0099 eq freqs= 0.2403 rel rates= 0.7561 ins/del rates= 0.0754) pass 2 : -3329.0411 (branch= 0.3511 alpha= 0.0000 pinv= 0.0096 eq freqs= 0.0000 rel rates= 0.5271 ins/del rates= 0.0631) pass 3 : -3328.4283 (branch= 0.1466 alpha= 0.0039 pinv= 0.0146 eq freqs= 0.0187 rel rates= 0.3867 ins/del rates= 0.0424) pass 4 : -3327.9685 (branch= 0.0855 alpha= 0.0067 pinv= 0.0148 eq freqs= 0.0031 rel rates= 0.3207 ins/del rates= 0.0290) pass 5 : -3327.6169 (branch= 0.0530 alpha= 0.0080 pinv= 0.0147 eq freqs= 0.0017 rel rates= 0.2561 ins/del rates= 0.0181) pass 6 : -3327.3365 (branch= 0.0344 alpha= 0.0079 pinv= 0.0146 eq freqs= 0.0008 rel rates= 0.2111 ins/del rates= 0.0115) pass 7 : -3327.1138 (branch= 0.0219 alpha= 0.0094 pinv= 0.0140 eq freqs= 0.0007 rel rates= 0.1690 ins/del rates= 0.0077) pass 8 : -3326.9319 (branch= 0.0143 alpha= 0.0098 pinv= 0.0133 eq freqs= 0.0006 rel rates= 0.1388 ins/del rates= 0.0051) pass 9 : -3326.7851 (branch= 0.0094 alpha= 0.0099 pinv= 0.0125 eq freqs= 0.0004 rel rates= 0.1113 ins/del rates= 0.0034) pass 10: -3326.6639 (branch= 0.0063 alpha= 0.0097 pinv= 0.0123 eq freqs= 0.0003 rel rates= 0.0903 ins/del rates= 0.0023) pass 11: -3326.5636 (branch= 0.0042 alpha= 0.0095 pinv= 0.0114 eq freqs= 0.0002 rel rates= 0.0735 ins/del rates= 0.0015) pass 12: -3326.4810 (branch= 0.0028 alpha= 0.0090 pinv= 0.0099 eq freqs= 0.0002 rel rates= 0.0596 ins/del rates= 0.0010) pass 13: -3326.4117 (branch= 0.0019 alpha= 0.0085 pinv= 0.0091 eq freqs= 0.0001 rel rates= 0.0490 ins/del rates= 0.0007) pass 14: -3326.3528 (branch= 0.0013 alpha= 0.0080 pinv= 0.0083 eq freqs= 0.0001 rel rates= 0.0408 ins/del rates= 0.0005) pass 15: -3326.3023 (branch= 0.0009 alpha= 0.0074 pinv= 0.0076 eq freqs= 0.0001 rel rates= 0.0342 ins/del rates= 0.0003) pass 16: -3326.2594 (branch= 0.0006 alpha= 0.0069 pinv= 0.0068 eq freqs= 0.0001 rel rates= 0.0283 ins/del rates= 0.0002) pass 17: -3326.2227 (branch= 0.0004 alpha= 0.0064 pinv= 0.0062 eq freqs= 0.0001 rel rates= 0.0235 ins/del rates= 0.0001) pass 18: -3326.1910 (branch= 0.0002 alpha= 0.0057 pinv= 0.0056 eq freqs= 0.0001 rel rates= 0.0201 ins/del rates= 0.0001) pass 19: -3326.1634 (branch= 0.0001 alpha= 0.0052 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0171 ins/del rates= 0.0000) pass 20: -3326.1395 (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= 0.0001 rel rates= 0.0688 ins/del rates= 0.0001) optimization up to ... pass 40: -3325.9908 (branch= 0.0000 alpha= 0.0068 pinv= 0.0064 eq freqs= 0.0000 rel rates= 0.0157 ins/del rates= 0.0000) optimization up to ... pass 50: -3325.9841 (branch= 0.0000 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 76: -3325.9822 (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 = -3325.9822 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 : -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: 3.062 10.26 2.656 0.001 21.52 1 0.333 0.222 0.157 0.288 0.574 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 3325.98220 ***Expected is 3325.98222 ***SCORE DIFFERENCE IS -.00002 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 2061.640 (branch=1982.89 scale= 74.28 freqs= 0.89 rel rates= 3.59) pass 2:+ 221.898 (branch= 220.63 scale= 0.00 freqs= 0.84 rel rates= 0.43) pass 3:+ 4.926 (branch= 4.77 scale= 0.00 freqs= 0.07 rel rates= 0.09) pass 4:+ 0.328 (branch= 0.31 scale= 0.00 freqs= 0.00 rel rates= 0.02) pass 5:+ 0.069 (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: -16071.0881 gen current_lnL precision last_tree_imp 0 -16071.0881 0.010 0 100 -14502.1424 0.010 73 200 -14502.1082 0.010 73 300 -14501.0360 0.010 73 400 -14500.4215 0.010 73 500 -14500.0792 0.010 73 600 -14499.5615 0.010 73 700 -14499.2365 0.010 73 800 -14499.1060 0.010 73 900 -14499.1049 0.010 73 1000 -14499.1049 0.010 73 1100 -14498.9970 0.010 73 1200 -14498.9970 0.010 73 1300 -14498.9879 0.010 73 1400 -14498.9879 0.010 73 1500 -14498.9852 0.010 73 1600 -14498.9678 0.010 73 Reached termination condition! last topological improvement at gen 73 Improvement over last 500 gen = 0.02921 Current score = -14498.9678 Performing final optimizations... pass 1 : -14498.9160 (branch= 0.0243 eq freqs= 0.0185 rel rates= 0.0090) pass 2 : -14498.8971 (branch= 0.0099 eq freqs= 0.0002 rel rates= 0.0089) pass 3 : -14498.8909 (branch= 0.0037 eq freqs= 0.0001 rel rates= 0.0023) pass 4 : -14498.8878 (branch= 0.0010 eq freqs= 0.0019 rel rates= 0.0002) pass 5 : -14498.8866 (branch= 0.0006 eq freqs= 0.0004 rel rates= 0.0002) pass 6 : -14498.8859 (branch= 0.0004 eq freqs= 0.0000 rel rates= 0.0002) pass 7 : -14498.8857 (branch= 0.0002 eq freqs= 0.0000 rel rates= 0.0001) pass 8 : -14498.8855 (branch= 0.0002 eq freqs= 0.0000 rel rates= 0.0000) pass 9 : -14498.8854 (branch= 0.0001 eq freqs= 0.0000 rel rates= 0.0000) pass 10: -14498.8853 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 11: -14498.8853 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 12: -14498.8853 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -14498.8853 Time used = 0 hours, 0 minutes and 2 seconds MODEL REPORT - Parameter values are FINAL 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 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 : -14498.8853 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 1.869 3.671 1.221 1.853 4.414 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 14486.03850 ***Expected is 14486.03829 ***SCORE DIFFERENCE IS .00021 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 36.660 (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: -13315.7939 Current score = -13315.7939 Performing final optimizations... pass 1 : -13309.3700 (branch= 2.8300 alpha= 0.8831 pinv= 0.0158 eq freqs= 0.2323 rel rates= 1.8454 subset rates= 0.6173) pass 2 : -13307.8842 (branch= 0.4328 alpha= 0.2019 pinv= 0.0134 eq freqs= 0.1232 rel rates= 0.6633 subset rates= 0.0513) pass 3 : -13307.2657 (branch= 0.1095 alpha= 0.0595 pinv= 0.0031 eq freqs= 0.0081 rel rates= 0.4287 subset rates= 0.0096) pass 4 : -13306.9109 (branch= 0.0241 alpha= 0.0171 pinv= 0.0026 eq freqs= 0.0085 rel rates= 0.2993 subset rates= 0.0032) pass 5 : -13306.6767 (branch= 0.0088 alpha= 0.0057 pinv= 0.0013 eq freqs= 0.0072 rel rates= 0.2110 subset rates= 0.0002) pass 6 : -13306.5232 (branch= 0.0036 alpha= 0.0020 pinv= 0.0004 eq freqs= 0.0043 rel rates= 0.1433 subset rates= 0.0000) pass 7 : -13306.4217 (branch= 0.0011 alpha= 0.0004 pinv= 0.0001 eq freqs= 0.0035 rel rates= 0.0964 subset rates= 0.0000) pass 8 : -13306.3532 (branch= 0.0006 alpha= 0.0002 pinv= 0.0001 eq freqs= 0.0020 rel rates= 0.0656 subset rates= 0.0000) pass 9 : -13306.3069 (branch= 0.0003 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0015 rel rates= 0.0444 subset rates= 0.0000) pass 10: -13306.2750 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0012 rel rates= 0.0306 subset rates= 0.0000) pass 11: -13306.2534 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0206 subset rates= 0.0002) pass 12: -13306.2381 (branch= 0.0001 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0142 subset rates= 0.0005) pass 13: -13306.2280 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0097 subset rates= 0.0000) pass 14: -13306.2211 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0067 subset rates= 0.0000) pass 15: -13306.2164 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0045 subset rates= 0.0000) pass 16: -13306.2134 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0030 subset rates= 0.0000) pass 17: -13306.2112 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0021 subset rates= 0.0000) pass 18: -13306.2097 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014 subset rates= 0.0000) pass 19: -13306.2087 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010 subset rates= 0.0000) pass 20: -13306.2080 (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: -13306.2065 (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: -13306.2063 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0001) Looking for minimum length branches... Final score = -13306.2063 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 : -13306.2063 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 1.413 1.413 3.72 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: 4.369 7.051 1.608 7.051 4.369 1 0.270 0.164 0.161 0.406 0.361 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 4.034 0.033 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 1.694 0.540 0.300 2.160 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 13306.20634 ***Expected is 13306.20608 ***SCORE DIFFERENCE IS .00026 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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= 4.30) pass 2:+ 9.055 (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:+ 0.303 (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: -467.8152 Current score = -467.8152 Performing final optimizations... pass 1 : -467.7873 (branch= 0.0213 subset rates= 0.0066) pass 2 : -467.7197 (branch= 0.0649 subset rates= 0.0027) pass 3 : -467.6968 (branch= 0.0229 subset rates= 0.0000) pass 4 : -467.6869 (branch= 0.0099 subset rates= 0.0000) pass 5 : -467.6823 (branch= 0.0046 subset rates= 0.0000) pass 6 : -467.6802 (branch= 0.0020 subset rates= 0.0000) pass 7 : -467.6793 (branch= 0.0009 subset rates= 0.0000) pass 8 : -467.6788 (branch= 0.0005 subset rates= 0.0000) pass 9 : -467.6785 (branch= 0.0003 subset rates= 0.0000) pass 10: -467.6784 (branch= 0.0001 subset rates= 0.0000) pass 11: -467.6783 (branch= 0.0000 subset rates= 0.0000) pass 12: -467.6783 (branch= 0.0000 subset rates= 0.0000) pass 13: -467.6783 (branch= 0.0000 subset rates= 0.0000) pass 14: -467.6783 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6783 Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -467.6783 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: 3.842 0.786 1.480 2.177 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 467.67829 ***Expected is 467.6783 ***SCORE DIFFERENCE IS -.00001 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 12.450 (branch= 8.46 scale= 0.00 subset rates= 3.99) pass 3:+ 3.552 (branch= 2.32 scale= 0.03 subset rates= 1.21) pass 4:+ 0.758 (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: -477.9401 Current score = -477.9401 Performing final optimizations... pass 1 : -477.8535 (branch= 0.0858 subset rates= 0.0008) pass 2 : -477.7572 (branch= 0.0963 subset rates= 0.0000) pass 3 : -477.7255 (branch= 0.0301 subset rates= 0.0016) pass 4 : -477.7048 (branch= 0.0207 subset rates= 0.0000) pass 5 : -477.6964 (branch= 0.0085 subset rates= 0.0000) pass 6 : -477.6921 (branch= 0.0043 subset rates= 0.0000) pass 7 : -477.6900 (branch= 0.0021 subset rates= 0.0000) pass 8 : -477.6888 (branch= 0.0011 subset rates= 0.0000) pass 9 : -477.6882 (branch= 0.0007 subset rates= 0.0000) pass 10: -477.6861 (branch= 0.0004 subset rates= 0.0016) pass 11: -477.6854 (branch= 0.0008 subset rates= 0.0000) pass 12: -477.6850 (branch= 0.0003 subset rates= 0.0000) pass 13: -477.6849 (branch= 0.0002 subset rates= 0.0000) pass 14: -477.6847 (branch= 0.0001 subset rates= 0.0000) pass 15: -477.6847 (branch= 0.0000 subset rates= 0.0000) pass 16: -477.6847 (branch= 0.0000 subset rates= 0.0000) pass 17: -477.6847 (branch= 0.0000 subset rates= 0.0000) pass 18: -477.6846 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.6846 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 : -477.6846 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: 4.914 0.631 1.899 2.807 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 477.68463 ***Expected is 477.6848 ***SCORE DIFFERENCE IS -.00017 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 129.564 (branch= 123.99 scale= 0.59 subset rates= 4.98) pass 2:+ 9.273 (branch= 7.97 scale= 0.00 subset rates= 1.30) pass 3:+ 1.739 (branch= 1.57 scale= 0.00 subset rates= 0.17) pass 4:+ 0.312 (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: -464.7107 Current score = -464.7107 Performing final optimizations... pass 1 : -464.6735 (branch= 0.0277 subset rates= 0.0095) pass 2 : -464.5879 (branch= 0.0823 subset rates= 0.0033) pass 3 : -464.5682 (branch= 0.0185 subset rates= 0.0012) pass 4 : -464.5557 (branch= 0.0125 subset rates= 0.0000) pass 5 : -464.5526 (branch= 0.0031 subset rates= 0.0000) pass 6 : -464.5498 (branch= 0.0022 subset rates= 0.0006) pass 7 : -464.5490 (branch= 0.0007 subset rates= 0.0000) pass 8 : -464.5482 (branch= 0.0008 subset rates= 0.0000) pass 9 : -464.5478 (branch= 0.0004 subset rates= 0.0000) pass 10: -464.5477 (branch= 0.0001 subset rates= 0.0000) pass 11: -464.5476 (branch= 0.0001 subset rates= 0.0000) pass 12: -464.5476 (branch= 0.0000 subset rates= 0.0000) pass 13: -464.5476 (branch= 0.0000 subset rates= 0.0000) pass 14: -464.5476 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -464.5476 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 : -464.5476 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 0.772 1.641 2.452 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 464.54756 ***Expected is 464.5473 ***SCORE DIFFERENCE IS .00026 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 3.846 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.161 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.158 (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: -474.8622 Current score = -474.8622 Performing final optimizations... pass 1 : -474.7981 (branch= 0.0576 subset rates= 0.0066) pass 2 : -474.6999 (branch= 0.0911 subset rates= 0.0071) pass 3 : -474.6746 (branch= 0.0233 subset rates= 0.0020) pass 4 : -474.6609 (branch= 0.0137 subset rates= 0.0000) pass 5 : -474.6539 (branch= 0.0070 subset rates= 0.0000) pass 6 : -474.6510 (branch= 0.0029 subset rates= 0.0000) pass 7 : -474.6490 (branch= 0.0011 subset rates= 0.0009) pass 8 : -474.6470 (branch= 0.0012 subset rates= 0.0008) pass 9 : -474.6464 (branch= 0.0007 subset rates= 0.0000) pass 10: -474.6460 (branch= 0.0004 subset rates= 0.0000) pass 11: -474.6458 (branch= 0.0002 subset rates= 0.0000) pass 12: -474.6457 (branch= 0.0001 subset rates= 0.0001) pass 13: -474.6456 (branch= 0.0001 subset rates= 0.0000) pass 14: -474.6455 (branch= 0.0000 subset rates= 0.0000) pass 15: -474.6455 (branch= 0.0000 subset rates= 0.0000) pass 16: -474.6455 (branch= 0.0000 subset rates= 0.0000) pass 17: -474.6455 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -474.6455 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 : -474.6455 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: 4.585 0.585 2.017 2.998 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 474.64547 ***Expected is 474.6455633 ***SCORE DIFFERENCE IS -.0000933 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 -210.8784 0.010 1215 2000 -210.6679 0.010 1215 2500 -210.6042 0.010 1215 3000 -210.5103 0.010 1215 3500 -210.4074 0.010 1215 Reached termination condition! last topological improvement at gen 1215 Improvement over last 500 gen = 0.04856 Current score = -210.3682 Performing final optimizations... pass 1 : -210.0050 (branch= 0.0000 alpha= 0.0802 pinv= 0.2366 eq freqs= 0.0000 rel rates= 0.0463) pass 2 : -209.4569 (branch= 0.0070 alpha= 0.3208 pinv= 0.2046 eq freqs= 0.0043 rel rates= 0.0115) pass 3 : -209.3004 (branch= 0.0331 alpha= 0.0941 pinv= 0.0091 eq freqs= 0.0085 rel rates= 0.0117) pass 4 : -209.2399 (branch= 0.0368 alpha= 0.0184 pinv= 0.0014 eq freqs= 0.0008 rel rates= 0.0031) pass 5 : -209.1932 (branch= 0.0307 alpha= 0.0102 pinv= 0.0005 eq freqs= 0.0000 rel rates= 0.0052) pass 6 : -209.1657 (branch= 0.0133 alpha= 0.0051 pinv= 0.0005 eq freqs= 0.0009 rel rates= 0.0076) pass 7 : -209.1439 (branch= 0.0077 alpha= 0.0024 pinv= 0.0002 eq freqs= 0.0005 rel rates= 0.0110) pass 8 : -209.1281 (branch= 0.0045 alpha= 0.0005 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0104) pass 9 : -209.1165 (branch= 0.0016 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0095) pass 10: -209.1072 (branch= 0.0007 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0082) pass 11: -209.0991 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0074) pass 12: -209.0921 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0067) pass 13: -209.0857 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0061) pass 14: -209.0798 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0057) pass 15: -209.0744 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0053) pass 16: -209.0691 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0051) pass 17: -209.0644 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 18: -209.0596 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 19: -209.0547 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 20: -209.0495 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) optimization up to ... pass 30: -208.9548 (branch= 0.0159 alpha= 0.0000 pinv= 0.0005 eq freqs= 0.0028 rel rates= 0.0755) optimization up to ... pass 40: -208.7782 (branch= 0.0289 alpha= 0.0000 pinv= 0.0019 eq freqs= 0.0089 rel rates= 0.1370) optimization up to ... pass 50: -208.6671 (branch= 0.0060 alpha= 0.0000 pinv= 0.0008 eq freqs= 0.0032 rel rates= 0.1009) optimization up to ... pass 60: -208.6038 (branch= 0.0007 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0623) optimization up to ... pass 70: -208.5599 (branch= 0.0002 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0434) optimization up to ... pass 80: -208.5276 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0321) optimization up to ... pass 90: -208.5027 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0247) optimization up to ... pass 100: -208.4832 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0194) optimization up to ... pass 110: -208.4674 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0156) optimization up to ... pass 120: -208.4545 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0129) optimization up to ... pass 130: -208.4437 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0107) optimization up to ... pass 140: -208.4345 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0091) optimization up to ... pass 150: -208.4266 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0078) optimization up to ... pass 160: -208.4199 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) optimization up to ... pass 170: -208.4141 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) optimization up to ... pass 180: -208.4090 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0051) optimization up to ... pass 190: -208.4044 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0045) optimization up to ... pass 200: -208.4004 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) optimization up to ... pass 210: -208.3969 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0036) optimization up to ... pass 220: -208.3936 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... pass 230: -208.3907 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) optimization up to ... pass 240: -208.3880 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0027) optimization up to ... pass 250: -208.3856 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0025) optimization up to ... pass 260: -208.3833 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... pass 270: -208.3813 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) optimization up to ... pass 280: -208.3794 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 290: -208.3776 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) optimization up to ... pass 300: -208.3760 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 310: -208.3744 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... pass 320: -208.3730 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 330: -208.3716 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 340: -208.3704 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 350: -208.3692 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 360: -208.3681 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 370: -208.3671 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 380: -208.3661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 390: -208.3652 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 400: -208.3644 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 410: -208.3635 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 420: -208.3627 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 430: -208.3620 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 440: -208.3613 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 450: -208.3606 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 460: -208.3600 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 470: -208.3594 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 480: -208.3590 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0004) optimization up to ... pass 490: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) optimization up to ... pass 492: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.3587 Time used = 0 hours, 0 minutes and 2 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 121.128, AG = 186.935, AT = 6.902, CG = 202.957, CT = 193.125, 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. ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -208.3587 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: 121.1 186.9 6.902 203 193.1 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 -212.3288 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 = 0.03824 Current score = -211.2855 Performing final optimizations... pass 1 : -208.9608 (branch= 0.0000 alpha= 0.7627 pinv= 1.4695 eq freqs= 0.0065 rel rates= 0.0860) pass 2 : -208.5654 (branch= 0.0411 alpha= 0.3048 pinv= 0.0095 eq freqs= 0.0118 rel rates= 0.0282) pass 3 : -208.5084 (branch= 0.0299 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0018 rel rates= 0.0253) pass 4 : -208.4811 (branch= 0.0032 alpha= 0.0022 pinv= 0.0017 eq freqs= 0.0000 rel rates= 0.0202) pass 5 : -208.4608 (branch= 0.0022 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0176) pass 6 : -208.4423 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0177) pass 7 : -208.4250 (branch= 0.0009 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0160) pass 8 : -208.4103 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0144) pass 9 : -208.3965 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0135) pass 10: -208.3839 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0124) pass 11: -208.3723 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0115) pass 12: -208.3618 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0104) pass 13: -208.3520 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0098) pass 14: -208.3430 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0090) pass 15: -208.3347 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0083) pass 16: -208.3272 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0075) pass 17: -208.3199 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0072) pass 18: -208.3133 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) pass 19: -208.3068 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0064) pass 20: -208.3010 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) optimization up to ... pass 30: -208.2568 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0440) optimization up to ... pass 40: -208.2293 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0274) optimization up to ... pass 50: -208.2106 (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: -208.1865 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0104) optimization up to ... pass 80: -208.1782 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0082) optimization up to ... pass 90: -208.1716 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) optimization up to ... pass 100: -208.1661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0055) optimization up to ... pass 110: -208.1615 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) 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: -208.1260 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 350: -208.1254 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... 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 3 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 22.242, AG = 32.319, AT = 0.001, CG = 36.406, CT = 80.314, 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 80.31 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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: -219.1444 gen current_lnL precision last_tree_imp 0 -219.1444 0.500 0 500 -216.3490 0.500 474 1000 -215.0097 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 -210.9688 0.010 1502 2500 -210.8711 0.010 1502 3000 -210.7510 0.010 2883 3500 -210.7005 0.010 2883 4000 -210.6775 0.010 2883 4500 -210.6277 0.010 2883 5000 -210.5646 0.010 2883 5500 -210.5008 0.010 2883 6000 -210.3538 0.010 2883 Reached termination condition! last topological improvement at gen 2883 Improvement over last 500 gen = 0.04187 Current score = -210.3452 Performing final optimizations... pass 1 : -209.7259 (branch= 0.0025 alpha= 0.1839 pinv= 0.3304 eq freqs= 0.0000 rel rates= 0.1026) pass 2 : -209.3742 (branch= 0.0078 alpha= 0.2626 pinv= 0.0730 eq freqs= 0.0000 rel rates= 0.0083) pass 3 : -209.2734 (branch= 0.0558 alpha= 0.0257 pinv= 0.0046 eq freqs= 0.0058 rel rates= 0.0088) pass 4 : -209.2185 (branch= 0.0250 alpha= 0.0158 pinv= 0.0000 eq freqs= 0.0049 rel rates= 0.0093) pass 5 : -209.1816 (branch= 0.0224 alpha= 0.0077 pinv= 0.0012 eq freqs= 0.0004 rel rates= 0.0052) pass 6 : -209.1540 (branch= 0.0130 alpha= 0.0052 pinv= 0.0002 eq freqs= 0.0012 rel rates= 0.0080) pass 7 : -209.1308 (branch= 0.0091 alpha= 0.0028 pinv= 0.0001 eq freqs= 0.0006 rel rates= 0.0106) pass 8 : -209.1164 (branch= 0.0042 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0094) pass 9 : -209.1063 (branch= 0.0014 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0082) pass 10: -209.0981 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0073) pass 11: -209.0910 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0065) pass 12: -209.0847 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0059) pass 13: -209.0791 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0054) pass 14: -209.0738 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0051) pass 15: -209.0686 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) pass 16: -209.0634 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) pass 17: -209.0579 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0051) pass 18: -209.0519 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0052) pass 19: -209.0454 (branch= 0.0009 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0056) pass 20: -209.0380 (branch= 0.0012 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0061) optimization up to ... pass 30: -208.9100 (branch= 0.0260 alpha= 0.0000 pinv= 0.0009 eq freqs= 0.0049 rel rates= 0.0963) optimization up to ... pass 40: -208.7402 (branch= 0.0229 alpha= 0.0000 pinv= 0.0019 eq freqs= 0.0080 rel rates= 0.1371) optimization up to ... pass 50: -208.6479 (branch= 0.0029 alpha= 0.0000 pinv= 0.0004 eq freqs= 0.0017 rel rates= 0.0873) optimization up to ... pass 60: -208.5911 (branch= 0.0005 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0560) optimization up to ... pass 70: -208.5508 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0399) optimization up to ... pass 80: -208.5205 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0301) optimization up to ... pass 90: -208.4972 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0231) optimization up to ... pass 100: -208.4788 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0182) optimization up to ... pass 110: -208.4638 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0149) optimization up to ... pass 120: -208.4514 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0123) optimization up to ... pass 130: -208.4411 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0103) optimization up to ... pass 140: -208.4322 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0088) optimization up to ... pass 150: -208.4247 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0075) optimization up to ... pass 160: -208.4183 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0064) optimization up to ... pass 170: -208.4127 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0056) optimization up to ... pass 180: -208.4077 (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= 0.0044) optimization up to ... pass 200: -208.3995 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0039) optimization up to ... pass 210: -208.3960 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0035) optimization up to ... pass 220: -208.3929 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... pass 230: -208.3900 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0028) optimization up to ... pass 240: -208.3874 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) optimization up to ... pass 250: -208.3850 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... pass 260: -208.3828 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... pass 270: -208.3808 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... pass 280: -208.3789 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 290: -208.3772 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 300: -208.3756 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 310: -208.3741 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... pass 320: -208.3727 (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: -208.3701 (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: -208.3679 (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= 0.0010) 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: -208.3626 (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: -208.3605 (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 488: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... Final score = -208.3586 Time used = 0 hours, 0 minutes and 3 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 121.794, AG = 187.954, AT = 6.949, CG = 204.067, CT = 194.168, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2225 0.2905 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 : -208.3586 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: 121.8 188 6.949 204.1 194.2 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 -210.6026 0.010 1230 Reached termination condition! last topological improvement at gen 1230 Improvement over last 500 gen = 0.04161 Current score = -210.5932 Performing final optimizations... pass 1 : -210.1850 (branch= 0.0000 alpha= 0.1339 pinv= 0.2110 eq freqs= 0.0000 rel rates= 0.0632) pass 2 : -209.5580 (branch= 0.0093 alpha= 0.3569 pinv= 0.2371 eq freqs= 0.0050 rel rates= 0.0187) pass 3 : -209.3359 (branch= 0.0380 alpha= 0.1430 pinv= 0.0187 eq freqs= 0.0077 rel rates= 0.0147) pass 4 : -209.2571 (branch= 0.0476 alpha= 0.0199 pinv= 0.0030 eq freqs= 0.0034 rel rates= 0.0049) pass 5 : -209.2088 (branch= 0.0334 alpha= 0.0098 pinv= 0.0009 eq freqs= 0.0000 rel rates= 0.0043) pass 6 : -209.1769 (branch= 0.0177 alpha= 0.0054 pinv= 0.0005 eq freqs= 0.0014 rel rates= 0.0069) pass 7 : -209.1511 (branch= 0.0101 alpha= 0.0036 pinv= 0.0002 eq freqs= 0.0009 rel rates= 0.0110) pass 8 : -209.1300 (branch= 0.0071 alpha= 0.0017 pinv= 0.0000 eq freqs= 0.0009 rel rates= 0.0115) pass 9 : -209.1160 (branch= 0.0031 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0008 rel rates= 0.0100) pass 10: -209.1057 (branch= 0.0011 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0087) pass 11: -209.0970 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0078) pass 12: -209.0897 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0068) pass 13: -209.0833 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0061) pass 14: -209.0775 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0056) pass 15: -209.0720 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0053) pass 16: -209.0670 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0049) pass 17: -209.0621 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 18: -209.0573 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 19: -209.0525 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) pass 20: -209.0471 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) optimization up to ... pass 30: -208.9462 (branch= 0.0176 alpha= 0.0000 pinv= 0.0006 eq freqs= 0.0033 rel rates= 0.0793) optimization up to ... pass 40: -208.7696 (branch= 0.0280 alpha= 0.0000 pinv= 0.0020 eq freqs= 0.0088 rel rates= 0.1378) optimization up to ... pass 50: -208.6633 (branch= 0.0052 alpha= 0.0000 pinv= 0.0007 eq freqs= 0.0028 rel rates= 0.0976) optimization up to ... pass 60: -208.6013 (branch= 0.0006 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0609) optimization up to ... pass 70: -208.5582 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0427) optimization up to ... pass 80: -208.5262 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0317) optimization up to ... pass 90: -208.5016 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0244) optimization up to ... pass 100: -208.4824 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0192) optimization up to ... pass 110: -208.4668 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0155) optimization up to ... pass 120: -208.4539 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0128) optimization up to ... pass 130: -208.4432 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0107) optimization up to ... pass 140: -208.4341 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0090) optimization up to ... pass 150: -208.4263 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0078) optimization up to ... pass 160: -208.4196 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) optimization up to ... pass 170: -208.4138 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) optimization up to ... pass 180: -208.4087 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) optimization up to ... pass 190: -208.4043 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0044) optimization up to ... pass 200: -208.4003 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) optimization up to ... pass 210: -208.3967 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0036) optimization up to ... pass 220: -208.3935 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... pass 230: -208.3906 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) optimization up to ... pass 240: -208.3879 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0027) optimization up to ... pass 250: -208.3854 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... pass 260: -208.3832 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... pass 270: -208.3812 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... pass 280: -208.3792 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 290: -208.3775 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 300: -208.3758 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 310: -208.3743 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... pass 320: -208.3729 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 330: -208.3716 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... pass 340: -208.3703 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 350: -208.3692 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 360: -208.3681 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 370: -208.3671 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 380: -208.3661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 390: -208.3652 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 400: -208.3643 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 410: -208.3635 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 420: -208.3627 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 430: -208.3620 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 440: -208.3613 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 450: -208.3606 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 460: -208.3600 (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: -208.3588 (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= 0.0003) optimization up to ... pass 493: -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 3 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 122.551, AG = 189.112, AT = 6.991, CG = 205.325, CT = 195.363, 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: 122.6 189.1 6.991 205.3 195.4 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 0.925 (branch= 0.64 scale= 0.00 omega= 0.28 rel rates= 0.00) pass 3:+ 0.733 (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: -213.0379 gen current_lnL precision last_tree_imp 0 -213.0379 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) = 0.130445 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 : -210.2321 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 77.066 (branch= 2.27 scale= 0.00 alpha= 4.14 freqs= 10.82 rel rates= 3.11 pinv= 0.78 subset rates= 55.95) pass 3:+ 49.994 (branch= 6.88 scale= 0.78 alpha= 5.67 freqs= 1.20 rel rates= 1.34 pinv= 0.01 subset rates= 34.11) pass 4:+ 15.059 (branch= 0.00 scale= 0.72 alpha= 0.64 freqs= 1.21 rel rates= 0.50 pinv= 0.00 subset rates= 12.00) pass 5:+ 5.778 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.10 rel rates= 0.77 pinv= 0.00 subset rates= 4.91) pass 6:+ 0.115 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.09 rel rates= 0.01 pinv= 0.00 subset rates= 0.00) lnL after optimization: -13342.2046 gen current_lnL precision last_tree_imp 0 -13342.2046 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 = 1.337, CG = 1.337, CT = 3.999, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3134 0.1755 0.2988 0.2122 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 = 6.057, AT = 1.217, CG = 6.057, CT = 3.969, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2816 0.1661 0.1574 0.3949 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.3385 Substitution rate categories under this model: rate proportion 0.0089 0.2500 0.1346 0.2500 0.6551 0.2500 3.2014 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 = 4.110, AT = 2.501, CG = 0.382, CT = 4.110, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1597 0.3517 0.2835 0.2051 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 4.3250 with an invariant (invariable) site category, proportion estimated 0.0388 Substitution rate categories under this model: rate proportion 0.0000 0.0388 0.4714 0.2403 0.7857 0.2403 1.0842 0.2403 1.6587 0.2403 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 : -13323.9616 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 1.337 1.337 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 6.057 1.217 6.057 3.969 1 0.282 0.166 0.157 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 4.11 2.501 0.3821 4.11 1 0.160 0.352 0.284 0.205 4.325 0.039 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 1.695 0.539 0.326 2.136 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 3.846 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.161 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.158 (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: -474.8622 gen current_lnL precision last_tree_imp 0 -474.8622 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 : -474.8614 (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 2.019 2.820 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:+ 5.106 (branch= 3.29 scale= 0.00 subset rates= 1.82) pass 4:+ 0.827 (branch= 0.20 scale= 0.00 subset rates= 0.62) pass 5:+ 0.064 (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 : -474.8614 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 2.019 2.820 rep 2: 4.516 0.599 2.014 2.839 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:+ 0.939 (branch= 0.38 scale= 0.00 subset rates= 0.56) pass 5:+ 0.207 (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: -474.8925 gen current_lnL precision last_tree_imp 0 -474.8925 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 : -474.8614 Replicate 2 : -474.8505 (best) Replicate 3 : -474.8831 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 2.019 2.820 rep 2: 4.516 0.599 2.014 2.839 rep 3: 4.460 0.600 2.010 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 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:+ 3.711 (branch= 2.16 scale= 0.00 subset rates= 1.55) pass 4:+ 1.981 (branch= 1.40 scale= 0.00 subset rates= 0.58) pass 5:+ 0.364 (branch= 0.33 scale= 0.00 subset rates= 0.03) pass 6:+ 0.110 (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: -474.8512 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 2.85 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 : -474.8614 Replicate 2 : -474.8505 Replicate 3 : -474.8831 Replicate 4 : -474.8498 (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 2.019 2.820 rep 2: 4.516 0.599 2.014 2.839 rep 3: 4.460 0.600 2.010 2.838 rep 4: 4.504 0.598 2.010 2.854 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:+ 0.168 (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: -474.9109 gen current_lnL precision last_tree_imp 0 -474.9109 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 : -474.8614 Replicate 2 : -474.8505 Replicate 3 : -474.8831 Replicate 4 : -474.8498 (best) Replicate 5 : -474.9076 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 2.019 2.820 rep 2: 4.516 0.599 2.014 2.839 rep 3: 4.460 0.600 2.010 2.838 rep 4: 4.504 0.598 2.010 2.854 rep 5: 4.499 0.597 2.021 2.840 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 0.500 215 800 -90.1648 0.500 215 Optimization precision reduced Optimizing parameters... improved 0.159 lnL Optimizing branchlengths... improved 0.317 lnL 900 -88.9507 0.010 879 1000 -88.8871 0.010 879 1100 -88.8475 0.010 879 1200 -88.8463 0.010 879 1300 -88.8312 0.010 879 1400 -88.8046 0.010 879 1500 -88.7999 0.010 879 1600 -88.7604 0.010 879 1700 -88.7532 0.010 879 1800 -88.7145 0.010 879 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 1892, seed 1659727313, best lnL -88.698 gen current_lnL precision last_tree_imp 1892 -88.6979 0.010 879 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0165 0.0083 0.0496 0.0909 0.0909 0.0083 0.0744 0.0083 0.0083 0.1074 0.1157 0.0248 0.1240 0.0331 0.0083 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 1.5379 with an invariant (invariable) site category, proportion estimated 0.1862 Substitution rate categories under this model: rate proportion 0.0000 0.1862 0.2908 0.2713 0.8063 0.2713 1.9029 0.2713 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -88.6979 Parameter estimates: alpha pinv rep 1: 1.538 0.186 Treelengths: TL rep 1: 2.363 Saving best tree to bootstrap file ch.a.G3.boot.tre >>>Completed Bootstrap rep 1<<< ####################################################### 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 84 600 -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 -110.5066 0.010 707 1100 -110.4789 0.010 707 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 1178, seed 1189642758, best lnL -110.448 gen current_lnL precision last_tree_imp 1178 -110.4480 0.010 707 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: 4 discrete gamma distributed rate categories, alpha param estimated 1.4529 with an invariant (invariable) site category, proportion estimated 0.0935 Substitution rate categories under this model: rate proportion 0.0000 0.0935 0.2180 0.2266 0.5805 0.2266 1.0475 0.2266 2.1540 0.2266 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file ch.a.G4.sitelikes.log ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -110.4480 Parameter estimates: alpha pinv rep 1: 1.453 0.094 Treelengths: TL rep 1: 2.615 Saving final tree from best search rep (#1) to ch.a.G4.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.G4.internalstates.log ####################################################### TREEFILES PASS Running checkpoint test ./check/a.conf Running checkpoint test ./check/a.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 2000 -111.6817 0.010 563 2100 -111.6817 0.010 563 2200 -111.6817 0.010 563 2300 -111.6817 0.010 563 2400 -111.6817 0.010 563 2500 -111.6817 0.010 563 2600 -111.6816 0.010 563 2700 -111.6816 0.010 563 2800 -111.6816 0.010 563 2900 -111.6815 0.010 563 3000 -111.6815 0.010 563 3100 -111.6815 0.010 563 3200 -111.6815 0.010 563 Reached termination condition! last topological improvement at gen 563 Improvement over last 500 gen = 0.00009 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) No branches were short enough to be collapsed. Saving site likelihoods to file ch.a.sitelikes.log ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -111.6815 Parameter estimates: Model contains no estimated parameters Treelengths: TL rep 1: 2.607 Saving final tree from best search rep (#1) to ch.a.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.internalstates.log ####################################################### Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 3200, seed 1669543796, best lnL -111.681 gen current_lnL precision last_tree_imp 3200 -111.6815 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) No branches were short enough to be collapsed. Saving site likelihoods to file ch.a.sitelikes.log ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -111.6815 Parameter estimates: Model contains no estimated parameters Treelengths: TL rep 1: 2.607 Saving final tree from best search rep (#1) to ch.a.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.internalstates.log ####################################################### 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 70 -205.5741 0.500 53 80 -205.4022 0.500 76 90 -205.3871 0.500 76 100 -205.3829 0.500 76 110 -205.3431 0.500 106 120 -205.3431 0.500 106 130 -205.2505 0.500 121 140 -205.2440 0.500 121 150 -205.1047 0.500 121 160 -205.0609 0.500 121 170 -204.9812 0.500 121 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 171, seed 1312101128, best lnL -204.981 gen current_lnL precision last_tree_imp 171 -204.9812 0.500 121 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.586, AG = 4.036, 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 0.0473 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 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -204.9812 Parameter estimates: w(0) p(0) w(1) p(1) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) rep 1: 0.047 0.521 0.499 0.479 1.586 4.036 0.04 2.453 3.968 1 Treelengths: TL rep 1: 7.813 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 ####################################################### TREEFILES PASS Running checkpoint test ./check/c.conf Running checkpoint test ./check/c.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 -195.2554 0.500 0 50 -195.2137 0.500 0 60 -195.1629 0.500 0 70 -195.0042 0.500 0 80 -194.9478 0.500 0 90 -194.9092 0.500 0 100 -194.9092 0.500 0 110 -194.8986 0.500 0 120 -194.8986 0.500 0 130 -194.8984 0.500 0 140 -194.8500 0.500 0 150 -194.7085 0.500 0 160 -194.7085 0.500 0 170 -194.5936 0.500 168 180 -194.5926 0.500 168 190 -194.5693 0.500 168 200 -194.2413 0.500 196 210 -194.2413 0.500 196 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 215, seed 276267568, best lnL -194.204 gen current_lnL precision last_tree_imp 215 -194.2043 0.500 196 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 61 (codon data, standard code) One estimated dN/dS ratio (aka omega) = 0.120507 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.637, AG = 5.880, AT = 0.011, CG = 4.174, CT = 2.304, 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. ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -194.2043 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 5.88 0.01146 4.174 2.304 1 Treelengths: TL rep 1: 10.277 Saving best tree to bootstrap file ch.c.boot.tre >>>Completed Bootstrap rep 1<<< ####################################################### 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 0.831 lnL Optimizing branchlengths... improved 0.085 lnL 1100 -3352.7180 0.010 0 1200 -3352.6366 0.010 0 1300 -3352.5137 0.010 0 1400 -3352.4036 0.010 0 1500 -3352.3987 0.010 0 1600 -3352.2919 0.010 0 1700 -3352.2843 0.010 0 1800 -3352.2036 0.010 0 1900 -3351.8476 0.010 0 2000 -3351.7698 0.010 0 2100 -3351.6181 0.010 0 2200 -3351.3750 0.010 0 2300 -3351.3499 0.010 0 2400 -3351.3426 0.010 0 2500 -3351.2398 0.010 0 2600 -3351.1737 0.010 0 2700 -3351.1734 0.010 0 2800 -3351.1196 0.010 0 2900 -3351.1184 0.010 0 3000 -3351.1143 0.010 0 3100 -3351.1019 0.010 0 3200 -3351.0899 0.010 0 3300 -3351.0880 0.010 0 3400 -3351.0866 0.010 0 3500 -3351.0854 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 3560, seed 284781261, best lnL -3351.085 gen current_lnL precision last_tree_imp 3560 -3351.0848 0.010 0 3600 -3351.0827 0.010 0 3700 -3351.0495 0.010 0 3800 -3351.0374 0.010 0 3900 -3350.9831 0.010 0 4000 -3350.9831 0.010 0 4100 -3350.9762 0.010 0 4200 -3350.9697 0.010 0 4300 -3350.9691 0.010 0 4400 -3350.9650 0.010 0 4500 -3350.9650 0.010 0 4600 -3350.9243 0.010 0 4700 -3350.9241 0.010 0 4800 -3350.9231 0.010 0 4900 -3350.9231 0.010 0 5000 -3350.9221 0.010 0 5100 -3350.8994 0.010 0 5200 -3350.8809 0.010 0 5300 -3350.8796 0.010 0 5400 -3350.8607 0.010 0 5500 -3350.8014 0.010 0 5600 -3350.7518 0.010 0 5700 -3350.7432 0.010 0 5800 -3350.6963 0.010 0 5900 -3350.6922 0.010 0 6000 -3350.6866 0.010 0 6100 -3350.6725 0.010 0 6200 -3350.6725 0.010 0 6300 -3350.6688 0.010 0 6400 -3350.6676 0.010 0 6500 -3350.6676 0.010 0 6600 -3350.6636 0.010 0 6700 -3350.6636 0.010 0 6800 -3350.6588 0.010 0 6900 -3350.6246 0.010 0 7000 -3350.6208 0.010 0 7100 -3350.6204 0.010 0 7200 -3350.6204 0.010 0 7300 -3350.6197 0.010 0 7400 -3350.5966 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... Current score = -3350.5954 Performing final optimizations... pass 1 : -3350.5551 (branch= 0.0000 alpha= 0.0000 pinv= 0.0225 eq freqs= 0.0115 rel rates= 0.0063 subset rates= 0.0000) pass 2 : -3350.5211 (branch= 0.0000 alpha= 0.0195 pinv= 0.0144 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) pass 3 : -3350.4834 (branch= 0.0015 alpha= 0.0147 pinv= 0.0131 eq freqs= 0.0017 rel rates= 0.0069 subset rates= 0.0000) pass 4 : -3350.4561 (branch= 0.0025 alpha= 0.0116 pinv= 0.0123 eq freqs= 0.0000 rel rates= 0.0008 subset rates= 0.0000) pass 5 : -3350.4283 (branch= 0.0022 alpha= 0.0128 pinv= 0.0111 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0017) pass 6 : -3350.4049 (branch= 0.0015 alpha= 0.0108 pinv= 0.0101 eq freqs= 0.0004 rel rates= 0.0006 subset rates= 0.0000) pass 7 : -3350.3854 (branch= 0.0002 alpha= 0.0094 pinv= 0.0091 eq freqs= 0.0000 rel rates= 0.0007 subset rates= 0.0000) pass 8 : -3350.3665 (branch= 0.0006 alpha= 0.0085 pinv= 0.0082 eq freqs= 0.0001 rel rates= 0.0004 subset rates= 0.0012) pass 9 : -3350.3503 (branch= 0.0010 alpha= 0.0076 pinv= 0.0074 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) pass 10: -3350.3363 (branch= 0.0002 alpha= 0.0068 pinv= 0.0066 eq freqs= 0.0000 rel rates= 0.0004 subset rates= 0.0000) pass 11: -3350.3235 (branch= 0.0001 alpha= 0.0065 pinv= 0.0058 eq freqs= 0.0000 rel rates= 0.0004 subset rates= 0.0000) pass 12: -3350.3120 (branch= 0.0000 alpha= 0.0059 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0004 subset rates= 0.0000) pass 13: -3350.3018 (branch= 0.0000 alpha= 0.0053 pinv= 0.0046 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) pass 14: -3350.2928 (branch= 0.0000 alpha= 0.0047 pinv= 0.0041 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) pass 15: -3350.2849 (branch= 0.0000 alpha= 0.0041 pinv= 0.0036 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) pass 16: -3350.2780 (branch= 0.0000 alpha= 0.0036 pinv= 0.0031 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) pass 17: -3350.2719 (branch= 0.0000 alpha= 0.0032 pinv= 0.0028 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) pass 18: -3350.2665 (branch= 0.0000 alpha= 0.0028 pinv= 0.0024 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) pass 19: -3350.2619 (branch= 0.0000 alpha= 0.0024 pinv= 0.0021 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) pass 20: -3350.2578 (branch= 0.0000 alpha= 0.0021 pinv= 0.0018 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) optimization up to ... pass 30: -3350.2380 (branch= 0.0000 alpha= 0.0103 pinv= 0.0091 eq freqs= 0.0000 rel rates= 0.0004 subset rates= 0.0000) optimization up to ... pass 40: -3350.2338 (branch= 0.0000 alpha= 0.0021 pinv= 0.0019 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) optimization up to ... pass 50: -3350.2331 (branch= 0.0000 alpha= 0.0004 pinv= 0.0004 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) optimization up to ... pass 54: -3350.2330 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -3350.2330 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 3.136, AG = 10.490, AT = 2.711, CG = 0.001, CT = 22.089, 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 0.5750 with an invariant (invariable) site category, proportion estimated 0.3648 Substitution rate categories under this model: rate proportion 0.0000 0.3648 0.0480 0.1588 0.2981 0.1588 0.8680 0.1588 2.7859 0.1588 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 : -3350.2330 (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: 3.136 10.49 2.711 0.001 22.09 1 0.333 0.222 0.157 0.288 0.575 0.365 Partition model subset 2: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) rep 1: 0.790 1.821 0.179 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 1 500 -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 -3321.3650 0.255 1 800 -3321.0295 0.255 1 900 -3321.0142 0.255 1 1000 -3320.9667 0.255 1 1100 -3320.8654 0.255 1 Optimization precision reduced Optimizing parameters... improved 0.578 lnL Optimizing branchlengths... improved 0.060 lnL 1200 -3320.1462 0.010 1 1300 -3320.0857 0.010 1 1400 -3320.0695 0.010 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 1428, seed 585325787, best lnL -3320.025 gen current_lnL precision last_tree_imp 1428 -3320.0255 0.010 1 1500 -3320.0226 0.010 1 1600 -3320.0183 0.010 1 1700 -3320.0152 0.010 1 1800 -3319.8191 0.010 1 1900 -3319.6008 0.010 1 2000 -3319.5579 0.010 1 2100 -3319.5506 0.010 1 2200 -3319.4670 0.010 1 2300 -3319.3661 0.010 1 2400 -3319.3307 0.010 1 NOTE: ****Specified time limit (5 seconds) reached... Current score = -3319.3293 Performing final optimizations... pass 1 : -3319.0714 (branch= 0.0074 alpha= 0.0000 pinv= 0.0160 eq freqs= 0.0110 rel rates= 0.1612 ins/del rates= 0.0623) pass 2 : -3318.8830 (branch= 0.0321 alpha= 0.0083 pinv= 0.0161 eq freqs= 0.0000 rel rates= 0.1227 ins/del rates= 0.0092) pass 3 : -3318.7273 (branch= 0.0274 alpha= 0.0122 pinv= 0.0146 eq freqs= 0.0018 rel rates= 0.0931 ins/del rates= 0.0066) pass 4 : -3318.5910 (branch= 0.0180 alpha= 0.0114 pinv= 0.0140 eq freqs= 0.0014 rel rates= 0.0860 ins/del rates= 0.0055) pass 5 : -3318.4830 (branch= 0.0116 alpha= 0.0108 pinv= 0.0133 eq freqs= 0.0006 rel rates= 0.0672 ins/del rates= 0.0044) pass 6 : -3318.3923 (branch= 0.0074 alpha= 0.0101 pinv= 0.0125 eq freqs= 0.0002 rel rates= 0.0573 ins/del rates= 0.0032) pass 7 : -3318.3126 (branch= 0.0049 alpha= 0.0096 pinv= 0.0116 eq freqs= 0.0006 rel rates= 0.0511 ins/del rates= 0.0020) pass 8 : -3318.2433 (branch= 0.0034 alpha= 0.0098 pinv= 0.0106 eq freqs= 0.0002 rel rates= 0.0438 ins/del rates= 0.0014) pass 9 : -3318.1846 (branch= 0.0022 alpha= 0.0091 pinv= 0.0097 eq freqs= 0.0001 rel rates= 0.0367 ins/del rates= 0.0009) pass 10: -3318.1330 (branch= 0.0014 alpha= 0.0085 pinv= 0.0089 eq freqs= 0.0001 rel rates= 0.0322 ins/del rates= 0.0006) pass 11: -3318.0887 (branch= 0.0010 alpha= 0.0078 pinv= 0.0081 eq freqs= 0.0000 rel rates= 0.0270 ins/del rates= 0.0004) pass 12: -3318.0500 (branch= 0.0006 alpha= 0.0074 pinv= 0.0073 eq freqs= 0.0001 rel rates= 0.0230 ins/del rates= 0.0003) pass 13: -3318.0163 (branch= 0.0004 alpha= 0.0067 pinv= 0.0066 eq freqs= 0.0000 rel rates= 0.0198 ins/del rates= 0.0002) pass 14: -3317.9868 (branch= 0.0003 alpha= 0.0061 pinv= 0.0060 eq freqs= 0.0000 rel rates= 0.0170 ins/del rates= 0.0001) pass 15: -3317.9610 (branch= 0.0002 alpha= 0.0056 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0146 ins/del rates= 0.0001) pass 16: -3317.9384 (branch= 0.0001 alpha= 0.0050 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0126 ins/del rates= 0.0000) pass 17: -3317.9187 (branch= 0.0001 alpha= 0.0046 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0108 ins/del rates= 0.0000) pass 18: -3317.9015 (branch= 0.0000 alpha= 0.0041 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0092 ins/del rates= 0.0000) pass 19: -3317.8865 (branch= 0.0000 alpha= 0.0037 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0080 ins/del rates= 0.0000) pass 20: -3317.8733 (branch= 0.0000 alpha= 0.0033 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0069 ins/del rates= 0.0000) optimization up to ... pass 30: -3317.8073 (branch= 0.0001 alpha= 0.0170 pinv= 0.0156 eq freqs= 0.0001 rel rates= 0.0332 ins/del rates= 0.0000) optimization up to ... pass 40: -3317.7916 (branch= 0.0001 alpha= 0.0041 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0078 ins/del rates= 0.0000) optimization up to ... pass 50: -3317.7880 (branch= 0.0000 alpha= 0.0009 pinv= 0.0008 eq freqs= 0.0000 rel rates= 0.0019 ins/del rates= 0.0000) optimization up to ... pass 60: -3317.7873 (branch= 0.0000 alpha= 0.0002 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0004 ins/del rates= 0.0000) optimization up to ... pass 69: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3317.7871 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 3.064, AG = 10.257, AT = 2.654, CG = 0.001, CT = 21.525, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3328 0.2223 0.1567 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5745 with an invariant (invariable) site category, proportion estimated 0.3611 Substitution rate categories under this model: rate proportion 0.0000 0.3611 0.0479 0.1597 0.2978 0.1597 0.8677 0.1597 2.7866 0.1597 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: 3.064 10.26 2.654 0.001 21.53 1 0.333 0.222 0.157 0.288 0.574 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: 1.418 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 1.264 lnL Optimizing branchlengths... improved 0.275 lnL 1200 -211.1652 0.010 1104 1400 -211.1318 0.010 1104 1600 -211.0218 0.010 1104 1800 -210.9997 0.010 1104 2000 -210.9460 0.010 1104 2200 -210.8946 0.010 1104 2400 -210.8864 0.010 1104 2600 -210.8436 0.010 1104 2800 -210.8249 0.010 1104 3000 -210.8188 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 -210.6946 0.010 1104 4200 -210.6740 0.010 1104 4400 -210.6493 0.010 1104 4600 -210.6257 0.010 1104 4800 -210.5948 0.010 1104 5000 -210.5740 0.010 1104 5200 -210.5693 0.010 1104 5400 -210.5461 0.010 1104 5600 -210.5151 0.010 1104 5800 -210.4823 0.010 1104 6000 -210.4632 0.010 1104 6200 -210.4596 0.010 1104 6400 -210.4468 0.010 1104 6600 -210.4214 0.010 1104 6800 -210.3964 0.010 1104 7000 -210.3383 0.010 1104 7200 -210.3217 0.010 1104 7400 -210.2807 0.010 1104 7600 -210.2625 0.010 1104 7800 -210.1872 0.010 1104 8000 -210.1732 0.010 1104 8200 -210.1275 0.010 1104 8400 -210.1090 0.010 1104 8600 -210.0887 0.010 1104 8800 -210.0539 0.010 1104 9000 -210.0488 0.010 1104 9200 -209.9764 0.010 1104 9400 -209.9612 0.010 1104 9600 -209.9440 0.010 1104 9800 -209.9190 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 9996, seed 428919122, best lnL -209.886 gen current_lnL precision last_tree_imp 9996 -209.8863 0.010 1104 10000 -209.8863 0.010 1104 Optimizing parameters... improved 0.505 lnL Optimizing branchlengths... improved 0.011 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 = 5.150, AG = 9.093, AT = 0.233, CG = 9.359, CT = 14.077, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2377 0.3274 0.2094 0.2255 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 4.1580 with an invariant (invariable) site category, proportion estimated 0.2914 Substitution rate categories under this model: rate proportion 0.0000 0.2914 0.5191 0.2362 0.9259 0.2362 1.5550 0.2362 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. Saving site likelihoods to file ch.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 : -209.3698 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: 5.15 9.093 0.2328 9.359 14.08 1 0.238 0.327 0.209 0.225 4.158 0.291 Treelengths: TL rep 1: 2.284 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 WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 0.319 lnL 1000 -167.2082 0.010 843 1200 -167.1487 0.010 843 1400 -167.0497 0.010 843 1600 -166.9651 0.010 843 1800 -166.8256 0.010 843 2000 -166.7014 0.010 843 2200 -166.6037 0.010 843 2400 -166.5437 0.010 843 2600 -166.4761 0.010 843 2800 -166.4631 0.010 843 3000 -166.4054 0.010 843 3200 -166.3555 0.010 843 3400 -166.2985 0.010 843 3600 -166.2506 0.010 843 3800 -166.1403 0.010 843 4000 -166.1354 0.010 843 4200 -166.0869 0.010 843 4400 -166.0244 0.010 843 4600 -165.9672 0.010 843 4800 -165.9475 0.010 843 5000 -165.8859 0.010 843 5200 -165.8689 0.010 843 5400 -165.8337 0.010 843 5600 -165.6916 0.010 843 5800 -165.5811 0.010 843 6000 -165.5435 0.010 843 6200 -165.4997 0.010 843 6400 -165.3822 0.010 843 6600 -165.3045 0.010 843 6800 -165.1802 0.010 6750 7000 -165.1486 0.010 6750 7200 -165.1326 0.010 6750 7400 -164.9712 0.010 6750 7600 -164.9063 0.010 7540 7800 -164.7723 0.010 7540 8000 -164.6934 0.010 7540 8200 -164.5487 0.010 7540 8400 -164.4148 0.010 7540 8600 -164.2339 0.010 7540 8800 -164.0455 0.010 7540 9000 -163.8878 0.010 7540 9200 -163.8773 0.010 7540 9400 -163.8424 0.010 7540 9600 -163.7592 0.010 7540 9800 -163.7102 0.010 7540 10000 -163.6729 0.010 7540 Optimizing parameters... improved 1.625 lnL Optimizing branchlengths... improved 0.033 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 = 0.657, AG = 11.198, AT = 2.634, CG = 4.227, CT = 35.803, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1301 0.4168 0.2379 0.2153 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 522.6859 with an invariant (invariable) site category, proportion estimated 0.3437 Substitution rate categories under this model: rate proportion 0.0000 0.3437 0.9450 0.1641 0.9853 0.1641 1.0136 0.1641 1.0561 0.1641 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 : -162.0153 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: 0.6571 11.2 2.634 4.227 35.8 1 0.130 0.417 0.238 0.215 522.686 0.344 Treelengths: TL rep 1: 2.891 Saving best tree to bootstrap file ch.n.G4.boot.tre WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 10001, seed 258537382, best lnL -162.015 gen current_lnL precision last_tree_imp 10001 -162.0153 0.010 7540 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 0.657, AG = 11.198, AT = 2.634, CG = 4.227, CT = 35.803, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1301 0.4168 0.2379 0.2153 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 522.6859 with an invariant (invariable) site category, proportion estimated 0.3437 Substitution rate categories under this model: rate proportion 0.0000 0.3437 0.9450 0.1641 0.9853 0.1641 1.0136 0.1641 1.0561 0.1641 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 3 branches were collapsed. ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -162.0153 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: 0.6571 11.2 2.634 4.227 35.8 1 0.130 0.417 0.238 0.215 522.686 0.344 Treelengths: TL rep 1: 2.891 Saving best tree to bootstrap file ch.n.G4.boot.tre >>>Completed Bootstrap rep 1<<< ####################################################### TREEFILES PASS Running checkpoint test ./check/n.conf Running checkpoint test ./check/n.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 -213.6190 0.010 530 1400 -213.5800 0.010 530 1600 -213.5576 0.010 530 1800 -213.3951 0.010 530 2000 -213.3646 0.010 530 2200 -213.3318 0.010 530 2400 -213.2445 0.010 530 2600 -213.2282 0.010 530 2800 -213.2193 0.010 530 3000 -213.2001 0.010 530 3200 -213.1945 0.010 530 3400 -213.1682 0.010 530 3600 -213.1580 0.010 530 3800 -213.0250 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 -212.8760 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 -212.6654 0.010 3769 8000 -212.6638 0.010 3769 8200 -212.6580 0.010 3769 8400 -212.6570 0.010 3769 8600 -212.6362 0.010 3769 8800 -212.5814 0.010 3769 9000 -212.5437 0.010 3769 9200 -212.5310 0.010 3769 9400 -212.5139 0.010 3769 9600 -212.5123 0.010 3769 9800 -212.5095 0.010 3769 10000 -212.5014 0.010 3769 Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 0.000 lnL NOTE: ****Specified generation limit (10000) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 7.821, AG = 15.066, AT = 0.614, CG = 15.031, CT = 9.551, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2189 0.2871 0.1831 0.3108 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. Saving site likelihoods to file ch.n.sitelikes.log ... WARNING: Site likelihoods being output on prematurely terminated search ... NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -212.5014 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 7.821 15.07 0.6138 15.03 9.551 1 0.219 0.287 0.183 0.311 Treelengths: TL rep 1: 1.722 Saving final tree from best search rep (#1) to ch.n.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 10001, seed 1459438551, best lnL -212.501 gen current_lnL precision last_tree_imp 10001 -212.5014 0.010 3769 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 7.821, AG = 15.066, AT = 0.614, CG = 15.031, CT = 9.551, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2189 0.2871 0.1831 0.3108 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. Saving site likelihoods to file ch.n.sitelikes.log ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -212.5014 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 7.821 15.07 0.6138 15.03 9.551 1 0.219 0.287 0.183 0.311 Treelengths: TL rep 1: 1.722 Saving final tree from best search rep (#1) to ch.n.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log ####################################################### 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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: -219.1444 gen current_lnL precision last_tree_imp 0 -219.1444 0.500 0 200 -217.4629 0.500 32 400 -216.6525 0.500 363 600 -216.1292 0.500 474 800 -215.4112 0.500 669 1000 -215.0097 0.500 936 1200 -214.3653 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 -210.9688 0.010 1502 2200 -210.8960 0.010 1502 2400 -210.8906 0.010 1502 2600 -210.8172 0.010 1502 2800 -210.7847 0.010 1502 3000 -210.7510 0.010 2883 3200 -210.7243 0.010 2883 3400 -210.7006 0.010 2883 3600 -210.6993 0.010 2883 3800 -210.6778 0.010 2883 4000 -210.6775 0.010 2883 4200 -210.6505 0.010 2883 4400 -210.6306 0.010 2883 4600 -210.6208 0.010 2883 4800 -210.5769 0.010 2883 5000 -210.5646 0.010 2883 5200 -210.5368 0.010 2883 5400 -210.5093 0.010 2883 5600 -210.5005 0.010 2883 5800 -210.3871 0.010 2883 6000 -210.3538 0.010 2883 6200 -210.3498 0.010 2883 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 6242, seed 1195716606, best lnL -210.348 gen current_lnL precision last_tree_imp 6242 -210.3483 0.010 2883 6300 -210.3452 0.010 2883 Reached termination condition! last topological improvement at gen 2883 Improvement over last 500 gen = 0.04187 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 2.043, AG = 4.107, AT = 0.207, CG = 3.802, CT = 7.237, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2421 0.3373 0.2121 0.2085 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 1.4302 with an invariant (invariable) site category, proportion estimated 0.1960 Substitution rate categories under this model: rate proportion 0.0000 0.1960 0.2143 0.2010 0.5765 0.2010 1.0460 0.2010 2.1631 0.2010 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 : -210.3452 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: 2.043 4.107 0.2071 3.802 7.237 1 0.242 0.337 0.212 0.208 1.430 0.196 Treelengths: TL rep 1: 2.430 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 222.682 (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 -13375.8794 0.500 0 200 -13373.8436 0.500 0 300 -13372.9678 0.500 0 400 -13371.8986 0.500 0 500 -13371.5865 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 -13371.0755 0.402 0 800 -13370.9489 0.402 0 900 -13370.7802 0.402 0 1000 -13370.6791 0.402 0 Optimization precision reduced Optimizing parameters... improved 0.037 lnL Optimizing branchlengths... improved 0.000 lnL 1100 -13370.5869 0.304 0 1200 -13370.5241 0.304 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 1208, seed 528078057, best lnL -13370.524 gen current_lnL precision last_tree_imp 1208 -13370.5241 0.304 0 1300 -13370.5104 0.304 0 1400 -13370.5063 0.304 0 1500 -13370.4967 0.304 0 Optimization precision reduced Optimizing parameters... improved 0.015 lnL Optimizing branchlengths... improved 0.000 lnL 1600 -13370.4816 0.206 0 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 = 1.605, AG = 2.506, AT = 1.208, CG = 1.208, CT = 4.152, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3082 0.1811 0.3085 0.2021 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.3642 Substitution rate categories under this model: rate proportion 0.0119 0.2500 0.1545 0.2500 0.6894 0.2500 3.1441 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 = 2.624, AG = 4.245, AT = 0.821, CG = 4.245, CT = 2.624, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2815 0.1769 0.1594 0.3822 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.2458 Substitution rate categories under this model: rate proportion 0.0019 0.2500 0.0637 0.2500 0.4925 0.2500 3.4419 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 = 5.332, AT = 4.291, CG = 0.633, CT = 5.332, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1554 0.3462 0.2765 0.2219 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 4.1103 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 : -13370.4688 (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: 1.605 2.506 1.208 1.208 4.152 1 0.308 0.181 0.309 0.202 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: 2.624 4.245 0.821 4.245 2.624 1 0.281 0.177 0.159 0.382 0.246 Partition model subset 3: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 1 5.332 4.291 0.6327 5.332 1 0.155 0.346 0.276 0.222 4.110 0.049 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 1.762 0.530 0.287 2.183 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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= 4.30) pass 2:+ 9.055 (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:+ 0.303 (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: -467.8152 gen current_lnL precision last_tree_imp 0 -467.8152 0.010 0 100 -467.7854 0.010 76 200 -467.7768 0.010 76 300 -467.7654 0.010 76 400 -467.7615 0.010 76 500 -467.7562 0.010 76 600 -467.7505 0.010 76 700 -467.7495 0.010 76 800 -467.7483 0.010 76 900 -467.7471 0.010 76 1000 -467.7427 0.010 76 1100 -467.7372 0.010 76 1200 -467.7330 0.010 76 1300 -467.7317 0.010 76 1400 -467.7307 0.010 76 1500 -467.7301 0.010 76 1600 -467.7294 0.010 76 1700 -467.7252 0.010 76 1800 -467.7239 0.010 76 1900 -467.7239 0.010 76 2000 -467.7234 0.010 76 2100 -467.7228 0.010 76 2200 -467.7218 0.010 76 2300 -467.7216 0.010 76 2400 -467.7209 0.010 76 2500 -467.7205 0.010 76 2600 -467.7205 0.010 76 2700 -467.7197 0.010 76 2800 -467.7190 0.010 76 2900 -467.7186 0.010 76 3000 -467.7184 0.010 76 3100 -467.7181 0.010 76 3200 -467.7180 0.010 76 3300 -467.7179 0.010 76 3400 -467.7178 0.010 76 Reached termination condition! last topological improvement at gen 76 Improvement over last 500 gen = 0.00072 Current score = -467.7178 Performing final optimizations... pass 1 : -467.7126 (branch= 0.0000 subset rates= 0.0052) pass 2 : -467.6927 (branch= 0.0182 subset rates= 0.0018) pass 3 : -467.6906 (branch= 0.0018 subset rates= 0.0003) pass 4 : -467.6866 (branch= 0.0040 subset rates= 0.0000) pass 5 : -467.6836 (branch= 0.0018 subset rates= 0.0011) pass 6 : -467.6820 (branch= 0.0017 subset rates= 0.0000) pass 7 : -467.6809 (branch= 0.0010 subset rates= 0.0000) pass 8 : -467.6803 (branch= 0.0006 subset rates= 0.0000) pass 9 : -467.6800 (branch= 0.0003 subset rates= 0.0000) pass 10: -467.6799 (branch= 0.0001 subset rates= 0.0000) pass 11: -467.6798 (branch= 0.0001 subset rates= 0.0000) pass 12: -467.6798 (branch= 0.0000 subset rates= 0.0000) pass 13: -467.6798 (branch= 0.0000 subset rates= 0.0000) pass 14: -467.6798 (branch= 0.0000 subset rates= 0.0000) pass 15: -467.6797 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6797 Time used so far = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate 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 2.15 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=864977241 Initial ln Likelihood: -614.0831 optimizing: starting branch lengths, subset rates... pass 1:+ 127.392 (branch= 121.24 scale= 1.98 subset rates= 4.16) pass 2:+ 15.987 (branch= 15.02 scale= 0.02 subset rates= 0.96) pass 3:+ 2.694 (branch= 2.46 scale= 0.04 subset rates= 0.20) pass 4:+ 0.135 (branch= 0.13 scale= 0.00 subset rates= 0.00) pass 5:+ 0.039 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -467.8359 gen current_lnL precision last_tree_imp 0 -467.8359 0.010 0 100 -467.8013 0.010 0 200 -467.7836 0.010 0 300 -467.7721 0.010 0 400 -467.7470 0.010 0 500 -467.7426 0.010 0 600 -467.7398 0.010 0 700 -467.7362 0.010 0 800 -467.7332 0.010 0 900 -467.7319 0.010 0 1000 -467.7290 0.010 0 1100 -467.7275 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 1155, seed 640071195, best lnL -467.722 gen current_lnL precision last_tree_imp 1155 -467.7217 0.010 0 1200 -467.7204 0.010 0 1300 -467.7192 0.010 0 1400 -467.7176 0.010 0 1500 -467.7150 0.010 0 1600 -467.7149 0.010 0 1700 -467.7133 0.010 0 1800 -467.7124 0.010 0 1900 -467.7123 0.010 0 2000 -467.7121 0.010 0 2100 -467.7105 0.010 0 2200 -467.7090 0.010 0 2300 -467.7089 0.010 0 2400 -467.7088 0.010 0 2500 -467.7081 0.010 0 2600 -467.7078 0.010 0 2700 -467.7077 0.010 0 2800 -467.7071 0.010 0 2900 -467.7069 0.010 0 3000 -467.7067 0.010 0 3100 -467.7060 0.010 0 3200 -467.7054 0.010 0 3300 -467.7038 0.010 0 3400 -467.7033 0.010 0 3500 -467.7031 0.010 0 3600 -467.7029 0.010 0 3700 -467.7027 0.010 0 3800 -467.7026 0.010 0 3900 -467.7019 0.010 0 4000 -467.7013 0.010 0 4100 -467.7011 0.010 0 4200 -467.7011 0.010 0 4300 -467.7006 0.010 0 4400 -467.7005 0.010 0 4500 -467.7004 0.010 0 Reached termination condition! last topological improvement at gen 0 Improvement over last 500 gen = 0.00086 Current score = -467.7004 Performing final optimizations... pass 1 : -467.7004 (branch= 0.0000 subset rates= 0.0000) pass 2 : -467.6882 (branch= 0.0122 subset rates= 0.0000) pass 3 : -467.6834 (branch= 0.0048 subset rates= 0.0000) pass 4 : -467.6825 (branch= 0.0009 subset rates= 0.0000) pass 5 : -467.6814 (branch= 0.0011 subset rates= 0.0000) pass 6 : -467.6800 (branch= 0.0014 subset rates= 0.0000) pass 7 : -467.6790 (branch= 0.0010 subset rates= 0.0000) pass 8 : -467.6787 (branch= 0.0002 subset rates= 0.0000) pass 9 : -467.6785 (branch= 0.0002 subset rates= 0.0000) pass 10: -467.6784 (branch= 0.0002 subset rates= 0.0000) pass 11: -467.6783 (branch= 0.0000 subset rates= 0.0000) pass 12: -467.6783 (branch= 0.0000 subset rates= 0.0000) pass 13: -467.6783 (branch= 0.0000 subset rates= 0.0000) pass 14: -467.6783 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6783 Time used so far = 0 hours, 0 minutes and 9 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 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=1668858692 Initial ln Likelihood: -630.9240 optimizing: starting branch lengths, subset rates... pass 1:+ 146.354 (branch= 140.50 scale= 1.37 subset rates= 4.49) pass 2:+ 13.171 (branch= 11.99 scale= 0.01 subset rates= 1.17) pass 3:+ 3.302 (branch= 3.17 scale= 0.00 subset rates= 0.13) pass 4:+ 0.252 (branch= 0.25 scale= 0.00 subset rates= 0.00) pass 5:+ 0.024 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -467.8203 gen current_lnL precision last_tree_imp 0 -467.8203 0.010 0 100 -467.7944 0.010 0 200 -467.7835 0.010 0 300 -467.7680 0.010 0 400 -467.7552 0.010 0 500 -467.7483 0.010 0 600 -467.7437 0.010 0 700 -467.7409 0.010 0 800 -467.7404 0.010 0 900 -467.7397 0.010 0 1000 -467.7346 0.010 0 1100 -467.7325 0.010 0 1200 -467.7292 0.010 0 1300 -467.7278 0.010 0 1400 -467.7254 0.010 0 1500 -467.7245 0.010 0 1600 -467.7242 0.010 0 1700 -467.7234 0.010 0 1800 -467.7219 0.010 0 1900 -467.7211 0.010 0 2000 -467.7200 0.010 0 2100 -467.7198 0.010 0 2200 -467.7194 0.010 0 2300 -467.7194 0.010 0 2400 -467.7185 0.010 0 2500 -467.7184 0.010 0 2600 -467.7182 0.010 0 2700 -467.7174 0.010 0 2800 -467.7172 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... Current score = -467.7169 Performing final optimizations... pass 1 : -467.7169 (branch= 0.0000 subset rates= 0.0000) pass 2 : -467.7016 (branch= 0.0153 subset rates= 0.0000) pass 3 : -467.6941 (branch= 0.0075 subset rates= 0.0000) pass 4 : -467.6900 (branch= 0.0042 subset rates= 0.0000) pass 5 : -467.6859 (branch= 0.0040 subset rates= 0.0000) pass 6 : -467.6829 (branch= 0.0030 subset rates= 0.0000) pass 7 : -467.6814 (branch= 0.0015 subset rates= 0.0000) pass 8 : -467.6805 (branch= 0.0009 subset rates= 0.0000) pass 9 : -467.6800 (branch= 0.0004 subset rates= 0.0000) pass 10: -467.6797 (branch= 0.0003 subset rates= 0.0000) pass 11: -467.6791 (branch= 0.0001 subset rates= 0.0005) pass 12: -467.6788 (branch= 0.0003 subset rates= 0.0000) pass 13: -467.6785 (branch= 0.0002 subset rates= 0.0000) pass 14: -467.6782 (branch= 0.0001 subset rates= 0.0003) pass 15: -467.6782 (branch= 0.0000 subset rates= 0.0000) pass 16: -467.6782 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6782 Time used so far = 0 hours, 0 minutes and 12 seconds 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 : -467.6797 Replicate 2 : -467.6783 (same topology as 1) Replicate 3 : -467.6782 (best) (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: 3.838 0.789 1.477 2.150 rep 2: 3.841 0.787 1.478 2.178 rep 3: 3.843 0.786 1.480 2.184 Saving final tree from best search rep (#3) 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 12.450 (branch= 8.46 scale= 0.00 subset rates= 3.99) pass 3:+ 3.552 (branch= 2.32 scale= 0.03 subset rates= 1.21) pass 4:+ 0.758 (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: -477.9401 gen current_lnL precision last_tree_imp 0 -477.9401 0.010 0 100 -477.8632 0.010 76 200 -477.8299 0.010 152 300 -477.7567 0.010 215 400 -477.5628 0.010 373 500 -477.5393 0.010 373 600 -477.5302 0.010 373 700 -477.5293 0.010 373 800 -477.5220 0.010 373 900 -477.5163 0.010 373 1000 -477.5148 0.010 373 1100 -477.5133 0.010 373 1200 -477.5083 0.010 373 1300 -477.5075 0.010 373 1400 -477.4995 0.010 373 1500 -477.4940 0.010 373 1600 -477.4867 0.010 373 1700 -477.4839 0.010 373 1800 -477.4824 0.010 373 1900 -477.4794 0.010 373 2000 -477.4782 0.010 373 2100 -477.4777 0.010 373 2200 -477.4766 0.010 373 2300 -477.4758 0.010 373 2400 -477.4754 0.010 373 2500 -477.4753 0.010 373 2600 -477.4749 0.010 373 2700 -477.4738 0.010 373 2800 -477.4737 0.010 373 2900 -477.4725 0.010 373 3000 -477.4725 0.010 373 3100 -477.4725 0.010 373 3200 -477.4718 0.010 373 3300 -477.4718 0.010 373 3400 -477.4717 0.010 373 Reached termination condition! last topological improvement at gen 373 Improvement over last 500 gen = 0.00083 Current score = -477.4717 Performing final optimizations... pass 1 : -477.4695 (branch= 0.0000 subset rates= 0.0022) pass 2 : -477.4423 (branch= 0.0272 subset rates= 0.0000) pass 3 : -477.4395 (branch= 0.0028 subset rates= 0.0000) pass 4 : -477.4388 (branch= 0.0007 subset rates= 0.0000) pass 5 : -477.4372 (branch= 0.0016 subset rates= 0.0000) pass 6 : -477.4355 (branch= 0.0016 subset rates= 0.0000) pass 7 : -477.4339 (branch= 0.0009 subset rates= 0.0007) pass 8 : -477.4330 (branch= 0.0010 subset rates= 0.0000) pass 9 : -477.4322 (branch= 0.0006 subset rates= 0.0001) pass 10: -477.4320 (branch= 0.0003 subset rates= 0.0000) pass 11: -477.4319 (branch= 0.0001 subset rates= 0.0000) pass 12: -477.4318 (branch= 0.0001 subset rates= 0.0000) pass 13: -477.4318 (branch= 0.0000 subset rates= 0.0000) pass 14: -477.4318 (branch= 0.0000 subset rates= 0.0000) pass 15: -477.4318 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.4318 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 2.72 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=425957087 Initial ln Likelihood: -636.0761 optimizing: starting branch lengths, subset rates... pass 1:+ 138.672 (branch= 128.04 scale= 0.72 subset rates= 9.91) pass 2:+ 13.747 (branch= 9.73 scale= 0.00 subset rates= 4.02) pass 3:+ 3.414 (branch= 2.10 scale= 0.00 subset rates= 1.31) pass 4:+ 1.365 (branch= 1.09 scale= 0.00 subset rates= 0.27) pass 5:+ 0.834 (branch= 0.80 scale= 0.01 subset rates= 0.02) pass 6:+ 0.191 (branch= 0.19 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -477.8544 gen current_lnL precision last_tree_imp 0 -477.8544 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 17, seed 689186569, best lnL -477.847 gen current_lnL precision last_tree_imp 17 -477.8469 0.010 0 100 -477.7502 0.010 36 200 -477.7249 0.010 149 300 -477.4594 0.010 203 400 -477.3874 0.010 366 500 -477.3748 0.010 366 600 -477.3633 0.010 366 700 -477.3569 0.010 366 800 -477.3520 0.010 366 900 -477.3483 0.010 366 1000 -477.3445 0.010 366 1100 -477.3365 0.010 366 1200 -477.3113 0.010 1197 1300 -477.2903 0.010 1197 1400 -477.2877 0.010 1197 1500 -477.2841 0.010 1197 1600 -477.2783 0.010 1197 1700 -477.2762 0.010 1197 1800 -477.2729 0.010 1197 1900 -477.2723 0.010 1197 2000 -477.2721 0.010 1197 2100 -477.2715 0.010 1197 2200 -477.2703 0.010 1197 2300 -477.2696 0.010 1197 2400 -477.2695 0.010 1197 2500 -477.2686 0.010 1197 2600 -477.2680 0.010 1197 2700 -477.2670 0.010 1197 2800 -477.2662 0.010 1197 2900 -477.2654 0.010 1197 3000 -477.2649 0.010 1197 3100 -477.2645 0.010 1197 3200 -477.2631 0.010 1197 3300 -477.2630 0.010 1197 3400 -477.2630 0.010 1197 3500 -477.2625 0.010 1197 3600 -477.2619 0.010 1197 3700 -477.2618 0.010 1197 3800 -477.2615 0.010 1197 3900 -477.2611 0.010 1197 4000 -477.2611 0.010 1197 4100 -477.2609 0.010 1197 4200 -477.2609 0.010 1197 Reached termination condition! last topological improvement at gen 1197 Improvement over last 500 gen = 0.00088 Current score = -477.2609 Performing final optimizations... pass 1 : -477.2399 (branch= 0.0055 subset rates= 0.0155) pass 2 : -477.2268 (branch= 0.0069 subset rates= 0.0062) pass 3 : -477.2118 (branch= 0.0143 subset rates= 0.0007) pass 4 : -477.2095 (branch= 0.0022 subset rates= 0.0000) pass 5 : -477.2078 (branch= 0.0018 subset rates= 0.0000) pass 6 : -477.2070 (branch= 0.0008 subset rates= 0.0000) pass 7 : -477.2060 (branch= 0.0010 subset rates= 0.0000) pass 8 : -477.2054 (branch= 0.0006 subset rates= 0.0000) pass 9 : -477.2052 (branch= 0.0002 subset rates= 0.0000) pass 10: -477.2051 (branch= 0.0001 subset rates= 0.0000) pass 11: -477.2051 (branch= 0.0000 subset rates= 0.0000) pass 12: -477.2050 (branch= 0.0000 subset rates= 0.0000) pass 13: -477.2050 (branch= 0.0000 subset rates= 0.0000) pass 14: -477.2050 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.2050 Time used so far = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.63 1.94 2.64 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 (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=792142821 Initial ln Likelihood: -607.1513 optimizing: starting branch lengths, subset rates... pass 1:+ 108.828 (branch= 98.09 scale= 0.82 subset rates= 9.92) pass 2:+ 14.908 (branch= 10.91 scale= 0.01 subset rates= 3.98) pass 3:+ 3.027 (branch= 1.70 scale= 0.00 subset rates= 1.32) pass 4:+ 1.411 (branch= 1.08 scale= 0.00 subset rates= 0.33) pass 5:+ 0.976 (branch= 0.95 scale= 0.00 subset rates= 0.03) pass 6:+ 0.207 (branch= 0.19 scale= 0.01 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -477.7945 gen current_lnL precision last_tree_imp 0 -477.7945 0.010 0 100 -477.7794 0.010 0 200 -477.7563 0.010 0 300 -477.7529 0.010 0 400 -477.7432 0.010 0 500 -477.7418 0.010 0 600 -477.3413 0.010 537 700 -477.3275 0.010 537 800 -477.3202 0.010 537 900 -477.3116 0.010 537 1000 -477.3054 0.010 537 1100 -477.3026 0.010 537 1200 -477.3003 0.010 537 1300 -477.2955 0.010 537 1400 -477.2902 0.010 537 1500 -477.2883 0.010 537 1600 -477.2865 0.010 537 1700 -477.2852 0.010 537 1800 -477.2835 0.010 537 1900 -477.2826 0.010 537 2000 -477.2805 0.010 537 2100 -477.2787 0.010 537 2200 -477.2785 0.010 537 NOTE: ****Specified time limit (5 seconds) reached... Current score = -477.2779 Performing final optimizations... pass 1 : -477.2779 (branch= 0.0000 subset rates= 0.0000) pass 2 : -477.2503 (branch= 0.0103 subset rates= 0.0173) pass 3 : -477.2221 (branch= 0.0072 subset rates= 0.0209) pass 4 : -477.2178 (branch= 0.0015 subset rates= 0.0028) pass 5 : -477.2147 (branch= 0.0031 subset rates= 0.0000) pass 6 : -477.2111 (branch= 0.0036 subset rates= 0.0000) pass 7 : -477.2096 (branch= 0.0015 subset rates= 0.0000) pass 8 : -477.2092 (branch= 0.0004 subset rates= 0.0000) pass 9 : -477.2092 (branch= 0.0001 subset rates= 0.0000) pass 10: -477.2091 (branch= 0.0000 subset rates= 0.0000) pass 11: -477.2088 (branch= 0.0001 subset rates= 0.0002) pass 12: -477.2062 (branch= 0.0000 subset rates= 0.0026) pass 13: -477.2061 (branch= 0.0001 subset rates= 0.0000) pass 14: -477.2047 (branch= 0.0000 subset rates= 0.0013) pass 15: -477.2046 (branch= 0.0001 subset rates= 0.0000) pass 16: -477.2046 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.2046 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 1.94 2.64 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 : -477.4318 Replicate 2 : -477.2050 Replicate 3 : -477.2046 (best) (same topology as 2) (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: 4.927 0.632 1.917 2.725 rep 2: 4.703 0.632 1.943 2.641 rep 3: 4.701 0.633 1.940 2.642 Saving final tree from best search rep (#3) to ch.p.mkO.ssr.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkv.ssr.conf Running checkpoint test ./check/p.mkv.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 0.368 (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 -430.2565 0.010 92 200 -427.7102 0.010 179 300 -426.9763 0.010 293 400 -425.6930 0.010 365 500 -425.6677 0.010 365 600 -425.6512 0.010 365 700 -425.6318 0.010 365 800 -425.6212 0.010 365 900 -425.6126 0.010 365 1000 -425.6095 0.010 365 1100 -425.6090 0.010 365 1200 -425.6083 0.010 365 1300 -425.6068 0.010 365 1400 -425.6058 0.010 365 1500 -425.6042 0.010 365 1600 -425.6022 0.010 365 1700 -425.5976 0.010 365 1800 -425.5972 0.010 365 1900 -425.5954 0.010 365 2000 -425.5950 0.010 365 2100 -425.5942 0.010 365 2200 -425.5913 0.010 365 2300 -425.5899 0.010 365 2400 -425.5893 0.010 365 2500 -425.5891 0.010 365 2600 -425.5890 0.010 365 2700 -425.5888 0.010 365 2800 -425.5883 0.010 365 2900 -425.5869 0.010 365 3000 -425.5868 0.010 365 3100 -425.5859 0.010 365 3200 -425.5858 0.010 365 3300 -425.5850 0.010 365 3400 -425.5843 0.010 365 3500 -425.5843 0.010 365 3600 -425.5841 0.010 365 3700 -425.5839 0.010 365 3800 -425.5839 0.010 365 3900 -425.5839 0.010 365 Reached termination condition! last topological improvement at gen 365 Improvement over last 500 gen = 0.00044 Current score = -425.5839 Performing final optimizations... pass 1 : -425.5730 (branch= 0.0000 subset rates= 0.0109) pass 2 : -425.5586 (branch= 0.0144 subset rates= 0.0000) pass 3 : -425.5516 (branch= 0.0070 subset rates= 0.0000) 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 : -425.5488 (branch= 0.0005 subset rates= 0.0000) pass 9 : -425.5487 (branch= 0.0001 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 3 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:+ 1.686 (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: -439.2276 gen current_lnL precision last_tree_imp 0 -439.2276 0.010 0 100 -428.8676 0.010 98 200 -428.0499 0.010 164 300 -427.6003 0.010 249 400 -427.5649 0.010 249 500 -427.4911 0.010 499 600 -427.3864 0.010 511 700 -425.7188 0.010 668 800 -425.6951 0.010 722 900 -425.6795 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 -425.6341 0.010 722 1600 -425.6274 0.010 722 1700 -425.6239 0.010 722 1800 -425.6235 0.010 722 1900 -425.6225 0.010 722 2000 -425.6202 0.010 722 2100 -425.6196 0.010 722 2200 -425.6174 0.010 722 2300 -425.6146 0.010 722 2400 -425.6135 0.010 722 2500 -425.6104 0.010 722 2600 -425.6099 0.010 722 2700 -425.6088 0.010 722 2800 -425.6077 0.010 722 2900 -425.6073 0.010 722 3000 -425.6058 0.010 722 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 2 (of 5) generation 3031, seed 1887747887, best lnL -425.606 gen current_lnL precision last_tree_imp 3031 -425.6058 0.010 722 3100 -425.6056 0.010 722 3200 -425.6055 0.010 722 3300 -425.6051 0.010 722 3400 -425.6049 0.010 722 3500 -425.6048 0.010 722 3600 -425.6048 0.010 722 Reached termination condition! last topological improvement at gen 722 Improvement over last 500 gen = 0.00084 Current score = -425.6048 Performing final optimizations... pass 1 : -425.5779 (branch= 0.0000 subset rates= 0.0269) pass 2 : -425.5572 (branch= 0.0188 subset rates= 0.0018) pass 3 : -425.5530 (branch= 0.0041 subset rates= 0.0001) pass 4 : -425.5518 (branch= 0.0012 subset rates= 0.0000) pass 5 : -425.5505 (branch= 0.0013 subset rates= 0.0000) pass 6 : -425.5498 (branch= 0.0007 subset rates= 0.0000) pass 7 : -425.5491 (branch= 0.0007 subset rates= 0.0000) pass 8 : -425.5489 (branch= 0.0003 subset rates= 0.0000) pass 9 : -425.5487 (branch= 0.0001 subset rates= 0.0000) pass 10: -425.5487 (branch= 0.0001 subset rates= 0.0000) pass 11: -425.5486 (branch= 0.0001 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 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.87 1.53 1.12 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 9 branches were collapsed. >>>Completed Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< >>>Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< Obtained starting tree 1 from Nexus Starting with seed=2129292874 Initial ln Likelihood: -588.2493 optimizing: starting branch lengths, subset rates... pass 1:+ 141.030 (branch= 140.49 scale= 0.38 subset rates= 0.17) pass 2:+ 6.536 (branch= 6.52 scale= 0.00 subset rates= 0.02) pass 3:+ 1.051 (branch= 1.03 scale= 0.00 subset rates= 0.02) pass 4:+ 0.060 (branch= 0.06 scale= 0.00 subset rates= 0.00) pass 5:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -439.5713 gen current_lnL precision last_tree_imp 0 -439.5713 0.010 0 100 -431.1391 0.010 95 200 -428.6585 0.010 167 300 -427.6514 0.010 295 400 -427.2438 0.010 295 500 -427.2138 0.010 295 600 -427.1679 0.010 568 700 -427.1487 0.010 568 800 -425.4817 0.010 762 900 -425.4264 0.010 803 1000 -425.4085 0.010 803 1100 -425.4058 0.010 803 1200 -425.3915 0.010 803 1300 -425.3912 0.010 803 1400 -425.3887 0.010 803 1500 -425.3865 0.010 803 1600 -425.3820 0.010 803 1700 -425.3760 0.010 803 1800 -425.3759 0.010 803 1900 -425.3750 0.010 803 2000 -425.3712 0.010 803 2100 -425.3702 0.010 803 2200 -425.3666 0.010 803 2300 -425.3654 0.010 803 2400 -425.3635 0.010 803 2500 -425.3629 0.010 803 2600 -425.3622 0.010 803 2700 -425.3619 0.010 803 2800 -425.3613 0.010 803 2900 -425.3592 0.010 803 3000 -425.3583 0.010 803 3100 -425.3581 0.010 803 3200 -425.3571 0.010 803 3300 -425.3567 0.010 803 3400 -425.3566 0.010 803 3500 -425.3564 0.010 803 3600 -425.3558 0.010 803 3700 -425.3553 0.010 803 3800 -425.3549 0.010 803 3900 -425.3540 0.010 803 4000 -425.3540 0.010 803 4100 -425.3536 0.010 803 4200 -425.3534 0.010 803 4300 -425.3533 0.010 803 4400 -425.3532 0.010 803 Reached termination condition! last topological improvement at gen 803 Improvement over last 500 gen = 0.00083 Current score = -425.3532 Performing final optimizations... pass 1 : -425.3514 (branch= 0.0000 subset rates= 0.0018) pass 2 : -425.3324 (branch= 0.0164 subset rates= 0.0026) pass 3 : -425.3254 (branch= 0.0070 subset rates= 0.0000) pass 4 : -425.3219 (branch= 0.0026 subset rates= 0.0009) pass 5 : -425.3216 (branch= 0.0003 subset rates= 0.0000) pass 6 : -425.3216 (branch= 0.0000 subset rates= 0.0000) pass 7 : -425.3212 (branch= 0.0005 subset rates= 0.0000) pass 8 : -425.3205 (branch= 0.0006 subset rates= 0.0000) pass 9 : -425.3204 (branch= 0.0001 subset rates= 0.0000) pass 10: -425.3203 (branch= 0.0001 subset rates= 0.0000) pass 11: -425.3202 (branch= 0.0001 subset rates= 0.0000) pass 12: -425.3202 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.3202 Time used so far = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.86 1.54 1.15 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 9 branches were collapsed. >>>Completed Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< >>>Bootstrap rep 1 (of 1) Search rep 4 (of 5)<<< Obtained starting tree 1 from Nexus Starting with seed=1573911897 Initial ln Likelihood: -585.3657 optimizing: starting branch lengths, subset rates... pass 1:+ 128.924 (branch= 128.21 scale= 0.69 subset rates= 0.02) pass 2:+ 11.959 (branch= 11.78 scale= 0.03 subset rates= 0.15) pass 3:+ 4.421 (branch= 4.33 scale= 0.00 subset rates= 0.09) pass 4:+ 0.779 (branch= 0.76 scale= 0.00 subset rates= 0.01) pass 5:+ 0.057 (branch= 0.06 scale= 0.00 subset rates= 0.00) pass 6:+ 0.012 (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: -439.2135 gen current_lnL precision last_tree_imp 0 -439.2135 0.010 0 100 -428.1779 0.010 67 200 -427.4638 0.010 189 300 -427.4437 0.010 226 400 -427.1435 0.010 393 500 -427.1285 0.010 393 600 -427.1120 0.010 393 700 -427.1022 0.010 393 800 -427.1003 0.010 393 900 -427.0977 0.010 393 1000 -427.0972 0.010 393 1100 -427.0948 0.010 393 1200 -427.0919 0.010 393 1300 -427.0909 0.010 393 1400 -427.0892 0.010 393 1500 -427.0880 0.010 393 1600 -427.0868 0.010 393 1700 -427.0861 0.010 393 1800 -427.0846 0.010 393 1900 -425.5433 0.010 1890 2000 -425.5081 0.010 1942 2100 -425.3789 0.010 2010 2200 -425.3685 0.010 2010 NOTE: ****Specified time limit (5 seconds) reached... Current score = -425.3666 Performing final optimizations... pass 1 : -425.3666 (branch= 0.0000 subset rates= 0.0000) pass 2 : -425.3329 (branch= 0.0336 subset rates= 0.0001) pass 3 : -425.3299 (branch= 0.0030 subset rates= 0.0000) pass 4 : -425.3268 (branch= 0.0031 subset rates= 0.0000) pass 5 : -425.3226 (branch= 0.0042 subset rates= 0.0000) pass 6 : -425.3212 (branch= 0.0014 subset rates= 0.0000) pass 7 : -425.3209 (branch= 0.0003 subset rates= 0.0000) pass 8 : -425.3206 (branch= 0.0003 subset rates= 0.0000) pass 9 : -425.3205 (branch= 0.0001 subset rates= 0.0000) pass 10: -425.3204 (branch= 0.0001 subset rates= 0.0000) pass 11: -425.3204 (branch= 0.0000 subset rates= 0.0000) pass 12: -425.3204 (branch= 0.0000 subset rates= 0.0000) pass 13: -425.3204 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.3204 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: 0.86 1.54 1.14 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 10 branches were collapsed. >>>Terminated Bootstrap rep 1 (of 1) Search rep 4 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### 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 : -425.5486 Replicate 2 : -425.5486 Replicate 3 : -425.3202 (best) Replicate 4 : -425.3204 (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 1.530 1.121 rep 2: 3.038 0.868 1.529 1.123 rep 3: 2.977 0.864 1.541 1.155 rep 4: 2.982 0.865 1.539 1.142 Saving tree from best search rep (#3) 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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:+ 3.846 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.161 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.158 (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: -474.8622 gen current_lnL precision last_tree_imp 0 -474.8622 0.010 0 100 -474.7511 0.010 68 200 -474.7181 0.010 68 300 -474.6977 0.010 68 400 -474.6394 0.010 329 500 -474.1564 0.010 455 600 -474.1360 0.010 560 700 -474.0348 0.010 653 800 -474.0229 0.010 653 900 -474.0144 0.010 653 1000 -474.0143 0.010 653 1100 -474.0135 0.010 653 1200 -474.0077 0.010 653 1300 -474.0014 0.010 653 1400 -473.9965 0.010 653 1500 -473.9958 0.010 653 1600 -473.9945 0.010 653 1700 -473.9894 0.010 653 1800 -473.9877 0.010 653 1900 -473.9867 0.010 653 2000 -473.9852 0.010 653 2100 -473.9830 0.010 653 2200 -473.9824 0.010 653 2300 -473.9816 0.010 653 2400 -473.9807 0.010 653 2500 -473.9801 0.010 653 2600 -473.9795 0.010 653 2700 -473.9790 0.010 653 2800 -473.9779 0.010 653 2900 -473.9776 0.010 653 3000 -473.9775 0.010 653 3100 -473.9771 0.010 653 3200 -473.9769 0.010 653 3300 -473.9766 0.010 653 3400 -473.9762 0.010 653 3500 -473.9761 0.010 653 3600 -473.9761 0.010 653 3700 -473.9759 0.010 653 Reached termination condition! last topological improvement at gen 653 Improvement over last 500 gen = 0.00096 Current score = -473.9759 Performing final optimizations... pass 1 : -473.9758 (branch= 0.0001 subset rates= 0.0000) pass 2 : -473.9558 (branch= 0.0183 subset rates= 0.0016) pass 3 : -473.9558 (branch= 0.0000 subset rates= 0.0000) pass 4 : -473.9550 (branch= 0.0009 subset rates= 0.0000) pass 5 : -473.9525 (branch= 0.0007 subset rates= 0.0018) pass 6 : -473.9521 (branch= 0.0004 subset rates= 0.0000) pass 7 : -473.9516 (branch= 0.0004 subset rates= 0.0000) pass 8 : -473.9512 (branch= 0.0004 subset rates= 0.0000) pass 9 : -473.9510 (branch= 0.0002 subset rates= 0.0000) pass 10: -473.9509 (branch= 0.0001 subset rates= 0.0000) pass 11: -473.9508 (branch= 0.0001 subset rates= 0.0000) pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) pass 13: -473.9508 (branch= 0.0000 subset rates= 0.0000) pass 14: -473.9508 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -473.9508 Time used so far = 0 hours, 0 minutes and 3 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.59 2.07 2.81 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. >>>Completed Search rep 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=74284197 Initial ln Likelihood: -646.1143 optimizing: starting branch lengths, subset rates... pass 1:+ 146.023 (branch= 135.13 scale= 0.95 subset rates= 9.94) pass 2:+ 17.326 (branch= 12.98 scale= 0.01 subset rates= 4.33) pass 3:+ 4.642 (branch= 3.12 scale= 0.00 subset rates= 1.52) pass 4:+ 2.490 (branch= 1.89 scale= 0.00 subset rates= 0.60) pass 5:+ 0.684 (branch= 0.61 scale= 0.02 subset rates= 0.05) pass 6:+ 0.130 (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: -474.8185 gen current_lnL precision last_tree_imp 0 -474.8185 0.010 0 100 -474.7244 0.010 55 200 -474.7128 0.010 55 300 -474.7037 0.010 55 400 -474.6654 0.010 339 500 -474.5695 0.010 496 600 -474.0703 0.010 585 700 -474.0481 0.010 585 800 -474.0412 0.010 585 900 -474.0316 0.010 585 1000 -474.0282 0.010 585 1100 -474.0225 0.010 585 1200 -474.0142 0.010 585 1300 -474.0116 0.010 585 1400 -474.0080 0.010 585 1500 -474.0041 0.010 585 1600 -474.0016 0.010 585 1700 -474.0010 0.010 585 1800 -473.9994 0.010 585 1900 -473.9983 0.010 585 2000 -473.9971 0.010 585 2100 -473.9968 0.010 585 2200 -473.9964 0.010 585 2300 -473.9963 0.010 585 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0 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 2 (of 5) generation 2327, seed 1905945318, best lnL -473.996 gen current_lnL precision last_tree_imp 2327 -473.9960 0.010 585 2400 -473.9952 0.010 585 2500 -473.9949 0.010 585 2600 -473.9933 0.010 585 2700 -473.9932 0.010 585 2800 -473.9932 0.010 585 2900 -473.9930 0.010 585 3000 -473.9930 0.010 585 3100 -473.9925 0.010 585 Reached termination condition! last topological improvement at gen 585 Improvement over last 500 gen = 0.00079 Current score = -473.9925 Performing final optimizations... pass 1 : -473.9818 (branch= 0.0000 subset rates= 0.0107) pass 2 : -473.9604 (branch= 0.0189 subset rates= 0.0025) pass 3 : -473.9545 (branch= 0.0058 subset rates= 0.0000) pass 4 : -473.9538 (branch= 0.0007 subset rates= 0.0000) pass 5 : -473.9535 (branch= 0.0003 subset rates= 0.0000) pass 6 : -473.9521 (branch= 0.0014 subset rates= 0.0000) pass 7 : -473.9516 (branch= 0.0003 subset rates= 0.0002) pass 8 : -473.9513 (branch= 0.0002 subset rates= 0.0000) pass 9 : -473.9511 (branch= 0.0002 subset rates= 0.0000) pass 10: -473.9510 (branch= 0.0001 subset rates= 0.0000) pass 11: -473.9510 (branch= 0.0001 subset rates= 0.0000) pass 12: -473.9510 (branch= 0.0000 subset rates= 0.0000) pass 13: -473.9509 (branch= 0.0000 subset rates= 0.0000) pass 14: -473.9508 (branch= 0.0000 subset rates= 0.0001) Looking for minimum length branches... Final score = -473.9508 Time used so far = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.59 2.06 2.81 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 (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=663269721 Initial ln Likelihood: -659.0351 optimizing: starting branch lengths, subset rates... pass 1:+ 164.999 (branch= 154.40 scale= 0.48 subset rates= 10.12) pass 2:+ 14.317 (branch= 9.49 scale= 0.03 subset rates= 4.79) pass 3:+ 3.819 (branch= 2.06 scale= 0.02 subset rates= 1.74) pass 4:+ 0.906 (branch= 0.30 scale= 0.00 subset rates= 0.60) pass 5:+ 0.122 (branch= 0.09 scale= 0.00 subset rates= 0.03) pass 6:+ 0.038 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -474.8340 gen current_lnL precision last_tree_imp 0 -474.8340 0.010 0 100 -474.7919 0.010 0 200 -474.7307 0.010 183 300 -474.7187 0.010 183 400 -474.7036 0.010 183 500 -474.6871 0.010 183 600 -474.5395 0.010 535 700 -474.5271 0.010 535 800 -474.5227 0.010 535 900 -474.5120 0.010 535 1000 -474.5077 0.010 535 1100 -474.5053 0.010 535 1200 -474.5039 0.010 535 1300 -474.5013 0.010 535 1400 -474.4986 0.010 535 1500 -474.4981 0.010 535 1600 -474.4956 0.010 535 1700 -474.4907 0.010 535 1800 -474.4796 0.010 535 1900 -474.4760 0.010 535 2000 -474.4747 0.010 535 2100 -474.4733 0.010 535 2200 -474.4720 0.010 535 2300 -474.4709 0.010 535 2400 -474.4703 0.010 535 2500 -474.4697 0.010 535 2600 -474.4676 0.010 535 2700 -474.4670 0.010 535 2800 -474.4665 0.010 535 2900 -474.4661 0.010 535 3000 -474.4649 0.010 535 3100 -474.4642 0.010 535 3200 -474.4636 0.010 535 3300 -474.4636 0.010 535 3400 -474.4619 0.010 535 3500 -474.4614 0.010 535 3600 -474.4611 0.010 535 3700 -474.4608 0.010 535 3800 -474.4608 0.010 535 3900 -474.4607 0.010 535 4000 -474.4607 0.010 535 Reached termination condition! last topological improvement at gen 535 Improvement over last 500 gen = 0.00071 Current score = -474.4607 Performing final optimizations... pass 1 : -474.4602 (branch= 0.0000 subset rates= 0.0005) pass 2 : -474.4430 (branch= 0.0172 subset rates= 0.0000) pass 3 : -474.4430 (branch= 0.0000 subset rates= 0.0000) pass 4 : -474.4383 (branch= 0.0047 subset rates= 0.0000) pass 5 : -474.4338 (branch= 0.0046 subset rates= 0.0000) pass 6 : -474.4316 (branch= 0.0021 subset rates= 0.0000) pass 7 : -474.4301 (branch= 0.0016 subset rates= 0.0000) pass 8 : -474.4294 (branch= 0.0006 subset rates= 0.0001) pass 9 : -474.4289 (branch= 0.0005 subset rates= 0.0000) pass 10: -474.4285 (branch= 0.0003 subset rates= 0.0000) pass 11: -474.4283 (branch= 0.0002 subset rates= 0.0001) pass 12: -474.4282 (branch= 0.0001 subset rates= 0.0000) pass 13: -474.4281 (branch= 0.0000 subset rates= 0.0000) pass 14: -474.4281 (branch= 0.0000 subset rates= 0.0000) pass 15: -474.4281 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -474.4281 Time used so far = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate 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. >>>Completed Search rep 3 (of 5)<<< >>>Search rep 4 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=17311967 Initial ln Likelihood: -692.6191 optimizing: starting branch lengths, subset rates... pass 1:+ 190.070 (branch= 177.15 scale= 2.85 subset rates= 10.07) pass 2:+ 19.411 (branch= 14.64 scale= 0.00 subset rates= 4.77) pass 3:+ 6.755 (branch= 5.00 scale= 0.00 subset rates= 1.76) pass 4:+ 1.361 (branch= 0.80 scale= 0.00 subset rates= 0.56) pass 5:+ 0.120 (branch= 0.09 scale= 0.00 subset rates= 0.03) pass 6:+ 0.055 (branch= 0.05 scale= 0.00 subset rates= 0.00) pass 7:+ 0.014 (branch= 0.01 scale= 0.00 subset rates= 0.00) pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -474.8342 gen current_lnL precision last_tree_imp 0 -474.8342 0.010 0 100 -474.7467 0.010 62 200 -474.1735 0.010 145 300 -474.1515 0.010 145 400 -474.1337 0.010 145 500 -474.0523 0.010 463 600 -474.0185 0.010 523 700 -474.0121 0.010 523 800 -474.0051 0.010 523 900 -474.0040 0.010 523 1000 -473.9974 0.010 523 1100 -473.9955 0.010 523 1200 -473.9908 0.010 523 1300 -473.9892 0.010 523 1400 -473.9877 0.010 523 1500 -473.9860 0.010 523 NOTE: ****Specified time limit (5 seconds) reached... Current score = -473.9855 Performing final optimizations... pass 1 : -473.9847 (branch= 0.0000 subset rates= 0.0008) pass 2 : -473.9652 (branch= 0.0157 subset rates= 0.0038) pass 3 : -473.9594 (branch= 0.0057 subset rates= 0.0002) pass 4 : -473.9561 (branch= 0.0032 subset rates= 0.0000) pass 5 : -473.9539 (branch= 0.0020 subset rates= 0.0003) pass 6 : -473.9526 (branch= 0.0013 subset rates= 0.0000) pass 7 : -473.9514 (branch= 0.0012 subset rates= 0.0000) pass 8 : -473.9509 (branch= 0.0005 subset rates= 0.0000) pass 9 : -473.9509 (branch= 0.0001 subset rates= 0.0000) pass 10: -473.9508 (branch= 0.0000 subset rates= 0.0000) pass 11: -473.9508 (branch= 0.0000 subset rates= 0.0000) pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -473.9508 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 2.07 2.80 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. >>>Terminated Search rep 4 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### 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 : -473.9508 Replicate 2 : -473.9508 (best) (same topology as 1) Replicate 3 : -474.4281 Replicate 4 : -473.9508 (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: 4.351 0.587 2.066 2.813 rep 2: 4.349 0.588 2.064 2.806 rep 3: 4.601 0.587 2.035 2.918 rep 4: 4.350 0.588 2.069 2.800 Saving final tree from best search rep (#2) 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 -j42 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-dbgsym' in '../garli-dbgsym_2.1-9_amd64.deb'. dpkg-deb: building package 'garli' in '../garli_2.1-9_amd64.deb'. dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-9_amd64.deb'. dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-9_amd64.deb'. dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-9_all.deb'. dpkg-genbuildinfo --build=binary -O../garli_2.1-9_amd64.buildinfo dpkg-genchanges --build=binary -O../garli_2.1-9_amd64.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: user script /srv/workspace/pbuilder/1872835/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1872835/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1872835 and its subdirectories I: Current time: Thu Oct 22 04:15:41 +14 2026 I: pbuilder-time-stamp: 1792592141 + false + set +x Wed Oct 21 14:15:41 UTC 2026 I: Signing ./b2/garli_2.1-9_amd64.buildinfo as garli_2.1-9_amd64.buildinfo.asc Wed Oct 21 14:15:41 UTC 2026 I: Signed ./b2/garli_2.1-9_amd64.buildinfo as ./b2/garli_2.1-9_amd64.buildinfo.asc Wed Oct 21 14:15:41 UTC 2026 - build #2 for garli/forky/amd64 on ionos5-amd64 done. Starting cleanup. All cleanup done. Wed Oct 21 14:15:41 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-7bqFSjWH, removing. /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w: total 884 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 07:43 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 07:52 b2 -rw-rw-r-- 1 jenkins jenkins 2186 Dec 19 2024 garli_2.1-9.dsc -rw------- 1 jenkins jenkins 888754 Sep 18 07:43 rbuildlog.IszsNDe /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/b1: total 21348 -rw-r--r-- 1 jenkins jenkins 885211 Sep 18 07:43 build.log -rw-r--r-- 1 jenkins jenkins 9531080 Sep 18 07:43 garli-dbgsym_2.1-9_amd64.deb -rw-r--r-- 1 jenkins jenkins 103464 Sep 18 07:43 garli-examples_2.1-9_all.deb -rw-r--r-- 1 jenkins jenkins 9915936 Sep 18 07:43 garli-mpi-dbgsym_2.1-9_amd64.deb -rw-r--r-- 1 jenkins jenkins 650548 Sep 18 07:43 garli-mpi_2.1-9_amd64.deb -rw-r--r-- 1 jenkins jenkins 5072 Sep 18 07:43 garli_2.1-9.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2186 Sep 18 07:43 garli_2.1-9.dsc -rw-r--r-- 1 jenkins jenkins 8131 Sep 18 07:43 garli_2.1-9_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 9013 Sep 18 07:43 garli_2.1-9_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2388 Sep 18 07:43 garli_2.1-9_amd64.changes -rw-r--r-- 1 jenkins jenkins 673680 Sep 18 07:43 garli_2.1-9_amd64.deb -rw-r--r-- 1 jenkins jenkins 1220 Sep 18 07:43 garli_2.1-9_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/b2: total 21336 -rw-rw-r-- 1 jenkins jenkins 915278 Sep 18 07:52 build.log -rw-r--r-- 1 jenkins jenkins 9531080 Sep 18 07:52 garli-dbgsym_2.1-9_amd64.deb -rw-r--r-- 1 jenkins jenkins 103464 Sep 18 07:52 garli-examples_2.1-9_all.deb -rw-r--r-- 1 jenkins jenkins 9915936 Sep 18 07:52 garli-mpi-dbgsym_2.1-9_amd64.deb -rw-r--r-- 1 jenkins jenkins 650548 Sep 18 07:52 garli-mpi_2.1-9_amd64.deb -rw-r--r-- 1 jenkins jenkins 5072 Sep 18 07:52 garli_2.1-9.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2186 Sep 18 07:52 garli_2.1-9.dsc -rw-rw-r-- 1 jenkins jenkins 8131 Sep 18 07:52 garli_2.1-9_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 9013 Sep 18 07:52 garli_2.1-9_amd64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 2388 Sep 18 07:52 garli_2.1-9_amd64.changes -rw-r--r-- 1 jenkins jenkins 673680 Sep 18 07:52 garli_2.1-9_amd64.deb -rw-rw-r-- 1 jenkins jenkins 1220 Sep 18 07:52 garli_2.1-9_source.changes Thu Sep 18 07:52:42 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Thu Sep 18 07:52:42 UTC 2025 I: garli_2.1-9_amd64.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: amd64 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: f0e348f807a865fc76a1815c992172c2c738ef72 9531080 garli-dbgsym_2.1-9_amd64.deb 9190fdad700fcdc0fc9fe53c5c92c112dc23d533 103464 garli-examples_2.1-9_all.deb af1cfe4002f6b2e1f014e8fd39426a7cdbbeeeb1 9915936 garli-mpi-dbgsym_2.1-9_amd64.deb 60599830a4e4672fcfb67e3d56433ef29f1257a4 650548 garli-mpi_2.1-9_amd64.deb f5e9379bf1dcffeaa56dbfbd8cc99060020849ed 8131 garli_2.1-9_amd64.buildinfo 8072dd631944efda66a544481357b3df47f46da6 673680 garli_2.1-9_amd64.deb Checksums-Sha256: 82e261ee7fbdcfc5b9960506b1f0583afd854c4f4307c5140aeaea07e000280a 9531080 garli-dbgsym_2.1-9_amd64.deb 932b8ad8935349f05f0abbf62fbba0c7f312a7d912d9bc30ec9287833081b095 103464 garli-examples_2.1-9_all.deb b971280b73162b3a4548712a58fe7a7a8f80ef996fb2df2572dbff336b69ff8d 9915936 garli-mpi-dbgsym_2.1-9_amd64.deb 7a16f288359a4c9ff8315cfd3947a7343dff38b8bb02362848544d85036051f5 650548 garli-mpi_2.1-9_amd64.deb 2c6297197edb57831867d09dbaad0e1c9e605b0741eaa0504070755f7737e1b0 8131 garli_2.1-9_amd64.buildinfo 290e4095de1a0b1875a3334c691bcc2fa3591454496a72e2b9472e88ea034b0a 673680 garli_2.1-9_amd64.deb Files: 858723f3a456d88956c4571663e1ab42 9531080 debug optional garli-dbgsym_2.1-9_amd64.deb d7e71d1f8908fce11e935020473b4b15 103464 science optional garli-examples_2.1-9_all.deb 68273696e05eaaae94c3a1a839ac9ac0 9915936 debug optional garli-mpi-dbgsym_2.1-9_amd64.deb 91acbce80208551c52484b11fd0810d4 650548 science optional garli-mpi_2.1-9_amd64.deb 94f6633dfdad81ae49bace201be7b438 8131 science optional garli_2.1-9_amd64.buildinfo 0ac916bb665a8661dcaf499f22a854ca 673680 science optional garli_2.1-9_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/garli_2.1-9.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/garli_2.1-9.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/forky/amd64/garli_2.1-9.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/forky/amd64/garli_2.1-9.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/forky/amd64/garli_2.1-9_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/amd64/garli_2.1-9.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-09-18 07:43:57.029161238 +0000 +++ b2/build.log 2025-09-18 07:52:42.053834777 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Sep 17 19:29:14 -12 2025 -I: pbuilder-time-stamp: 1758180554 +I: Current time: Thu Oct 22 04:06:58 +14 2026 +I: pbuilder-time-stamp: 1792591618 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -22,53 +22,85 @@ 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/4082616/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1872835/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 21 14:07 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1872835/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1872835/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='fcede2e9c9734edeb0817bb04baae1cf' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='4082616' - PS1='# ' - PS2='> ' + INVOCATION_ID=3d335d2935234f7e87ed5379c3129348 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1872835 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.sP9jpE6w/pbuilderrc_CBRI --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/b1 --logfile b1/build.log garli_2.1-9.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/pbuilderrc_iBiM --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/b2 --logfile b2/build.log garli_2.1-9.dsc' + SUDO_GID=110 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4082616/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1872835/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -215,7 +247,7 @@ Get: 101 http://deb.debian.org/debian forky/main amd64 libopenmpi-dev amd64 5.0.8-9 [1228 kB] Get: 102 http://deb.debian.org/debian forky/main amd64 mpi-default-dev amd64 1.18 [3372 B] Get: 103 http://deb.debian.org/debian forky/main amd64 ncl-tools amd64 2.1.21+git20210811.b1213a7-6 [190 kB] -Fetched 164 MB in 26s (6364 kB/s) +Fetched 164 MB in 21s (7894 kB/s) Preconfiguring packages ... Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) @@ -650,7 +682,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/garli-2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../garli_2.1-9_source.changes +I: user script /srv/workspace/pbuilder/1872835/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/1872835/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/garli-2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../garli_2.1-9_source.changes dpkg-buildpackage: info: source package garli dpkg-buildpackage: info: source version 2.1-9 dpkg-buildpackage: info: source distribution unstable @@ -755,8 +791,8 @@ checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking for gcc... gcc @@ -825,7 +861,7 @@ config.status: creating config.h config.status: executing depfiles commands dh_auto_build - make -j40 + make -j42 make[2]: Entering directory '/build/reproducible-path/garli-2.1' make all-recursive make[3]: Entering directory '/build/reproducible-path/garli-2.1' @@ -852,39 +888,16 @@ mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp +linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)': +linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1322 | register int nsq = n * n; + | ^~~ garlimain.cpp:434:66: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ garlimain.cpp:434:76: warning: macro '__TIME__' might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ -linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)': -linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1322 | register int nsq = n * n; - | ^~~ -In file included from /usr/include/stdio.h:970, - from /usr/include/c++/15/cstdio:47, - from /usr/include/c++/15/ext/string_conversions.h:47, - from /usr/include/c++/15/bits/basic_string.h:4444, - from /usr/include/c++/15/string:56, - from /usr/include/c++/15/bits/locale_classes.h:42, - from /usr/include/c++/15/bits/ios_base.h:43, - from /usr/include/c++/15/ios:46, - from /usr/include/c++/15/bits/ostream.h:43, - from /usr/include/c++/15/ostream:42, - from /usr/include/c++/15/iostream:43, - from configoptions.cpp:20: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] 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{ @@ -929,26 +942,32 @@ /usr/include/c++/15/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 file included from /usr/include/stdio.h:970, + from /usr/include/c++/15/cstdio:47, + from /usr/include/c++/15/ext/string_conversions.h:47, + from /usr/include/c++/15/bits/basic_string.h:4444, + from /usr/include/c++/15/string:56, + from /usr/include/c++/15/bits/locale_classes.h:42, + from /usr/include/c++/15/bits/ios_base.h:43, + from /usr/include/c++/15/ios:46, + from /usr/include/c++/15/bits/ostream.h:43, + from /usr/include/c++/15/ostream:42, + from /usr/include/c++/15/iostream:43, + from configoptions.cpp:20: In function 'int sprintf(char*, const char*, ...)', - inlined from 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)' at configoptions.cpp:337:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from tree.h:35, from individual.h:21, - from population.h:31, - from garlimain.cpp:40: + from model.cpp:26: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -959,7 +978,7 @@ from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, - from population.h:23: + from model.cpp:17: /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -997,14 +1016,11 @@ /usr/include/c++/15/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{ | ^~~~~~~~~~~~~~~ @@ -1015,7 +1031,38 @@ from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, - from model.cpp:17: + from population.h:23: +/usr/include/c++/15/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++/15/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++/15/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from tree.h:35, + from individual.h:21, + from population.h:31, + from funcs.h:25, + from 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++/15/string:51, + from /usr/include/c++/15/bits/locale_classes.h:42, + from /usr/include/c++/15/bits/ios_base.h:43, + from /usr/include/c++/15/ios:46, + from /usr/include/c++/15/bits/ostream.h:43, + from /usr/include/c++/15/ostream:42, + from /usr/include/c++/15/iostream:43, + from adaptation.cpp:18: /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1046,6 +1093,28 @@ /usr/include/c++/15/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++/15/bits/stl_function.h:1441: +/usr/include/c++/15/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++/15/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++/15/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; @@ -1054,13 +1123,18 @@ 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from tree.h:35, - from optimization.cpp:19: + 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++/15/bits/refwrap.h:41, - from /usr/include/c++/15/vector:70, - from tree.h:24: +In file included from /usr/include/c++/15/string:51, + from /usr/include/c++/15/bits/locale_classes.h:42, + from /usr/include/c++/15/bits/ios_base.h:43, + from /usr/include/c++/15/iomanip:47, + from individual.cpp:21: /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1101,19 +1175,13 @@ In file included from tree.h:35, from individual.h:21, from population.h:31, - from funcs.h:25, - from adaptation.cpp:25: + 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++/15/string:51, - from /usr/include/c++/15/bits/locale_classes.h:42, - from /usr/include/c++/15/bits/ios_base.h:43, - from /usr/include/c++/15/ios:46, - from /usr/include/c++/15/bits/ostream.h:43, - from /usr/include/c++/15/ostream:42, - from /usr/include/c++/15/iostream:43, - from adaptation.cpp:18: +In file included from /usr/include/c++/15/bits/refwrap.h:41, + from /usr/include/c++/15/vector:70, + from population.cpp:23: /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1152,21 +1220,13 @@ 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 configreader.cpp:30: + 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++/15/string:51, - from /usr/include/c++/15/bits/locale_classes.h:42, - from /usr/include/c++/15/bits/ios_base.h:43, - from /usr/include/c++/15/ios:46, - from /usr/include/c++/15/bits/ostream.h:43, - from /usr/include/c++/15/ostream:42, - from /usr/include/c++/15/iostream:43, - from configreader.cpp:21: +In file included from /usr/include/c++/15/bits/refwrap.h:41, + from /usr/include/c++/15/vector:70, + from tree.h:24: /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1201,49 +1261,31 @@ 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; | ~~~~~~~^~~~~~~~~~~~~~~~~~ -In file included from optimization.cpp:21: +/usr/include/c++/15/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++/15/string:51, - from /usr/include/c++/15/bits/locale_classes.h:42, - from /usr/include/c++/15/bits/ios_base.h:43, - from /usr/include/c++/15/ios:46, - from /usr/include/c++/15/bits/ostream.h:43, - from /usr/include/c++/15/ostream:42, - from /usr/include/c++/15/iostream:43, - from population.h:23: -/usr/include/c++/15/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++/15/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++/15/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i 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++/15/bits/stl_function.h:1441: -/usr/include/c++/15/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++/15/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++/15/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; @@ -1323,25 +1343,38 @@ 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++/15/bits/refwrap.h:41, - from /usr/include/c++/15/vector:70, - from tree.cpp:21: +In file included from /usr/include/c++/15/string:51, + from /usr/include/c++/15/bits/locale_classes.h:42, + from /usr/include/c++/15/bits/ios_base.h:43, + from /usr/include/c++/15/ios:46, + from /usr/include/c++/15/bits/ostream.h:43, + from /usr/include/c++/15/ostream:42, + from /usr/include/c++/15/iostream:43, + from configreader.cpp:21: /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1372,16 +1405,28 @@ /usr/include/c++/15/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++/15/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, - from population.cpp:45: + from garlimain.cpp:40: 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++/15/bits/refwrap.h:41, - from /usr/include/c++/15/vector:70, - from population.cpp:23: +In file included from /usr/include/c++/15/string:51, + from /usr/include/c++/15/bits/locale_classes.h:42, + from /usr/include/c++/15/bits/ios_base.h:43, + from /usr/include/c++/15/ios:46, + from /usr/include/c++/15/bits/ostream.h:43, + from /usr/include/c++/15/ostream:42, + from /usr/include/c++/15/iostream:43, + from population.h:23: /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1397,13 +1442,6 @@ /usr/include/c++/15/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++/15/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)); @@ -1426,19 +1464,26 @@ /usr/include/c++/15/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++/15/string:51, - from /usr/include/c++/15/bits/locale_classes.h:42, - from /usr/include/c++/15/bits/ios_base.h:43, - from /usr/include/c++/15/iomanip:47, - from individual.cpp:21: +In file included from /usr/include/c++/15/bits/refwrap.h:41, + from /usr/include/c++/15/vector:70, + from tree.cpp:21: /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1476,15 +1521,6 @@ /usr/include/c++/15/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from population.cpp:49: -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;idlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -reconnode.h: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)': -reconnode.h:388:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 388 | fread(&unique, scalarSize, 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -reconnode.h: In constructor 'Swap::Swap(FILE*&)': -reconnode.h:264:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 264 | fread(&count, scalarSize, 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from treenode.h:30, - from tree.h:31: -bipartition.h: In member function 'void Bipartition::BinaryInput(FILE*&)': -bipartition.h:518:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 518 | fread((char*) rep, sizeof(unsigned int), nBlocks, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp: In member function 'void Population::ReadPopulationCheckpoint()': -population.cpp:1880:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1880 | fread((char *) &seed, sizeof(seed), 1, pin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp:1887:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1887 | fread((char *) &t, sizeof(t), 1, pin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp:1896:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(this, scalarSize, 1, pin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, @@ -1716,9 +1752,7 @@ from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, - from model.h:25, - from clamanager.h:25, - from condlike.cpp:22: + from treenode.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1734,15 +1768,7 @@ from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, - from /usr/include/c++/15/string:56, - from /usr/include/c++/15/bits/locale_classes.h:42, - from /usr/include/c++/15/bits/ios_base.h:43, - from /usr/include/c++/15/ios:46, - from /usr/include/c++/15/bits/ostream.h:43, - from /usr/include/c++/15/ostream:42, - from /usr/include/c++/15/iostream:43, - from rng.h:36, - from tree.h:30: + from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1771,7 +1797,13 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, - from configreader.cpp:18: + from /usr/include/c++/15/cstdio:47, + from /usr/include/c++/15/ext/string_conversions.h:47, + from /usr/include/c++/15/bits/basic_string.h:4444, + from /usr/include/c++/15/string:56, + 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/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1794,7 +1826,8 @@ from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, - from treenode.cpp:21: + from rng.h:36, + from tree.h:30: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1843,9 +1876,15 @@ from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, - from datamatr.h:23, - from sequencedata.h:27, - from sequencedata.cpp:21: + from /usr/include/c++/15/bits/locale_classes.h:42, + from /usr/include/c++/15/bits/ios_base.h:43, + from /usr/include/c++/15/ios:46, + from /usr/include/c++/15/bits/ostream.h:43, + from /usr/include/c++/15/ostream:42, + from /usr/include/c++/15/iostream:43, + from model.h:25, + from clamanager.h:25, + from condlike.cpp:22: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1856,6 +1895,7 @@ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/ncl/ncl.h:27, @@ -1870,13 +1910,8 @@ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -/usr/include/x86_64-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++/15/cstdio:47, - from /usr/include/c++/15/ext/string_conversions.h:47, - from /usr/include/c++/15/bits/basic_string.h:4444, - from /usr/include/c++/15/string:56: + from configreader.cpp:18: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1888,6 +1923,7 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +/usr/include/x86_64-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++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, @@ -1931,6 +1967,23 @@ from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, + from /usr/include/c++/15/string:56, + from population.cpp:25: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +In file included from /usr/include/stdio.h:970, + from /usr/include/c++/15/cstdio:47, + from /usr/include/c++/15/ext/string_conversions.h:47, + from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: @@ -1948,7 +2001,9 @@ from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, - from population.cpp:25: + from datamatr.h:23, + from sequencedata.h:27, + from tree.cpp:31: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -1992,25 +2047,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:970, - from /usr/include/c++/15/cstdio:47, - from /usr/include/c++/15/ext/string_conversions.h:47, - from /usr/include/c++/15/bits/basic_string.h:4444, - from /usr/include/c++/15/string:56, - 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/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': population.cpp:3066:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 3066 | sprintf(oStr, "R(%d)", d + 1); @@ -2104,8 +2140,8 @@ checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking for gcc... gcc @@ -2172,7 +2208,7 @@ config.status: executing depfiles commands make[1]: Leaving directory '/build/reproducible-path/garli-2.1' dh_auto_build - make -j40 + make -j42 make[1]: Entering directory '/build/reproducible-path/garli-2.1' make all-recursive make[2]: Entering directory '/build/reproducible-path/garli-2.1' @@ -2199,16 +2235,39 @@ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp +linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)': +linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1322 | register int nsq = n * n; + | ^~~ garlimain.cpp:434:66: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ garlimain.cpp:434:76: warning: macro '__TIME__' might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ -linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)': -linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1322 | register int nsq = n * n; - | ^~~ +In file included from /usr/include/stdio.h:970, + from /usr/include/c++/15/cstdio:47, + from /usr/include/c++/15/ext/string_conversions.h:47, + from /usr/include/c++/15/bits/basic_string.h:4444, + from /usr/include/c++/15/string:56, + from /usr/include/c++/15/bits/locale_classes.h:42, + from /usr/include/c++/15/bits/ios_base.h:43, + from /usr/include/c++/15/ios:46, + from /usr/include/c++/15/bits/ostream.h:43, + from /usr/include/c++/15/ostream:42, + from /usr/include/c++/15/iostream:43, + from configoptions.cpp:20: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/x86_64-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/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] 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{ @@ -2253,58 +2312,30 @@ /usr/include/c++/15/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from /usr/include/stdio.h:970, - from /usr/include/c++/15/cstdio:47, - from /usr/include/c++/15/ext/string_conversions.h:47, - from /usr/include/c++/15/bits/basic_string.h:4444, - from /usr/include/c++/15/string:56, - from /usr/include/c++/15/bits/locale_classes.h:42, - from /usr/include/c++/15/bits/ios_base.h:43, - from /usr/include/c++/15/ios:46, - from /usr/include/c++/15/bits/ostream.h:43, - from /usr/include/c++/15/ostream:42, - from /usr/include/c++/15/iostream:43, - from configoptions.cpp:20: +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 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + inlined from 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)' at configoptions.cpp:337:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] 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++/15/string:51, - from /usr/include/c++/15/bits/locale_classes.h:42, - from /usr/include/c++/15/bits/ios_base.h:43, - from /usr/include/c++/15/iomanip:47, - from individual.cpp:21: -/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from tree.h:35, - from individual.h:21, - from population.h:31, - from garlimain.cpp:40: + from funcs.cpp:30: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public 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++/15/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, @@ -2316,12 +2347,6 @@ /usr/include/c++/15/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++/15/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{ | ^~~~~~~~~~~~~~~ @@ -2342,21 +2367,6 @@ /usr/include/c++/15/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++/15/bits/stl_function.h:1441: -/usr/include/c++/15/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++/15/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)); @@ -2371,13 +2381,6 @@ /usr/include/c++/15/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++/15/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, @@ -2424,23 +2427,21 @@ /usr/include/c++/15/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++/15/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, - from population.cpp:45: + from garlimain.cpp:40: 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++/15/bits/refwrap.h:41, - from /usr/include/c++/15/vector:70, - from population.cpp:23: +In file included from /usr/include/c++/15/string:51, + from /usr/include/c++/15/bits/locale_classes.h:42, + from /usr/include/c++/15/bits/ios_base.h:43, + from /usr/include/c++/15/ios:46, + from /usr/include/c++/15/bits/ostream.h:43, + from /usr/include/c++/15/ostream:42, + from /usr/include/c++/15/iostream:43, + from population.h:23: /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2471,6 +2472,24 @@ /usr/include/c++/15/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++/15/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++/15/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; - | ~~~~~~~^~~~~~~~~~~~~~~~~~ -/usr/include/c++/15/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)); @@ -2533,36 +2545,49 @@ 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++/15/bits/refwrap.h:41, + from /usr/include/c++/15/vector:70, + from tree.h:24: +/usr/include/c++/15/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++/15/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++/15/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from garlimain.cpp:46: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i std::bind2nd(const _Operation&, const _Tp&) [with _Operation = 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++/15/bits/stl_function.h:1441: +/usr/include/c++/15/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++/15/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, @@ -2594,6 +2619,13 @@ /usr/include/c++/15/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++/15/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)); @@ -2617,13 +2649,18 @@ 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from tree.h:35, - from optimization.cpp:19: + 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++/15/bits/refwrap.h:41, - from /usr/include/c++/15/vector:70, - from tree.h:24: +In file included from /usr/include/c++/15/string:51, + from /usr/include/c++/15/bits/locale_classes.h:42, + from /usr/include/c++/15/bits/ios_base.h:43, + from /usr/include/c++/15/iomanip:47, + from individual.cpp:21: /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2661,6 +2698,7 @@ /usr/include/c++/15/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++/15/bits/refwrap.h:41, from /usr/include/c++/15/vector:70, - from tree.cpp:21: + from population.cpp:23: /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2691,7 +2728,6 @@ /usr/include/c++/15/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/string:51, - from /usr/include/c++/15/bits/locale_classes.h:42, - from /usr/include/c++/15/bits/ios_base.h:43, - from /usr/include/c++/15/ios:46, - from /usr/include/c++/15/bits/ostream.h:43, - from /usr/include/c++/15/ostream:42, - from /usr/include/c++/15/iostream:43, - from population.h:23: +In file included from /usr/include/c++/15/bits/refwrap.h:41, + from /usr/include/c++/15/vector:70, + from tree.cpp:21: /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2768,6 +2799,11 @@ /usr/include/c++/15/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 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; @@ -2775,6 +2811,10 @@ /usr/include/c++/15/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>>Completed Bootstrap rep 1<<< ####################################################### TREEFILES PASS Running checkpoint test ./check/a.G4.conf @@ -13363,6 +13402,9 @@ 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 -110.5066 0.010 707 +1100 -110.4789 0.010 707 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13449,14 +13491,11 @@ STARTING RUN Restarting from checkpoint... - generation 800, seed 1245259246, best lnL -110.564 + generation 1178, seed 1189642758, best lnL -110.448 gen current_lnL precision last_tree_imp -800 -110.5642 0.010 707 -900 -110.5555 0.010 707 -1000 -110.5066 0.010 707 -NOTE: ****Specified generation limit (1000) reached... +1178 -110.4480 0.010 707 -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones @@ -13468,46 +13507,39 @@ 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 1.3049 + 1.4529 with an invariant (invariable) site category, proportion estimated - 0.0988 + 0.0935 Substitution rate categories under this model: rate proportion - 0.0000 0.0988 - 0.1935 0.2253 - 0.5525 0.2253 - 1.0366 0.2253 - 2.2174 0.2253 + 0.0000 0.0935 + 0.2180 0.2266 + 0.5805 0.2266 + 1.0475 0.2266 + 2.1540 0.2266 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 1 branches were collapsed. + No branches were short enough to be collapsed. Saving site likelihoods to file ch.a.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 : -110.5066 +Replicate 1 : -110.4480 Parameter estimates: alpha pinv -rep 1: 1.305 0.099 +rep 1: 1.453 0.094 Treelengths: TL -rep 1: 2.534 +rep 1: 2.615 Saving final tree from best search rep (#1) to ch.a.G4.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.G4.internalstates.log -WARNING: Internal states inferred on tree from prematurely terminated search - ####################################################### TREEFILES PASS Running checkpoint test ./check/a.conf @@ -13643,15 +13675,54 @@ 2100 -111.6817 0.010 563 2200 -111.6817 0.010 563 2300 -111.6817 0.010 563 -NOTE: ****Specified time limit (5 seconds) reached... +2400 -111.6817 0.010 563 +2500 -111.6817 0.010 563 +2600 -111.6816 0.010 563 +2700 -111.6816 0.010 563 +2800 -111.6816 0.010 563 +2900 -111.6815 0.010 563 +3000 -111.6815 0.010 563 +3100 -111.6815 0.010 563 +3200 -111.6815 0.010 563 +Reached termination condition! +last topological improvement at gen 563 +Improvement over last 500 gen = 0.00009 -NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY -TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE -FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF -(set restart = 1 in the config file). IF YOU WANT TO USE THE -PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY -ADD "end;" TO THE TREE FILES. +MODEL REPORT - 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) + No branches were short enough to be collapsed. + +Saving site likelihoods to file ch.a.sitelikes.log ... + +####################################################### + +Completed 1 replicate search(es) (of 1). +Results: +Replicate 1 : -111.6815 + +Parameter estimates: + Model contains no estimated parameters + +Treelengths: + TL +rep 1: 2.607 + +Saving final tree from best search rep (#1) to ch.a.best.tre +Inferring internal state probabilities on best tree... saving to file ch.a.internalstates.log + +####################################################### Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## @@ -13728,9 +13799,9 @@ STARTING RUN Restarting from checkpoint... - generation 2300, seed 1579946663, best lnL -111.682 + generation 3200, seed 1669543796, best lnL -111.681 gen current_lnL precision last_tree_imp -2300 -111.6817 0.010 563 +3200 -111.6815 0.010 563 MODEL REPORT - Parameter values are FINAL Model 1 @@ -13754,14 +13825,14 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -111.6817 +Replicate 1 : -111.6815 Parameter estimates: Model contains no estimated parameters Treelengths: TL -rep 1: 2.605 +rep 1: 2.607 Saving final tree from best search rep (#1) to ch.a.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.internalstates.log @@ -13896,6 +13967,15 @@ 60 -205.5990 0.500 53 70 -205.5741 0.500 53 80 -205.4022 0.500 76 +90 -205.3871 0.500 76 +100 -205.3829 0.500 76 +110 -205.3431 0.500 106 +120 -205.3431 0.500 106 +130 -205.2505 0.500 121 +140 -205.2440 0.500 121 +150 -205.1047 0.500 121 +160 -205.0609 0.500 121 +170 -204.9812 0.500 121 NOTE: ****Specified time limit (10 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13982,18 +14062,15 @@ STARTING RUN Restarting from checkpoint... - generation 80, seed 1732378755, best lnL -205.402 + generation 171, seed 1312101128, best lnL -204.981 gen current_lnL precision last_tree_imp -80 -205.4022 0.500 76 -90 -205.3871 0.500 76 -100 -205.3829 0.500 76 -NOTE: ****Specified generation limit (100) reached... +171 -204.9812 0.500 121 -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates - AC = 1.586, AG = 3.999, AT = 0.040, CG = 2.453, CT = 3.968, GT = 1.000 + AC = 1.586, AG = 4.036, 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) @@ -14014,38 +14091,31 @@ 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 + 0.0473 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 +Replicate 1 : -204.9812 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 +rep 1: 0.047 0.521 0.499 0.479 1.586 4.036 0.04 2.453 3.968 1 Treelengths: TL -rep 1: 7.371 +rep 1: 7.813 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 @@ -14176,6 +14246,22 @@ 30 -195.2776 0.500 0 40 -195.2554 0.500 0 50 -195.2137 0.500 0 +60 -195.1629 0.500 0 +70 -195.0042 0.500 0 +80 -194.9478 0.500 0 +90 -194.9092 0.500 0 +100 -194.9092 0.500 0 +110 -194.8986 0.500 0 +120 -194.8986 0.500 0 +130 -194.8984 0.500 0 +140 -194.8500 0.500 0 +150 -194.7085 0.500 0 +160 -194.7085 0.500 0 +170 -194.5936 0.500 168 +180 -194.5926 0.500 168 +190 -194.5693 0.500 168 +200 -194.2413 0.500 196 +210 -194.2413 0.500 196 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14263,22 +14349,16 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 51, seed 1784766670, best lnL -195.214 +Bootstrap rep 1 (of 1) generation 215, seed 276267568, best lnL -194.204 gen current_lnL precision last_tree_imp -51 -195.2137 0.500 0 -60 -195.1629 0.500 0 -70 -195.0042 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... +215 -194.2043 0.500 196 -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 61 (codon data, standard code) One estimated dN/dS ratio (aka omega) = 0.120507 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 + AC = 1.637, AG = 5.880, AT = 0.011, CG = 4.174, CT = 2.304, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) @@ -14302,27 +14382,23 @@ 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 +Replicate 1 : -194.2043 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 +rep 1: 0.121 1.000 1.637 5.88 0.01146 4.174 2.304 1 Treelengths: TL -rep 1: 9.255 +rep 1: 10.277 Saving best tree to bootstrap file ch.c.boot.tre -WARNING: Tree from prematurely terminated search saved to bootstrap file +>>>Completed Bootstrap rep 1<<< ####################################################### TREEFILES PASS Running checkpoint test ./check/g.dnaBnoZ.conf @@ -14487,6 +14563,27 @@ 1200 -3352.6366 0.010 0 1300 -3352.5137 0.010 0 1400 -3352.4036 0.010 0 +1500 -3352.3987 0.010 0 +1600 -3352.2919 0.010 0 +1700 -3352.2843 0.010 0 +1800 -3352.2036 0.010 0 +1900 -3351.8476 0.010 0 +2000 -3351.7698 0.010 0 +2100 -3351.6181 0.010 0 +2200 -3351.3750 0.010 0 +2300 -3351.3499 0.010 0 +2400 -3351.3426 0.010 0 +2500 -3351.2398 0.010 0 +2600 -3351.1737 0.010 0 +2700 -3351.1734 0.010 0 +2800 -3351.1196 0.010 0 +2900 -3351.1184 0.010 0 +3000 -3351.1143 0.010 0 +3100 -3351.1019 0.010 0 +3200 -3351.0899 0.010 0 +3300 -3351.0880 0.010 0 +3400 -3351.0866 0.010 0 +3500 -3351.0854 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14590,81 +14687,102 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 1431, seed 2054937967, best lnL -3352.404 +Search rep 1 (of 2) generation 3560, seed 284781261, best lnL -3351.085 gen current_lnL precision last_tree_imp -1431 -3352.4036 0.010 0 -1500 -3352.3987 0.010 0 -1600 -3352.2919 0.010 0 -1700 -3352.2843 0.010 0 -1800 -3352.2036 0.010 0 -1900 -3351.8476 0.010 0 -2000 -3351.7698 0.010 0 -2100 -3351.6181 0.010 0 -2200 -3351.3750 0.010 0 -2300 -3351.3499 0.010 0 -2400 -3351.3426 0.010 0 -2500 -3351.2398 0.010 0 -2600 -3351.1737 0.010 0 -2700 -3351.1734 0.010 0 -2800 -3351.1196 0.010 0 -2900 -3351.1184 0.010 0 -3000 -3351.1143 0.010 0 +3560 -3351.0848 0.010 0 +3600 -3351.0827 0.010 0 +3700 -3351.0495 0.010 0 +3800 -3351.0374 0.010 0 +3900 -3350.9831 0.010 0 +4000 -3350.9831 0.010 0 +4100 -3350.9762 0.010 0 +4200 -3350.9697 0.010 0 +4300 -3350.9691 0.010 0 +4400 -3350.9650 0.010 0 +4500 -3350.9650 0.010 0 +4600 -3350.9243 0.010 0 +4700 -3350.9241 0.010 0 +4800 -3350.9231 0.010 0 +4900 -3350.9231 0.010 0 +5000 -3350.9221 0.010 0 +5100 -3350.8994 0.010 0 +5200 -3350.8809 0.010 0 +5300 -3350.8796 0.010 0 +5400 -3350.8607 0.010 0 +5500 -3350.8014 0.010 0 +5600 -3350.7518 0.010 0 +5700 -3350.7432 0.010 0 +5800 -3350.6963 0.010 0 +5900 -3350.6922 0.010 0 +6000 -3350.6866 0.010 0 +6100 -3350.6725 0.010 0 +6200 -3350.6725 0.010 0 +6300 -3350.6688 0.010 0 +6400 -3350.6676 0.010 0 +6500 -3350.6676 0.010 0 +6600 -3350.6636 0.010 0 +6700 -3350.6636 0.010 0 +6800 -3350.6588 0.010 0 +6900 -3350.6246 0.010 0 +7000 -3350.6208 0.010 0 +7100 -3350.6204 0.010 0 +7200 -3350.6204 0.010 0 +7300 -3350.6197 0.010 0 +7400 -3350.5966 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3351.1019 +Current score = -3350.5954 Performing final optimizations... -pass 1 : -3351.0533 (branch= 0.0000 alpha= 0.0000 pinv= 0.0100 eq freqs= 0.0001 rel rates= 0.0384 subset rates= 0.0000) -pass 2 : -3350.9538 (branch= 0.0000 alpha= 0.0117 pinv= 0.0197 eq freqs= 0.0100 rel rates= 0.0582 subset rates= 0.0000) -pass 3 : -3350.8653 (branch= 0.0034 alpha= 0.0189 pinv= 0.0170 eq freqs= 0.0020 rel rates= 0.0471 subset rates= 0.0000) -pass 4 : -3350.7873 (branch= 0.0049 alpha= 0.0175 pinv= 0.0160 eq freqs= 0.0000 rel rates= 0.0369 subset rates= 0.0026) -pass 5 : -3350.7205 (branch= 0.0049 alpha= 0.0139 pinv= 0.0149 eq freqs= 0.0009 rel rates= 0.0310 subset rates= 0.0012) -pass 6 : -3350.6609 (branch= 0.0041 alpha= 0.0133 pinv= 0.0137 eq freqs= 0.0002 rel rates= 0.0272 subset rates= 0.0010) -pass 7 : -3350.6103 (branch= 0.0024 alpha= 0.0123 pinv= 0.0126 eq freqs= 0.0002 rel rates= 0.0231 subset rates= 0.0000) -pass 8 : -3350.5641 (branch= 0.0003 alpha= 0.0116 pinv= 0.0114 eq freqs= 0.0000 rel rates= 0.0213 subset rates= 0.0015) -pass 9 : -3350.5239 (branch= 0.0013 alpha= 0.0108 pinv= 0.0104 eq freqs= 0.0001 rel rates= 0.0176 subset rates= 0.0000) -pass 10: -3350.4880 (branch= 0.0002 alpha= 0.0098 pinv= 0.0100 eq freqs= 0.0000 rel rates= 0.0159 subset rates= 0.0000) -pass 11: -3350.4557 (branch= 0.0000 alpha= 0.0094 pinv= 0.0090 eq freqs= 0.0000 rel rates= 0.0139 subset rates= 0.0000) -pass 12: -3350.4266 (branch= 0.0000 alpha= 0.0085 pinv= 0.0075 eq freqs= 0.0000 rel rates= 0.0120 subset rates= 0.0011) -pass 13: -3350.4023 (branch= 0.0007 alpha= 0.0072 pinv= 0.0068 eq freqs= 0.0000 rel rates= 0.0096 subset rates= 0.0000) -pass 14: -3350.3812 (branch= 0.0001 alpha= 0.0063 pinv= 0.0061 eq freqs= 0.0000 rel rates= 0.0086 subset rates= 0.0000) -pass 15: -3350.3622 (branch= 0.0000 alpha= 0.0060 pinv= 0.0054 eq freqs= 0.0000 rel rates= 0.0075 subset rates= 0.0000) -pass 16: -3350.3453 (branch= 0.0000 alpha= 0.0054 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0067 subset rates= 0.0000) -pass 17: -3350.3306 (branch= 0.0000 alpha= 0.0048 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0057 subset rates= 0.0000) -pass 18: -3350.3177 (branch= 0.0000 alpha= 0.0042 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0049 subset rates= 0.0000) -pass 19: -3350.3063 (branch= 0.0000 alpha= 0.0037 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0042 subset rates= 0.0000) -pass 20: -3350.2965 (branch= 0.0000 alpha= 0.0033 pinv= 0.0029 eq freqs= 0.0000 rel rates= 0.0036 subset rates= 0.0000) - optimization up to ... -pass 30: -3350.2472 (branch= 0.0000 alpha= 0.0166 pinv= 0.0150 eq freqs= 0.0000 rel rates= 0.0176 subset rates= 0.0000) +pass 1 : -3350.5551 (branch= 0.0000 alpha= 0.0000 pinv= 0.0225 eq freqs= 0.0115 rel rates= 0.0063 subset rates= 0.0000) +pass 2 : -3350.5211 (branch= 0.0000 alpha= 0.0195 pinv= 0.0144 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 3 : -3350.4834 (branch= 0.0015 alpha= 0.0147 pinv= 0.0131 eq freqs= 0.0017 rel rates= 0.0069 subset rates= 0.0000) +pass 4 : -3350.4561 (branch= 0.0025 alpha= 0.0116 pinv= 0.0123 eq freqs= 0.0000 rel rates= 0.0008 subset rates= 0.0000) +pass 5 : -3350.4283 (branch= 0.0022 alpha= 0.0128 pinv= 0.0111 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0017) +pass 6 : -3350.4049 (branch= 0.0015 alpha= 0.0108 pinv= 0.0101 eq freqs= 0.0004 rel rates= 0.0006 subset rates= 0.0000) +pass 7 : -3350.3854 (branch= 0.0002 alpha= 0.0094 pinv= 0.0091 eq freqs= 0.0000 rel rates= 0.0007 subset rates= 0.0000) +pass 8 : -3350.3665 (branch= 0.0006 alpha= 0.0085 pinv= 0.0082 eq freqs= 0.0001 rel rates= 0.0004 subset rates= 0.0012) +pass 9 : -3350.3503 (branch= 0.0010 alpha= 0.0076 pinv= 0.0074 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) +pass 10: -3350.3363 (branch= 0.0002 alpha= 0.0068 pinv= 0.0066 eq freqs= 0.0000 rel rates= 0.0004 subset rates= 0.0000) +pass 11: -3350.3235 (branch= 0.0001 alpha= 0.0065 pinv= 0.0058 eq freqs= 0.0000 rel rates= 0.0004 subset rates= 0.0000) +pass 12: -3350.3120 (branch= 0.0000 alpha= 0.0059 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0004 subset rates= 0.0000) +pass 13: -3350.3018 (branch= 0.0000 alpha= 0.0053 pinv= 0.0046 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) +pass 14: -3350.2928 (branch= 0.0000 alpha= 0.0047 pinv= 0.0041 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) +pass 15: -3350.2849 (branch= 0.0000 alpha= 0.0041 pinv= 0.0036 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 16: -3350.2780 (branch= 0.0000 alpha= 0.0036 pinv= 0.0031 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 17: -3350.2719 (branch= 0.0000 alpha= 0.0032 pinv= 0.0028 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 18: -3350.2665 (branch= 0.0000 alpha= 0.0028 pinv= 0.0024 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 19: -3350.2619 (branch= 0.0000 alpha= 0.0024 pinv= 0.0021 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 20: -3350.2578 (branch= 0.0000 alpha= 0.0021 pinv= 0.0018 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) optimization up to ... -pass 40: -3350.2360 (branch= 0.0000 alpha= 0.0037 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0041 subset rates= 0.0000) +pass 30: -3350.2380 (branch= 0.0000 alpha= 0.0103 pinv= 0.0091 eq freqs= 0.0000 rel rates= 0.0004 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2337 (branch= 0.0000 alpha= 0.0007 pinv= 0.0006 eq freqs= 0.0000 rel rates= 0.0010 subset rates= 0.0000) +pass 40: -3350.2338 (branch= 0.0000 alpha= 0.0021 pinv= 0.0019 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) optimization up to ... -pass 60: -3350.2332 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) +pass 50: -3350.2331 (branch= 0.0000 alpha= 0.0004 pinv= 0.0004 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) optimization up to ... -pass 68: -3350.2331 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 54: -3350.2330 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -3350.2331 -Time used so far = 0 hours, 0 minutes and 15 seconds +Final score = -3350.2330 +Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.115, AG = 10.420, AT = 2.692, CG = 0.001, CT = 21.928, GT = 1.000 + AC = 3.136, AG = 10.490, AT = 2.711, CG = 0.001, CT = 22.089, 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 - 0.5773 + 0.5750 with an invariant (invariable) site category, proportion estimated - 0.3656 + 0.3648 Substitution rate categories under this model: rate proportion - 0.0000 0.3656 - 0.0485 0.1586 - 0.2994 0.1586 - 0.8693 0.1586 - 2.7828 0.1586 + 0.0000 0.3648 + 0.0480 0.1588 + 0.2981 0.1588 + 0.8680 0.1588 + 2.7859 0.1588 Model 2 Number of states = 2 (binary data) @@ -14689,20 +14807,20 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3350.2331 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3350.2330 (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: 3.115 10.42 2.692 0.001 21.93 1 0.333 0.222 0.157 0.288 0.577 0.366 +rep 1: 3.136 10.49 2.711 0.001 22.09 1 0.333 0.222 0.157 0.288 0.575 0.365 Partition model subset 2: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) -rep 1: 0.789 1.820 0.180 +rep 1: 0.790 1.821 0.179 Saving final tree from best search rep (#1) to ch.g.dnaBnoZ.best.tre ####################################################### @@ -14852,6 +14970,22 @@ 200 -3324.7543 0.500 1 300 -3324.3007 0.500 1 400 -3323.9848 0.500 1 +500 -3323.6818 0.500 1 +600 -3323.3459 0.500 1 +Optimization precision reduced + Optimizing parameters... improved 1.812 lnL + Optimizing branchlengths... improved 0.023 lnL +700 -3321.3650 0.255 1 +800 -3321.0295 0.255 1 +900 -3321.0142 0.255 1 +1000 -3320.9667 0.255 1 +1100 -3320.8654 0.255 1 +Optimization precision reduced + Optimizing parameters... improved 0.578 lnL + Optimizing branchlengths... improved 0.060 lnL +1200 -3320.1462 0.010 1 +1300 -3320.0857 0.010 1 +1400 -3320.0695 0.010 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14952,76 +15086,75 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 400, seed 198833985, best lnL -3323.985 +Search rep 1 (of 2) generation 1428, seed 585325787, best lnL -3320.025 gen current_lnL precision last_tree_imp -400 -3323.9848 0.500 1 -500 -3323.6818 0.500 1 -600 -3323.3459 0.500 1 -Optimization precision reduced - Optimizing parameters... improved 1.812 lnL - Optimizing branchlengths... improved 0.023 lnL -700 -3321.3650 0.255 1 -800 -3321.0295 0.255 1 -900 -3321.0142 0.255 1 -1000 -3320.9667 0.255 1 +1428 -3320.0255 0.010 1 +1500 -3320.0226 0.010 1 +1600 -3320.0183 0.010 1 +1700 -3320.0152 0.010 1 +1800 -3319.8191 0.010 1 +1900 -3319.6008 0.010 1 +2000 -3319.5579 0.010 1 +2100 -3319.5506 0.010 1 +2200 -3319.4670 0.010 1 +2300 -3319.3661 0.010 1 +2400 -3319.3307 0.010 1 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3320.8988 +Current score = -3319.3293 Performing final optimizations... -pass 1 : -3320.2605 (branch= 0.0468 alpha= 0.0000 pinv= 0.0155 eq freqs= 0.0001 rel rates= 0.5593 ins/del rates= 0.0166) -pass 2 : -3319.8108 (branch= 0.0687 alpha= 0.0065 pinv= 0.0159 eq freqs= 0.0000 rel rates= 0.3405 ins/del rates= 0.0180) -pass 3 : -3319.4666 (branch= 0.0455 alpha= 0.0079 pinv= 0.0157 eq freqs= 0.0000 rel rates= 0.2549 ins/del rates= 0.0201) -pass 4 : -3319.2019 (branch= 0.0263 alpha= 0.0102 pinv= 0.0153 eq freqs= 0.0024 rel rates= 0.2005 ins/del rates= 0.0101) -pass 5 : -3318.9818 (branch= 0.0182 alpha= 0.0103 pinv= 0.0147 eq freqs= 0.0011 rel rates= 0.1683 ins/del rates= 0.0075) -pass 6 : -3318.8010 (branch= 0.0120 alpha= 0.0105 pinv= 0.0139 eq freqs= 0.0012 rel rates= 0.1381 ins/del rates= 0.0051) -pass 7 : -3318.6466 (branch= 0.0085 alpha= 0.0099 pinv= 0.0130 eq freqs= 0.0004 rel rates= 0.1192 ins/del rates= 0.0035) -pass 8 : -3318.5179 (branch= 0.0056 alpha= 0.0099 pinv= 0.0121 eq freqs= 0.0003 rel rates= 0.0983 ins/del rates= 0.0024) -pass 9 : -3318.4100 (branch= 0.0037 alpha= 0.0099 pinv= 0.0112 eq freqs= 0.0003 rel rates= 0.0812 ins/del rates= 0.0016) -pass 10: -3318.3186 (branch= 0.0024 alpha= 0.0095 pinv= 0.0109 eq freqs= 0.0002 rel rates= 0.0673 ins/del rates= 0.0011) -pass 11: -3318.2438 (branch= 0.0016 alpha= 0.0089 pinv= 0.0094 eq freqs= 0.0002 rel rates= 0.0540 ins/del rates= 0.0007) -pass 12: -3318.1803 (branch= 0.0011 alpha= 0.0083 pinv= 0.0086 eq freqs= 0.0001 rel rates= 0.0449 ins/del rates= 0.0005) -pass 13: -3318.1262 (branch= 0.0007 alpha= 0.0078 pinv= 0.0078 eq freqs= 0.0001 rel rates= 0.0374 ins/del rates= 0.0003) -pass 14: -3318.0801 (branch= 0.0004 alpha= 0.0073 pinv= 0.0071 eq freqs= 0.0001 rel rates= 0.0309 ins/del rates= 0.0002) -pass 15: -3318.0410 (branch= 0.0003 alpha= 0.0066 pinv= 0.0064 eq freqs= 0.0001 rel rates= 0.0256 ins/del rates= 0.0001) -pass 16: -3318.0073 (branch= 0.0002 alpha= 0.0060 pinv= 0.0058 eq freqs= 0.0001 rel rates= 0.0216 ins/del rates= 0.0001) -pass 17: -3317.9780 (branch= 0.0001 alpha= 0.0054 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0184 ins/del rates= 0.0000) -pass 18: -3317.9527 (branch= 0.0001 alpha= 0.0049 pinv= 0.0046 eq freqs= 0.0000 rel rates= 0.0157 ins/del rates= 0.0000) -pass 19: -3317.9307 (branch= 0.0000 alpha= 0.0044 pinv= 0.0041 eq freqs= 0.0000 rel rates= 0.0134 ins/del rates= 0.0000) -pass 20: -3317.9115 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0114 ins/del rates= 0.0000) - optimization up to ... -pass 30: -3317.8163 (branch= 0.0001 alpha= 0.0212 pinv= 0.0196 eq freqs= 0.0001 rel rates= 0.0542 ins/del rates= 0.0000) - optimization up to ... -pass 40: -3317.7937 (branch= 0.0001 alpha= 0.0053 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0124 ins/del rates= 0.0000) +pass 1 : -3319.0714 (branch= 0.0074 alpha= 0.0000 pinv= 0.0160 eq freqs= 0.0110 rel rates= 0.1612 ins/del rates= 0.0623) +pass 2 : -3318.8830 (branch= 0.0321 alpha= 0.0083 pinv= 0.0161 eq freqs= 0.0000 rel rates= 0.1227 ins/del rates= 0.0092) +pass 3 : -3318.7273 (branch= 0.0274 alpha= 0.0122 pinv= 0.0146 eq freqs= 0.0018 rel rates= 0.0931 ins/del rates= 0.0066) +pass 4 : -3318.5910 (branch= 0.0180 alpha= 0.0114 pinv= 0.0140 eq freqs= 0.0014 rel rates= 0.0860 ins/del rates= 0.0055) +pass 5 : -3318.4830 (branch= 0.0116 alpha= 0.0108 pinv= 0.0133 eq freqs= 0.0006 rel rates= 0.0672 ins/del rates= 0.0044) +pass 6 : -3318.3923 (branch= 0.0074 alpha= 0.0101 pinv= 0.0125 eq freqs= 0.0002 rel rates= 0.0573 ins/del rates= 0.0032) +pass 7 : -3318.3126 (branch= 0.0049 alpha= 0.0096 pinv= 0.0116 eq freqs= 0.0006 rel rates= 0.0511 ins/del rates= 0.0020) +pass 8 : -3318.2433 (branch= 0.0034 alpha= 0.0098 pinv= 0.0106 eq freqs= 0.0002 rel rates= 0.0438 ins/del rates= 0.0014) +pass 9 : -3318.1846 (branch= 0.0022 alpha= 0.0091 pinv= 0.0097 eq freqs= 0.0001 rel rates= 0.0367 ins/del rates= 0.0009) +pass 10: -3318.1330 (branch= 0.0014 alpha= 0.0085 pinv= 0.0089 eq freqs= 0.0001 rel rates= 0.0322 ins/del rates= 0.0006) +pass 11: -3318.0887 (branch= 0.0010 alpha= 0.0078 pinv= 0.0081 eq freqs= 0.0000 rel rates= 0.0270 ins/del rates= 0.0004) +pass 12: -3318.0500 (branch= 0.0006 alpha= 0.0074 pinv= 0.0073 eq freqs= 0.0001 rel rates= 0.0230 ins/del rates= 0.0003) +pass 13: -3318.0163 (branch= 0.0004 alpha= 0.0067 pinv= 0.0066 eq freqs= 0.0000 rel rates= 0.0198 ins/del rates= 0.0002) +pass 14: -3317.9868 (branch= 0.0003 alpha= 0.0061 pinv= 0.0060 eq freqs= 0.0000 rel rates= 0.0170 ins/del rates= 0.0001) +pass 15: -3317.9610 (branch= 0.0002 alpha= 0.0056 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0146 ins/del rates= 0.0001) +pass 16: -3317.9384 (branch= 0.0001 alpha= 0.0050 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0126 ins/del rates= 0.0000) +pass 17: -3317.9187 (branch= 0.0001 alpha= 0.0046 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0108 ins/del rates= 0.0000) +pass 18: -3317.9015 (branch= 0.0000 alpha= 0.0041 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0092 ins/del rates= 0.0000) +pass 19: -3317.8865 (branch= 0.0000 alpha= 0.0037 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0080 ins/del rates= 0.0000) +pass 20: -3317.8733 (branch= 0.0000 alpha= 0.0033 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0069 ins/del rates= 0.0000) + optimization up to ... +pass 30: -3317.8073 (branch= 0.0001 alpha= 0.0170 pinv= 0.0156 eq freqs= 0.0001 rel rates= 0.0332 ins/del rates= 0.0000) optimization up to ... -pass 50: -3317.7885 (branch= 0.0000 alpha= 0.0011 pinv= 0.0010 eq freqs= 0.0000 rel rates= 0.0030 ins/del rates= 0.0000) +pass 40: -3317.7916 (branch= 0.0001 alpha= 0.0041 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0078 ins/del rates= 0.0000) optimization up to ... -pass 60: -3317.7874 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0007 ins/del rates= 0.0000) +pass 50: -3317.7880 (branch= 0.0000 alpha= 0.0009 pinv= 0.0008 eq freqs= 0.0000 rel rates= 0.0019 ins/del rates= 0.0000) optimization up to ... -pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) +pass 60: -3317.7873 (branch= 0.0000 alpha= 0.0002 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0004 ins/del rates= 0.0000) optimization up to ... -pass 74: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) +pass 69: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3317.7871 -Time used so far = 0 hours, 0 minutes and 13 seconds +Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.064, AG = 10.260, AT = 2.655, CG = 0.001, CT = 21.528, GT = 1.000 + AC = 3.064, AG = 10.257, AT = 2.654, CG = 0.001, CT = 21.525, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3328 0.2223 0.1566 0.2882 + (ACGT) 0.3328 0.2223 0.1567 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.5750 + 0.5745 with an invariant (invariable) site category, proportion estimated - 0.3614 + 0.3611 Substitution rate categories under this model: rate proportion - 0.0000 0.3614 - 0.0480 0.1597 - 0.2981 0.1597 - 0.8680 0.1597 - 2.7859 0.1597 + 0.0000 0.3611 + 0.0479 0.1597 + 0.2978 0.1597 + 0.8677 0.1597 + 2.7866 0.1597 Model 2 Number of states = 2 (0/1 coding of gaps) @@ -15053,7 +15186,7 @@ Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.064 10.26 2.655 0.001 21.53 1 0.333 0.222 0.157 0.288 0.575 0.361 +rep 1: 3.064 10.26 2.654 0.001 21.53 1 0.333 0.222 0.157 0.288 0.574 0.361 Partition model subset 2: ins del @@ -15199,6 +15332,33 @@ 4000 -210.6946 0.010 1104 4200 -210.6740 0.010 1104 4400 -210.6493 0.010 1104 +4600 -210.6257 0.010 1104 +4800 -210.5948 0.010 1104 +5000 -210.5740 0.010 1104 +5200 -210.5693 0.010 1104 +5400 -210.5461 0.010 1104 +5600 -210.5151 0.010 1104 +5800 -210.4823 0.010 1104 +6000 -210.4632 0.010 1104 +6200 -210.4596 0.010 1104 +6400 -210.4468 0.010 1104 +6600 -210.4214 0.010 1104 +6800 -210.3964 0.010 1104 +7000 -210.3383 0.010 1104 +7200 -210.3217 0.010 1104 +7400 -210.2807 0.010 1104 +7600 -210.2625 0.010 1104 +7800 -210.1872 0.010 1104 +8000 -210.1732 0.010 1104 +8200 -210.1275 0.010 1104 +8400 -210.1090 0.010 1104 +8600 -210.0887 0.010 1104 +8800 -210.0539 0.010 1104 +9000 -210.0488 0.010 1104 +9200 -209.9764 0.010 1104 +9400 -209.9612 0.010 1104 +9600 -209.9440 0.010 1104 +9800 -209.9190 0.010 1104 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15278,55 +15438,62 @@ STARTING RUN Restarting from checkpoint... - generation 4420, seed 2050063237, best lnL -210.649 + generation 9996, seed 428919122, best lnL -209.886 gen current_lnL precision last_tree_imp -4420 -210.6493 0.010 1104 -4500 -210.6477 0.010 1104 -Reached termination condition! -last topological improvement at gen 1104 -Improvement over last 500 gen = 0.04686 +9996 -209.8863 0.010 1104 +10000 -209.8863 0.010 1104 + Optimizing parameters... improved 0.505 lnL + Optimizing branchlengths... improved 0.011 lnL +NOTE: ****Specified generation limit (10000) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 2.570, AG = 4.891, AT = 0.202, CG = 4.460, CT = 7.252, GT = 1.000 + AC = 5.150, AG = 9.093, AT = 0.233, CG = 9.359, CT = 14.077, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2331 0.3366 0.2107 0.2196 + (ACGT) 0.2377 0.3274 0.2094 0.2255 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 1.1902 + 4.1580 with an invariant (invariable) site category, proportion estimated - 0.1208 + 0.2914 Substitution rate categories under this model: rate proportion - 0.0000 0.1208 - 0.2293 0.2931 - 0.7543 0.2931 - 2.0165 0.2931 + 0.0000 0.2914 + 0.5191 0.2362 + 0.9259 0.2362 + 1.5550 0.2362 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. Saving site likelihoods to file ch.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 : -210.6477 +Replicate 1 : -209.3698 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: 2.57 4.891 0.2023 4.46 7.252 1 0.233 0.337 0.211 0.220 1.190 0.121 +rep 1: 5.15 9.093 0.2328 9.359 14.08 1 0.238 0.327 0.209 0.225 4.158 0.291 Treelengths: TL -rep 1: 2.247 +rep 1: 2.284 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 +WARNING: Internal states inferred on tree from prematurely terminated search + ####################################################### TREEFILES PASS Running checkpoint test ./check/n.G4.conf @@ -15451,15 +15618,97 @@ 1400 -167.0497 0.010 843 1600 -166.9651 0.010 843 1800 -166.8256 0.010 843 -NOTE: ****Specified time limit (5 seconds) reached... +2000 -166.7014 0.010 843 +2200 -166.6037 0.010 843 +2400 -166.5437 0.010 843 +2600 -166.4761 0.010 843 +2800 -166.4631 0.010 843 +3000 -166.4054 0.010 843 +3200 -166.3555 0.010 843 +3400 -166.2985 0.010 843 +3600 -166.2506 0.010 843 +3800 -166.1403 0.010 843 +4000 -166.1354 0.010 843 +4200 -166.0869 0.010 843 +4400 -166.0244 0.010 843 +4600 -165.9672 0.010 843 +4800 -165.9475 0.010 843 +5000 -165.8859 0.010 843 +5200 -165.8689 0.010 843 +5400 -165.8337 0.010 843 +5600 -165.6916 0.010 843 +5800 -165.5811 0.010 843 +6000 -165.5435 0.010 843 +6200 -165.4997 0.010 843 +6400 -165.3822 0.010 843 +6600 -165.3045 0.010 843 +6800 -165.1802 0.010 6750 +7000 -165.1486 0.010 6750 +7200 -165.1326 0.010 6750 +7400 -164.9712 0.010 6750 +7600 -164.9063 0.010 7540 +7800 -164.7723 0.010 7540 +8000 -164.6934 0.010 7540 +8200 -164.5487 0.010 7540 +8400 -164.4148 0.010 7540 +8600 -164.2339 0.010 7540 +8800 -164.0455 0.010 7540 +9000 -163.8878 0.010 7540 +9200 -163.8773 0.010 7540 +9400 -163.8424 0.010 7540 +9600 -163.7592 0.010 7540 +9800 -163.7102 0.010 7540 +10000 -163.6729 0.010 7540 + Optimizing parameters... improved 1.625 lnL + Optimizing branchlengths... improved 0.033 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 = 0.657, AG = 11.198, AT = 2.634, CG = 4.227, CT = 35.803, GT = 1.000 + Equilibrium State Frequencies: estimated + (ACGT) 0.1301 0.4168 0.2379 0.2153 + Rate Heterogeneity Model: + 4 discrete gamma distributed rate categories, alpha param estimated + 522.6859 + with an invariant (invariable) site category, proportion estimated + 0.3437 + Substitution rate categories under this model: + rate proportion + 0.0000 0.3437 + 0.9450 0.1641 + 0.9853 0.1641 + 1.0136 0.1641 + 1.0561 0.1641 + +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 3 branches were collapsed. -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. +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 : -162.0153 + +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: 0.6571 11.2 2.634 4.227 35.8 1 0.130 0.417 0.238 0.215 522.686 0.344 + +Treelengths: + TL +rep 1: 2.891 + +Saving best tree to bootstrap file ch.n.G4.boot.tre + +WARNING: Tree from prematurely terminated search saved to bootstrap file +####################################################### Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## @@ -15531,121 +15780,51 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 1800, seed 174826483, best lnL -166.826 +Bootstrap rep 1 (of 1) generation 10001, seed 258537382, best lnL -162.015 gen current_lnL precision last_tree_imp -1800 -166.8256 0.010 843 -1900 -166.7180 0.010 843 -2000 -166.7014 0.010 843 -2100 -166.6757 0.010 843 -2200 -166.6037 0.010 843 -2300 -166.5465 0.010 843 -2400 -166.5437 0.010 843 -2500 -166.5375 0.010 843 -2600 -166.4761 0.010 843 -2700 -166.4664 0.010 843 -2800 -166.4631 0.010 843 -2900 -166.4514 0.010 843 -3000 -166.4054 0.010 843 -3100 -166.3571 0.010 843 -3200 -166.3555 0.010 843 -3300 -166.3530 0.010 843 -3400 -166.2985 0.010 843 -3500 -166.2534 0.010 843 -3600 -166.2506 0.010 843 -3700 -166.1918 0.010 843 -3800 -166.1403 0.010 843 -3900 -166.1393 0.010 843 -4000 -166.1354 0.010 843 -4100 -166.1094 0.010 843 -4200 -166.0869 0.010 843 -4300 -166.0372 0.010 843 -4400 -166.0244 0.010 843 -4500 -165.9962 0.010 843 -4600 -165.9672 0.010 843 -4700 -165.9608 0.010 843 -4800 -165.9475 0.010 843 -4900 -165.8872 0.010 843 -5000 -165.8859 0.010 843 -5100 -165.8706 0.010 843 -5200 -165.8689 0.010 843 -5300 -165.8440 0.010 843 -5400 -165.8337 0.010 843 -5500 -165.7368 0.010 843 -5600 -165.6916 0.010 843 -5700 -165.6356 0.010 843 -5800 -165.5811 0.010 843 -5900 -165.5485 0.010 843 -6000 -165.5435 0.010 843 -6100 -165.5044 0.010 843 -6200 -165.4997 0.010 843 -6300 -165.4047 0.010 843 -6400 -165.3822 0.010 843 -6500 -165.3294 0.010 843 -6600 -165.3045 0.010 843 -6700 -165.2908 0.010 843 -6800 -165.1802 0.010 6750 -6900 -165.1514 0.010 6750 -7000 -165.1486 0.010 6750 -7100 -165.1452 0.010 6750 -7200 -165.1326 0.010 6750 -7300 -165.0450 0.010 6750 -7400 -164.9712 0.010 6750 -7500 -164.9350 0.010 6750 -7600 -164.9063 0.010 7540 -7700 -164.7982 0.010 7540 -7800 -164.7723 0.010 7540 -7900 -164.7470 0.010 7540 -8000 -164.6934 0.010 7540 -8100 -164.5821 0.010 7540 -8200 -164.5487 0.010 7540 -NOTE: ****Specified time limit (5 seconds) reached... +10001 -162.0153 0.010 7540 -MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT +MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 0.743, AG = 9.547, AT = 1.586, CG = 3.762, CT = 20.251, GT = 1.000 + AC = 0.657, AG = 11.198, AT = 2.634, CG = 4.227, CT = 35.803, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1288 0.4051 0.2333 0.2328 + (ACGT) 0.1301 0.4168 0.2379 0.2153 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 2.9470 + 522.6859 with an invariant (invariable) site category, proportion estimated - 0.3098 + 0.3437 Substitution rate categories under this model: rate proportion - 0.0000 0.3098 - 0.3851 0.1725 - 0.7286 0.1725 - 1.0822 0.1725 - 1.8041 0.1725 + 0.0000 0.3437 + 0.9450 0.1641 + 0.9853 0.1641 + 1.0136 0.1641 + 1.0561 0.1641 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 2 branches were 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!*** + 3 branches were collapsed. ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -164.4785 (TERMINATED PREMATURELY) +Replicate 1 : -162.0153 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: 0.7427 9.547 1.586 3.762 20.25 1 0.129 0.405 0.233 0.233 2.947 0.310 +rep 1: 0.6571 11.2 2.634 4.227 35.8 1 0.130 0.417 0.238 0.215 522.686 0.344 Treelengths: TL -rep 1: 2.446 +rep 1: 2.891 Saving best tree to bootstrap file ch.n.G4.boot.tre -WARNING: Tree from prematurely terminated search saved to bootstrap file +>>>Completed Bootstrap rep 1<<< ####################################################### TREEFILES PASS Running checkpoint test ./check/n.conf @@ -15778,15 +15957,68 @@ 6000 -212.7263 0.010 3769 6200 -212.7248 0.010 3769 6400 -212.7244 0.010 3769 -NOTE: ****Specified time limit (5 seconds) reached... +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 -212.6654 0.010 3769 +8000 -212.6638 0.010 3769 +8200 -212.6580 0.010 3769 +8400 -212.6570 0.010 3769 +8600 -212.6362 0.010 3769 +8800 -212.5814 0.010 3769 +9000 -212.5437 0.010 3769 +9200 -212.5310 0.010 3769 +9400 -212.5139 0.010 3769 +9600 -212.5123 0.010 3769 +9800 -212.5095 0.010 3769 +10000 -212.5014 0.010 3769 + Optimizing parameters... improved 0.000 lnL + Optimizing branchlengths... improved 0.000 lnL +NOTE: ****Specified generation limit (10000) reached... -NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY -TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE -FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF -(set restart = 1 in the config file). IF YOU WANT TO USE THE -PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY -ADD "end;" TO THE TREE FILES. +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +Model 1 + Number of states = 4 (nucleotide data) + Nucleotide Relative Rate Matrix: 6 rates + AC = 7.821, AG = 15.066, AT = 0.614, CG = 15.031, CT = 9.551, GT = 1.000 + Equilibrium State Frequencies: estimated + (ACGT) 0.2189 0.2871 0.1831 0.3108 + Rate Heterogeneity Model: + no rate heterogeneity + +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 1 branches were collapsed. + +Saving site likelihoods to file ch.n.sitelikes.log ... +WARNING: Site likelihoods being output on prematurely terminated search ... + +NOTE: ***Search was terminated before full auto-termination condition was reached! +Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** + + +####################################################### + +Completed 1 replicate search(es) (of 1). +Results: +Replicate 1 : -212.5014 +Parameter estimates: + r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) +rep 1: 7.821 15.07 0.6138 15.03 9.551 1 0.219 0.287 0.183 0.311 + +Treelengths: + TL +rep 1: 1.722 + +Saving final tree from best search rep (#1) to ch.n.best.tre +Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log + +WARNING: Internal states inferred on tree from prematurely terminated search + +####################################################### Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## @@ -15857,21 +16089,17 @@ STARTING RUN Restarting from checkpoint... - generation 6400, seed 300440726, best lnL -212.724 + generation 10001, seed 1459438551, best lnL -212.501 gen current_lnL precision last_tree_imp -6400 -212.7244 0.010 3769 -6500 -212.7244 0.010 3769 -Reached termination condition! -last topological improvement at gen 3769 -Improvement over last 500 gen = 0.00190 +10001 -212.5014 0.010 3769 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 4.839, AG = 9.614, AT = 0.397, CG = 9.744, CT = 6.243, GT = 1.000 + AC = 7.821, AG = 15.066, AT = 0.614, CG = 15.031, CT = 9.551, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2222 0.2881 0.1826 0.3071 + (ACGT) 0.2189 0.2871 0.1831 0.3108 Rate Heterogeneity Model: no rate heterogeneity @@ -15884,15 +16112,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -212.7244 +Replicate 1 : -212.5014 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) -rep 1: 4.839 9.614 0.397 9.744 6.243 1 0.222 0.288 0.183 0.307 +rep 1: 7.821 15.07 0.6138 15.03 9.551 1 0.219 0.287 0.183 0.311 Treelengths: TL -rep 1: 1.732 +rep 1: 1.722 Saving final tree from best search rep (#1) to ch.n.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log @@ -16046,7 +16274,6 @@ 5800 -210.3871 0.010 2883 6000 -210.3538 0.010 2883 6200 -210.3498 0.010 2883 -6400 -210.3399 0.010 2883 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16134,36 +16361,36 @@ STARTING RUN Restarting from checkpoint... - generation 6420, seed 1385520058, best lnL -210.339 + generation 6242, seed 1195716606, best lnL -210.348 gen current_lnL precision last_tree_imp -6420 -210.3390 0.010 2883 -6500 -210.3384 0.010 2883 +6242 -210.3483 0.010 2883 +6300 -210.3452 0.010 2883 Reached termination condition! last topological improvement at gen 2883 -Improvement over last 500 gen = 0.01539 +Improvement over last 500 gen = 0.04187 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 2.043, AG = 4.107, AT = 0.207, CG = 3.870, CT = 7.237, GT = 1.000 + AC = 2.043, AG = 4.107, AT = 0.207, CG = 3.802, CT = 7.237, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2409 0.3408 0.2110 0.2074 + (ACGT) 0.2421 0.3373 0.2121 0.2085 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 1.4302 with an invariant (invariable) site category, proportion estimated - 0.1961 + 0.1960 Substitution rate categories under this model: rate proportion - 0.0000 0.1961 + 0.0000 0.1960 0.2143 0.2010 0.5765 0.2010 1.0460 0.2010 2.1631 0.2010 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - No branches were short enough to be collapsed. + 1 branches were collapsed. NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with @@ -16176,15 +16403,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -210.3384 +Replicate 1 : -210.3452 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: 2.043 4.107 0.2071 3.87 7.237 1 0.241 0.341 0.211 0.207 1.430 0.196 +rep 1: 2.043 4.107 0.2071 3.802 7.237 1 0.242 0.337 0.212 0.208 1.430 0.196 Treelengths: TL -rep 1: 2.440 +rep 1: 2.430 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 @@ -16398,6 +16625,8 @@ Optimization precision reduced Optimizing parameters... improved 0.037 lnL Optimizing branchlengths... improved 0.000 lnL +1100 -13370.5869 0.304 0 +1200 -13370.5241 0.304 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16520,13 +16749,16 @@ Subset 3: Random seed for bootstrap reweighting: 486988955 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 1000, seed 355230265, best lnL -13370.642 +Bootstrap rep 1 (of 1) generation 1208, seed 528078057, best lnL -13370.524 gen current_lnL precision last_tree_imp -1000 -13370.6422 0.304 0 -1100 -13370.5869 0.304 0 -1200 -13370.5241 0.304 0 +1208 -13370.5241 0.304 0 1300 -13370.5104 0.304 0 1400 -13370.5063 0.304 0 +1500 -13370.4967 0.304 0 +Optimization precision reduced + Optimizing parameters... improved 0.015 lnL + Optimizing branchlengths... improved 0.000 lnL +1600 -13370.4816 0.206 0 NOTE: ****Specified time limit (1 seconds) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -16534,46 +16766,46 @@ 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 = 1.208, CG = 1.208, CT = 4.135, GT = 1.000 + AC = 1.605, AG = 2.506, AT = 1.208, CG = 1.208, CT = 4.152, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3079 0.1814 0.3083 0.2024 + (ACGT) 0.3082 0.1811 0.3085 0.2021 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.3640 + 0.3642 Substitution rate categories under this model: rate proportion 0.0119 0.2500 - 0.1544 0.2500 - 0.6892 0.2500 - 3.1446 0.2500 + 0.1545 0.2500 + 0.6894 0.2500 + 3.1441 0.2500 Model 2 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) - AC = 2.627, AG = 4.239, AT = 0.821, CG = 4.239, CT = 2.627, GT = 1.000 + AC = 2.624, AG = 4.245, AT = 0.821, CG = 4.245, CT = 2.624, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2812 0.1772 0.1597 0.3819 + (ACGT) 0.2815 0.1769 0.1594 0.3822 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.2460 + 0.2458 Substitution rate categories under this model: rate proportion 0.0019 0.2500 - 0.0638 0.2500 - 0.4929 0.2500 - 3.4413 0.2500 + 0.0637 0.2500 + 0.4925 0.2500 + 3.4419 0.2500 Model 3 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) - AC = 1.000, AG = 5.347, AT = 4.290, CG = 0.632, CT = 5.347, GT = 1.000 + AC = 1.000, AG = 5.332, AT = 4.291, CG = 0.633, CT = 5.332, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1555 0.3460 0.2768 0.2217 + (ACGT) 0.1554 0.3462 0.2765 0.2219 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.1101 + 4.1103 with an invariant (invariable) site category, proportion estimated 0.0486 Substitution rate categories under this model: @@ -16599,25 +16831,25 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13370.5063 (TERMINATED PREMATURELY) +Replicate 1 : -13370.4688 (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 1.208 1.208 4.135 1 0.308 0.181 0.308 0.202 0.364 +rep 1: 1.605 2.506 1.208 1.208 4.152 1 0.308 0.181 0.309 0.202 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 +rep 1: 2.624 4.245 0.821 4.245 2.624 1 0.281 0.177 0.159 0.382 0.246 Partition model subset 3: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 1 5.347 4.29 0.6325 5.347 1 0.155 0.346 0.277 0.222 4.110 0.049 +rep 1: 1 5.332 4.291 0.6327 5.332 1 0.155 0.346 0.276 0.222 4.110 0.049 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 1.763 0.530 0.287 2.183 +rep 1: 1.762 0.530 0.287 2.183 Saving best tree to bootstrap file ch.p.3diff.boot.tre @@ -16839,7 +17071,7 @@ pass 15: -467.6797 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6797 -Time used so far = 0 hours, 0 minutes and 5 seconds +Time used so far = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -16921,6 +17153,11 @@ 400 -467.7470 0.010 0 500 -467.7426 0.010 0 600 -467.7398 0.010 0 +700 -467.7362 0.010 0 +800 -467.7332 0.010 0 +900 -467.7319 0.010 0 +1000 -467.7290 0.010 0 +1100 -467.7275 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17046,14 +17283,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 634, seed 34875524, best lnL -467.739 +Search rep 2 (of 5) generation 1155, seed 640071195, best lnL -467.722 gen current_lnL precision last_tree_imp -634 -467.7393 0.010 0 -700 -467.7362 0.010 0 -800 -467.7332 0.010 0 -900 -467.7319 0.010 0 -1000 -467.7290 0.010 0 -1100 -467.7275 0.010 0 +1155 -467.7217 0.010 0 1200 -467.7204 0.010 0 1300 -467.7192 0.010 0 1400 -467.7176 0.010 0 @@ -17109,7 +17341,7 @@ pass 14: -467.6783 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6783 -Time used so far = 0 hours, 0 minutes and 10 seconds +Time used so far = 0 hours, 0 minutes and 9 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17199,28 +17431,41 @@ 1200 -467.7292 0.010 0 1300 -467.7278 0.010 0 1400 -467.7254 0.010 0 +1500 -467.7245 0.010 0 +1600 -467.7242 0.010 0 +1700 -467.7234 0.010 0 +1800 -467.7219 0.010 0 +1900 -467.7211 0.010 0 +2000 -467.7200 0.010 0 +2100 -467.7198 0.010 0 +2200 -467.7194 0.010 0 +2300 -467.7194 0.010 0 +2400 -467.7185 0.010 0 +2500 -467.7184 0.010 0 +2600 -467.7182 0.010 0 +2700 -467.7174 0.010 0 +2800 -467.7172 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -467.7254 +Current score = -467.7169 Performing final optimizations... -pass 1 : -467.7254 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -467.7070 (branch= 0.0183 subset rates= 0.0000) -pass 3 : -467.6961 (branch= 0.0109 subset rates= 0.0000) -pass 4 : -467.6901 (branch= 0.0060 subset rates= 0.0000) -pass 5 : -467.6843 (branch= 0.0058 subset rates= 0.0000) -pass 6 : -467.6824 (branch= 0.0019 subset rates= 0.0000) -pass 7 : -467.6809 (branch= 0.0014 subset rates= 0.0000) -pass 8 : -467.6803 (branch= 0.0006 subset rates= 0.0000) -pass 9 : -467.6799 (branch= 0.0004 subset rates= 0.0000) -pass 10: -467.6797 (branch= 0.0002 subset rates= 0.0000) -pass 11: -467.6796 (branch= 0.0001 subset rates= 0.0000) -pass 12: -467.6792 (branch= 0.0000 subset rates= 0.0003) -pass 13: -467.6792 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6789 (branch= 0.0000 subset rates= 0.0003) -pass 15: -467.6788 (branch= 0.0001 subset rates= 0.0000) -pass 16: -467.6788 (branch= 0.0000 subset rates= 0.0000) -pass 17: -467.6788 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -467.7169 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -467.7016 (branch= 0.0153 subset rates= 0.0000) +pass 3 : -467.6941 (branch= 0.0075 subset rates= 0.0000) +pass 4 : -467.6900 (branch= 0.0042 subset rates= 0.0000) +pass 5 : -467.6859 (branch= 0.0040 subset rates= 0.0000) +pass 6 : -467.6829 (branch= 0.0030 subset rates= 0.0000) +pass 7 : -467.6814 (branch= 0.0015 subset rates= 0.0000) +pass 8 : -467.6805 (branch= 0.0009 subset rates= 0.0000) +pass 9 : -467.6800 (branch= 0.0004 subset rates= 0.0000) +pass 10: -467.6797 (branch= 0.0003 subset rates= 0.0000) +pass 11: -467.6791 (branch= 0.0001 subset rates= 0.0005) +pass 12: -467.6788 (branch= 0.0003 subset rates= 0.0000) +pass 13: -467.6785 (branch= 0.0002 subset rates= 0.0000) +pass 14: -467.6782 (branch= 0.0001 subset rates= 0.0003) +pass 15: -467.6782 (branch= 0.0000 subset rates= 0.0000) +pass 16: -467.6782 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -467.6788 +Final score = -467.6782 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -17249,7 +17494,7 @@ no rate heterogeneity Subset rate multipliers: - 0.78 1.49 2.18 + 0.79 1.48 2.18 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. @@ -17267,8 +17512,8 @@ same topology, you should assume that they found different topologies. Results: Replicate 1 : -467.6797 -Replicate 2 : -467.6783 (best) (same topology as 1) -Replicate 3 : -467.6788 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 2 : -467.6783 (same topology as 1) +Replicate 3 : -467.6782 (best) (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17285,9 +17530,9 @@ TL R(1) R(2) R(3) rep 1: 3.838 0.789 1.477 2.150 rep 2: 3.841 0.787 1.478 2.178 -rep 3: 3.845 0.784 1.486 2.184 +rep 3: 3.843 0.786 1.480 2.184 -Saving final tree from best search rep (#2) to ch.p.mk.ssr.best.tre +Saving final tree from best search rep (#3) to ch.p.mk.ssr.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkO.ssr.conf @@ -17506,7 +17751,7 @@ pass 15: -477.4318 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.4318 -Time used so far = 0 hours, 0 minutes and 4 seconds +Time used so far = 0 hours, 0 minutes and 5 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17583,25 +17828,6 @@ lnL after optimization: -477.8544 gen current_lnL precision last_tree_imp 0 -477.8544 0.010 0 -100 -477.7502 0.010 36 -200 -477.7249 0.010 149 -300 -477.4594 0.010 203 -400 -477.3874 0.010 366 -500 -477.3748 0.010 366 -600 -477.3633 0.010 366 -700 -477.3569 0.010 366 -800 -477.3520 0.010 366 -900 -477.3483 0.010 366 -1000 -477.3445 0.010 366 -1100 -477.3365 0.010 366 -1200 -477.3113 0.010 1197 -1300 -477.2903 0.010 1197 -1400 -477.2877 0.010 1197 -1500 -477.2841 0.010 1197 -1600 -477.2783 0.010 1197 -1700 -477.2762 0.010 1197 -1800 -477.2729 0.010 1197 -1900 -477.2723 0.010 1197 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17727,9 +17953,28 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 1949, seed 894358758, best lnL -477.272 +Search rep 2 (of 5) generation 17, seed 689186569, best lnL -477.847 gen current_lnL precision last_tree_imp -1949 -477.2722 0.010 1197 +17 -477.8469 0.010 0 +100 -477.7502 0.010 36 +200 -477.7249 0.010 149 +300 -477.4594 0.010 203 +400 -477.3874 0.010 366 +500 -477.3748 0.010 366 +600 -477.3633 0.010 366 +700 -477.3569 0.010 366 +800 -477.3520 0.010 366 +900 -477.3483 0.010 366 +1000 -477.3445 0.010 366 +1100 -477.3365 0.010 366 +1200 -477.3113 0.010 1197 +1300 -477.2903 0.010 1197 +1400 -477.2877 0.010 1197 +1500 -477.2841 0.010 1197 +1600 -477.2783 0.010 1197 +1700 -477.2762 0.010 1197 +1800 -477.2729 0.010 1197 +1900 -477.2723 0.010 1197 2000 -477.2721 0.010 1197 2100 -477.2715 0.010 1197 2200 -477.2703 0.010 1197 @@ -17774,7 +18019,7 @@ pass 14: -477.2050 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.2050 -Time used so far = 0 hours, 0 minutes and 9 seconds +Time used so far = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17871,24 +18116,29 @@ 1800 -477.2835 0.010 537 1900 -477.2826 0.010 537 2000 -477.2805 0.010 537 +2100 -477.2787 0.010 537 +2200 -477.2785 0.010 537 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -477.2805 +Current score = -477.2779 Performing final optimizations... -pass 1 : -477.2425 (branch= 0.0000 subset rates= 0.0379) -pass 2 : -477.2286 (branch= 0.0103 subset rates= 0.0036) -pass 3 : -477.2191 (branch= 0.0092 subset rates= 0.0004) -pass 4 : -477.2155 (branch= 0.0034 subset rates= 0.0002) -pass 5 : -477.2088 (branch= 0.0066 subset rates= 0.0000) -pass 6 : -477.2059 (branch= 0.0030 subset rates= 0.0000) -pass 7 : -477.2056 (branch= 0.0003 subset rates= 0.0000) -pass 8 : -477.2054 (branch= 0.0002 subset rates= 0.0000) -pass 9 : -477.2046 (branch= 0.0003 subset rates= 0.0005) -pass 10: -477.2043 (branch= 0.0002 subset rates= 0.0000) -pass 11: -477.2043 (branch= 0.0000 subset rates= 0.0000) -pass 12: -477.2043 (branch= 0.0000 subset rates= 0.0000) -pass 13: -477.2043 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -477.2779 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -477.2503 (branch= 0.0103 subset rates= 0.0173) +pass 3 : -477.2221 (branch= 0.0072 subset rates= 0.0209) +pass 4 : -477.2178 (branch= 0.0015 subset rates= 0.0028) +pass 5 : -477.2147 (branch= 0.0031 subset rates= 0.0000) +pass 6 : -477.2111 (branch= 0.0036 subset rates= 0.0000) +pass 7 : -477.2096 (branch= 0.0015 subset rates= 0.0000) +pass 8 : -477.2092 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -477.2092 (branch= 0.0001 subset rates= 0.0000) +pass 10: -477.2091 (branch= 0.0000 subset rates= 0.0000) +pass 11: -477.2088 (branch= 0.0001 subset rates= 0.0002) +pass 12: -477.2062 (branch= 0.0000 subset rates= 0.0026) +pass 13: -477.2061 (branch= 0.0001 subset rates= 0.0000) +pass 14: -477.2047 (branch= 0.0000 subset rates= 0.0013) +pass 15: -477.2046 (branch= 0.0001 subset rates= 0.0000) +pass 16: -477.2046 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.2043 +Final score = -477.2046 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -17917,7 +18167,7 @@ no rate heterogeneity Subset rate multipliers: - 0.63 1.94 2.63 + 0.63 1.94 2.64 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. @@ -17936,7 +18186,7 @@ Results: Replicate 1 : -477.4318 Replicate 2 : -477.2050 -Replicate 3 : -477.2043 (best) (same topology as 2) (TERMINATED PREMATURELY) +Replicate 3 : -477.2046 (best) (same topology as 2) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17953,7 +18203,7 @@ TL R(1) R(2) R(3) rep 1: 4.927 0.632 1.917 2.725 rep 2: 4.703 0.632 1.943 2.641 -rep 3: 4.696 0.635 1.935 2.629 +rep 3: 4.701 0.633 1.940 2.642 Saving final tree from best search rep (#3) to ch.p.mkO.ssr.best.tre ####################################################### @@ -18140,6 +18390,132 @@ 1700 -425.5976 0.010 365 1800 -425.5972 0.010 365 1900 -425.5954 0.010 365 +2000 -425.5950 0.010 365 +2100 -425.5942 0.010 365 +2200 -425.5913 0.010 365 +2300 -425.5899 0.010 365 +2400 -425.5893 0.010 365 +2500 -425.5891 0.010 365 +2600 -425.5890 0.010 365 +2700 -425.5888 0.010 365 +2800 -425.5883 0.010 365 +2900 -425.5869 0.010 365 +3000 -425.5868 0.010 365 +3100 -425.5859 0.010 365 +3200 -425.5858 0.010 365 +3300 -425.5850 0.010 365 +3400 -425.5843 0.010 365 +3500 -425.5843 0.010 365 +3600 -425.5841 0.010 365 +3700 -425.5839 0.010 365 +3800 -425.5839 0.010 365 +3900 -425.5839 0.010 365 +Reached termination condition! +last topological improvement at gen 365 +Improvement over last 500 gen = 0.00044 +Current score = -425.5839 +Performing final optimizations... +pass 1 : -425.5730 (branch= 0.0000 subset rates= 0.0109) +pass 2 : -425.5586 (branch= 0.0144 subset rates= 0.0000) +pass 3 : -425.5516 (branch= 0.0070 subset rates= 0.0000) +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 : -425.5488 (branch= 0.0005 subset rates= 0.0000) +pass 9 : -425.5487 (branch= 0.0001 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 3 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:+ 1.686 (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: -439.2276 +gen current_lnL precision last_tree_imp +0 -439.2276 0.010 0 +100 -428.8676 0.010 98 +200 -428.0499 0.010 164 +300 -427.6003 0.010 249 +400 -427.5649 0.010 249 +500 -427.4911 0.010 499 +600 -427.3864 0.010 511 +700 -425.7188 0.010 668 +800 -425.6951 0.010 722 +900 -425.6795 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 -425.6341 0.010 722 +1600 -425.6274 0.010 722 +1700 -425.6239 0.010 722 +1800 -425.6235 0.010 722 +1900 -425.6225 0.010 722 +2000 -425.6202 0.010 722 +2100 -425.6196 0.010 722 +2200 -425.6174 0.010 722 +2300 -425.6146 0.010 722 +2400 -425.6135 0.010 722 +2500 -425.6104 0.010 722 +2600 -425.6099 0.010 722 +2700 -425.6088 0.010 722 +2800 -425.6077 0.010 722 +2900 -425.6073 0.010 722 +3000 -425.6058 0.010 722 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -18268,49 +18644,35 @@ Subset 3: Random seed for bootstrap reweighting: 974568031 Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 1 (of 5) generation 1933, seed 413780019, best lnL -425.595 +Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 3031, seed 1887747887, best lnL -425.606 gen current_lnL precision last_tree_imp -1933 -425.5950 0.010 365 -2000 -425.5950 0.010 365 -2100 -425.5942 0.010 365 -2200 -425.5913 0.010 365 -2300 -425.5899 0.010 365 -2400 -425.5893 0.010 365 -2500 -425.5891 0.010 365 -2600 -425.5890 0.010 365 -2700 -425.5888 0.010 365 -2800 -425.5883 0.010 365 -2900 -425.5869 0.010 365 -3000 -425.5868 0.010 365 -3100 -425.5859 0.010 365 -3200 -425.5858 0.010 365 -3300 -425.5850 0.010 365 -3400 -425.5843 0.010 365 -3500 -425.5843 0.010 365 -3600 -425.5841 0.010 365 -3700 -425.5839 0.010 365 -3800 -425.5839 0.010 365 -3900 -425.5839 0.010 365 +3031 -425.6058 0.010 722 +3100 -425.6056 0.010 722 +3200 -425.6055 0.010 722 +3300 -425.6051 0.010 722 +3400 -425.6049 0.010 722 +3500 -425.6048 0.010 722 +3600 -425.6048 0.010 722 Reached termination condition! -last topological improvement at gen 365 -Improvement over last 500 gen = 0.00044 -Current score = -425.5839 +last topological improvement at gen 722 +Improvement over last 500 gen = 0.00084 +Current score = -425.6048 Performing final optimizations... -pass 1 : -425.5730 (branch= 0.0000 subset rates= 0.0109) -pass 2 : -425.5586 (branch= 0.0144 subset rates= 0.0000) -pass 3 : -425.5516 (branch= 0.0070 subset rates= 0.0000) -pass 4 : -425.5509 (branch= 0.0007 subset rates= 0.0000) -pass 5 : -425.5505 (branch= 0.0004 subset rates= 0.0000) +pass 1 : -425.5779 (branch= 0.0000 subset rates= 0.0269) +pass 2 : -425.5572 (branch= 0.0188 subset rates= 0.0018) +pass 3 : -425.5530 (branch= 0.0041 subset rates= 0.0001) +pass 4 : -425.5518 (branch= 0.0012 subset rates= 0.0000) +pass 5 : -425.5505 (branch= 0.0013 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 : -425.5488 (branch= 0.0005 subset rates= 0.0000) +pass 7 : -425.5491 (branch= 0.0007 subset rates= 0.0000) +pass 8 : -425.5489 (branch= 0.0003 subset rates= 0.0000) pass 9 : -425.5487 (branch= 0.0001 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 11: -425.5486 (branch= 0.0001 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 9 seconds +Time used so far = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18340,62 +18702,177 @@ Subset rate multipliers: 0.87 1.53 1.12 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 10 branches were collapsed. + 9 branches were collapsed. ->>>Completed Bootstrap rep 1 (of 1) Search rep 1 (of 5)<<< +>>>Completed Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< ->>>Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< +>>>Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< Obtained starting tree 1 from Nexus -Starting with seed=222492842 +Starting with seed=2129292874 -Initial ln Likelihood: -586.0233 +Initial ln Likelihood: -588.2493 optimizing: starting branch lengths, subset rates... -pass 1:+ 129.358 (branch= 127.50 scale= 1.82 subset rates= 0.04) -pass 2:+ 11.580 (branch= 11.46 scale= 0.04 subset rates= 0.07) -pass 3:+ 3.728 (branch= 3.71 scale= 0.00 subset rates= 0.02) -pass 4:+ 1.686 (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: -439.2276 +pass 1:+ 141.030 (branch= 140.49 scale= 0.38 subset rates= 0.17) +pass 2:+ 6.536 (branch= 6.52 scale= 0.00 subset rates= 0.02) +pass 3:+ 1.051 (branch= 1.03 scale= 0.00 subset rates= 0.02) +pass 4:+ 0.060 (branch= 0.06 scale= 0.00 subset rates= 0.00) +pass 5:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -439.5713 gen current_lnL precision last_tree_imp -0 -439.2276 0.010 0 -100 -428.8676 0.010 98 -200 -428.0499 0.010 164 -300 -427.6003 0.010 249 -400 -427.5649 0.010 249 -500 -427.4911 0.010 499 -600 -427.3864 0.010 511 -700 -425.7188 0.010 668 -800 -425.6951 0.010 722 -900 -425.6795 0.010 722 -1000 -425.6689 0.010 722 -1100 -425.6640 0.010 722 +0 -439.5713 0.010 0 +100 -431.1391 0.010 95 +200 -428.6585 0.010 167 +300 -427.6514 0.010 295 +400 -427.2438 0.010 295 +500 -427.2138 0.010 295 +600 -427.1679 0.010 568 +700 -427.1487 0.010 568 +800 -425.4817 0.010 762 +900 -425.4264 0.010 803 +1000 -425.4085 0.010 803 +1100 -425.4058 0.010 803 +1200 -425.3915 0.010 803 +1300 -425.3912 0.010 803 +1400 -425.3887 0.010 803 +1500 -425.3865 0.010 803 +1600 -425.3820 0.010 803 +1700 -425.3760 0.010 803 +1800 -425.3759 0.010 803 +1900 -425.3750 0.010 803 +2000 -425.3712 0.010 803 +2100 -425.3702 0.010 803 +2200 -425.3666 0.010 803 +2300 -425.3654 0.010 803 +2400 -425.3635 0.010 803 +2500 -425.3629 0.010 803 +2600 -425.3622 0.010 803 +2700 -425.3619 0.010 803 +2800 -425.3613 0.010 803 +2900 -425.3592 0.010 803 +3000 -425.3583 0.010 803 +3100 -425.3581 0.010 803 +3200 -425.3571 0.010 803 +3300 -425.3567 0.010 803 +3400 -425.3566 0.010 803 +3500 -425.3564 0.010 803 +3600 -425.3558 0.010 803 +3700 -425.3553 0.010 803 +3800 -425.3549 0.010 803 +3900 -425.3540 0.010 803 +4000 -425.3540 0.010 803 +4100 -425.3536 0.010 803 +4200 -425.3534 0.010 803 +4300 -425.3533 0.010 803 +4400 -425.3532 0.010 803 +Reached termination condition! +last topological improvement at gen 803 +Improvement over last 500 gen = 0.00083 +Current score = -425.3532 +Performing final optimizations... +pass 1 : -425.3514 (branch= 0.0000 subset rates= 0.0018) +pass 2 : -425.3324 (branch= 0.0164 subset rates= 0.0026) +pass 3 : -425.3254 (branch= 0.0070 subset rates= 0.0000) +pass 4 : -425.3219 (branch= 0.0026 subset rates= 0.0009) +pass 5 : -425.3216 (branch= 0.0003 subset rates= 0.0000) +pass 6 : -425.3216 (branch= 0.0000 subset rates= 0.0000) +pass 7 : -425.3212 (branch= 0.0005 subset rates= 0.0000) +pass 8 : -425.3205 (branch= 0.0006 subset rates= 0.0000) +pass 9 : -425.3204 (branch= 0.0001 subset rates= 0.0000) +pass 10: -425.3203 (branch= 0.0001 subset rates= 0.0000) +pass 11: -425.3202 (branch= 0.0001 subset rates= 0.0000) +pass 12: -425.3202 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -425.3202 +Time used so far = 0 hours, 0 minutes and 10 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (standard data) + Character change matrix: + One rate (symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.86 1.54 1.15 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 9 branches were collapsed. + +>>>Completed Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< + +>>>Bootstrap rep 1 (of 1) Search rep 4 (of 5)<<< +Obtained starting tree 1 from Nexus +Starting with seed=1573911897 + +Initial ln Likelihood: -585.3657 +optimizing: starting branch lengths, subset rates... +pass 1:+ 128.924 (branch= 128.21 scale= 0.69 subset rates= 0.02) +pass 2:+ 11.959 (branch= 11.78 scale= 0.03 subset rates= 0.15) +pass 3:+ 4.421 (branch= 4.33 scale= 0.00 subset rates= 0.09) +pass 4:+ 0.779 (branch= 0.76 scale= 0.00 subset rates= 0.01) +pass 5:+ 0.057 (branch= 0.06 scale= 0.00 subset rates= 0.00) +pass 6:+ 0.012 (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: -439.2135 +gen current_lnL precision last_tree_imp +0 -439.2135 0.010 0 +100 -428.1779 0.010 67 +200 -427.4638 0.010 189 +300 -427.4437 0.010 226 +400 -427.1435 0.010 393 +500 -427.1285 0.010 393 +600 -427.1120 0.010 393 +700 -427.1022 0.010 393 +800 -427.1003 0.010 393 +900 -427.0977 0.010 393 +1000 -427.0972 0.010 393 +1100 -427.0948 0.010 393 +1200 -427.0919 0.010 393 +1300 -427.0909 0.010 393 +1400 -427.0892 0.010 393 +1500 -427.0880 0.010 393 +1600 -427.0868 0.010 393 +1700 -427.0861 0.010 393 +1800 -427.0846 0.010 393 +1900 -425.5433 0.010 1890 +2000 -425.5081 0.010 1942 +2100 -425.3789 0.010 2010 +2200 -425.3685 0.010 2010 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -425.6509 +Current score = -425.3666 Performing final optimizations... -pass 1 : -425.6081 (branch= 0.0136 subset rates= 0.0292) -pass 2 : -425.5757 (branch= 0.0324 subset rates= 0.0000) -pass 3 : -425.5588 (branch= 0.0169 subset rates= 0.0000) -pass 4 : -425.5546 (branch= 0.0041 subset rates= 0.0000) -pass 5 : -425.5523 (branch= 0.0024 subset rates= 0.0000) -pass 6 : -425.5501 (branch= 0.0022 subset rates= 0.0000) -pass 7 : -425.5495 (branch= 0.0006 subset rates= 0.0000) -pass 8 : -425.5491 (branch= 0.0003 subset rates= 0.0000) -pass 9 : -425.5490 (branch= 0.0001 subset rates= 0.0000) -pass 10: -425.5490 (branch= 0.0001 subset rates= 0.0000) -pass 11: -425.5489 (branch= 0.0001 subset rates= 0.0000) -pass 12: -425.5489 (branch= 0.0000 subset rates= 0.0000) -pass 13: -425.5489 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -425.3666 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -425.3329 (branch= 0.0336 subset rates= 0.0001) +pass 3 : -425.3299 (branch= 0.0030 subset rates= 0.0000) +pass 4 : -425.3268 (branch= 0.0031 subset rates= 0.0000) +pass 5 : -425.3226 (branch= 0.0042 subset rates= 0.0000) +pass 6 : -425.3212 (branch= 0.0014 subset rates= 0.0000) +pass 7 : -425.3209 (branch= 0.0003 subset rates= 0.0000) +pass 8 : -425.3206 (branch= 0.0003 subset rates= 0.0000) +pass 9 : -425.3205 (branch= 0.0001 subset rates= 0.0000) +pass 10: -425.3204 (branch= 0.0001 subset rates= 0.0000) +pass 11: -425.3204 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.3204 (branch= 0.0000 subset rates= 0.0000) +pass 13: -425.3204 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -425.5489 +Final score = -425.3204 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -18424,11 +18901,11 @@ no rate heterogeneity Subset rate multipliers: - 0.87 1.52 1.13 + 0.86 1.54 1.14 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 10 branches were collapsed. ->>>Terminated Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< +>>>Terminated Bootstrap rep 1 (of 1) Search rep 4 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -18436,13 +18913,15 @@ ####################################################### -Completed 2 replicate search(es) (of 5). +Completed 4 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -425.5486 (best) -Replicate 2 : -425.5489 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 1 : -425.5486 +Replicate 2 : -425.5486 +Replicate 3 : -425.3202 (best) +Replicate 4 : -425.3204 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -18458,9 +18937,11 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 3.038 0.868 1.530 1.121 -rep 2: 3.038 0.869 1.525 1.128 +rep 2: 3.038 0.868 1.529 1.123 +rep 3: 2.977 0.864 1.541 1.155 +rep 4: 2.982 0.865 1.539 1.142 -Saving tree from best search rep (#1) to bootstrap file ch.p.mkv.ssr.boot.tre +Saving tree from best search rep (#3) to bootstrap file ch.p.mkv.ssr.boot.tre ####################################################### TREEFILES PASS @@ -18655,6 +19136,134 @@ 2800 -473.9779 0.010 653 2900 -473.9776 0.010 653 3000 -473.9775 0.010 653 +3100 -473.9771 0.010 653 +3200 -473.9769 0.010 653 +3300 -473.9766 0.010 653 +3400 -473.9762 0.010 653 +3500 -473.9761 0.010 653 +3600 -473.9761 0.010 653 +3700 -473.9759 0.010 653 +Reached termination condition! +last topological improvement at gen 653 +Improvement over last 500 gen = 0.00096 +Current score = -473.9759 +Performing final optimizations... +pass 1 : -473.9758 (branch= 0.0001 subset rates= 0.0000) +pass 2 : -473.9558 (branch= 0.0183 subset rates= 0.0016) +pass 3 : -473.9558 (branch= 0.0000 subset rates= 0.0000) +pass 4 : -473.9550 (branch= 0.0009 subset rates= 0.0000) +pass 5 : -473.9525 (branch= 0.0007 subset rates= 0.0018) +pass 6 : -473.9521 (branch= 0.0004 subset rates= 0.0000) +pass 7 : -473.9516 (branch= 0.0004 subset rates= 0.0000) +pass 8 : -473.9512 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -473.9510 (branch= 0.0002 subset rates= 0.0000) +pass 10: -473.9509 (branch= 0.0001 subset rates= 0.0000) +pass 11: -473.9508 (branch= 0.0001 subset rates= 0.0000) +pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 13: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 14: -473.9508 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -473.9508 +Time used so far = 0 hours, 0 minutes and 3 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.59 2.07 2.81 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 8 branches were collapsed. + +>>>Completed Search rep 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=74284197 + +Initial ln Likelihood: -646.1143 +optimizing: starting branch lengths, subset rates... +pass 1:+ 146.023 (branch= 135.13 scale= 0.95 subset rates= 9.94) +pass 2:+ 17.326 (branch= 12.98 scale= 0.01 subset rates= 4.33) +pass 3:+ 4.642 (branch= 3.12 scale= 0.00 subset rates= 1.52) +pass 4:+ 2.490 (branch= 1.89 scale= 0.00 subset rates= 0.60) +pass 5:+ 0.684 (branch= 0.61 scale= 0.02 subset rates= 0.05) +pass 6:+ 0.130 (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: -474.8185 +gen current_lnL precision last_tree_imp +0 -474.8185 0.010 0 +100 -474.7244 0.010 55 +200 -474.7128 0.010 55 +300 -474.7037 0.010 55 +400 -474.6654 0.010 339 +500 -474.5695 0.010 496 +600 -474.0703 0.010 585 +700 -474.0481 0.010 585 +800 -474.0412 0.010 585 +900 -474.0316 0.010 585 +1000 -474.0282 0.010 585 +1100 -474.0225 0.010 585 +1200 -474.0142 0.010 585 +1300 -474.0116 0.010 585 +1400 -474.0080 0.010 585 +1500 -474.0041 0.010 585 +1600 -474.0016 0.010 585 +1700 -474.0010 0.010 585 +1800 -473.9994 0.010 585 +1900 -473.9983 0.010 585 +2000 -473.9971 0.010 585 +2100 -473.9968 0.010 585 +2200 -473.9964 0.010 585 +2300 -473.9963 0.010 585 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -18780,38 +19389,39 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 5) generation 3050, seed 1821801759, best lnL -473.977 +Search rep 2 (of 5) generation 2327, seed 1905945318, best lnL -473.996 gen current_lnL precision last_tree_imp -3050 -473.9772 0.010 653 -3100 -473.9771 0.010 653 -3200 -473.9769 0.010 653 -3300 -473.9766 0.010 653 -3400 -473.9762 0.010 653 -3500 -473.9761 0.010 653 -3600 -473.9761 0.010 653 -3700 -473.9759 0.010 653 +2327 -473.9960 0.010 585 +2400 -473.9952 0.010 585 +2500 -473.9949 0.010 585 +2600 -473.9933 0.010 585 +2700 -473.9932 0.010 585 +2800 -473.9932 0.010 585 +2900 -473.9930 0.010 585 +3000 -473.9930 0.010 585 +3100 -473.9925 0.010 585 Reached termination condition! -last topological improvement at gen 653 -Improvement over last 500 gen = 0.00096 -Current score = -473.9759 +last topological improvement at gen 585 +Improvement over last 500 gen = 0.00079 +Current score = -473.9925 Performing final optimizations... -pass 1 : -473.9758 (branch= 0.0001 subset rates= 0.0000) -pass 2 : -473.9558 (branch= 0.0183 subset rates= 0.0016) -pass 3 : -473.9558 (branch= 0.0000 subset rates= 0.0000) -pass 4 : -473.9550 (branch= 0.0009 subset rates= 0.0000) -pass 5 : -473.9525 (branch= 0.0007 subset rates= 0.0018) -pass 6 : -473.9521 (branch= 0.0004 subset rates= 0.0000) -pass 7 : -473.9516 (branch= 0.0004 subset rates= 0.0000) -pass 8 : -473.9512 (branch= 0.0004 subset rates= 0.0000) -pass 9 : -473.9510 (branch= 0.0002 subset rates= 0.0000) -pass 10: -473.9509 (branch= 0.0001 subset rates= 0.0000) -pass 11: -473.9508 (branch= 0.0001 subset rates= 0.0000) -pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9508 (branch= 0.0000 subset rates= 0.0000) -pass 14: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -473.9818 (branch= 0.0000 subset rates= 0.0107) +pass 2 : -473.9604 (branch= 0.0189 subset rates= 0.0025) +pass 3 : -473.9545 (branch= 0.0058 subset rates= 0.0000) +pass 4 : -473.9538 (branch= 0.0007 subset rates= 0.0000) +pass 5 : -473.9535 (branch= 0.0003 subset rates= 0.0000) +pass 6 : -473.9521 (branch= 0.0014 subset rates= 0.0000) +pass 7 : -473.9516 (branch= 0.0003 subset rates= 0.0002) +pass 8 : -473.9513 (branch= 0.0002 subset rates= 0.0000) +pass 9 : -473.9511 (branch= 0.0002 subset rates= 0.0000) +pass 10: -473.9510 (branch= 0.0001 subset rates= 0.0000) +pass 11: -473.9510 (branch= 0.0001 subset rates= 0.0000) +pass 12: -473.9510 (branch= 0.0000 subset rates= 0.0000) +pass 13: -473.9509 (branch= 0.0000 subset rates= 0.0000) +pass 14: -473.9508 (branch= 0.0000 subset rates= 0.0001) Looking for minimum length branches... Final score = -473.9508 -Time used so far = 0 hours, 0 minutes and 7 seconds +Time used so far = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18839,13 +19449,13 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.07 2.81 + 0.59 2.06 2.81 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. ->>>Completed Search rep 1 (of 5)<<< +>>>Completed Search rep 2 (of 5)<<< ->>>Search rep 2 (of 5)<<< +>>>Search rep 3 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 @@ -18874,57 +19484,192 @@ Subset rate multipliers: 1.00 1.00 1.00 -Starting with seed=74284197 +Starting with seed=663269721 -Initial ln Likelihood: -646.1143 +Initial ln Likelihood: -659.0351 optimizing: starting branch lengths, subset rates... -pass 1:+ 146.023 (branch= 135.13 scale= 0.95 subset rates= 9.94) -pass 2:+ 17.326 (branch= 12.98 scale= 0.01 subset rates= 4.33) -pass 3:+ 4.642 (branch= 3.12 scale= 0.00 subset rates= 1.52) -pass 4:+ 2.490 (branch= 1.89 scale= 0.00 subset rates= 0.60) -pass 5:+ 0.684 (branch= 0.61 scale= 0.02 subset rates= 0.05) -pass 6:+ 0.130 (branch= 0.13 scale= 0.00 subset rates= 0.00) +pass 1:+ 164.999 (branch= 154.40 scale= 0.48 subset rates= 10.12) +pass 2:+ 14.317 (branch= 9.49 scale= 0.03 subset rates= 4.79) +pass 3:+ 3.819 (branch= 2.06 scale= 0.02 subset rates= 1.74) +pass 4:+ 0.906 (branch= 0.30 scale= 0.00 subset rates= 0.60) +pass 5:+ 0.122 (branch= 0.09 scale= 0.00 subset rates= 0.03) +pass 6:+ 0.038 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8185 +lnL after optimization: -474.8340 gen current_lnL precision last_tree_imp -0 -474.8185 0.010 0 -100 -474.7244 0.010 55 -200 -474.7128 0.010 55 -300 -474.7037 0.010 55 -400 -474.6654 0.010 339 -500 -474.5695 0.010 496 -600 -474.0703 0.010 585 -700 -474.0481 0.010 585 -800 -474.0412 0.010 585 -900 -474.0316 0.010 585 -1000 -474.0282 0.010 585 -1100 -474.0225 0.010 585 -1200 -474.0142 0.010 585 -1300 -474.0116 0.010 585 -1400 -474.0080 0.010 585 -1500 -474.0041 0.010 585 -1600 -474.0016 0.010 585 -1700 -474.0010 0.010 585 -1800 -473.9994 0.010 585 -1900 -473.9983 0.010 585 +0 -474.8340 0.010 0 +100 -474.7919 0.010 0 +200 -474.7307 0.010 183 +300 -474.7187 0.010 183 +400 -474.7036 0.010 183 +500 -474.6871 0.010 183 +600 -474.5395 0.010 535 +700 -474.5271 0.010 535 +800 -474.5227 0.010 535 +900 -474.5120 0.010 535 +1000 -474.5077 0.010 535 +1100 -474.5053 0.010 535 +1200 -474.5039 0.010 535 +1300 -474.5013 0.010 535 +1400 -474.4986 0.010 535 +1500 -474.4981 0.010 535 +1600 -474.4956 0.010 535 +1700 -474.4907 0.010 535 +1800 -474.4796 0.010 535 +1900 -474.4760 0.010 535 +2000 -474.4747 0.010 535 +2100 -474.4733 0.010 535 +2200 -474.4720 0.010 535 +2300 -474.4709 0.010 535 +2400 -474.4703 0.010 535 +2500 -474.4697 0.010 535 +2600 -474.4676 0.010 535 +2700 -474.4670 0.010 535 +2800 -474.4665 0.010 535 +2900 -474.4661 0.010 535 +3000 -474.4649 0.010 535 +3100 -474.4642 0.010 535 +3200 -474.4636 0.010 535 +3300 -474.4636 0.010 535 +3400 -474.4619 0.010 535 +3500 -474.4614 0.010 535 +3600 -474.4611 0.010 535 +3700 -474.4608 0.010 535 +3800 -474.4608 0.010 535 +3900 -474.4607 0.010 535 +4000 -474.4607 0.010 535 +Reached termination condition! +last topological improvement at gen 535 +Improvement over last 500 gen = 0.00071 +Current score = -474.4607 +Performing final optimizations... +pass 1 : -474.4602 (branch= 0.0000 subset rates= 0.0005) +pass 2 : -474.4430 (branch= 0.0172 subset rates= 0.0000) +pass 3 : -474.4430 (branch= 0.0000 subset rates= 0.0000) +pass 4 : -474.4383 (branch= 0.0047 subset rates= 0.0000) +pass 5 : -474.4338 (branch= 0.0046 subset rates= 0.0000) +pass 6 : -474.4316 (branch= 0.0021 subset rates= 0.0000) +pass 7 : -474.4301 (branch= 0.0016 subset rates= 0.0000) +pass 8 : -474.4294 (branch= 0.0006 subset rates= 0.0001) +pass 9 : -474.4289 (branch= 0.0005 subset rates= 0.0000) +pass 10: -474.4285 (branch= 0.0003 subset rates= 0.0000) +pass 11: -474.4283 (branch= 0.0002 subset rates= 0.0001) +pass 12: -474.4282 (branch= 0.0001 subset rates= 0.0000) +pass 13: -474.4281 (branch= 0.0000 subset rates= 0.0000) +pass 14: -474.4281 (branch= 0.0000 subset rates= 0.0000) +pass 15: -474.4281 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -474.4281 +Time used so far = 0 hours, 0 minutes and 10 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate 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. + +>>>Completed Search rep 3 (of 5)<<< + +>>>Search rep 4 (of 5)<<< +Obtained starting tree 1 from Nexus +MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 1.00 1.00 1.00 +Starting with seed=17311967 + +Initial ln Likelihood: -692.6191 +optimizing: starting branch lengths, subset rates... +pass 1:+ 190.070 (branch= 177.15 scale= 2.85 subset rates= 10.07) +pass 2:+ 19.411 (branch= 14.64 scale= 0.00 subset rates= 4.77) +pass 3:+ 6.755 (branch= 5.00 scale= 0.00 subset rates= 1.76) +pass 4:+ 1.361 (branch= 0.80 scale= 0.00 subset rates= 0.56) +pass 5:+ 0.120 (branch= 0.09 scale= 0.00 subset rates= 0.03) +pass 6:+ 0.055 (branch= 0.05 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.014 (branch= 0.01 scale= 0.00 subset rates= 0.00) +pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -474.8342 +gen current_lnL precision last_tree_imp +0 -474.8342 0.010 0 +100 -474.7467 0.010 62 +200 -474.1735 0.010 145 +300 -474.1515 0.010 145 +400 -474.1337 0.010 145 +500 -474.0523 0.010 463 +600 -474.0185 0.010 523 +700 -474.0121 0.010 523 +800 -474.0051 0.010 523 +900 -474.0040 0.010 523 +1000 -473.9974 0.010 523 +1100 -473.9955 0.010 523 +1200 -473.9908 0.010 523 +1300 -473.9892 0.010 523 +1400 -473.9877 0.010 523 +1500 -473.9860 0.010 523 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -473.9971 +Current score = -473.9855 Performing final optimizations... -pass 1 : -473.9874 (branch= 0.0000 subset rates= 0.0097) -pass 2 : -473.9638 (branch= 0.0207 subset rates= 0.0030) -pass 3 : -473.9574 (branch= 0.0063 subset rates= 0.0000) -pass 4 : -473.9566 (branch= 0.0009 subset rates= 0.0000) -pass 5 : -473.9545 (branch= 0.0021 subset rates= 0.0000) -pass 6 : -473.9532 (branch= 0.0013 subset rates= 0.0000) -pass 7 : -473.9520 (branch= 0.0012 subset rates= 0.0000) -pass 8 : -473.9515 (branch= 0.0005 subset rates= 0.0000) -pass 9 : -473.9513 (branch= 0.0002 subset rates= 0.0000) -pass 10: -473.9512 (branch= 0.0001 subset rates= 0.0000) -pass 11: -473.9512 (branch= 0.0001 subset rates= 0.0000) -pass 12: -473.9511 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9511 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -473.9847 (branch= 0.0000 subset rates= 0.0008) +pass 2 : -473.9652 (branch= 0.0157 subset rates= 0.0038) +pass 3 : -473.9594 (branch= 0.0057 subset rates= 0.0002) +pass 4 : -473.9561 (branch= 0.0032 subset rates= 0.0000) +pass 5 : -473.9539 (branch= 0.0020 subset rates= 0.0003) +pass 6 : -473.9526 (branch= 0.0013 subset rates= 0.0000) +pass 7 : -473.9514 (branch= 0.0012 subset rates= 0.0000) +pass 8 : -473.9509 (branch= 0.0005 subset rates= 0.0000) +pass 9 : -473.9509 (branch= 0.0001 subset rates= 0.0000) +pass 10: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 11: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -473.9511 +Final score = -473.9508 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -18953,11 +19698,11 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.06 2.81 + 0.59 2.07 2.80 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. ->>>Terminated Search rep 2 (of 5)<<< +>>>Terminated Search rep 4 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -18965,13 +19710,15 @@ ####################################################### -Completed 2 replicate search(es) (of 5). +Completed 4 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -473.9508 (best) -Replicate 2 : -473.9511 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 1 : -473.9508 +Replicate 2 : -473.9508 (best) (same topology as 1) +Replicate 3 : -474.4281 +Replicate 4 : -473.9508 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -18987,9 +19734,11 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.351 0.587 2.066 2.813 -rep 2: 4.347 0.590 2.059 2.806 +rep 2: 4.349 0.588 2.064 2.806 +rep 3: 4.601 0.587 2.035 2.918 +rep 4: 4.350 0.588 2.069 2.800 -Saving final tree from best search rep (#1) to ch.p.mkvO.ssr.best.tre +Saving final tree from best search rep (#2) to ch.p.mkvO.ssr.best.tre ####################################################### TREEFILES PASS ALL TESTS COMPLETED SUCCESSFULLY @@ -19005,13 +19754,13 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j40 install DESTDIR=/build/reproducible-path/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no + make -j42 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' - /usr/bin/mkdir -p '/build/reproducible-path/garli-2.1/debian/tmp/usr/bin' 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' @@ -19054,11 +19803,11 @@ dh_gencontrol dh_md5sums dh_builddeb +dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-9_amd64.deb'. +dpkg-deb: building package 'garli' in '../garli_2.1-9_amd64.deb'. dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-9_amd64.deb'. -dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-9_all.deb'. dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-9_amd64.deb'. -dpkg-deb: building package 'garli' in '../garli_2.1-9_amd64.deb'. -dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-9_amd64.deb'. +dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-9_all.deb'. dpkg-genbuildinfo --build=binary -O../garli_2.1-9_amd64.buildinfo dpkg-genchanges --build=binary -O../garli_2.1-9_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -19066,12 +19815,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1872835/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1872835/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/4082616 and its subdirectories -I: Current time: Wed Sep 17 19:43:56 -12 2025 -I: pbuilder-time-stamp: 1758181436 +I: removing directory /srv/workspace/pbuilder/1872835 and its subdirectories +I: Current time: Thu Oct 22 04:15:41 +14 2026 +I: pbuilder-time-stamp: 1792592141 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/amd64/garli_2.1-9.diff: 87.2% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/amd64/garli_2.1-9.diff.gz b2/build.log: 91.6% -- replaced with stdout Compressing the 1st log... b1/build.log: 91.8% -- replaced with stdout Thu Sep 18 07:52:43 UTC 2025 I: diffoscope 306 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_garli_forky_amd64_1758181963 + touch /var/log/reproducible-builds/diffoscope_stamp_garli_forky_amd64_1758181963 + RESULT=0 + systemd-run '--description=diffoscope on garli/2.1-9 in forky/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_25-54238 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w --run-session -c jenkins-reproducible-forky-diffoscope-56f38430-6295-444b-beec-8e26240358b9 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/dbd-tmp-AqX4RxH ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/garli_2.1-9.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/garli_2.1-9.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/garli_2.1-9.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/b1/garli_2.1-9_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/b2/garli_2.1-9_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_25-54238.service; invocation ID: e10842af4c9e46a8a64edf75a128d37b # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/garli_2.1-9.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/garli_2.1-9.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/garli_2.1-9.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/b1/garli_2.1-9_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.sP9jpE6w/b2/garli_2.1-9_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 221ms CPU time consumed: 182ms Memory peak: 16.9M (swap: 0B) _ _ __ _ __ _ _ __| (_) / _` |/ _` | '__| | | | (_| | (_| | | | | | \__, |\__,_|_| |_|_| |___/ Thu Sep 18 07:52:43 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Thu Sep 18 07:52:43 UTC 2025 I: garli from forky built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-09-18 07:52:44] INFO: Starting at 2025-09-18 07:52:44.181820 [2025-09-18 07:52:44] INFO: Generating the pages of 1 package(s) [2025-09-18 07:52:44] CRITICAL: https://tests.reproducible-builds.org/debian/forky/amd64/garli didn't produce a buildlog, even though it has been built. [2025-09-18 07:52:44] INFO: Finished at 2025-09-18 07:52:44.455294, took: 0:00:00.273477 Thu Sep 18 07:52:44 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/forky/amd64/garli.html Thu Sep 18 07:52:44 UTC 2025 I: Removing signed garli_2.1-9_amd64.buildinfo.asc files: removed './b1/garli_2.1-9_amd64.buildinfo.asc' removed './b2/garli_2.1-9_amd64.buildinfo.asc' 1758181964 amd64 forky garli Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/garli_2.1-9.rbuild.log: 91.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/garli_2.1-9.rbuild.log.gz [2025-09-18 07:52:44] INFO: Starting at 2025-09-18 07:52:44.809033 [2025-09-18 07:52:44] INFO: Generating the pages of 1 package(s) [2025-09-18 07:52:45] INFO: Finished at 2025-09-18 07:52:45.068920, took: 0:00:00.259892 All cleanup done. Thu Sep 18 07:52:45 UTC 2025 - total duration: 0h 23m 37s. Thu Sep 18 07:52:45 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-y8Nflwfw, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 23min 39.061s CPU time consumed: 4.389s Memory peak: 85.4M (swap: 0B)