Fri May 5 04:26:51 UTC 2023 I: starting to build garli/bookworm/armhf on jenkins on '2023-05-05 04:26' Fri May 5 04:26:51 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_27/8247/console.log Fri May 5 04:26:51 UTC 2023 I: Downloading source for bookworm/garli=2.1-7 --2023-05-05 04:26:51-- http://cdn-fastly.deb.debian.org/debian/pool/main/g/garli/garli_2.1-7.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2047 (2.0K) [text/prs.lines.tag] Saving to: ‘garli_2.1-7.dsc’ 0K . 100% 168M=0s 2023-05-05 04:26:51 (168 MB/s) - ‘garli_2.1-7.dsc’ saved [2047/2047] Fri May 5 04:26:51 UTC 2023 I: garli_2.1-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: garli Binary: garli, garli-mpi, garli-examples Architecture: any all Version: 2.1-7 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/Ashod/garli Standards-Version: 4.6.0 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, libopenmpi-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 8867c1a2f13f8697af3c34b306968f43b53ebe35 4788 garli_2.1-7.debian.tar.xz Checksums-Sha256: 00aa31af5d8ecc2cb9bd276ce93b6580ae6cff93f4f5e1145d95d5fe6359e1b6 1248730 garli_2.1.orig.tar.gz e20b992291e1e313188bc2351c988e0b2129e7b0543b9e088f17cf1a0882d27c 4788 garli_2.1-7.debian.tar.xz Files: 83d6720df816365182291306383d056c 1248730 garli_2.1.orig.tar.gz fe894843d93d33864ab58bb4015e09b4 4788 garli_2.1-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAmISUVwACgkQ6NN64vCf SHIKug//eCdWTZVppWlDvM+BKXLfelwLC3Qe8KIuo5UKgz7THR4TqjpysIQNxhoI DC+z6Ik7orUkIuL/otT186kQrOOtWRdYd5VCqBKhgaC4rtlLe/iQ5WBQk8otWIWb ASWBTDi+NoKNqm9oG3W35kfjn8AarPfruKsVNeqvO/YhjEf0F/gGWFe8CDtzRbZG hhEnx0NkXUGqKu15GPgxjvAxgMbPcnDmAuQ0mLmhmFdpKGKyK5F44eOA0ai2Ufog uh516xGLa9VvpyuG8Tgj6eEb4rbyPN+LsBZQioyHU2YlcmDzqFwkockLMFxaJkjM dRuWx+P1+7zBmf0HxJJMKGTOZGkbqyFXY/To4a/0vZmRl+b6l1bVyCzts/HSkaA8 OxtcJ983VQV2SG1xEcXLIdcwEW3nEmPh04YSDJ4q3W9nvf7jpyVvL8eBMYg0BlRF 8dY7ntJC504kpiU2h87Z+YPS8Z1rCRwZ0plHgp7swnMwphHZNzdJEhon1dy9eYA3 36Zfa4TqHbz4tIv120t2UoR9OiPLLmGq1MisTVgv7VOce1pKnwxmTE0AKkc5pvtB difTDkM77v268vcP+IzhkqdM6xg2aT+h4eUudEsYnaC5rewrOhslj6BrynHefxqS Iia8Y4CMftmS6qUtdAu6O2WmNpCOS+Mfh5YRIAQ07ZIV7GUo9lU= =7lh0 -----END PGP SIGNATURE----- Fri May 5 04:26:51 UTC 2023 I: Checking whether the package is not for us Fri May 5 04:26:51 UTC 2023 I: Starting 1st build on remote node jtx1a-armhf-rb.debian.net. Fri May 5 04:26:51 UTC 2023 I: Preparing to do remote build '1' on jtx1a-armhf-rb.debian.net. Fri May 5 04:41:12 UTC 2023 I: Deleting $TMPDIR on jtx1a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu May 4 16:26:56 -12 2023 I: pbuilder-time-stamp: 1683260816 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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_2.1-7.dsc] I: copying [./garli_2.1.orig.tar.gz] I: copying [./garli_2.1-7.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Feb 20 02:34:04 2022 -12 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./garli_2.1-7.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_2.1-7.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/32726/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='a9fb300977a04cb8aeb73fa4d471fed5' 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='32726' 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.q427glx6/pbuilderrc_yWBT --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.q427glx6/b1 --logfile b1/build.log garli_2.1-7.dsc' SUDO_GID='114' SUDO_UID='108' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux jtx1a 5.10.0-22-arm64 #1 SMP Debian 5.10.178-3 (2023-04-22) aarch64 GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash -rwxr-xr-x 1 root root 133220 Sep 20 2022 date -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd -rwxr-xr-x 1 root root 68104 Sep 20 2022 df -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 67548 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch -rwxr-xr-x 1 root root 67548 Sep 20 2022 true -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/32726/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: armhf 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, libopenmpi-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 ... 19329 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 libopenmpi-dev; however: Package libopenmpi-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-12{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcbor0.8{a} libdebhelper-perl{a} libedit2{a} libelf1{a} libevent-2.1-7{a} libevent-core-2.1-7{a} libevent-dev{a} libevent-extra-2.1-7{a} libevent-openssl-2.1-7{a} libevent-pthreads-2.1-7{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-12-dev{a} libgfortran5{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libicu72{a} libjs-jquery{a} libjs-jquery-ui{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libmunge2{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} libopenmpi3{a} libpciaccess0{a} libpipeline1{a} libpmix-dev{a} libpmix2{a} librdmacm1{a} libreadline8{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} m4{a} man-db{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 libarchive-cpio-perl libcoarrays-openmpi-dev libmail-sendmail-perl lynx wget xauth 0 packages upgraded, 85 newly installed, 0 to remove and 0 not upgraded. Need to get 39.1 MB of archives. After unpacking 136 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf readline-common all 8.2-1.3 [69.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 11 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf libbsd0 armhf 0.11.7-2 [113 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf libedit2 armhf 3.1-20221030-2 [77.0 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf libcbor0.8 armhf 0.8.0-2+b1 [23.1 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf libfido2-1 armhf 1.12.0-2+b1 [69.3 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf openssh-client armhf 1:9.2p1-2 [893 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 21 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf libreadline8 armhf 8.2-1.3 [144 kB] Get: 23 http://deb.debian.org/debian bookworm/main armhf bc armhf 1.07.1-3 [104 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 29 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 31 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 34 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 35 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf libgfortran5 armhf 12.2.0-14 [246 kB] Get: 40 http://deb.debian.org/debian bookworm/main armhf libgfortran-12-dev armhf 12.2.0-14 [298 kB] Get: 41 http://deb.debian.org/debian bookworm/main armhf gfortran-12 armhf 12.2.0-14 [7633 kB] Get: 42 http://deb.debian.org/debian bookworm/main armhf libnl-3-200 armhf 3.7.0-0.2+b1 [55.8 kB] Get: 43 http://deb.debian.org/debian bookworm/main armhf libnl-route-3-200 armhf 3.7.0-0.2+b1 [156 kB] Get: 44 http://deb.debian.org/debian bookworm/main armhf libibverbs1 armhf 44.0-2 [53.6 kB] Get: 45 http://deb.debian.org/debian bookworm/main armhf ibverbs-providers armhf 44.0-2 [28.4 kB] Get: 46 http://deb.debian.org/debian bookworm/main armhf libevent-2.1-7 armhf 2.1.12-stable-8 [161 kB] Get: 47 http://deb.debian.org/debian bookworm/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-8 [120 kB] Get: 48 http://deb.debian.org/debian bookworm/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-8 [97.5 kB] Get: 49 http://deb.debian.org/debian bookworm/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-8 [53.2 kB] Get: 50 http://deb.debian.org/debian bookworm/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-8 [58.3 kB] Get: 51 http://deb.debian.org/debian bookworm/main armhf libevent-dev armhf 2.1.12-stable-8 [290 kB] Get: 52 http://deb.debian.org/debian bookworm/main armhf librdmacm1 armhf 44.0-2 [60.6 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf libfabric1 armhf 1.17.0-3 [385 kB] Get: 54 http://deb.debian.org/debian bookworm/main armhf libhwloc15 armhf 2.9.0-1 [127 kB] Get: 55 http://deb.debian.org/debian bookworm/main armhf libnuma1 armhf 2.0.16-1 [17.8 kB] Get: 56 http://deb.debian.org/debian bookworm/main armhf libnuma-dev armhf 2.0.16-1 [33.0 kB] Get: 57 http://deb.debian.org/debian bookworm/main armhf libltdl7 armhf 2.4.7-5 [390 kB] Get: 58 http://deb.debian.org/debian bookworm/main armhf libltdl-dev armhf 2.4.7-5 [162 kB] Get: 59 http://deb.debian.org/debian bookworm/main armhf libhwloc-dev armhf 2.9.0-1 [214 kB] Get: 60 http://deb.debian.org/debian bookworm/main armhf libpciaccess0 armhf 0.17-2 [48.7 kB] Get: 61 http://deb.debian.org/debian bookworm/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB] Get: 62 http://deb.debian.org/debian bookworm/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 63 http://deb.debian.org/debian bookworm/main armhf libxcb1 armhf 1.15-1 [140 kB] Get: 64 http://deb.debian.org/debian bookworm/main armhf libx11-data all 2:1.8.4-2 [292 kB] Get: 65 http://deb.debian.org/debian bookworm/main armhf libx11-6 armhf 2:1.8.4-2 [695 kB] Get: 66 http://deb.debian.org/debian bookworm/main armhf libxext6 armhf 2:1.3.4-1+b1 [47.8 kB] Get: 67 http://deb.debian.org/debian bookworm/main armhf libxnvctrl0 armhf 525.85.05-1 [12.2 kB] Get: 68 http://deb.debian.org/debian bookworm/main armhf ocl-icd-libopencl1 armhf 2.3.1-1 [40.1 kB] Get: 69 http://deb.debian.org/debian bookworm/main armhf libhwloc-plugins armhf 2.9.0-1 [15.9 kB] Get: 70 http://deb.debian.org/debian bookworm/main armhf libnl-3-dev armhf 3.7.0-0.2+b1 [98.4 kB] Get: 71 http://deb.debian.org/debian bookworm/main armhf libnl-route-3-dev armhf 3.7.0-0.2+b1 [183 kB] Get: 72 http://deb.debian.org/debian bookworm/main armhf libibverbs-dev armhf 44.0-2 [195 kB] Get: 73 http://deb.debian.org/debian bookworm/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 74 http://deb.debian.org/debian bookworm/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 75 http://deb.debian.org/debian bookworm/main armhf libmunge2 armhf 0.5.15-2 [15.7 kB] Get: 76 http://deb.debian.org/debian bookworm/main armhf libncl2 armhf 2.1.21+git20210811.b1213a7-4 [359 kB] Get: 77 http://deb.debian.org/debian bookworm/main armhf libncl-dev armhf 2.1.21+git20210811.b1213a7-4 [526 kB] Get: 78 http://deb.debian.org/debian bookworm/main armhf libpmix2 armhf 4.2.2-1+b1 [553 kB] Get: 79 http://deb.debian.org/debian bookworm/main armhf libopenmpi3 armhf 4.1.4-3+b1 [1849 kB] Get: 80 http://deb.debian.org/debian bookworm/main armhf openmpi-common all 4.1.4-3 [167 kB] Get: 81 http://deb.debian.org/debian bookworm/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB] Get: 82 http://deb.debian.org/debian bookworm/main armhf libpmix-dev armhf 4.2.2-1+b1 [864 kB] Get: 83 http://deb.debian.org/debian bookworm/main armhf openmpi-bin armhf 4.1.4-3+b1 [194 kB] Get: 84 http://deb.debian.org/debian bookworm/main armhf libopenmpi-dev armhf 4.1.4-3+b1 [920 kB] Get: 85 http://deb.debian.org/debian bookworm/main armhf ncl-tools armhf 2.1.21+git20210811.b1213a7-4 [138 kB] Fetched 39.1 MB in 3s (11.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19329 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.44-3_armhf.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../03-libmagic1_1%3a5.44-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.44-3_armhf.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-12_armhf.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../06-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.22.4-10_armhf.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.38.1-5+b1_armhf.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../09-libpipeline1_1.5.7-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.11.2-2_armhf.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package libbsd0:armhf. Preparing to unpack .../11-libbsd0_0.11.7-2_armhf.deb ... Unpacking libbsd0:armhf (0.11.7-2) ... Selecting previously unselected package libedit2:armhf. Preparing to unpack .../12-libedit2_3.1-20221030-2_armhf.deb ... Unpacking libedit2:armhf (3.1-20221030-2) ... Selecting previously unselected package libcbor0.8:armhf. Preparing to unpack .../13-libcbor0.8_0.8.0-2+b1_armhf.deb ... Unpacking libcbor0.8:armhf (0.8.0-2+b1) ... Selecting previously unselected package libfido2-1:armhf. Preparing to unpack .../14-libfido2-1_1.12.0-2+b1_armhf.deb ... Unpacking libfido2-1:armhf (1.12.0-2+b1) ... Selecting previously unselected package openssh-client. Preparing to unpack .../15-openssh-client_1%3a9.2p1-2_armhf.deb ... Unpacking openssh-client (1:9.2p1-2) ... Selecting previously unselected package m4. Preparing to unpack .../16-m4_1.4.19-3_armhf.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../17-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../18-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../19-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../20-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libreadline8:armhf. Preparing to unpack .../21-libreadline8_8.2-1.3_armhf.deb ... Unpacking libreadline8:armhf (8.2-1.3) ... Selecting previously unselected package bc. Preparing to unpack .../22-bc_1.07.1-3_armhf.deb ... Unpacking bc (1.07.1-3) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../23-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../24-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../25-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../26-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../27-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../28-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../29-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../30-libelf1_0.188-2.1_armhf.deb ... Unpacking libelf1:armhf (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../31-dwz_0.15-1_armhf.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../32-libicu72_72.1-3_armhf.deb ... Unpacking libicu72:armhf (72.1-3) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../33-libxml2_2.9.14+dfsg-1.2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../34-gettext_0.21-12_armhf.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../35-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 .../36-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../37-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package libgfortran5:armhf. Preparing to unpack .../38-libgfortran5_12.2.0-14_armhf.deb ... Unpacking libgfortran5:armhf (12.2.0-14) ... Selecting previously unselected package libgfortran-12-dev:armhf. Preparing to unpack .../39-libgfortran-12-dev_12.2.0-14_armhf.deb ... Unpacking libgfortran-12-dev:armhf (12.2.0-14) ... Selecting previously unselected package gfortran-12. Preparing to unpack .../40-gfortran-12_12.2.0-14_armhf.deb ... Unpacking gfortran-12 (12.2.0-14) ... Selecting previously unselected package libnl-3-200:armhf. Preparing to unpack .../41-libnl-3-200_3.7.0-0.2+b1_armhf.deb ... Unpacking libnl-3-200:armhf (3.7.0-0.2+b1) ... Selecting previously unselected package libnl-route-3-200:armhf. Preparing to unpack .../42-libnl-route-3-200_3.7.0-0.2+b1_armhf.deb ... Unpacking libnl-route-3-200:armhf (3.7.0-0.2+b1) ... Selecting previously unselected package libibverbs1:armhf. Preparing to unpack .../43-libibverbs1_44.0-2_armhf.deb ... Unpacking libibverbs1:armhf (44.0-2) ... Selecting previously unselected package ibverbs-providers:armhf. Preparing to unpack .../44-ibverbs-providers_44.0-2_armhf.deb ... Unpacking ibverbs-providers:armhf (44.0-2) ... Selecting previously unselected package libevent-2.1-7:armhf. Preparing to unpack .../45-libevent-2.1-7_2.1.12-stable-8_armhf.deb ... Unpacking libevent-2.1-7:armhf (2.1.12-stable-8) ... Selecting previously unselected package libevent-core-2.1-7:armhf. Preparing to unpack .../46-libevent-core-2.1-7_2.1.12-stable-8_armhf.deb ... Unpacking libevent-core-2.1-7:armhf (2.1.12-stable-8) ... Selecting previously unselected package libevent-extra-2.1-7:armhf. Preparing to unpack .../47-libevent-extra-2.1-7_2.1.12-stable-8_armhf.deb ... Unpacking libevent-extra-2.1-7:armhf (2.1.12-stable-8) ... Selecting previously unselected package libevent-pthreads-2.1-7:armhf. Preparing to unpack .../48-libevent-pthreads-2.1-7_2.1.12-stable-8_armhf.deb ... Unpacking libevent-pthreads-2.1-7:armhf (2.1.12-stable-8) ... Selecting previously unselected package libevent-openssl-2.1-7:armhf. Preparing to unpack .../49-libevent-openssl-2.1-7_2.1.12-stable-8_armhf.deb ... Unpacking libevent-openssl-2.1-7:armhf (2.1.12-stable-8) ... Selecting previously unselected package libevent-dev. Preparing to unpack .../50-libevent-dev_2.1.12-stable-8_armhf.deb ... Unpacking libevent-dev (2.1.12-stable-8) ... Selecting previously unselected package librdmacm1:armhf. Preparing to unpack .../51-librdmacm1_44.0-2_armhf.deb ... Unpacking librdmacm1:armhf (44.0-2) ... Selecting previously unselected package libfabric1:armhf. Preparing to unpack .../52-libfabric1_1.17.0-3_armhf.deb ... Unpacking libfabric1:armhf (1.17.0-3) ... Selecting previously unselected package libhwloc15:armhf. Preparing to unpack .../53-libhwloc15_2.9.0-1_armhf.deb ... Unpacking libhwloc15:armhf (2.9.0-1) ... Selecting previously unselected package libnuma1:armhf. Preparing to unpack .../54-libnuma1_2.0.16-1_armhf.deb ... Unpacking libnuma1:armhf (2.0.16-1) ... Selecting previously unselected package libnuma-dev:armhf. Preparing to unpack .../55-libnuma-dev_2.0.16-1_armhf.deb ... Unpacking libnuma-dev:armhf (2.0.16-1) ... Selecting previously unselected package libltdl7:armhf. Preparing to unpack .../56-libltdl7_2.4.7-5_armhf.deb ... Unpacking libltdl7:armhf (2.4.7-5) ... Selecting previously unselected package libltdl-dev:armhf. Preparing to unpack .../57-libltdl-dev_2.4.7-5_armhf.deb ... Unpacking libltdl-dev:armhf (2.4.7-5) ... Selecting previously unselected package libhwloc-dev:armhf. Preparing to unpack .../58-libhwloc-dev_2.9.0-1_armhf.deb ... Unpacking libhwloc-dev:armhf (2.9.0-1) ... Selecting previously unselected package libpciaccess0:armhf. Preparing to unpack .../59-libpciaccess0_0.17-2_armhf.deb ... Unpacking libpciaccess0:armhf (0.17-2) ... Selecting previously unselected package libxau6:armhf. Preparing to unpack .../60-libxau6_1%3a1.0.9-1_armhf.deb ... Unpacking libxau6:armhf (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:armhf. Preparing to unpack .../61-libxdmcp6_1%3a1.1.2-3_armhf.deb ... Unpacking libxdmcp6:armhf (1:1.1.2-3) ... Selecting previously unselected package libxcb1:armhf. Preparing to unpack .../62-libxcb1_1.15-1_armhf.deb ... Unpacking libxcb1:armhf (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../63-libx11-data_2%3a1.8.4-2_all.deb ... Unpacking libx11-data (2:1.8.4-2) ... Selecting previously unselected package libx11-6:armhf. Preparing to unpack .../64-libx11-6_2%3a1.8.4-2_armhf.deb ... Unpacking libx11-6:armhf (2:1.8.4-2) ... Selecting previously unselected package libxext6:armhf. Preparing to unpack .../65-libxext6_2%3a1.3.4-1+b1_armhf.deb ... Unpacking libxext6:armhf (2:1.3.4-1+b1) ... Selecting previously unselected package libxnvctrl0:armhf. Preparing to unpack .../66-libxnvctrl0_525.85.05-1_armhf.deb ... Unpacking libxnvctrl0:armhf (525.85.05-1) ... Selecting previously unselected package ocl-icd-libopencl1:armhf. Preparing to unpack .../67-ocl-icd-libopencl1_2.3.1-1_armhf.deb ... Unpacking ocl-icd-libopencl1:armhf (2.3.1-1) ... Selecting previously unselected package libhwloc-plugins:armhf. Preparing to unpack .../68-libhwloc-plugins_2.9.0-1_armhf.deb ... Unpacking libhwloc-plugins:armhf (2.9.0-1) ... Selecting previously unselected package libnl-3-dev:armhf. Preparing to unpack .../69-libnl-3-dev_3.7.0-0.2+b1_armhf.deb ... Unpacking libnl-3-dev:armhf (3.7.0-0.2+b1) ... Selecting previously unselected package libnl-route-3-dev:armhf. Preparing to unpack .../70-libnl-route-3-dev_3.7.0-0.2+b1_armhf.deb ... Unpacking libnl-route-3-dev:armhf (3.7.0-0.2+b1) ... Selecting previously unselected package libibverbs-dev:armhf. Preparing to unpack .../71-libibverbs-dev_44.0-2_armhf.deb ... Unpacking libibverbs-dev:armhf (44.0-2) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../72-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-jquery-ui. Preparing to unpack .../73-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... Selecting previously unselected package libmunge2. Preparing to unpack .../74-libmunge2_0.5.15-2_armhf.deb ... Unpacking libmunge2 (0.5.15-2) ... Selecting previously unselected package libncl2:armhf. Preparing to unpack .../75-libncl2_2.1.21+git20210811.b1213a7-4_armhf.deb ... Unpacking libncl2:armhf (2.1.21+git20210811.b1213a7-4) ... Selecting previously unselected package libncl-dev:armhf. Preparing to unpack .../76-libncl-dev_2.1.21+git20210811.b1213a7-4_armhf.deb ... Unpacking libncl-dev:armhf (2.1.21+git20210811.b1213a7-4) ... Selecting previously unselected package libpmix2:armhf. Preparing to unpack .../77-libpmix2_4.2.2-1+b1_armhf.deb ... Unpacking libpmix2:armhf (4.2.2-1+b1) ... Selecting previously unselected package libopenmpi3:armhf. Preparing to unpack .../78-libopenmpi3_4.1.4-3+b1_armhf.deb ... Unpacking libopenmpi3:armhf (4.1.4-3+b1) ... Selecting previously unselected package openmpi-common. Preparing to unpack .../79-openmpi-common_4.1.4-3_all.deb ... Unpacking openmpi-common (4.1.4-3) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../80-zlib1g-dev_1%3a1.2.13.dfsg-1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.13.dfsg-1) ... Selecting previously unselected package libpmix-dev:armhf. Preparing to unpack .../81-libpmix-dev_4.2.2-1+b1_armhf.deb ... Unpacking libpmix-dev:armhf (4.2.2-1+b1) ... Selecting previously unselected package openmpi-bin. Preparing to unpack .../82-openmpi-bin_4.1.4-3+b1_armhf.deb ... Unpacking openmpi-bin (4.1.4-3+b1) ... Selecting previously unselected package libopenmpi-dev:armhf. Preparing to unpack .../83-libopenmpi-dev_4.1.4-3+b1_armhf.deb ... Unpacking libopenmpi-dev:armhf (4.1.4-3+b1) ... Selecting previously unselected package ncl-tools. Preparing to unpack .../84-ncl-tools_2.1.21+git20210811.b1213a7-4_armhf.deb ... Unpacking ncl-tools (2.1.21+git20210811.b1213a7-4) ... Setting up libpipeline1:armhf (1.5.7-1) ... Setting up libpciaccess0:armhf (0.17-2) ... Setting up libxau6:armhf (1:1.0.9-1) ... Setting up libicu72:armhf (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libcbor0.8:armhf (0.8.0-2+b1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:armhf (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libncl2:armhf (2.1.21+git20210811.b1213a7-4) ... Setting up libncl-dev:armhf (2.1.21+git20210811.b1213a7-4) ... Setting up autotools-dev (20220109.1) ... Setting up libmunge2 (0.5.15-2) ... Setting up libx11-data (2:1.8.4-2) ... Setting up libhwloc15:armhf (2.9.0-1) ... Setting up libevent-core-2.1-7:armhf (2.1.12-stable-8) ... Setting up libevent-2.1-7:armhf (2.1.12-stable-8) ... Setting up autopoint (0.21-12) ... Setting up libltdl7:armhf (2.4.7-5) ... Setting up libgfortran5:armhf (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-1) ... Setting up libnuma1:armhf (2.0.16-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up ocl-icd-libopencl1:armhf (2.3.1-1) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libnl-3-200:armhf (3.7.0-0.2+b1) ... Setting up openmpi-common (4.1.4-3) ... Setting up libsub-override-perl (0.09-4) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:armhf (1.12.0-2+b1) ... Setting up libbsd0:armhf (0.11.7-2) ... Setting up libelf1:armhf (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:armhf (2.9.14+dfsg-1.2) ... Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-8) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libxdmcp6:armhf (1:1.1.2-3) ... Setting up libevent-extra-2.1-7:armhf (2.1.12-stable-8) ... Setting up libxcb1:armhf (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libedit2:armhf (3.1-20221030-2) ... Setting up libreadline8:armhf (8.2-1.3) ... Setting up libevent-openssl-2.1-7:armhf (2.1.12-stable-8) ... Setting up bc (1.07.1-3) ... Setting up ncl-tools (2.1.21+git20210811.b1213a7-4) ... Setting up libgfortran-12-dev:armhf (12.2.0-14) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:armhf (2.0.16-1) ... Setting up libnl-route-3-200:armhf (3.7.0-0.2+b1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:armhf (2.4.7-5) ... Setting up gfortran-12 (12.2.0-14) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libevent-dev (2.1.12-stable-8) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up libnl-3-dev:armhf (3.7.0-0.2+b1) ... Setting up groff-base (1.22.4-10) ... Setting up libx11-6:armhf (2:1.8.4-2) ... Setting up libhwloc-dev:armhf (2.9.0-1) ... Setting up libibverbs1:armhf (44.0-2) ... Setting up ibverbs-providers:armhf (44.0-2) ... Setting up openssh-client (1:9.2p1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:armhf (2:1.3.4-1+b1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxnvctrl0:armhf (525.85.05-1) ... Setting up libnl-route-3-dev:armhf (3.7.0-0.2+b1) ... Setting up librdmacm1:armhf (44.0-2) ... Setting up debhelper (13.11.4) ... Setting up libibverbs-dev:armhf (44.0-2) ... Setting up libhwloc-plugins:armhf (2.9.0-1) ... Setting up libfabric1:armhf (1.17.0-3) ... Setting up libpmix2:armhf (4.2.2-1+b1) ... Setting up libopenmpi3:armhf (4.1.4-3+b1) ... Setting up libpmix-dev:armhf (4.2.2-1+b1) ... Setting up openmpi-bin (4.1.4-3+b1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:armhf (4.1.4-3+b1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode Processing triggers for libc-bin (2.36-9) ... 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/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_2.1-7_source.changes dpkg-buildpackage: info: source package garli dpkg-buildpackage: info: source version 2.1-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf 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.m4:704: 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.m4:2847: 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.m4:2920: 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.m4:2920: 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.m4:2823: _AC_COMPILE_IFELSE is expanded from... ./lib/autoconf/general.m4:2839: 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/garli-2.1' # First build MPI version of Garli dh_auto_configure -- --with-ncl=/usr --enable-mpi ./configure --build=arm-linux-gnueabihf --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/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-ncl=/usr --enable-mpi checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking target system type... arm-unknown-linux-gnueabihf checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '1111' is supported by ustar format... yes checking whether GID '1111' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking for ranlib... ranlib checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /bin/grep checking for egrep... /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... 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 -j3 make[2]: Entering directory '/build/garli-2.1' make all-recursive make[3]: Entering directory '/build/garli-2.1' Making all in src make[4]: Entering directory '/build/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/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o adaptation.o adaptation.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o bipartition.o bipartition.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o condlike.o condlike.cpp 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++/12/string:48, from bipartition.h:23, from bipartition.cpp:19: /usr/include/c++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from adaptation.cpp:18: /usr/include/c++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from configreader.cpp:21: /usr/include/c++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from population.h:23: /usr/include/c++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from population.h:23: /usr/include/c++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/iomanip:40, from individual.cpp:21: /usr/include/c++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/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 >; _ForwardIterator = ProcessedNxsToken*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; _Tp = ProcessedNxsToken]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44, inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:316:21: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; _Tp = ProcessedNxsToken]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::_List_node >]' at /usr/include/c++/12/bits/new_allocator.h:175:4, inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::_List_node >]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, inlined from 'std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const std::vector >&}; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:713:33, inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const std::vector >&}; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:2005:32, inlined from 'std::__cxx11::list<_Tp, _Alloc>::reference std::__cxx11::list<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {const std::vector >&}; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:1321:19, inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_initialize_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:1934:18, inlined from 'std::__cxx11::list<_Tp, _Alloc>::list(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = std::_List_const_iterator >; = void; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:882:26, inlined from 'std::__cxx11::list<_Tp, _Alloc>::iterator std::__cxx11::list<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = std::_List_const_iterator >; = void; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:137:7, inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:320:17: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from population.h:24: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Tree::StoreBranchlengths(std::vector&)' at tree.h:313:20, inlined from 'void Individual::RefineStartingConditions(bool, FLOAT_TYPE)' at individual.cpp:755:33: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp 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; | ^~~ 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/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp 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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from model.cpp:17: /usr/include/c++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp 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++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from tree.h:24: /usr/include/c++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/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 Tree::CalcDerivativesRateHet(TreeNode*, TreeNode*)': optimization.cpp:1099:87: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1099 | pair Tree::CalcDerivativesRateHet(TreeNode *nd1, TreeNode *nd2){ | ^ model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:3675:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3675 | fread(&o, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:3677:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3677 | fread(&o, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:3684:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3684 | fread((char*) &(b[i]), sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:3691:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3691 | fread((char*) &(rateMults[i]), sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:3692:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3692 | fread((char*) &(rateProbs[i]), sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:3699:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3699 | fread((char*) &a, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:3705:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3705 | fread((char*) &p, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:3710:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3710 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:3713:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3713 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from population.cpp:23: /usr/include/c++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/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' when C++17 is enabled changed to match C++14 in GCC 10.1 875 | tree0->CalcDerivativesRateHet(nd->anc, nd); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ reconnode.h: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)': reconnode.h:388:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 388 | fread(&unique, scalarSize, 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ reconnode.h: In constructor 'Swap::Swap(FILE*&)': reconnode.h:264:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 264 | fread(&count, scalarSize, 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from treenode.h:30, from tree.h:31: bipartition.h: In member function 'void Bipartition::BinaryInput(FILE*&)': bipartition.h:518:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 518 | fread((char*) rep, sizeof(unsigned int), nBlocks, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ population.cpp: In member function 'void Population::ReadPopulationCheckpoint()': population.cpp:1880:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1880 | fread((char *) &seed, sizeof(seed), 1, pin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ population.cpp:1887:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1887 | fread((char *) &t, sizeof(t), 1, pin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ population.cpp:1896:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(this, scalarSize, 1, pin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, from population.cpp:25: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': population.cpp:3066:50: warning: '%d' directive writing between 1 and 9 bytes into a region of size 8 [-Wformat-overflow=] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~ population.cpp:3066:47: note: directive argument in the range [1, 536870911] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 13 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from model.h:28, from model.cpp:25: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)' at model.cpp:4957:19: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void ModelPartition::SetSubsetRates(std::vector, bool)' at model.h:2109:25, inlined from 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)' at model.cpp:4959:17: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ 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/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void Model::ReadGarliFormattedModelString(std::string&)' at model.cpp:2801:16: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void Model::ReadGarliFormattedModelString(std::string&)' at model.cpp:2821:16: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void Model::ReadGarliFormattedModelString(std::string&)' at model.cpp:2825:16: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Tree::StoreBranchlengths(std::vector&)' at tree.h:313:20, inlined from 'void Population::BetterFinalOptimization()' at population.cpp:2541:30: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Tree::StoreBranchlengths(std::vector&)' at tree.h:313:20, inlined from 'void Population::InitialOptimization(Individual*, bool, FLOAT_TYPE)' at population.cpp:1449:33: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void ModelPartition::ReadGarliFormattedModelStrings(std::string&)' at model.cpp:4894:19: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void ModelPartition::SetSubsetRates(std::vector, bool)' at model.h:2109:25, inlined from 'void ModelPartition::ReadGarliFormattedModelStrings(std::string&)' at model.cpp:4896:19: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void Model::CalcSynonymousBranchlengthProportions(std::vector&)' at model.cpp:712:20: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void Model::CalcSynonymousBranchlengthProportions(std::vector&)' at model.cpp:723:19: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, inlined from 'InsertProportion::InsertProportion(FLOAT_TYPE**, int)' at model.h:340:149, inlined from 'void Model::CreateModelFromSpecification(int)' at model.cpp:3060:83: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, inlined from 'ProportionInvariant::ProportionInvariant(const char*, FLOAT_TYPE**, int)' at model.h:328:157, inlined from 'void Model::CreateModelFromSpecification(int)' at model.cpp:3086:112: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, inlined from 'RateProportions::RateProportions(FLOAT_TYPE**, int, int)' at model.h:278:125, inlined from 'void Model::CreateModelFromSpecification(int)' at model.cpp:3117:77: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, inlined from 'RateMultipliers::RateMultipliers(FLOAT_TYPE**, int, int)' at model.h:307:149, inlined from 'void Model::CreateModelFromSpecification(int)' at model.cpp:3124:77: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, inlined from 'StateFrequencies::StateFrequencies(FLOAT_TYPE**, int, int)' at model.h:146:133, inlined from 'void Model::CreateModelFromSpecification(int)' at model.cpp:3142:75: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, inlined from 'RelativeRates::RelativeRates(const char*, FLOAT_TYPE**, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:191:160, inlined from 'void Model::CreateModelFromSpecification(int)' at model.cpp:3216:94: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, inlined from 'SumConstrainedRelativeRates::SumConstrainedRelativeRates(const char*, FLOAT_TYPE**, int, FLOAT_TYPE, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:248:190, inlined from 'void Model::CreateModelFromSpecification(int)' at model.cpp:3266:202: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, inlined from 'RateMultipliers::RateMultipliers(FLOAT_TYPE**, int, int)' at model.h:307:149, inlined from 'void Model::CreateModelFromSpecification(int)' at model.cpp:3339:79: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'ModelPartition::ModelPartition()' at model.cpp:4686:25: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'ModelPartition::ModelPartition()' at model.cpp:4687:31: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, inlined from 'SubsetRates::SubsetRates(FLOAT_TYPE**, int, int)' at model.h:352:144, inlined from 'ModelPartition::ModelPartition()' at model.cpp:4699:71: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'ModelPartition::ModelPartition()' at model.cpp:4705:24: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'ModelPartition::ModelPartition()' at model.cpp:4706:30: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]', inlined from 'void Population::OptimizeSiteRates()' at population.cpp:7958:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ 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/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3846:17: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3887:24: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3897:52: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3902:35: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3906:52: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, from tree.cpp:33: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from tree.cpp:21: /usr/include/c++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/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 Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE)': tree.cpp:8463:87: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 8463 | pair Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE optPrecision){ | ^ mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp tree.cpp: In member function 'void Tree::ReadBinaryFormattedTree(FILE*)': tree.cpp:6808:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6808 | fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6815:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6815 | fread((char*) &lnL, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6816:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6816 | fread((char*) &numTipsAdded, sizeof(numTipsAdded), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6817:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6817 | fread((char*) &numNodesAdded, sizeof(numNodesAdded), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6818:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6818 | fread((char*) &numBranchesAdded, sizeof(numBranchesAdded), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6819:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6819 | fread((char*) &numNodesTotal, sizeof(numNodesTotal), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6823:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6823 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6826:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6826 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6829:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6829 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6833:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6833 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6837:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6837 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6841:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6841 | fread((char*) &allNodes[0]->dlen, 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:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from treenode.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, from mpitrick.cpp:27: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/map:60, from /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:42, from /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:2887, from mpitrick.cpp:20: /usr/include/c++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/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::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'FLOAT_TYPE Tree::OptimizeSubsetRates(FLOAT_TYPE)' at tree.cpp:7316:21: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void ModelPartition::SetSubsetRates(std::vector, bool)' at model.h:2109:25, inlined from 'FLOAT_TYPE Tree::OptimizeSubsetRates(FLOAT_TYPE)' at tree.cpp:7335:26: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ mpic++ -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -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/garli-2.1/src' Making all in tests make[4]: Entering directory '/build/garli-2.1/tests' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/garli-2.1/tests' make[4]: Entering directory '/build/garli-2.1' make[4]: Leaving directory '/build/garli-2.1' make[3]: Leaving directory '/build/garli-2.1' make[2]: Leaving directory '/build/garli-2.1' mkdir -p debian/mpi mv src/Garli debian/mpi/Garli-mpi make distclean make[2]: Entering directory '/build/garli-2.1' Making distclean in src make[3]: Entering directory '/build/garli-2.1/src' test -z "Garli" || rm -f Garli rm -f *.o rm -f *.tab.c test -z "" || rm -f test . = "." || test -z "" || 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/garli-2.1/src' Making distclean in tests make[3]: Entering directory '/build/garli-2.1/tests' test -z "" || rm -f test . = "." || test -z "" || rm -f rm -f Makefile make[3]: Leaving directory '/build/garli-2.1/tests' make[3]: Entering directory '/build/garli-2.1' test -z "" || rm -f test . = "." || test -z "" || 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/garli-2.1' rm -f config.status config.cache config.log configure.lineno config.status.lineno rm -f Makefile make[2]: Leaving directory '/build/garli-2.1' # Now build single processor binary dh_auto_configure -- --with-ncl=/usr ./configure --build=arm-linux-gnueabihf --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/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-ncl=/usr checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking target system type... arm-unknown-linux-gnueabihf checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '1111' is supported by ustar format... yes checking whether GID '1111' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking for ranlib... ranlib checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /bin/grep checking for egrep... /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... 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/garli-2.1' dh_auto_build make -j3 make[1]: Entering directory '/build/garli-2.1' make all-recursive make[2]: Entering directory '/build/garli-2.1' Making all in src make[3]: Entering directory '/build/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/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o condlike.o condlike.cpp 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++/12/string:48, from bipartition.h:23, from bipartition.cpp:19: /usr/include/c++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from adaptation.cpp:18: /usr/include/c++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from configreader.cpp:21: /usr/include/c++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from population.h:23: /usr/include/c++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from population.h:23: /usr/include/c++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/iomanip:40, from individual.cpp:21: /usr/include/c++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/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 >; _ForwardIterator = ProcessedNxsToken*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; _Tp = ProcessedNxsToken]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44, inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:316:21: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*; _Tp = ProcessedNxsToken]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = ProcessedNxsToken; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::_List_node >]' at /usr/include/c++/12/bits/new_allocator.h:175:4, inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector; _Args = {const std::vector >&}; _Tp = std::_List_node >]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, inlined from 'std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const std::vector >&}; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:713:33, inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const std::vector >&}; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:2005:32, inlined from 'std::__cxx11::list<_Tp, _Alloc>::reference std::__cxx11::list<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {const std::vector >&}; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:1321:19, inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_initialize_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:1934:18, inlined from 'std::__cxx11::list<_Tp, _Alloc>::list(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = std::_List_const_iterator >; = void; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_list.h:882:26, inlined from 'std::__cxx11::list<_Tp, _Alloc>::iterator std::__cxx11::list<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = std::_List_const_iterator >; = void; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:137:7, inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator >; _Tp = std::vector; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/list.tcc:320:17: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from population.h:24: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Tree::StoreBranchlengths(std::vector&)' at tree.h:313:20, inlined from 'void Individual::RefineStartingConditions(bool, FLOAT_TYPE)' at individual.cpp:755:33: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o 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/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.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; | ^~~ 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/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp 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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from model.cpp:17: /usr/include/c++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp 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++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from tree.h:24: /usr/include/c++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/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 Tree::CalcDerivativesRateHet(TreeNode*, TreeNode*)': optimization.cpp:1099:87: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1099 | pair Tree::CalcDerivativesRateHet(TreeNode *nd1, TreeNode *nd2){ | ^ model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:3675:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3675 | fread(&o, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:3677:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3677 | fread(&o, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:3684:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3684 | fread((char*) &(b[i]), sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:3691:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3691 | fread((char*) &(rateMults[i]), sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:3692:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3692 | fread((char*) &(rateProbs[i]), sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:3699:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3699 | fread((char*) &a, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:3705:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3705 | fread((char*) &p, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:3710:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3710 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp:3713:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3713 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/arm-linux-gnueabihf/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 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++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from population.cpp:23: /usr/include/c++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/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' when C++17 is enabled changed to match C++14 in GCC 10.1 875 | tree0->CalcDerivativesRateHet(nd->anc, nd); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ reconnode.h: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)': reconnode.h:388:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 388 | fread(&unique, scalarSize, 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ reconnode.h: In constructor 'Swap::Swap(FILE*&)': reconnode.h:264:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 264 | fread(&count, scalarSize, 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from treenode.h:30, from tree.h:31: bipartition.h: In member function 'void Bipartition::BinaryInput(FILE*&)': bipartition.h:518:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 518 | fread((char*) rep, sizeof(unsigned int), nBlocks, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ population.cpp: In member function 'void Population::ReadPopulationCheckpoint()': population.cpp:1880:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1880 | fread((char *) &seed, sizeof(seed), 1, pin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ population.cpp:1887:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1887 | fread((char *) &t, sizeof(t), 1, pin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ population.cpp:1896:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(this, scalarSize, 1, pin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 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/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp In file included from /usr/include/stdio.h:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, from population.cpp:25: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp In file included from /usr/include/c++/12/vector:70, from model.h:28, from model.cpp:25: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': population.cpp:3066:50: warning: '%d' directive writing between 1 and 9 bytes into a region of size 8 [-Wformat-overflow=] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~ population.cpp:3066:47: note: directive argument in the range [1, 536870911] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 13 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)' at model.cpp:4957:19: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void ModelPartition::SetSubsetRates(std::vector, bool)' at model.h:2109:25, inlined from 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)' at model.cpp:4959:17: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void Model::ReadGarliFormattedModelString(std::string&)' at model.cpp:2801:16: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void Model::ReadGarliFormattedModelString(std::string&)' at model.cpp:2821:16: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void Model::ReadGarliFormattedModelString(std::string&)' at model.cpp:2825:16: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Tree::StoreBranchlengths(std::vector&)' at tree.h:313:20, inlined from 'void Population::BetterFinalOptimization()' at population.cpp:2541:30: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Tree::StoreBranchlengths(std::vector&)' at tree.h:313:20, inlined from 'void Population::InitialOptimization(Individual*, bool, FLOAT_TYPE)' at population.cpp:1449:33: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void ModelPartition::ReadGarliFormattedModelStrings(std::string&)' at model.cpp:4894:19: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void ModelPartition::SetSubsetRates(std::vector, bool)' at model.h:2109:25, inlined from 'void ModelPartition::ReadGarliFormattedModelStrings(std::string&)' at model.cpp:4896:19: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/stdio.h:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void Model::CalcSynonymousBranchlengthProportions(std::vector&)' at model.cpp:712:20: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void Model::CalcSynonymousBranchlengthProportions(std::vector&)' at model.cpp:723:19: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, inlined from 'InsertProportion::InsertProportion(FLOAT_TYPE**, int)' at model.h:340:149, inlined from 'void Model::CreateModelFromSpecification(int)' at model.cpp:3060:83: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, inlined from 'ProportionInvariant::ProportionInvariant(const char*, FLOAT_TYPE**, int)' at model.h:328:157, inlined from 'void Model::CreateModelFromSpecification(int)' at model.cpp:3086:112: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, inlined from 'RateProportions::RateProportions(FLOAT_TYPE**, int, int)' at model.h:278:125, inlined from 'void Model::CreateModelFromSpecification(int)' at model.cpp:3117:77: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, inlined from 'RateMultipliers::RateMultipliers(FLOAT_TYPE**, int, int)' at model.h:307:149, inlined from 'void Model::CreateModelFromSpecification(int)' at model.cpp:3124:77: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, inlined from 'StateFrequencies::StateFrequencies(FLOAT_TYPE**, int, int)' at model.h:146:133, inlined from 'void Model::CreateModelFromSpecification(int)' at model.cpp:3142:75: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, inlined from 'RelativeRates::RelativeRates(const char*, FLOAT_TYPE**, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:191:160, inlined from 'void Model::CreateModelFromSpecification(int)' at model.cpp:3216:94: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, inlined from 'SumConstrainedRelativeRates::SumConstrainedRelativeRates(const char*, FLOAT_TYPE**, int, FLOAT_TYPE, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:248:190, inlined from 'void Model::CreateModelFromSpecification(int)' at model.cpp:3266:202: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, inlined from 'RateMultipliers::RateMultipliers(FLOAT_TYPE**, int, int)' at model.h:307:149, inlined from 'void Model::CreateModelFromSpecification(int)' at model.cpp:3339:79: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'ModelPartition::ModelPartition()' at model.cpp:4686:25: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'ModelPartition::ModelPartition()' at model.cpp:4687:31: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, inlined from 'SubsetRates::SubsetRates(FLOAT_TYPE**, int, int)' at model.h:352:144, inlined from 'ModelPartition::ModelPartition()' at model.cpp:4699:71: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'ModelPartition::ModelPartition()' at model.cpp:4705:24: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'ModelPartition::ModelPartition()' at model.cpp:4706:30: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp 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/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]', inlined from 'void Population::OptimizeSiteRates()' at population.cpp:7958:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3846:17: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3887:24: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3897:52: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3902:35: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3906:52: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp 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/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp 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/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, from tree.cpp:33: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from tree.cpp:21: /usr/include/c++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/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 Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE)': tree.cpp:8463:87: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 8463 | pair Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE optPrecision){ | ^ tree.cpp: In member function 'void Tree::ReadBinaryFormattedTree(FILE*)': tree.cpp:6808:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6808 | fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6815:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6815 | fread((char*) &lnL, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6816:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6816 | fread((char*) &numTipsAdded, sizeof(numTipsAdded), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6817:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6817 | fread((char*) &numNodesAdded, sizeof(numNodesAdded), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6818:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6818 | fread((char*) &numBranchesAdded, sizeof(numBranchesAdded), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6819:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6819 | fread((char*) &numNodesTotal, sizeof(numNodesTotal), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6823:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6823 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6826:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6826 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6829:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6829 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6833:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6833 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6837:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6837 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6841:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6841 | fread((char*) &allNodes[0]->dlen, 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:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from treenode.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'FLOAT_TYPE Tree::OptimizeSubsetRates(FLOAT_TYPE)' at tree.cpp:7316:21: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void ModelPartition::SetSubsetRates(std::vector, bool)' at model.h:2109:25, inlined from 'FLOAT_TYPE Tree::OptimizeSubsetRates(FLOAT_TYPE)' at tree.cpp:7335:26: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-z,relro -Wl,-z,now -L/usr/lib -o Garli adaptation.o bipartition.o condlike.o configoptions.o configreader.o datamatr.o funcs.o garlimain.o garlireader.o individual.o linalg.o model.o optimization.o population.o rng.o sequencedata.o set.o translatetable.o tree.o treenode.o mpitrick.o -lncl -lncl make[3]: Leaving directory '/build/garli-2.1/src' Making all in tests make[3]: Entering directory '/build/garli-2.1/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/garli-2.1/tests' make[3]: Entering directory '/build/garli-2.1' make[3]: Leaving directory '/build/garli-2.1' make[2]: Leaving directory '/build/garli-2.1' make[1]: Leaving directory '/build/garli-2.1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/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 -j3 check "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1 make[2]: Entering directory '/build/garli-2.1' Making check in src make[3]: Entering directory '/build/garli-2.1/src' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/garli-2.1/src' Making check in tests make[3]: Entering directory '/build/garli-2.1/tests' make check-local make[4]: Entering directory '/build/garli-2.1/tests' ./runtests.sh . ../src/Garli /usr/bin/NEXUSvalidator Linking to data .... data folder already exists ************************** Running internal tests ... ************************** Running internal test ./internal/a.G3.conf Running internal test ./internal/a.G3.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/a.G3.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/moore.matK90-120.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 86 sequences. 2 constant characters. 6 parsimony-informative characters. 2 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 5 MB good approx 4 MB to 2 MB low approx 2 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 5.8 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/moore.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0088 0.0022 0.0131 0.3020 0.0985 0.0088 0.0109 0.0284 0.0810 0.0503 0.1794 0.0022 0.0044 0.1575 0.0109 0.0109 0.0044 0.0044 0.0022 0.0197 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0500 Substitution rate categories under this model: rate proportion 0.0000 0.0500 0.0603 0.3167 0.4894 0.3167 2.4503 0.3167 Starting with seed=1 WARNING: Polytomies found in start tree. These were arbitrarily resolved. Initial ln Likelihood: -534.6163 optimizing: starting branch lengths, alpha shape, prop. invar... pass 1:+ 97.093 (branch= 90.61 scale= 6.48 alpha= 0.00 pinv= 0.00) pass 2:+ 26.504 (branch= 20.56 scale= 5.94 alpha= 0.00 pinv= 0.00) pass 3:+ 7.183 (branch= 6.27 scale= 0.91 alpha= 0.00 pinv= 0.00) pass 4:+ 2.513 (branch= 1.73 scale= 0.78 alpha= 0.00 pinv= 0.00) pass 5:+ 1.030 (branch= 0.48 scale= 0.55 alpha= 0.00 pinv= 0.00) pass 6:+ 0.375 (branch= 0.37 scale= 0.00 alpha= 0.00 pinv= 0.00) lnL after optimization: -399.9190 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/a.G4.conf Running internal test ./internal/a.G4.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/a.G4.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/moore.matK90-120.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 86 sequences. 2 constant characters. 6 parsimony-informative characters. 2 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 6 MB good approx 5 MB to 4 MB low approx 3 MB to 2 MB very low approx 2 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 7.7 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/moore.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0088 0.0022 0.0131 0.3020 0.0985 0.0088 0.0109 0.0284 0.0810 0.0503 0.1794 0.0022 0.0044 0.1575 0.0109 0.0109 0.0044 0.0044 0.0022 0.0197 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0500 Substitution rate categories under this model: rate proportion 0.0000 0.0500 0.0334 0.2375 0.2519 0.2375 0.8203 0.2375 2.8944 0.2375 Starting with seed=1 WARNING: Polytomies found in start tree. These were arbitrarily resolved. Initial ln Likelihood: -532.4673 optimizing: starting branch lengths, alpha shape, prop. invar... pass 1:+ 92.949 (branch= 88.74 scale= 4.20 alpha= 0.00 pinv= 0.00) pass 2:+ 25.801 (branch= 20.07 scale= 5.73 alpha= 0.00 pinv= 0.00) pass 3:+ 9.142 (branch= 7.26 scale= 1.88 alpha= 0.00 pinv= 0.00) pass 4:+ 3.445 (branch= 2.67 scale= 0.78 alpha= 0.00 pinv= 0.00) pass 5:+ 0.802 (branch= 0.25 scale= 0.55 alpha= 0.00 pinv= 0.00) pass 6:+ 0.294 (branch= 0.29 scale= 0.00 alpha= 0.00 pinv= 0.00) lnL after optimization: -400.0333 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/a.conf Running internal test ./internal/a.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/a.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/moore.matK90-120.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 86 sequences. 2 constant characters. 6 parsimony-informative characters. 2 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 2 MB good approx 2 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 2.0 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/moore.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0088 0.0022 0.0131 0.3020 0.0985 0.0088 0.0109 0.0284 0.0810 0.0503 0.1794 0.0022 0.0044 0.1575 0.0109 0.0109 0.0044 0.0044 0.0022 0.0197 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 WARNING: Polytomies found in start tree. These were arbitrarily resolved. NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -567.2416 optimizing: starting branch lengths... pass 1:+ 135.572 (branch= 118.31 scale= 17.26) pass 2:+ 21.497 (branch= 16.34 scale= 5.15) pass 3:+ 6.821 (branch= 6.09 scale= 0.73) pass 4:+ 2.066 (branch= 1.47 scale= 0.59) pass 5:+ 1.595 (branch= 1.59 scale= 0.00) pass 6:+ 1.322 (branch= 0.81 scale= 0.51) pass 7:+ 0.354 (branch= 0.35 scale= 0.00) lnL after optimization: -398.0145 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/c.M3x2.conf Running internal test ./internal/c.M3x2.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/c.M3x2.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x30.stop.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Codon data Warning: stop codon TAA found at codon site 11 (nuc site 31) in taxon MorNa6. Treating as missing data because ignorestopcodons = 1 is set in configuration file. Warning: stop codon TAA found at codon site 11 (nuc site 31) in taxon ClownNa6. Treating as missing data because ignorestopcodons = 1 is set in configuration file. Base usage at codon positions: A C G T pos 1 0.27184 0.35922 0.21359 0.15534 pos 2 0.32039 0.20388 0.07767 0.39806 pos 3 0.12621 0.37864 0.26214 0.23301 all pos 0.23948 0.31392 0.18447 0.26214 Summary of data: 11 sequences. 0 constant characters. 9 parsimony-informative characters. 1 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 10 total characters (11 before removing empty columns). 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 1.3 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### STARTING RUN starting internal tests... MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0112 0.0337 0.0233 0.0207 0.0071 0.0214 0.0148 0.0132 0.0027 0.0082 0.0057 0.0050 0.0139 0.0418 0.0290 0.0258 0.0148 0.0445 0.0308 0.0274 0.0094 0.0283 0.0196 0.0174 0.0036 0.0108 0.0075 0.0066 0.0184 0.0553 0.0383 0.0340 0.0088 0.0265 0.0183 0.0163 0.0056 0.0168 0.0117 0.0104 0.0021 0.0064 0.0044 0.0039 0.0110 0.0329 0.0228 0.0202 0.0192 0.0118 0.0041 0.0122 0.0085 0.0075 0.0047 0.0032 0.0029 0.0080 0.0239 0.0166 0.0147 Rate Heterogeneity Model: 2 nonsynonymous rate categories, rate and proportion of each estimated (this is effectively the M3 model of PAML) dN/dS Proportion 0.2500 0.5000 0.5000 0.5000 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 4.421 lnL Optimizing branchlengths... improved 0.690 lnL 7 8 9 10 11 Initial ln Likelihood: -215.5693 optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters... pass 1:+ 6.143 (branch= 0.00 scale= 0.00 omega= 0.01 rel rates= 6.13) pass 2:+ 0.420 (branch= 0.00 scale= 0.00 omega= 0.01 rel rates= 0.41) lnL after optimization: -209.0069 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/c.conf Running internal test ./internal/c.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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: -213.0377 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/n.G3.conf Running internal test ./internal/n.G3.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/n.G3.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/moore.matK90-120.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 86 sequences. 10 constant characters. 13 parsimony-informative characters. 7 uninformative variable characters. 30 total characters. 24 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 2 MB good approx 2 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 2.9 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN starting internal tests... MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.4638 0.0976 0.2304 0.2082 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0833 Substitution rate categories under this model: rate proportion 0.0000 0.0833 0.0603 0.3056 0.4894 0.3056 2.4503 0.3056 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 Optimizing parameters... improved 2.070 lnL Optimizing branchlengths... improved 1.544 lnL 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 Initial ln Likelihood: -351.3160 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 11.635 (branch= 3.88 scale= 0.50 alpha= 0.97 freqs= 0.05 rel rates= 6.23 pinv= 0.01) pass 2:+ 1.385 (branch= 0.93 scale= 0.41 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.01) pass 3:+ 0.338 (branch= 0.30 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.01) lnL after optimization: -337.9573 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/n.G4.conf Running internal test ./internal/n.G4.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/n.G4.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/moore.matK90-120.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 86 sequences. 10 constant characters. 13 parsimony-informative characters. 7 uninformative variable characters. 30 total characters. 24 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 4 MB good approx 3 MB to 2 MB low approx 2 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 3.8 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN starting internal tests... MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.4638 0.0976 0.2304 0.2082 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0833 Substitution rate categories under this model: rate proportion 0.0000 0.0833 0.0334 0.2292 0.2519 0.2292 0.8203 0.2292 2.8944 0.2292 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 Optimizing parameters... improved 2.099 lnL Optimizing branchlengths... improved 1.492 lnL 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 Initial ln Likelihood: -363.1701 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 13.147 (branch= 2.38 scale= 2.97 alpha= 0.67 freqs= 1.24 rel rates= 5.88 pinv= 0.01) pass 2:+ 2.663 (branch= 2.63 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.00) pass 3:+ 0.035 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.00) lnL after optimization: -347.3249 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/n.conf Running internal test ./internal/n.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/n.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/moore.matK90-120.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 86 sequences. 10 constant characters. 13 parsimony-informative characters. 7 uninformative variable characters. 30 total characters. 24 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 1.0 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN starting internal tests... MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 1 rate Equilibrium State Frequencies: estimated (ACGT) 0.4638 0.0976 0.2304 0.2082 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 2.038 lnL 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 Initial ln Likelihood: -371.0442 optimizing: starting branch lengths, eq freqs... pass 1:+ 3.897 (branch= 2.20 scale= 0.00 freqs= 1.70) pass 2:+ 0.641 (branch= 0.60 scale= 0.00 freqs= 0.04) pass 3:+ 0.073 (branch= 0.03 scale= 0.00 freqs= 0.04) lnL after optimization: -366.4339 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.3diff.conf Running internal test ./internal/p.3diff.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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:+ 77.990 (branch= 2.27 scale= 0.00 alpha= 4.14 freqs= 11.22 rel rates= 3.32 pinv= 0.86 subset rates= 56.18) pass 3:+ 48.437 (branch= 6.88 scale= 0.73 alpha= 4.15 freqs= 1.22 rel rates= 1.34 pinv= 0.01 subset rates= 34.10) pass 4:+ 15.263 (branch= 0.00 scale= 0.79 alpha= 0.64 freqs= 1.21 rel rates= 0.57 pinv= 0.01 subset rates= 12.04) pass 5:+ 5.799 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.10 rel rates= 0.77 pinv= 0.02 subset rates= 4.91) pass 6:+ 0.133 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.10 rel rates= 0.01 pinv= 0.01 subset rates= 0.00) lnL after optimization: -13342.5949 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mk.conf Running internal test ./internal/p.mk.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/p.mk.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, modeled as Standard k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -609.1934 optimizing: starting branch lengths... pass 1:+ 125.912 (branch= 124.97 scale= 0.94) pass 2:+ 7.205 (branch= 7.20 scale= 0.00) pass 3:+ 1.518 (branch= 1.48 scale= 0.03) pass 4:+ 0.225 (branch= 0.22 scale= 0.00) pass 5:+ 0.014 (branch= 0.01 scale= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -474.3188 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mk.ssr.conf Running internal test ./internal/p.mk.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/p.mk.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, modeled as Standard k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -609.1934 optimizing: starting branch lengths, subset rates... pass 1:+ 130.207 (branch= 124.97 scale= 0.94 subset rates= 4.29) pass 2:+ 9.055 (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:+ 0.304 (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: -467.8138 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mkO.conf Running internal test ./internal/p.mkO.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/p.mkO.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, modeled as Standard ordered k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -641.9257 optimizing: starting branch lengths... pass 1:+ 137.411 (branch= 136.58 scale= 0.83) pass 2:+ 7.774 (branch= 7.77 scale= 0.00) pass 3:+ 1.542 (branch= 1.52 scale= 0.02) pass 4:+ 0.091 (branch= 0.09 scale= 0.00) pass 5:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -495.1076 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mkO.ssr.conf Running internal test ./internal/p.mkO.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/p.mkO.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, modeled as Standard ordered k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -641.9257 optimizing: starting branch lengths, subset rates... pass 1:+ 147.096 (branch= 136.58 scale= 0.83 subset rates= 9.68) pass 2:+ 12.451 (branch= 8.46 scale= 0.00 subset rates= 3.99) pass 3:+ 3.549 (branch= 2.32 scale= 0.03 subset rates= 1.20) pass 4:+ 0.759 (branch= 0.51 scale= 0.00 subset rates= 0.25) pass 5:+ 0.120 (branch= 0.11 scale= 0.00 subset rates= 0.01) pass 6:+ 0.011 (branch= 0.01 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -477.9402 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mkv.conf Running internal test ./internal/p.mkv.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/p.mkv.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, variable only, modeled as Standard k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -605.5989 optimizing: starting branch lengths... pass 1:+ 124.584 (branch= 123.99 scale= 0.59) pass 2:+ 6.980 (branch= 6.98 scale= 0.00) pass 3:+ 1.324 (branch= 1.31 scale= 0.02) pass 4:+ 0.161 (branch= 0.16 scale= 0.00) pass 5:+ 0.013 (branch= 0.01 scale= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -472.5370 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mkv.ssr.conf Running internal test ./internal/p.mkv.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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:+ 9.272 (branch= 7.97 scale= 0.00 subset rates= 1.30) pass 3:+ 1.741 (branch= 1.57 scale= 0.00 subset rates= 0.17) pass 4:+ 0.311 (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: -464.7113 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mkvO.conf Running internal test ./internal/p.mkvO.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/p.mkvO.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, variable only, modeled as Standard ordered k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -637.9212 optimizing: starting branch lengths... pass 1:+ 134.883 (branch= 134.40 scale= 0.48) pass 2:+ 7.290 (branch= 7.29 scale= 0.00) pass 3:+ 1.758 (branch= 1.73 scale= 0.03) pass 4:+ 0.187 (branch= 0.19 scale= 0.00) pass 5:+ 0.011 (branch= 0.01 scale= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -493.7915 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mkvO.ssr.conf Running internal test ./internal/p.mkvO.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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:+ 1.162 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.156 (branch= 0.12 scale= 0.00 subset rates= 0.03) pass 6:+ 0.044 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 7:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -474.8632 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** ************************** Running scoring tests ... ************************** Running scoring test ./scoring/a.G3.conf Running scoring test ./scoring/a.G3.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/a.G3.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x2178.AA.nex ... Reading TAXA block...storing read block: TAXA successful Reading CHARACTERS block...storing read block: CHARACTERS found protein data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful Reading CODONS block...storing read block: CODONS successful Reading MESQUITECHARMODELS block...storing read block: MESQUITECHARMODELS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Protein translation of Character Matrix") Data read as Amino acid data, modeled as Amino acid data Found wtset "equal" with data, applying... Summary of data: 11 sequences. 389 constant characters. 190 parsimony-informative characters. 147 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 726 total characters (727 before removing empty columns). 343 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 13 MB good approx 12 MB to 9 MB low approx 8 MB to 5 MB very low approx 4 MB to 2 MB the minimum required availablememory is 2 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 5 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 18.0 MB of memory ####################################################### Found outgroup specification: 1 2 ####################################################### Loading starting model and/or tree from file data/a.G3.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus Obtained starting or fixed model parameter values from configuration file: MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: WAG Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0500 0.0252 0.0458 0.0579 0.0750 0.0561 0.0078 0.0882 0.0489 0.1128 0.0438 0.0500 0.0296 0.0252 0.0373 0.0552 0.0444 0.0906 0.0217 0.0346 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.4368 Substitution rate categories under this model: rate proportion 0.0437 0.3333 0.4372 0.3333 2.5190 0.3333 Starting with seed=1 Initial ln Likelihood: -6242.8631 optimizing: starting branch lengths, alpha shape... pass 1:+ 0.000 (branch= 0.00 scale= 0.00 alpha= 0.00) lnL after optimization: -6242.8629 Current score = -6242.8629 Performing final optimizations... pass 1 : -6242.8629 (branch= 0.0000 alpha= 0.0000) pass 2 : -6242.8595 (branch= 0.0034 alpha= 0.0000) pass 3 : -6242.8595 (branch= 0.0000 alpha= 0.0000) pass 4 : -6242.8595 (branch= 0.0000 alpha= 0.0000) pass 5 : -6242.8591 (branch= 0.0004 alpha= 0.0000) pass 6 : -6242.8586 (branch= 0.0005 alpha= 0.0000) pass 7 : -6242.8585 (branch= 0.0001 alpha= 0.0000) pass 8 : -6242.8583 (branch= 0.0002 alpha= 0.0000) pass 9 : -6242.8582 (branch= 0.0001 alpha= 0.0000) pass 10: -6242.8581 (branch= 0.0001 alpha= 0.0000) pass 11: -6242.8580 (branch= 0.0000 alpha= 0.0000) pass 12: -6242.8580 (branch= 0.0000 alpha= 0.0000) pass 13: -6242.8580 (branch= 0.0000 alpha= 0.0000) Looking for minimum length branches... Final score = -6242.8580 Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -6242.8580 Parameter estimates: alpha rep 1: 0.436 Treelengths: TL rep 1: 1.345 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.a.G3.best.all.tre ***********TEST************** ***Score is 6242.85802 ***Expected is 6242.85802 ***SCORE DIFFERENCE IS 0 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/a.G3.conf *** Running scoring test ./scoring/a.G4.conf Running scoring test ./scoring/a.G4.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/a.G4.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x2178.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data Some sites treated as missing data for taxon SterNa6 due to ambiguity in translation. Aminoacids coded as missing for that taxon: 708 Summary of data: 11 sequences. 389 constant characters. 190 parsimony-informative characters. 147 uninformative variable characters. 726 total characters. 343 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 17 MB good approx 16 MB to 13 MB low approx 12 MB to 6 MB very low approx 5 MB to 3 MB the minimum required availablememory is 3 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 6 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 23.9 MB of memory ####################################################### Found outgroup specification: 1-5 ####################################################### Loading starting model and/or tree from file data/a.G4.start Reading TREES block...storing read block: TREES successful Reading GARLI block...storing read block: GARLI successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus Obtained starting or fixed model parameter values from Nexus: MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: values specified by user (fixed) Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0500 0.0252 0.0458 0.0579 0.0750 0.0561 0.0078 0.0882 0.0489 0.1128 0.0438 0.0500 0.0296 0.0252 0.0373 0.0552 0.0444 0.0906 0.0217 0.0346 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.4616 Substitution rate categories under this model: rate proportion 0.0265 0.2500 0.2261 0.2500 0.7902 0.2500 2.9572 0.2500 Starting with seed=1 Initial ln Likelihood: -6249.1664 optimizing: starting branch lengths, alpha shape... pass 1:+ 1.482 (branch= 0.00 scale= 1.47 alpha= 0.01) pass 2:+ 0.010 (branch= 0.00 scale= 0.00 alpha= 0.01) lnL after optimization: -6247.6743 Current score = -6247.6743 Performing final optimizations... pass 1 : -6247.0539 (branch= 0.2066 alpha= 0.4138) pass 2 : -6247.0347 (branch= 0.0192 alpha= 0.0000) pass 3 : -6247.0279 (branch= 0.0068 alpha= 0.0000) pass 4 : -6247.0255 (branch= 0.0023 alpha= 0.0000) pass 5 : -6247.0234 (branch= 0.0022 alpha= 0.0000) pass 6 : -6247.0228 (branch= 0.0005 alpha= 0.0000) pass 7 : -6247.0226 (branch= 0.0002 alpha= 0.0000) pass 8 : -6247.0223 (branch= 0.0002 alpha= 0.0000) pass 9 : -6247.0222 (branch= 0.0001 alpha= 0.0000) pass 10: -6247.0222 (branch= 0.0000 alpha= 0.0000) Looking for minimum length branches... Final score = -6247.0222 Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -6247.0222 Parameter estimates: alpha rep 1: 0.423 Treelengths: TL rep 1: 1.467 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.a.G4.best.all.tre ***********TEST************** ***Score is 6247.02222 ***Expected is 6247.02222 ***SCORE DIFFERENCE IS 0 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/a.G4.conf *** Running scoring test ./scoring/a.conf Running scoring test ./scoring/a.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/a.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x2178.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data Some sites treated as missing data for taxon SterNa6 due to ambiguity in translation. Aminoacids coded as missing for that taxon: 708 Summary of data: 11 sequences. 389 constant characters. 190 parsimony-informative characters. 147 uninformative variable characters. 726 total characters. 343 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 4 MB good approx 3 MB to 3 MB low approx 2 MB to 2 MB very low approx 1 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 2 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 6.1 MB of memory ####################################################### Found outgroup specification: 1 ####################################################### Loading starting model and/or tree from file data/a.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: WAG Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0500 0.0252 0.0458 0.0579 0.0750 0.0561 0.0078 0.0882 0.0489 0.1128 0.0438 0.0500 0.0296 0.0252 0.0373 0.0552 0.0444 0.0906 0.0217 0.0346 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -6434.5146 optimizing: starting branch lengths... pass 1:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -6434.5146 Current score = -6434.5146 Performing final optimizations... pass 1 : -6434.5146 (branch= 0.0000) pass 2 : -6434.5101 (branch= 0.0045) pass 3 : -6434.5101 (branch= 0.0000) pass 4 : -6434.5101 (branch= 0.0000) pass 5 : -6434.5101 (branch= 0.0000) pass 6 : -6434.5092 (branch= 0.0009) pass 7 : -6434.5092 (branch= 0.0000) pass 8 : -6434.5092 (branch= 0.0000) pass 9 : -6434.5092 (branch= 0.0000) pass 10: -6434.5092 (branch= 0.0000) pass 11: -6434.5092 (branch= 0.0000) Looking for minimum length branches... Final score = -6434.5092 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -6434.5092 Parameter estimates: Model contains no estimated parameters Treelengths: TL rep 1: 1.143 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.a.best.all.tre ***********TEST************** ***Score is 6434.50916 ***Expected is 6434.50916 ***SCORE DIFFERENCE IS 0 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/a.conf *** Running scoring test ./scoring/c.M3x2.conf Running scoring test ./scoring/c.M3x2.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 36 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -12956.1235 Parameter estimates: w(0) p(0) w(1) p(1) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) rep 1: 0.020 0.696 0.294 0.304 1.26 2.449 1.259 0.6866 1.396 1 Treelengths: TL rep 1: 5.371 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.c.M3x2.best.all.tre ***********TEST************** ***Score is 12956.12351 ***Expected is 12956.1235 ***SCORE DIFFERENCE IS .00001 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/c.M3x2.conf *** Running scoring test ./scoring/c.conf Running scoring test ./scoring/c.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 26 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -13269.2298 Parameter estimates: w(0) p(0) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) rep 1: 0.087 1.000 1.265 2.362 1.151 0.7058 1.402 1 Treelengths: TL rep 1: 5.169 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.c.best.all.tre ***********TEST************** ***Score is 13269.22979 ***Expected is 13269.229793 ***SCORE DIFFERENCE IS -.000003 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/c.conf *** Running scoring test ./scoring/g.dnaBnoZ.conf Running scoring test ./scoring/g.dnaBnoZ.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 : -3355.4801 (branch= 0.9931 alpha= 0.0078 pinv= 0.0071 eq freqs= 0.1960 rel rates= 1.3008 subset rates= 0.3859) pass 2 : -3354.0738 (branch= 0.5295 alpha= 0.0090 pinv= 0.0117 eq freqs= 0.0202 rel rates= 0.6733 subset rates= 0.1627) pass 3 : -3353.2074 (branch= 0.3029 alpha= 0.0000 pinv= 0.0088 eq freqs= 0.0143 rel rates= 0.4607 subset rates= 0.0797) pass 4 : -3352.5841 (branch= 0.1779 alpha= 0.0022 pinv= 0.0160 eq freqs= 0.0064 rel rates= 0.3739 subset rates= 0.0469) pass 5 : -3352.1392 (branch= 0.0811 alpha= 0.0062 pinv= 0.0163 eq freqs= 0.0025 rel rates= 0.3066 subset rates= 0.0323) pass 6 : -3351.7984 (branch= 0.0566 alpha= 0.0067 pinv= 0.0165 eq freqs= 0.0008 rel rates= 0.2471 subset rates= 0.0132) pass 7 : -3351.5324 (branch= 0.0327 alpha= 0.0085 pinv= 0.0159 eq freqs= 0.0006 rel rates= 0.1993 subset rates= 0.0089) pass 8 : -3351.3163 (branch= 0.0193 alpha= 0.0099 pinv= 0.0150 eq freqs= 0.0005 rel rates= 0.1659 subset rates= 0.0054) pass 9 : -3351.1433 (branch= 0.0107 alpha= 0.0106 pinv= 0.0140 eq freqs= 0.0005 rel rates= 0.1334 subset rates= 0.0039) pass 10: -3351.0014 (branch= 0.0064 alpha= 0.0106 pinv= 0.0138 eq freqs= 0.0004 rel rates= 0.1081 subset rates= 0.0025) pass 11: -3350.8849 (branch= 0.0049 alpha= 0.0103 pinv= 0.0127 eq freqs= 0.0003 rel rates= 0.0871 subset rates= 0.0012) pass 12: -3350.7888 (branch= 0.0029 alpha= 0.0098 pinv= 0.0116 eq freqs= 0.0002 rel rates= 0.0715 subset rates= 0.0000) pass 13: -3350.7057 (branch= 0.0007 alpha= 0.0097 pinv= 0.0105 eq freqs= 0.0002 rel rates= 0.0604 subset rates= 0.0017) pass 14: -3350.6391 (branch= 0.0014 alpha= 0.0090 pinv= 0.0090 eq freqs= 0.0002 rel rates= 0.0470 subset rates= 0.0000) pass 15: -3350.5823 (branch= 0.0004 alpha= 0.0081 pinv= 0.0081 eq freqs= 0.0001 rel rates= 0.0401 subset rates= 0.0000) pass 16: -3350.5332 (branch= 0.0001 alpha= 0.0079 pinv= 0.0073 eq freqs= 0.0001 rel rates= 0.0338 subset rates= 0.0000) pass 17: -3350.4917 (branch= 0.0000 alpha= 0.0074 pinv= 0.0065 eq freqs= 0.0001 rel rates= 0.0274 subset rates= 0.0000) pass 18: -3350.4553 (branch= 0.0000 alpha= 0.0066 pinv= 0.0059 eq freqs= 0.0001 rel rates= 0.0228 subset rates= 0.0010) pass 19: -3350.4257 (branch= 0.0005 alpha= 0.0055 pinv= 0.0053 eq freqs= 0.0001 rel rates= 0.0183 subset rates= 0.0000) pass 20: -3350.3999 (branch= 0.0001 alpha= 0.0048 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0161 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= 0.0761 subset rates= 0.0000) optimization up to ... pass 40: -3350.2418 (branch= 0.0000 alpha= 0.0065 pinv= 0.0060 eq freqs= 0.0000 rel rates= 0.0171 subset rates= 0.0000) optimization up to ... pass 50: -3350.2352 (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: -3350.2336 (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: -3350.2333 (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 75: -3350.2332 (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: 3.112 10.41 2.688 0.001 21.89 1 0.333 0.222 0.157 0.288 0.578 0.366 Partition model subset 2: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) rep 1: 0.789 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 3350.23325 ***Expected is 3350.2345 ***SCORE DIFFERENCE IS -.00125 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/g.dnaBnoZ.conf *** Running scoring test ./scoring/g.dnaMix.conf Running scoring test ./scoring/g.dnaMix.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 : -3329.9872 (branch= 1.3745 alpha= 0.0217 pinv= 0.0099 eq freqs= 0.2403 rel rates= 0.7610 ins/del rates= 0.0754) pass 2 : -3328.9659 (branch= 0.3685 alpha= 0.0000 pinv= 0.0130 eq freqs= 0.0040 rel rates= 0.5672 ins/del rates= 0.0686) pass 3 : -3328.3611 (branch= 0.1485 alpha= 0.0057 pinv= 0.0143 eq freqs= 0.0130 rel rates= 0.3796 ins/del rates= 0.0437) pass 4 : -3327.9018 (branch= 0.0826 alpha= 0.0070 pinv= 0.0147 eq freqs= 0.0031 rel rates= 0.3239 ins/del rates= 0.0279) pass 5 : -3327.5623 (branch= 0.0510 alpha= 0.0076 pinv= 0.0148 eq freqs= 0.0008 rel rates= 0.2476 ins/del rates= 0.0177) pass 6 : -3327.2964 (branch= 0.0330 alpha= 0.0080 pinv= 0.0145 eq freqs= 0.0011 rel rates= 0.1981 ins/del rates= 0.0111) pass 7 : -3327.0823 (branch= 0.0212 alpha= 0.0094 pinv= 0.0139 eq freqs= 0.0007 rel rates= 0.1614 ins/del rates= 0.0075) pass 8 : -3326.9071 (branch= 0.0138 alpha= 0.0097 pinv= 0.0132 eq freqs= 0.0005 rel rates= 0.1331 ins/del rates= 0.0050) pass 9 : -3326.7651 (branch= 0.0091 alpha= 0.0099 pinv= 0.0124 eq freqs= 0.0004 rel rates= 0.1070 ins/del rates= 0.0033) pass 10: -3326.6477 (branch= 0.0061 alpha= 0.0096 pinv= 0.0122 eq freqs= 0.0003 rel rates= 0.0869 ins/del rates= 0.0022) pass 11: -3326.5503 (branch= 0.0041 alpha= 0.0093 pinv= 0.0113 eq freqs= 0.0002 rel rates= 0.0710 ins/del rates= 0.0015) pass 12: -3326.4699 (branch= 0.0028 alpha= 0.0089 pinv= 0.0098 eq freqs= 0.0002 rel rates= 0.0578 ins/del rates= 0.0010) pass 13: -3326.4023 (branch= 0.0019 alpha= 0.0084 pinv= 0.0090 eq freqs= 0.0001 rel rates= 0.0475 ins/del rates= 0.0007) pass 14: -3326.3449 (branch= 0.0013 alpha= 0.0079 pinv= 0.0082 eq freqs= 0.0001 rel rates= 0.0396 ins/del rates= 0.0005) pass 15: -3326.2956 (branch= 0.0009 alpha= 0.0073 pinv= 0.0075 eq freqs= 0.0001 rel rates= 0.0332 ins/del rates= 0.0003) pass 16: -3326.2539 (branch= 0.0005 alpha= 0.0069 pinv= 0.0068 eq freqs= 0.0001 rel rates= 0.0272 ins/del rates= 0.0002) pass 17: -3326.2181 (branch= 0.0003 alpha= 0.0063 pinv= 0.0061 eq freqs= 0.0001 rel rates= 0.0229 ins/del rates= 0.0001) pass 18: -3326.1870 (branch= 0.0002 alpha= 0.0056 pinv= 0.0055 eq freqs= 0.0000 rel rates= 0.0196 ins/del rates= 0.0001) pass 19: -3326.1600 (branch= 0.0001 alpha= 0.0051 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0167 ins/del rates= 0.0000) pass 20: -3326.1365 (branch= 0.0001 alpha= 0.0046 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0143 ins/del rates= 0.0000) optimization up to ... pass 30: -3326.0190 (branch= 0.0002 alpha= 0.0258 pinv= 0.0240 eq freqs= 0.0002 rel rates= 0.0674 ins/del rates= 0.0001) optimization up to ... pass 40: -3325.9906 (branch= 0.0001 alpha= 0.0067 pinv= 0.0062 eq freqs= 0.0000 rel rates= 0.0154 ins/del rates= 0.0000) optimization up to ... pass 50: -3325.9841 (branch= 0.0000 alpha= 0.0015 pinv= 0.0013 eq freqs= 0.0000 rel rates= 0.0037 ins/del rates= 0.0000) optimization up to ... pass 60: -3325.9825 (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: -3325.9822 (branch= 0.0000 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 ins/del rates= 0.0000) optimization up to ... pass 75: -3325.9822 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3325.9822 Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -3325.9822 Parameter estimates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 3.062 10.26 2.659 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: 0.053 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 3325.98218 ***Expected is 3325.98222 ***SCORE DIFFERENCE IS -.00004 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/g.dnaMix.conf *** Running scoring test ./scoring/n.G4.conf Running scoring test ./scoring/n.G4.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 1 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -13930.5180 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 1.531 3.879 1.558 1.283 4.736 1 0.244 0.243 0.250 0.263 1.252 0.302 Treelengths: TL rep 1: 1.577 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.n.G4.best.all.tre ***********TEST************** ***Score is 13917.56622 ***Expected is 13917.56622 ***SCORE DIFFERENCE IS 0 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/n.G4.conf *** Running scoring test ./scoring/n.G5.conf Running scoring test ./scoring/n.G5.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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:+ 2061.637 (branch=1982.89 scale= 74.28 freqs= 0.89 rel rates= 3.59) pass 2:+ 221.908 (branch= 220.60 scale= 0.00 freqs= 0.86 rel rates= 0.44) pass 3:+ 4.934 (branch= 4.75 scale= 0.00 freqs= 0.06 rel rates= 0.12) pass 4:+ 0.339 (branch= 0.30 scale= 0.00 freqs= 0.00 rel rates= 0.04) pass 5:+ 0.068 (branch= 0.07 scale= 0.00 freqs= 0.00 rel rates= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00 freqs= 0.00 rel rates= 0.00) lnL after optimization: -16071.0626 gen current_lnL precision last_tree_imp 0 -16071.0626 0.010 0 100 -14502.0375 0.010 73 200 -14502.0088 0.010 73 300 -14501.0114 0.010 73 400 -14500.3784 0.010 73 500 -14499.9764 0.010 73 600 -14499.5066 0.010 73 700 -14499.2227 0.010 73 800 -14499.0584 0.010 73 900 -14499.0522 0.010 73 1000 -14499.0522 0.010 73 1100 -14498.9752 0.010 73 1200 -14498.9747 0.010 73 1300 -14498.9744 0.010 73 1400 -14498.9744 0.010 73 1500 -14498.9744 0.010 73 1600 -14498.9598 0.010 73 Reached termination condition! last topological improvement at gen 73 Improvement over last 500 gen = 0.01547 Current score = -14498.9598 Performing final optimizations... pass 1 : -14498.9266 (branch= 0.0118 eq freqs= 0.0156 rel rates= 0.0058) pass 2 : -14498.8998 (branch= 0.0172 eq freqs= 0.0059 rel rates= 0.0037) pass 3 : -14498.8921 (branch= 0.0061 eq freqs= 0.0014 rel rates= 0.0002) pass 4 : -14498.8895 (branch= 0.0010 eq freqs= 0.0008 rel rates= 0.0008) pass 5 : -14498.8878 (branch= 0.0006 eq freqs= 0.0001 rel rates= 0.0010) pass 6 : -14498.8866 (branch= 0.0005 eq freqs= 0.0003 rel rates= 0.0005) pass 7 : -14498.8860 (branch= 0.0004 eq freqs= 0.0001 rel rates= 0.0001) pass 8 : -14498.8858 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) pass 9 : -14498.8856 (branch= 0.0001 eq freqs= 0.0000 rel rates= 0.0001) pass 10: -14498.8855 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) pass 11: -14498.8855 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) pass 12: -14498.8854 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 13: -14498.8854 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 14: -14498.8854 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 15: -14498.8853 (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 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.871, AG = 3.673, AT = 1.222, CG = 1.854, CT = 4.417, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2554 0.2085 0.2382 0.2978 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file scr.n.sitelikes.log ... WARNING: Site likelihoods are being output when wtset compensate is in effect. Sites with weight > 1 will only be output once! ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -14498.8853 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 1.871 3.673 1.222 1.854 4.417 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 14486.03877 ***Expected is 14486.03829 ***SCORE DIFFERENCE IS .00048 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/n.conf *** Running scoring test ./scoring/p.3diff.conf Running scoring test ./scoring/p.3diff.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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:+ 327.990 (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:+ 196.573 (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:+ 0.901 (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: -13315.7937 Current score = -13315.7937 Performing final optimizations... pass 1 : -13309.3589 (branch= 2.8300 alpha= 0.8831 pinv= 0.0157 eq freqs= 0.2322 rel rates= 1.8494 subset rates= 0.6243) pass 2 : -13307.8685 (branch= 0.4258 alpha= 0.1992 pinv= 0.0130 eq freqs= 0.1299 rel rates= 0.6663 subset rates= 0.0562) pass 3 : -13307.2724 (branch= 0.1089 alpha= 0.0561 pinv= 0.0031 eq freqs= 0.0074 rel rates= 0.4206 subset rates= 0.0000) pass 4 : -13306.9015 (branch= 0.0214 alpha= 0.0163 pinv= 0.0021 eq freqs= 0.0108 rel rates= 0.2990 subset rates= 0.0213) pass 5 : -13306.6670 (branch= 0.0102 alpha= 0.0063 pinv= 0.0015 eq freqs= 0.0062 rel rates= 0.2082 subset rates= 0.0021) pass 6 : -13306.5170 (branch= 0.0033 alpha= 0.0030 pinv= 0.0005 eq freqs= 0.0036 rel rates= 0.1397 subset rates= 0.0000) pass 7 : -13306.4171 (branch= 0.0023 alpha= 0.0006 pinv= 0.0001 eq freqs= 0.0031 rel rates= 0.0938 subset rates= 0.0000) pass 8 : -13306.3499 (branch= 0.0007 alpha= 0.0003 pinv= 0.0000 eq freqs= 0.0020 rel rates= 0.0641 subset rates= 0.0000) pass 9 : -13306.3046 (branch= 0.0003 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0015 rel rates= 0.0434 subset rates= 0.0000) pass 10: -13306.2733 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0011 rel rates= 0.0300 subset rates= 0.0000) pass 11: -13306.2525 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0201 subset rates= 0.0000) pass 12: -13306.2382 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0138 subset rates= 0.0000) pass 13: -13306.2276 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0095 subset rates= 0.0008) pass 14: -13306.2207 (branch= 0.0001 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0066 subset rates= 0.0000) pass 15: -13306.2160 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0045 subset rates= 0.0000) pass 16: -13306.2130 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0029 subset rates= 0.0000) pass 17: -13306.2108 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0021 subset rates= 0.0000) pass 18: -13306.2094 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014 subset rates= 0.0000) pass 19: -13306.2084 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010 subset rates= 0.0000) pass 20: -13306.2077 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007 subset rates= 0.0000) optimization up to ... pass 30: -13306.2062 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0014 subset rates= 0.0000) optimization up to ... pass 34: -13306.2061 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) Looking for minimum length branches... Final score = -13306.2061 Time used = 0 hours, 0 minutes and 10 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -13306.2061 Parameter estimates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha rep 1: 1.974 2.576 1.413 1.413 3.719 1 0.310 0.177 0.297 0.216 0.407 Partition model subset 2: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha rep 1: 4.371 7.055 1.608 7.055 4.371 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 3.388 0.4593 4.939 1 0.157 0.354 0.287 0.202 4.036 0.033 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 1.694 0.541 0.301 2.159 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.p.3diff.best.all.tre ***********TEST************** ***Score is 13306.20613 ***Expected is 13306.20608 ***SCORE DIFFERENCE IS .00005 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.3diff.conf *** Running scoring test ./scoring/p.mk.conf Running scoring test ./scoring/p.mk.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/p.mk.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, modeled as Standard k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -609.1934 optimizing: starting branch lengths... pass 1:+ 125.912 (branch= 124.97 scale= 0.94) pass 2:+ 7.205 (branch= 7.20 scale= 0.00) pass 3:+ 1.518 (branch= 1.48 scale= 0.03) pass 4:+ 0.225 (branch= 0.22 scale= 0.00) pass 5:+ 0.014 (branch= 0.01 scale= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -474.3188 Current score = -474.3188 Performing final optimizations... pass 1 : -474.2925 (branch= 0.0264) pass 2 : -474.2170 (branch= 0.0755) pass 3 : -474.1996 (branch= 0.0173) pass 4 : -474.1939 (branch= 0.0057) pass 5 : -474.1908 (branch= 0.0031) pass 6 : -474.1886 (branch= 0.0022) pass 7 : -474.1872 (branch= 0.0014) pass 8 : -474.1869 (branch= 0.0003) pass 9 : -474.1867 (branch= 0.0002) pass 10: -474.1865 (branch= 0.0002) pass 11: -474.1864 (branch= 0.0001) pass 12: -474.1864 (branch= 0.0000) pass 13: -474.1864 (branch= 0.0000) pass 14: -474.1864 (branch= 0.0000) Looking for minimum length branches... Final score = -474.1864 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -474.1864 Parameter estimates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths: TL rep 1: 3.854 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.p.mk.best.all.tre ***********TEST************** ***Score is 474.18638 ***Expected is 474.1864 ***SCORE DIFFERENCE IS -.00002 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mk.conf *** Running scoring test ./scoring/p.mk.ssr.conf Running scoring test ./scoring/p.mk.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/p.mk.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, modeled as Standard k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -609.1934 optimizing: starting branch lengths, subset rates... pass 1:+ 130.207 (branch= 124.97 scale= 0.94 subset rates= 4.29) pass 2:+ 9.055 (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:+ 0.304 (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: -467.8138 Current score = -467.8138 Performing final optimizations... pass 1 : -467.7837 (branch= 0.0218 subset rates= 0.0084) pass 2 : -467.7131 (branch= 0.0705 subset rates= 0.0000) pass 3 : -467.7054 (branch= 0.0077 subset rates= 0.0000) pass 4 : -467.6967 (branch= 0.0087 subset rates= 0.0000) pass 5 : -467.6866 (branch= 0.0073 subset rates= 0.0028) pass 6 : -467.6817 (branch= 0.0044 subset rates= 0.0004) pass 7 : -467.6801 (branch= 0.0016 subset rates= 0.0000) pass 8 : -467.6799 (branch= 0.0002 subset rates= 0.0000) pass 9 : -467.6796 (branch= 0.0003 subset rates= 0.0000) pass 10: -467.6789 (branch= 0.0001 subset rates= 0.0007) pass 11: -467.6785 (branch= 0.0004 subset rates= 0.0000) pass 12: -467.6784 (branch= 0.0001 subset rates= 0.0000) pass 13: -467.6784 (branch= 0.0000 subset rates= 0.0000) pass 14: -467.6784 (branch= 0.0000 subset rates= 0.0000) pass 15: -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: 3.841 0.787 1.478 2.174 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 467.67834 ***Expected is 467.6783 ***SCORE DIFFERENCE IS .00004 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mk.ssr.conf *** Running scoring test ./scoring/p.mkO.conf Running scoring test ./scoring/p.mkO.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/p.mkO.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, modeled as Standard ordered k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -641.9257 optimizing: starting branch lengths... pass 1:+ 137.411 (branch= 136.58 scale= 0.83) pass 2:+ 7.774 (branch= 7.77 scale= 0.00) pass 3:+ 1.542 (branch= 1.52 scale= 0.02) pass 4:+ 0.091 (branch= 0.09 scale= 0.00) pass 5:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -495.1076 Current score = -495.1076 Performing final optimizations... pass 1 : -495.0677 (branch= 0.0399) pass 2 : -494.9999 (branch= 0.0678) pass 3 : -494.9820 (branch= 0.0179) pass 4 : -494.9768 (branch= 0.0051) pass 5 : -494.9724 (branch= 0.0044) pass 6 : -494.9711 (branch= 0.0013) pass 7 : -494.9709 (branch= 0.0002) pass 8 : -494.9703 (branch= 0.0006) pass 9 : -494.9702 (branch= 0.0001) pass 10: -494.9701 (branch= 0.0001) pass 11: -494.9701 (branch= 0.0000) pass 12: -494.9700 (branch= 0.0000) pass 13: -494.9700 (branch= 0.0000) Looking for minimum length branches... Final score = -494.9700 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -494.9700 Parameter estimates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths: TL rep 1: 4.503 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.p.mkO.best.all.tre ***********TEST************** ***Score is 494.97003 ***Expected is 494.9700 ***SCORE DIFFERENCE IS .00003 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mkO.conf *** Running scoring test ./scoring/p.mkO.ssr.conf Running scoring test ./scoring/p.mkO.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/p.mkO.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, modeled as Standard ordered k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -641.9257 optimizing: starting branch lengths, subset rates... pass 1:+ 147.096 (branch= 136.58 scale= 0.83 subset rates= 9.68) pass 2:+ 12.451 (branch= 8.46 scale= 0.00 subset rates= 3.99) pass 3:+ 3.549 (branch= 2.32 scale= 0.03 subset rates= 1.20) pass 4:+ 0.759 (branch= 0.51 scale= 0.00 subset rates= 0.25) pass 5:+ 0.120 (branch= 0.11 scale= 0.00 subset rates= 0.01) pass 6:+ 0.011 (branch= 0.01 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -477.9402 Current score = -477.9402 Performing final optimizations... pass 1 : -477.8555 (branch= 0.0847 subset rates= 0.0000) pass 2 : -477.7620 (branch= 0.0916 subset rates= 0.0020) pass 3 : -477.7274 (branch= 0.0329 subset rates= 0.0017) pass 4 : -477.7065 (branch= 0.0201 subset rates= 0.0008) pass 5 : -477.6965 (branch= 0.0100 subset rates= 0.0000) pass 6 : -477.6924 (branch= 0.0041 subset rates= 0.0000) pass 7 : -477.6895 (branch= 0.0029 subset rates= 0.0000) pass 8 : -477.6881 (branch= 0.0014 subset rates= 0.0000) pass 9 : -477.6869 (branch= 0.0009 subset rates= 0.0003) pass 10: -477.6859 (branch= 0.0009 subset rates= 0.0001) pass 11: -477.6853 (branch= 0.0006 subset rates= 0.0000) pass 12: -477.6850 (branch= 0.0003 subset rates= 0.0000) pass 13: -477.6849 (branch= 0.0001 subset rates= 0.0000) pass 14: -477.6848 (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: -477.6847 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.6847 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 : -477.6847 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: 4.918 0.629 1.903 2.812 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 477.68468 ***Expected is 477.6848 ***SCORE DIFFERENCE IS -.00012 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mkO.ssr.conf *** Running scoring test ./scoring/p.mkv.conf Running scoring test ./scoring/p.mkv.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/p.mkv.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, variable only, modeled as Standard k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -605.5989 optimizing: starting branch lengths... pass 1:+ 124.584 (branch= 123.99 scale= 0.59) pass 2:+ 6.980 (branch= 6.98 scale= 0.00) pass 3:+ 1.324 (branch= 1.31 scale= 0.02) pass 4:+ 0.161 (branch= 0.16 scale= 0.00) pass 5:+ 0.013 (branch= 0.01 scale= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -472.5370 Current score = -472.5370 Performing final optimizations... pass 1 : -472.4890 (branch= 0.0480) pass 2 : -472.4195 (branch= 0.0694) pass 3 : -472.4053 (branch= 0.0142) pass 4 : -472.3958 (branch= 0.0095) pass 5 : -472.3935 (branch= 0.0024) pass 6 : -472.3921 (branch= 0.0013) pass 7 : -472.3917 (branch= 0.0005) pass 8 : -472.3912 (branch= 0.0004) pass 9 : -472.3908 (branch= 0.0004) pass 10: -472.3907 (branch= 0.0001) pass 11: -472.3906 (branch= 0.0001) pass 12: -472.3906 (branch= 0.0000) pass 13: -472.3906 (branch= 0.0000) pass 14: -472.3906 (branch= 0.0000) Looking for minimum length branches... Final score = -472.3906 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -472.3906 Parameter estimates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths: TL rep 1: 3.621 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.p.mkv.best.all.tre ***********TEST************** ***Score is 472.39058 ***Expected is 472.3906 ***SCORE DIFFERENCE IS -.00002 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mkv.conf *** Running scoring test ./scoring/p.mkv.ssr.conf Running scoring test ./scoring/p.mkv.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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:+ 9.272 (branch= 7.97 scale= 0.00 subset rates= 1.30) pass 3:+ 1.741 (branch= 1.57 scale= 0.00 subset rates= 0.17) pass 4:+ 0.311 (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: -464.7113 Current score = -464.7113 Performing final optimizations... pass 1 : -464.6741 (branch= 0.0277 subset rates= 0.0094) pass 2 : -464.5915 (branch= 0.0810 subset rates= 0.0016) pass 3 : -464.5742 (branch= 0.0137 subset rates= 0.0036) pass 4 : -464.5605 (branch= 0.0126 subset rates= 0.0012) pass 5 : -464.5544 (branch= 0.0061 subset rates= 0.0000) pass 6 : -464.5510 (branch= 0.0018 subset rates= 0.0016) pass 7 : -464.5497 (branch= 0.0008 subset rates= 0.0005) pass 8 : -464.5487 (branch= 0.0010 subset rates= 0.0000) pass 9 : -464.5480 (branch= 0.0007 subset rates= 0.0001) pass 10: -464.5476 (branch= 0.0004 subset rates= 0.0001) pass 11: -464.5474 (branch= 0.0002 subset rates= 0.0000) pass 12: -464.5473 (branch= 0.0001 subset rates= 0.0000) pass 13: -464.5473 (branch= 0.0000 subset rates= 0.0000) pass 14: -464.5473 (branch= 0.0000 subset rates= 0.0000) pass 15: -464.5473 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -464.5473 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 : -464.5473 Parameter estimates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 3.400 0.771 1.640 2.469 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 464.54728 ***Expected is 464.5473 ***SCORE DIFFERENCE IS -.00002 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mkv.ssr.conf *** Running scoring test ./scoring/p.mkvO.conf Running scoring test ./scoring/p.mkvO.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/p.mkvO.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, variable only, modeled as Standard ordered k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -637.9212 optimizing: starting branch lengths... pass 1:+ 134.883 (branch= 134.40 scale= 0.48) pass 2:+ 7.290 (branch= 7.29 scale= 0.00) pass 3:+ 1.758 (branch= 1.73 scale= 0.03) pass 4:+ 0.187 (branch= 0.19 scale= 0.00) pass 5:+ 0.011 (branch= 0.01 scale= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -493.7915 Current score = -493.7915 Performing final optimizations... pass 1 : -493.7599 (branch= 0.0316) pass 2 : -493.6921 (branch= 0.0678) pass 3 : -493.6791 (branch= 0.0130) pass 4 : -493.6729 (branch= 0.0062) pass 5 : -493.6703 (branch= 0.0026) pass 6 : -493.6691 (branch= 0.0012) pass 7 : -493.6680 (branch= 0.0011) pass 8 : -493.6679 (branch= 0.0001) pass 9 : -493.6678 (branch= 0.0001) pass 10: -493.6677 (branch= 0.0000) pass 11: -493.6677 (branch= 0.0001) pass 12: -493.6676 (branch= 0.0000) pass 13: -493.6676 (branch= 0.0000) Looking for minimum length branches... Final score = -493.6676 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -493.6676 Parameter estimates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths: TL rep 1: 4.301 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.p.mkvO.best.all.tre ***********TEST************** ***Score is 493.66764 ***Expected is 493.667 ***SCORE DIFFERENCE IS .00064 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mkvO.conf *** Running scoring test ./scoring/p.mkvO.ssr.conf Running scoring test ./scoring/p.mkvO.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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:+ 1.162 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.156 (branch= 0.12 scale= 0.00 subset rates= 0.03) pass 6:+ 0.044 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 7:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -474.8632 Current score = -474.8632 Performing final optimizations... pass 1 : -474.7998 (branch= 0.0575 subset rates= 0.0059) pass 2 : -474.6995 (branch= 0.0905 subset rates= 0.0099) pass 3 : -474.6708 (branch= 0.0286 subset rates= 0.0000) pass 4 : -474.6601 (branch= 0.0107 subset rates= 0.0000) pass 5 : -474.6536 (branch= 0.0055 subset rates= 0.0011) pass 6 : -474.6498 (branch= 0.0029 subset rates= 0.0010) pass 7 : -474.6476 (branch= 0.0021 subset rates= 0.0000) pass 8 : -474.6469 (branch= 0.0007 subset rates= 0.0000) pass 9 : -474.6465 (branch= 0.0003 subset rates= 0.0001) 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= 0.0000) pass 13: -474.6456 (branch= 0.0001 subset rates= 0.0000) pass 14: -474.6456 (branch= 0.0000 subset rates= 0.0000) pass 15: -474.6456 (branch= 0.0000 subset rates= 0.0000) pass 16: -474.6456 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -474.6456 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -474.6456 Parameter estimates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.583 0.587 2.014 2.996 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 474.64557 ***Expected is 474.6455633 ***SCORE DIFFERENCE IS .0000067 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mkvO.ssr.conf *** ************************** Running constraint tests ... ************************** Running constraint test n.neg.const Running constraint test n.neg.const Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 1.331 lnL Optimizing branchlengths... improved 0.015 lnL 1500 -210.8784 0.010 1215 2000 -210.6585 0.010 1215 2500 -210.6111 0.010 1215 3000 -210.5162 0.010 1215 Reached termination condition! last topological improvement at gen 1215 Improvement over last 500 gen = 0.03349 Current score = -210.5118 Performing final optimizations... pass 1 : -210.1433 (branch= 0.0000 alpha= 0.0977 pinv= 0.2249 eq freqs= 0.0000 rel rates= 0.0460) pass 2 : -209.5323 (branch= 0.0000 alpha= 0.3293 pinv= 0.2553 eq freqs= 0.0029 rel rates= 0.0235) pass 3 : -209.3312 (branch= 0.0357 alpha= 0.1375 pinv= 0.0146 eq freqs= 0.0067 rel rates= 0.0067) pass 4 : -209.2605 (branch= 0.0422 alpha= 0.0192 pinv= 0.0022 eq freqs= 0.0011 rel rates= 0.0060) pass 5 : -209.2228 (branch= 0.0234 alpha= 0.0075 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0069) pass 6 : -209.1997 (branch= 0.0108 alpha= 0.0028 pinv= 0.0010 eq freqs= 0.0002 rel rates= 0.0084) pass 7 : -209.1781 (branch= 0.0076 alpha= 0.0023 pinv= 0.0003 eq freqs= 0.0003 rel rates= 0.0110) pass 8 : -209.1598 (branch= 0.0049 alpha= 0.0013 pinv= 0.0001 eq freqs= 0.0005 rel rates= 0.0115) pass 9 : -209.1462 (branch= 0.0024 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0108) pass 10: -209.1345 (branch= 0.0010 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0102) pass 11: -209.1247 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0090) pass 12: -209.1160 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0082) pass 13: -209.1081 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0075) pass 14: -209.1010 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0069) pass 15: -209.0943 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0065) pass 16: -209.0881 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0060) pass 17: -209.0822 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) pass 18: -209.0768 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0054) pass 19: -209.0715 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0052) pass 20: -209.0667 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) optimization up to ... pass 30: -208.9988 (branch= 0.0077 alpha= 0.0000 pinv= 0.0003 eq freqs= 0.0013 rel rates= 0.0587) optimization up to ... pass 40: -208.8376 (branch= 0.0298 alpha= 0.0000 pinv= 0.0016 eq freqs= 0.0076 rel rates= 0.1223) optimization up to ... pass 50: -208.6967 (branch= 0.0131 alpha= 0.0000 pinv= 0.0014 eq freqs= 0.0057 rel rates= 0.1208) optimization up to ... pass 60: -208.6228 (branch= 0.0012 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0007 rel rates= 0.0719) optimization up to ... pass 70: -208.5734 (branch= 0.0003 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0488) optimization up to ... pass 80: -208.5377 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0354) optimization up to ... pass 90: -208.5105 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0269) optimization up to ... pass 100: -208.4894 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0209) optimization up to ... pass 110: -208.4724 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0169) optimization up to ... pass 120: -208.4587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0136) optimization up to ... pass 130: -208.4472 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0114) optimization up to ... pass 140: -208.4374 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0097) optimization up to ... pass 150: -208.4292 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0082) optimization up to ... pass 160: -208.4221 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0070) optimization up to ... pass 170: -208.4160 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0061) optimization up to ... pass 180: -208.4106 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0054) optimization up to ... pass 190: -208.4059 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) optimization up to ... pass 200: -208.4017 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0041) optimization up to ... pass 210: -208.3980 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0037) optimization up to ... pass 220: -208.3946 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0033) optimization up to ... pass 230: -208.3916 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0030) optimization up to ... pass 240: -208.3888 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0028) optimization up to ... pass 250: -208.3863 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0025) optimization up to ... pass 260: -208.3840 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0023) optimization up to ... pass 270: -208.3819 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) optimization up to ... pass 280: -208.3799 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... pass 290: -208.3781 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) optimization up to ... pass 300: -208.3764 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 310: -208.3749 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... pass 320: -208.3734 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 330: -208.3721 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 340: -208.3708 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... pass 350: -208.3696 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 360: -208.3685 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 370: -208.3674 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 380: -208.3664 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 390: -208.3655 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 400: -208.3646 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 410: -208.3638 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 420: -208.3630 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 430: -208.3623 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 440: -208.3615 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 450: -208.3608 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 460: -208.3602 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 470: -208.3596 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 480: -208.3590 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 490: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... pass 494: -208.3585 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... Final score = -208.3585 Time used = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 121.821, AG = 187.997, AT = 6.950, CG = 204.113, CT = 194.212, 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 999.8998 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 : -208.3585 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 121.8 188 6.95 204.1 194.2 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.neg.const.best.tre ####################################################### TREEFILES PASS Running constraint test n.negBack.const Running constraint test n.negBack.const Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 1.751 lnL Optimizing branchlengths... improved 0.106 lnL 1000 -212.3291 0.010 825 1500 -212.1959 0.010 825 2000 -211.9101 0.010 825 2500 -211.7710 0.010 825 3000 -211.6572 0.010 825 3500 -211.4394 0.010 825 4000 -211.3138 0.010 825 Reached termination condition! last topological improvement at gen 825 Improvement over last 500 gen = 0.03817 Current score = -211.2856 Performing final optimizations... pass 1 : -208.8370 (branch= 0.0000 alpha= 0.7695 pinv= 1.5819 eq freqs= 0.0061 rel rates= 0.0912) pass 2 : -208.5500 (branch= 0.0559 alpha= 0.1910 pinv= 0.0000 eq freqs= 0.0115 rel rates= 0.0286) pass 3 : -208.5121 (branch= 0.0133 alpha= 0.0021 pinv= 0.0028 eq freqs= 0.0015 rel rates= 0.0182) pass 4 : -208.4860 (branch= 0.0045 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0209) pass 5 : -208.4643 (branch= 0.0019 alpha= 0.0007 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0191) pass 6 : -208.4461 (branch= 0.0003 alpha= 0.0000 pinv= 0.0003 eq freqs= 0.0002 rel rates= 0.0175) pass 7 : -208.4282 (branch= 0.0008 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0170) pass 8 : -208.4134 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0146) pass 9 : -208.3990 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0140) pass 10: -208.3862 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0127) pass 11: -208.3744 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0117) pass 12: -208.3639 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0104) pass 13: -208.3540 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0098) pass 14: -208.3448 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0091) pass 15: -208.3363 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0084) pass 16: -208.3285 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0078) pass 17: -208.3214 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0071) pass 18: -208.3144 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0069) pass 19: -208.3081 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0063) pass 20: -208.3021 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0060) optimization up to ... pass 30: -208.2576 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0444) optimization up to ... pass 40: -208.2298 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0277) optimization up to ... pass 50: -208.2109 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0189) optimization up to ... pass 60: -208.1971 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0137) optimization up to ... pass 70: -208.1867 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0104) optimization up to ... pass 80: -208.1784 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0083) optimization up to ... pass 90: -208.1717 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) optimization up to ... pass 100: -208.1662 (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: -208.1576 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) optimization up to ... pass 130: -208.1542 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) optimization up to ... pass 140: -208.1512 (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: -208.1462 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... pass 170: -208.1441 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) optimization up to ... pass 180: -208.1422 (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: -208.1375 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 220: -208.1362 (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: -208.1266 (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 372: -208.1244 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.1244 Time used = 0 hours, 0 minutes and 5 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 22.230, AG = 32.301, AT = 0.001, CG = 36.387, CT = 80.287, 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 : -208.1244 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: 22.23 32.3 0.001 36.39 80.29 1 0.221 0.344 0.216 0.218 999.900 0.338 Treelengths: TL rep 1: 2.421 Saving final tree from best search rep (#1) to con.n.negBack.const.best.tre ####################################################### TREEFILES PASS Running constraint test n.pos.const Running constraint test n.pos.const Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./const/n.pos.const.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1-5 ####################################################### Loading constraints from file data/z.pos.const.tre Found 6 positively constrained bipartition(s) Bipartition 1: (1,2,3,5,6,7,8,9,10) | (4,11) Bipartition 2: (1,3,5,6,7,8,9,10) | (2,4,11) Bipartition 3: (1,5,6,7,8,9,10) | (2,3,4,11) Bipartition 4: (1,2,3,4,5,8,9,10,11) | (6,7) Bipartition 5: (1,2,3,4,5,8,9,11) | (6,7,10) Bipartition 6: (1,5) | (2,3,4,6,7,8,9,10,11) STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0334 0.2271 0.2519 0.2271 0.8203 0.2271 2.8944 0.2271 Starting with seed=1 creating likelihood stepwise addition starting tree (compatible with constraints)... number of taxa added: 4 5 6 Optimizing parameters... improved 0.006 lnL Optimizing branchlengths... improved 11.173 lnL 7 8 9 10 11 Initial ln Likelihood: -225.0726 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 5.893 (branch= 2.29 scale= 0.89 alpha= 0.00 freqs= 1.20 rel rates= 1.50 pinv= 0.00) pass 2:+ 0.035 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.00) lnL after optimization: -219.1445 gen current_lnL precision last_tree_imp 0 -219.1445 0.500 0 500 -216.3491 0.500 474 1000 -215.0098 0.500 936 1500 -213.9531 0.500 936 Optimization precision reduced Optimizing parameters... improved 1.908 lnL Optimizing branchlengths... improved 0.702 lnL 2000 -210.9688 0.010 1502 2500 -210.8711 0.010 1502 3000 -210.7511 0.010 2883 3500 -210.7006 0.010 2883 4000 -210.6776 0.010 2883 4500 -210.6277 0.010 2883 5000 -210.5647 0.010 2883 5500 -210.5012 0.010 2883 6000 -210.3408 0.010 2883 Reached termination condition! last topological improvement at gen 2883 Improvement over last 500 gen = 0.04248 Current score = -210.3311 Performing final optimizations... pass 1 : -209.7245 (branch= 0.0039 alpha= 0.2015 pinv= 0.3325 eq freqs= 0.0000 rel rates= 0.0687) pass 2 : -209.3594 (branch= 0.0155 alpha= 0.2666 pinv= 0.0590 eq freqs= 0.0034 rel rates= 0.0207) pass 3 : -209.2472 (branch= 0.0797 alpha= 0.0162 pinv= 0.0072 eq freqs= 0.0063 rel rates= 0.0029) pass 4 : -209.1979 (branch= 0.0266 alpha= 0.0165 pinv= 0.0000 eq freqs= 0.0013 rel rates= 0.0050) pass 5 : -209.1659 (branch= 0.0191 alpha= 0.0068 pinv= 0.0010 eq freqs= 0.0006 rel rates= 0.0045) pass 6 : -209.1419 (branch= 0.0094 alpha= 0.0044 pinv= 0.0002 eq freqs= 0.0008 rel rates= 0.0091) pass 7 : -209.1243 (branch= 0.0060 alpha= 0.0010 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0100) pass 8 : -209.1128 (branch= 0.0021 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0086) pass 9 : -209.1041 (branch= 0.0007 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0076) pass 10: -209.0965 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0069) pass 11: -209.0899 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0062) pass 12: -209.0839 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0057) pass 13: -209.0784 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0053) pass 14: -209.0732 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0050) pass 15: -209.0681 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) pass 16: -209.0626 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) pass 17: -209.0567 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0052) pass 18: -209.0503 (branch= 0.0008 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0056) pass 19: -209.0432 (branch= 0.0010 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0058) pass 20: -209.0353 (branch= 0.0013 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0064) optimization up to ... pass 30: -208.9014 (branch= 0.0269 alpha= 0.0000 pinv= 0.0010 eq freqs= 0.0054 rel rates= 0.1006) optimization up to ... pass 40: -208.7354 (branch= 0.0207 alpha= 0.0000 pinv= 0.0018 eq freqs= 0.0076 rel rates= 0.1358) optimization up to ... pass 50: -208.6460 (branch= 0.0024 alpha= 0.0000 pinv= 0.0004 eq freqs= 0.0014 rel rates= 0.0853) optimization up to ... pass 60: -208.5896 (branch= 0.0004 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0555) optimization up to ... pass 70: -208.5497 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0396) optimization up to ... pass 80: -208.5197 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0297) optimization up to ... pass 90: -208.4966 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0230) optimization up to ... pass 100: -208.4783 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0182) optimization up to ... pass 110: -208.4634 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0148) optimization up to ... pass 120: -208.4512 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0122) optimization up to ... pass 130: -208.4408 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0103) optimization up to ... pass 140: -208.4321 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0087) optimization up to ... pass 150: -208.4246 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0074) optimization up to ... pass 160: -208.4181 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0064) optimization up to ... pass 170: -208.4125 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0056) optimization up to ... pass 180: -208.4076 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) optimization up to ... pass 190: -208.4032 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0043) optimization up to ... pass 200: -208.3994 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0038) optimization up to ... pass 210: -208.3959 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0035) optimization up to ... pass 220: -208.3927 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... pass 230: -208.3898 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) optimization up to ... pass 240: -208.3872 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) optimization up to ... pass 250: -208.3848 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... pass 260: -208.3826 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... pass 270: -208.3806 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... pass 280: -208.3788 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) optimization up to ... pass 290: -208.3770 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 300: -208.3754 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 310: -208.3740 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... pass 320: -208.3726 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 330: -208.3713 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... pass 340: -208.3701 (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: -208.3678 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 370: -208.3668 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 380: -208.3659 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) 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= 0.0008) optimization up to ... pass 410: -208.3633 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 420: -208.3625 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 430: -208.3618 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 440: -208.3611 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 450: -208.3604 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 460: -208.3598 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 470: -208.3592 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 480: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 488: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... Final score = -208.3584 Time used = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 122.601, AG = 189.649, AT = 6.980, CG = 205.574, CT = 195.517, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2225 0.2906 0.2035 0.2834 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: 122.6 189.6 6.98 205.6 195.5 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL rep 1: 1.881 Saving final tree from best search rep (#1) to con.n.pos.const.best.tre ####################################################### TREEFILES PASS Running constraint test n.posBack.const Running constraint test n.posBack.const Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./const/n.posBack.const.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 2 ####################################################### Loading constraints from file data/z.posBack.const.tre All constraints are backbone All constraints involve the same backbone set of taxa Found 4 positively constrained bipartition(s) Bipartition 1 (backbone): (1,2,3,5,8,9,10) | (4,11) Bipartition 2 (backbone): (1,3,5,8,9,10) | (2,4,11) Bipartition 3 (backbone): (1,5,8,9,10) | (2,3,4,11) Bipartition 4 (backbone): (1,5) | (2,3,4,8,9,10,11) STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0334 0.2271 0.2519 0.2271 0.8203 0.2271 2.8944 0.2271 Starting with seed=1 creating likelihood stepwise addition starting tree (compatible with constraints)... number of taxa added: 4 5 6 Optimizing parameters... improved 0.006 lnL Optimizing branchlengths... improved 11.173 lnL 7 8 9 10 11 Initial ln Likelihood: -221.7983 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 5.406 (branch= 2.03 scale= 0.00 alpha= 0.00 freqs= 1.20 rel rates= 2.17 pinv= 0.00) pass 2:+ 0.072 (branch= 0.04 scale= 0.00 alpha= 0.00 freqs= 0.02 rel rates= 0.00 pinv= 0.00) lnL after optimization: -216.3203 gen current_lnL precision last_tree_imp 0 -216.3203 0.500 0 500 -213.9944 0.500 208 1000 -213.0248 0.500 547 Optimization precision reduced Optimizing parameters... improved 1.494 lnL Optimizing branchlengths... improved 0.350 lnL 1500 -210.9424 0.010 1230 2000 -210.7769 0.010 1230 2500 -210.6534 0.010 1230 3000 -210.6127 0.010 1230 Reached termination condition! last topological improvement at gen 1230 Improvement over last 500 gen = 0.03867 Current score = -210.5967 Performing final optimizations... pass 1 : -210.1948 (branch= 0.0000 alpha= 0.1301 pinv= 0.2110 eq freqs= 0.0000 rel rates= 0.0609) pass 2 : -209.5594 (branch= 0.0039 alpha= 0.3421 pinv= 0.2529 eq freqs= 0.0036 rel rates= 0.0330) pass 3 : -209.3328 (branch= 0.0569 alpha= 0.1302 pinv= 0.0195 eq freqs= 0.0092 rel rates= 0.0107) pass 4 : -209.2518 (branch= 0.0540 alpha= 0.0194 pinv= 0.0013 eq freqs= 0.0022 rel rates= 0.0041) pass 5 : -209.2022 (branch= 0.0348 alpha= 0.0091 pinv= 0.0010 eq freqs= 0.0004 rel rates= 0.0043) pass 6 : -209.1701 (branch= 0.0178 alpha= 0.0057 pinv= 0.0003 eq freqs= 0.0011 rel rates= 0.0072) pass 7 : -209.1440 (branch= 0.0102 alpha= 0.0039 pinv= 0.0002 eq freqs= 0.0006 rel rates= 0.0112) pass 8 : -209.1243 (branch= 0.0067 alpha= 0.0015 pinv= 0.0000 eq freqs= 0.0009 rel rates= 0.0107) pass 9 : -209.1109 (branch= 0.0029 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0097) pass 10: -209.1010 (branch= 0.0010 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0084) pass 11: -209.0929 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0074) pass 12: -209.0859 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0065) pass 13: -209.0797 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0060) pass 14: -209.0741 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0054) pass 15: -209.0688 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0051) pass 16: -209.0639 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0048) pass 17: -209.0591 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 18: -209.0542 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 19: -209.0490 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) pass 20: -209.0434 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0051) optimization up to ... pass 30: -208.9359 (branch= 0.0194 alpha= 0.0000 pinv= 0.0007 eq freqs= 0.0038 rel rates= 0.0836) optimization up to ... pass 40: -208.7600 (branch= 0.0269 alpha= 0.0000 pinv= 0.0020 eq freqs= 0.0087 rel rates= 0.1383) optimization up to ... pass 50: -208.6584 (branch= 0.0043 alpha= 0.0000 pinv= 0.0006 eq freqs= 0.0024 rel rates= 0.0944) optimization up to ... pass 60: -208.5979 (branch= 0.0006 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0595) optimization up to ... pass 70: -208.5556 (branch= 0.0002 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0419) optimization up to ... pass 80: -208.5242 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0311) optimization up to ... pass 90: -208.5002 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0238) optimization up to ... pass 100: -208.4812 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0189) optimization up to ... pass 110: -208.4658 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0153) optimization up to ... pass 120: -208.4532 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0126) optimization up to ... pass 130: -208.4425 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0106) optimization up to ... pass 140: -208.4334 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0090) optimization up to ... pass 150: -208.4257 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0076) optimization up to ... pass 160: -208.4192 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0065) optimization up to ... pass 170: -208.4134 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0057) optimization up to ... pass 180: -208.4084 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) optimization up to ... pass 190: -208.4039 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0045) optimization up to ... pass 200: -208.3999 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) optimization up to ... pass 210: -208.3964 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0035) optimization up to ... pass 220: -208.3932 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... pass 230: -208.3903 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) optimization up to ... pass 240: -208.3876 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) optimization up to ... pass 250: -208.3852 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... pass 260: -208.3830 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... pass 270: -208.3810 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... pass 280: -208.3791 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 290: -208.3773 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 300: -208.3757 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 310: -208.3742 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... pass 320: -208.3728 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 330: -208.3715 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... pass 340: -208.3703 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 350: -208.3691 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 360: -208.3680 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 370: -208.3670 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 380: -208.3660 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 390: -208.3651 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 400: -208.3643 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 410: -208.3634 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 420: -208.3627 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 430: -208.3619 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 440: -208.3612 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 450: -208.3605 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 460: -208.3599 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 470: -208.3593 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 480: -208.3588 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) optimization up to ... pass 489: -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 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 121.696, AG = 187.808, AT = 6.943, CG = 203.906, CT = 194.015, 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 : -208.3586 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: 121.7 187.8 6.943 203.9 194 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL rep 1: 1.881 Saving final tree from best search rep (#1) to con.n.posBack.const.best.tre ####################################################### TREEFILES PASS ************************** Running output tests ... ************************** Running output test a.G3 Running output test a.G3 Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./output/a.G3.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 11 sequences. 3 constant characters. 6 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0165 0.0083 0.0496 0.0909 0.0909 0.0083 0.0744 0.0083 0.0083 0.1074 0.1157 0.0248 0.1240 0.0331 0.0083 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0750 Substitution rate categories under this model: rate proportion 0.0000 0.0750 0.0603 0.3083 0.4894 0.3083 2.4503 0.3083 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.002 lnL Optimizing branchlengths... improved 0.000 lnL 7 8 9 10 11 Initial ln Likelihood: -116.5267 optimizing: starting branch lengths, alpha shape, prop. invar... pass 1:+ 0.949 (branch= 0.95 scale= 0.00 alpha= 0.00 pinv= 0.00) pass 2:+ 0.099 (branch= 0.10 scale= 0.00 alpha= 0.00 pinv= 0.00) lnL after optimization: -115.4785 gen current_lnL precision last_tree_imp 0 -115.4785 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0165 0.0083 0.0496 0.0909 0.0909 0.0083 0.0744 0.0083 0.0083 0.1074 0.1157 0.0248 0.1240 0.0331 0.0083 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.5015 with an invariant (invariable) site category, proportion estimated 0.0735 Substitution rate categories under this model: rate proportion 0.0000 0.0735 0.0607 0.3088 0.4905 0.3088 2.4487 0.3088 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.a.G3.sitelikes.log ... WARNING: Site likelihoods being output on prematurely terminated search ... NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -114.0488 Parameter estimates: alpha pinv rep 1: 0.501 0.073 Treelengths: TL rep 1: 1.377 Saving final tree from best search rep (#1) to out.a.G3.best.tre Inferring internal state probabilities on best tree... saving to file out.a.G3.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.a.G3.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found 11 instead at line 1, column (approximately) 4 (file position 3) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 16, column (approximately) 1 (file position 470) storing implied block: TAXA storing read block: TREES TREEFILES PASS Running output test a.G4 Running output test a.G4 Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./output/a.G4.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 11 sequences. 3 constant characters. 6 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.8 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 2 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0165 0.0083 0.0496 0.0909 0.0909 0.0083 0.0744 0.0083 0.0083 0.1074 0.1157 0.0248 0.1240 0.0331 0.0083 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0750 Substitution rate categories under this model: rate proportion 0.0000 0.0750 0.0334 0.2313 0.2519 0.2313 0.8203 0.2313 2.8944 0.2313 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.001 lnL Optimizing branchlengths... improved 0.006 lnL 7 8 9 10 11 Initial ln Likelihood: -117.7431 optimizing: starting branch lengths, alpha shape, prop. invar... pass 1:+ 1.466 (branch= 1.13 scale= 0.33 alpha= 0.00 pinv= 0.00) pass 2:+ 0.134 (branch= 0.13 scale= 0.00 alpha= 0.00 pinv= 0.00) lnL after optimization: -116.1434 gen current_lnL precision last_tree_imp 0 -116.1434 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0165 0.0083 0.0496 0.0909 0.0909 0.0083 0.0744 0.0083 0.0083 0.1074 0.1157 0.0248 0.1240 0.0331 0.0083 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5015 with an invariant (invariable) site category, proportion estimated 0.0735 Substitution rate categories under this model: rate proportion 0.0000 0.0735 0.0337 0.2316 0.2529 0.2316 0.8214 0.2316 2.8921 0.2316 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.a.G4.sitelikes.log ... WARNING: Site likelihoods being output on prematurely terminated search ... NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -114.3787 Parameter estimates: alpha pinv rep 1: 0.501 0.073 Treelengths: TL rep 1: 1.339 Saving final tree from best search rep (#1) to out.a.G4.best.tre Inferring internal state probabilities on best tree... saving to file out.a.G4.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.a.G4.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found 11 instead at line 1, column (approximately) 4 (file position 3) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 16, column (approximately) 1 (file position 470) storing implied block: TAXA storing read block: TREES TREEFILES PASS Running output test a Running output test a Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./output/a.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.AA.fas as Fasta amino acid format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Amino acid data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 11 sequences. 3 constant characters. 6 parsimony-informative characters. 1 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 10 total characters (11 before removing empty columns). 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.2 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1-3 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0165 0.0083 0.0496 0.0909 0.0909 0.0083 0.0744 0.0083 0.0083 0.1074 0.1157 0.0248 0.1240 0.0331 0.0083 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 0.121 lnL 7 8 9 10 11 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -117.7533 optimizing: starting branch lengths... pass 1:+ 0.632 (branch= 0.63 scale= 0.00) pass 2:+ 0.134 (branch= 0.13 scale= 0.00) lnL after optimization: -116.9881 gen current_lnL precision last_tree_imp 0 -116.9881 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0165 0.0083 0.0496 0.0909 0.0909 0.0083 0.0744 0.0083 0.0083 0.1074 0.1157 0.0248 0.1240 0.0331 0.0083 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.a.sitelikes.log ... WARNING: Site likelihoods being output on prematurely terminated search ... NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -115.6197 Parameter estimates: Model contains no estimated parameters Treelengths: TL rep 1: 2.324 Saving final tree from best search rep (#1) to out.a.best.tre Inferring internal state probabilities on best tree... saving to file out.a.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.a.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found > instead at line 1, column (approximately) 2 (file position 1) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 26, column (approximately) 1 (file position 310) storing implied block: TAXA storing read block: TREES TREEFILES PASS Running output test c.M3x2 Running output test c.M3x2 Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./output/c.M3x2.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Codon data Base usage at codon positions: A C G T pos 1 0.27723 0.36634 0.21782 0.13861 pos 2 0.30693 0.20792 0.07921 0.40594 pos 3 0.10891 0.38614 0.26733 0.23762 all pos 0.23102 0.32013 0.18812 0.26073 Summary of data: 11 sequences. 0 constant characters. 9 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 1.3 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1-5 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0094 0.0334 0.0231 0.0206 0.0064 0.0226 0.0157 0.0139 0.0024 0.0086 0.0060 0.0053 0.0125 0.0442 0.0306 0.0272 0.0125 0.0442 0.0306 0.0272 0.0084 0.0299 0.0207 0.0184 0.0032 0.0114 0.0079 0.0070 0.0165 0.0584 0.0405 0.0360 0.0074 0.0263 0.0182 0.0162 0.0050 0.0178 0.0123 0.0110 0.0019 0.0068 0.0047 0.0042 0.0098 0.0347 0.0241 0.0214 0.0167 0.0103 0.0032 0.0113 0.0078 0.0070 0.0043 0.0030 0.0027 0.0062 0.0221 0.0153 0.0136 Rate Heterogeneity Model: 2 nonsynonymous rate categories, rate and proportion of each estimated (this is effectively the M3 model of PAML) dN/dS Proportion 0.2500 0.5000 0.5000 0.5000 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 4.461 lnL Optimizing branchlengths... improved 0.701 lnL 7 8 9 10 11 Initial ln Likelihood: -215.8071 optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters... pass 1:+ 6.388 (branch= 0.00 scale= 0.44 omega= 0.01 rel rates= 5.93) pass 2:+ 0.434 (branch= 0.00 scale= 0.00 omega= 0.01 rel rates= 0.42) lnL after optimization: -208.9856 gen current_lnL precision last_tree_imp 0 -208.9856 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.586, AG = 3.999, AT = 0.040, CG = 2.453, CT = 3.999, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0094 0.0334 0.0231 0.0206 0.0064 0.0226 0.0157 0.0139 0.0024 0.0086 0.0060 0.0053 0.0125 0.0442 0.0306 0.0272 0.0125 0.0442 0.0306 0.0272 0.0084 0.0299 0.0207 0.0184 0.0032 0.0114 0.0079 0.0070 0.0165 0.0584 0.0405 0.0360 0.0074 0.0263 0.0182 0.0162 0.0050 0.0178 0.0123 0.0110 0.0019 0.0068 0.0047 0.0042 0.0098 0.0347 0.0241 0.0214 0.0167 0.0103 0.0032 0.0113 0.0078 0.0070 0.0043 0.0030 0.0027 0.0062 0.0221 0.0153 0.0136 Rate Heterogeneity Model: 2 nonsynonymous rate categories, rate and proportion of each estimated (this is effectively the M3 model of PAML) dN/dS Proportion 0.0490 0.5030 0.4995 0.4970 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.c.M3x2.sitelikes.log ... WARNING: Site likelihoods being output on prematurely terminated search ... NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -208.2373 Parameter estimates: w(0) p(0) w(1) p(1) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) rep 1: 0.049 0.503 0.499 0.497 1.586 3.999 0.04 2.453 3.999 1 Treelengths: TL rep 1: 9.626 Saving final tree from best search rep (#1) to out.c.M3x2.best.tre Inferring internal state probabilities on best tree... saving to file out.c.M3x2.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.c.M3x2.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found 11 instead at line 1, column (approximately) 4 (file position 3) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 16, column (approximately) 1 (file position 470) storing implied block: TAXA storing read block: TREES TREEFILES PASS Running output test c Running output test c Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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: -213.0377 gen current_lnL precision last_tree_imp 0 -213.0377 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) = 0.130452 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 : -210.2320 Parameter estimates: w(0) p(0) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) rep 1: 0.130 1.000 2.468 4.008 0.588 2.683 2.283 1 Treelengths: TL rep 1: 8.650 Saving final tree from best search rep (#1) to out.c.best.tre Inferring internal state probabilities on best tree... saving to file out.c.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.c.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found 11 instead at line 1, column (approximately) 4 (file position 3) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 16, column (approximately) 1 (file position 470) storing implied block: TAXA storing read block: TREES TREEFILES PASS Running output test n.G3 Running output test n.G3 Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./output/n.G3.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.3 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0603 0.3028 0.4894 0.3028 2.4503 0.3028 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.004 lnL Optimizing branchlengths... improved 0.000 lnL 7 8 9 10 11 Initial ln Likelihood: -226.8217 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 3.951 (branch= 0.75 scale= 0.00 alpha= 0.00 freqs= 1.76 rel rates= 1.44 pinv= 0.00) pass 2:+ 0.586 (branch= 0.56 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.00) pass 3:+ 1.297 (branch= 0.66 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.61 pinv= 0.00) pass 4:+ 0.021 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.02 rel rates= 0.00 pinv= 0.00) lnL after optimization: -220.9660 gen current_lnL precision last_tree_imp 0 -220.9660 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.002, AG = 3.998, AT = 0.998, CG = 2.322, CT = 3.998, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2184 0.3566 0.2049 0.2201 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.5025 with an invariant (invariable) site category, proportion estimated 0.0892 Substitution rate categories under this model: rate proportion 0.0000 0.0892 0.0610 0.3036 0.4913 0.3036 2.4477 0.3036 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.n.G3.sitelikes.log ... WARNING: Site likelihoods being output on prematurely terminated search ... NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -220.9571 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 1.002 3.998 0.998 2.322 3.998 1 0.218 0.357 0.205 0.220 0.502 0.089 Treelengths: TL rep 1: 2.169 Saving final tree from best search rep (#1) to out.n.G3.best.tre Inferring internal state probabilities on best tree... saving to file out.n.G3.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.n.G3.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found 11 instead at line 1, column (approximately) 4 (file position 3) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 16, column (approximately) 1 (file position 470) storing implied block: TAXA storing read block: TREES storing read block: PAUP TREEFILES PASS Running output test n.G4 Running output test n.G4 Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./output/n.G4.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1-4 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0334 0.2271 0.2519 0.2271 0.8203 0.2271 2.8944 0.2271 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.005 lnL Optimizing branchlengths... improved 0.292 lnL 7 8 9 10 11 Initial ln Likelihood: -226.2799 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 5.831 (branch= 2.05 scale= 0.00 alpha= 0.00 freqs= 1.45 rel rates= 2.33 pinv= 0.00) pass 2:+ 0.107 (branch= 0.07 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.00) lnL after optimization: -220.3414 gen current_lnL precision last_tree_imp 0 -220.3414 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.001, AG = 2.400, AT = 0.589, CG = 1.512, CT = 4.001, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2259 0.3629 0.1852 0.2261 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5015 with an invariant (invariable) site category, proportion estimated 0.0902 Substitution rate categories under this model: rate proportion 0.0000 0.0902 0.0337 0.2275 0.2529 0.2275 0.8214 0.2275 2.8921 0.2275 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.n.G4.sitelikes.log ... WARNING: Site likelihoods being output on prematurely terminated search ... NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -217.4380 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 1.001 2.4 0.589 1.512 4.001 1 0.226 0.363 0.185 0.226 0.501 0.090 Treelengths: TL rep 1: 1.694 Saving final tree from best search rep (#1) to out.n.G4.best.tre Inferring internal state probabilities on best tree... saving to file out.n.G4.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.n.G4.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found 11 instead at line 1, column (approximately) 4 (file position 3) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 16, column (approximately) 1 (file position 470) storing implied block: TAXA storing read block: TREES storing read block: PAUP TREEFILES PASS Running output test n Running output test n Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./output/n.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.1 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 2 3 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 3.458 lnL 7 8 9 10 11 Initial ln Likelihood: -225.5327 optimizing: starting branch lengths, rel rates, eq freqs... pass 1:+ 7.466 (branch= 0.77 scale= 0.00 freqs= 0.02 rel rates= 6.68) pass 2:+ 0.468 (branch= 0.45 scale= 0.00 freqs= 0.02 rel rates= 0.00) lnL after optimization: -217.5990 gen current_lnL precision last_tree_imp 0 -217.5990 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.511, AG = 3.999, AT = 0.200, CG = 2.619, CT = 2.047, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2300 0.3205 0.1884 0.2611 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.n.sitelikes.log ... WARNING: Site likelihoods being output on prematurely terminated search ... NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -217.2394 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 1.511 3.999 0.1995 2.619 2.047 1 0.230 0.321 0.188 0.261 Treelengths: TL rep 1: 1.686 Saving final tree from best search rep (#1) to out.n.best.tre Inferring internal state probabilities on best tree... saving to file out.n.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.n.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found 11 instead at line 1, column (approximately) 4 (file position 3) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 16, column (approximately) 1 (file position 470) storing implied block: TAXA storing read block: TREES storing read block: PAUP TREEFILES PASS Running output test n.wackyNames Running output test n.wackyNames Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./output/n.wackyNames.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x30.wackyNames.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.1 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 3.458 lnL 7 8 9 10 11 Initial ln Likelihood: -225.5327 optimizing: starting branch lengths, rel rates, eq freqs... pass 1:+ 7.466 (branch= 0.77 scale= 0.00 freqs= 0.02 rel rates= 6.68) pass 2:+ 0.468 (branch= 0.45 scale= 0.00 freqs= 0.02 rel rates= 0.00) lnL after optimization: -217.5990 gen current_lnL precision last_tree_imp 0 -217.5990 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.511, AG = 3.999, AT = 0.200, CG = 2.619, CT = 2.047, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2300 0.3205 0.1884 0.2611 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.n.sitelikes.log ... WARNING: Site likelihoods being output on prematurely terminated search ... NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -217.2394 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 1.511 3.999 0.1995 2.619 2.047 1 0.230 0.321 0.188 0.261 Treelengths: TL rep 1: 1.686 Saving final tree from best search rep (#1) to out.n.best.tre ####################################################### cat: out.n.wackyNames.best.tre: No such file or directory [Reading test.out.n.wackyNames.nex ] Executing storing implied block: TAXA storing read block: DATA TREEFILES PASS Running output test p.3diff Running output test p.3diff Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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:+ 77.990 (branch= 2.27 scale= 0.00 alpha= 4.14 freqs= 11.22 rel rates= 3.32 pinv= 0.86 subset rates= 56.18) pass 3:+ 48.437 (branch= 6.88 scale= 0.73 alpha= 4.15 freqs= 1.22 rel rates= 1.34 pinv= 0.01 subset rates= 34.10) pass 4:+ 15.263 (branch= 0.00 scale= 0.79 alpha= 0.64 freqs= 1.21 rel rates= 0.57 pinv= 0.01 subset rates= 12.04) pass 5:+ 5.799 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.10 rel rates= 0.77 pinv= 0.02 subset rates= 4.91) pass 6:+ 0.133 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.10 rel rates= 0.01 pinv= 0.01 subset rates= 0.00) lnL after optimization: -13342.5949 gen current_lnL precision last_tree_imp 0 -13342.5949 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) AC = 1.951, AG = 2.401, AT = 1.336, CG = 1.336, CT = 3.999, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3134 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 = 6.053, AT = 1.216, CG = 6.053, 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 0.3384 Substitution rate categories under this model: rate proportion 0.0089 0.2500 0.1345 0.2500 0.6550 0.2500 3.2015 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 = 2.520, CG = 0.377, CT = 4.110, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1591 0.3524 0.2842 0.2043 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 4.0328 with an invariant (invariable) site category, proportion estimated 0.0231 Substitution rate categories under this model: rate proportion 0.0000 0.0231 0.4562 0.2442 0.7763 0.2442 1.0844 0.2442 1.6831 0.2442 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 : -13324.2768 Parameter estimates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha rep 1: 1.951 2.401 1.336 1.336 3.999 1 0.313 0.176 0.299 0.212 0.366 Partition model subset 2: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha rep 1: 3.969 6.053 1.216 6.053 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 2.52 0.3775 4.11 1 0.159 0.352 0.284 0.204 4.033 0.023 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 1.695 0.538 0.326 2.137 Saving final tree from best search rep (#1) to out.p.3diff.best.tre Inferring internal state probabilities on best tree... saving to file out.p.3diff.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.p.3diff.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: SETS storing read block: ASSUMPTIONS storing read block: TREES TREEFILES PASS Running output test p.mkvO.ssr Running output test p.mkvO.ssr Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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:+ 1.162 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.156 (branch= 0.12 scale= 0.00 subset rates= 0.03) pass 6:+ 0.044 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 7:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -474.8632 gen current_lnL precision last_tree_imp 0 -474.8632 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 : -474.8624 (best) Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.474 0.599 2.020 2.815 Saving final tree from best search rep (#1) to out.p.mkvO.ssr.best.tre ####################################################### >>>Search rep 2 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1351934195 Initial ln Likelihood: -668.6258 optimizing: starting branch lengths, subset rates... pass 1:+ 167.892 (branch= 157.14 scale= 1.13 subset rates= 9.62) pass 2:+ 19.859 (branch= 15.03 scale= 0.02 subset rates= 4.81) pass 3:+ 5.107 (branch= 3.29 scale= 0.00 subset rates= 1.82) pass 4:+ 0.826 (branch= 0.20 scale= 0.00 subset rates= 0.62) pass 5:+ 0.065 (branch= 0.04 scale= 0.00 subset rates= 0.03) pass 6:+ 0.027 (branch= 0.03 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -474.8510 gen current_lnL precision last_tree_imp 0 -474.8510 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 : -474.8624 Replicate 2 : -474.8503 (best) Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.474 0.599 2.020 2.815 rep 2: 4.516 0.599 2.013 2.840 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:+ 0.941 (branch= 0.38 scale= 0.00 subset rates= 0.56) pass 5:+ 0.205 (branch= 0.17 scale= 0.00 subset rates= 0.03) 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: -474.8930 gen current_lnL precision last_tree_imp 0 -474.8930 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 2.83 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 : -474.8624 Replicate 2 : -474.8503 (best) Replicate 3 : -474.8837 Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.474 0.599 2.020 2.815 rep 2: 4.516 0.599 2.013 2.840 rep 3: 4.460 0.600 2.011 2.833 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:+ 0.365 (branch= 0.33 scale= 0.00 subset rates= 0.03) pass 6:+ 0.111 (branch= 0.11 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -474.8509 gen current_lnL precision last_tree_imp 0 -474.8509 0.010 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.60 2.01 2.86 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 5 branches were collapsed. NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 4 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -474.8624 Replicate 2 : -474.8503 Replicate 3 : -474.8837 Replicate 4 : -474.8494 (best) Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.474 0.599 2.020 2.815 rep 2: 4.516 0.599 2.013 2.840 rep 3: 4.460 0.600 2.011 2.833 rep 4: 4.504 0.598 2.009 2.858 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:+ 2.470 (branch= 0.79 scale= 0.00 subset rates= 1.68) pass 4:+ 0.825 (branch= 0.23 scale= 0.01 subset rates= 0.58) pass 5:+ 0.169 (branch= 0.13 scale= 0.00 subset rates= 0.04) pass 6:+ 0.011 (branch= 0.01 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -474.9108 gen current_lnL precision last_tree_imp 0 -474.9108 0.010 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.60 2.02 2.84 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 4 branches were collapsed. NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 5 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -474.8624 Replicate 2 : -474.8503 Replicate 3 : -474.8837 Replicate 4 : -474.8494 (best) Replicate 5 : -474.9075 Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.474 0.599 2.020 2.815 rep 2: 4.516 0.599 2.013 2.840 rep 3: 4.460 0.600 2.011 2.833 rep 4: 4.504 0.598 2.009 2.858 rep 5: 4.499 0.597 2.020 2.843 Saving final trees from all search reps to out.p.mkvO.ssr.best.all.tre Saving final tree from best search rep (#4) to out.p.mkvO.ssr.best.tre ####################################################### [Reading test.out.p.mkvO.ssr.nex ] Executing Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS storing read block: ASSUMPTIONS storing read block: TREES TREEFILES PASS ************************** Running checkpoint tests ... ************************** Running checkpoint test ./check/a.G3.conf Running checkpoint test ./check/a.G3.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 664, seed 1398765731, best lnL -90.230 gen current_lnL precision last_tree_imp 664 -90.2302 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 NOTE: ****Specified generation limit (1000) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0165 0.0083 0.0496 0.0909 0.0909 0.0083 0.0744 0.0083 0.0083 0.1074 0.1157 0.0248 0.1240 0.0331 0.0083 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.9045 with an invariant (invariable) site category, proportion estimated 0.1355 Substitution rate categories under this model: rate proportion 0.0000 0.1355 0.1669 0.2882 0.6855 0.2882 2.1476 0.2882 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -88.8871 Parameter estimates: alpha pinv rep 1: 0.904 0.136 Treelengths: TL rep 1: 2.441 Saving best tree to bootstrap file ch.a.G3.boot.tre WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/a.G4.conf Running checkpoint test ./check/a.G4.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 487, seed 147137001, best lnL -111.824 gen current_lnL precision last_tree_imp 487 -111.8239 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 -110.5065 0.010 707 NOTE: ****Specified generation limit (1000) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0165 0.0083 0.0496 0.0909 0.0909 0.0083 0.0744 0.0083 0.0083 0.1074 0.1157 0.0248 0.1240 0.0331 0.0083 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 1.3049 with an invariant (invariable) site category, proportion estimated 0.0988 Substitution rate categories under this model: rate proportion 0.0000 0.0988 0.1936 0.2253 0.5525 0.2253 1.0366 0.2253 2.2174 0.2253 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. Saving site likelihoods to file ch.a.G4.sitelikes.log ... WARNING: Site likelihoods being output on prematurely terminated search ... NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -110.5065 Parameter estimates: alpha pinv rep 1: 1.305 0.099 Treelengths: TL rep 1: 2.534 Saving final tree from best search rep (#1) to ch.a.G4.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.G4.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### TREEFILES PASS Running checkpoint test ./check/a.conf Running checkpoint test ./check/a.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 1596, seed 1731679210, best lnL -111.682 gen current_lnL precision last_tree_imp 1596 -111.6819 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 : -111.6819 Parameter estimates: Model contains no estimated parameters Treelengths: TL rep 1: 2.606 Saving final tree from best search rep (#1) to ch.a.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.internalstates.log ####################################################### TREEFILES PASS Running checkpoint test ./check/c.M3x2.conf Running checkpoint test ./check/c.M3x2.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 NOTE: ****Specified time limit (10 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 29, seed 2029909503, best lnL -205.650 gen current_lnL precision last_tree_imp 29 -205.6499 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 NOTE: ****Specified generation limit (100) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.586, AG = 3.999, AT = 0.040, CG = 2.453, CT = 3.968, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0094 0.0334 0.0231 0.0206 0.0064 0.0226 0.0157 0.0139 0.0024 0.0086 0.0060 0.0053 0.0125 0.0442 0.0306 0.0272 0.0125 0.0442 0.0306 0.0272 0.0084 0.0299 0.0207 0.0184 0.0032 0.0114 0.0079 0.0070 0.0165 0.0584 0.0405 0.0360 0.0074 0.0263 0.0182 0.0162 0.0050 0.0178 0.0123 0.0110 0.0019 0.0068 0.0047 0.0042 0.0098 0.0347 0.0241 0.0214 0.0167 0.0103 0.0032 0.0113 0.0078 0.0070 0.0043 0.0030 0.0027 0.0062 0.0221 0.0153 0.0136 Rate Heterogeneity Model: 2 nonsynonymous rate categories, rate and proportion of each estimated (this is effectively the M3 model of PAML) dN/dS Proportion 0.0490 0.5211 0.4995 0.4789 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file ch.c.M3x2.sitelikes.log ... WARNING: Site likelihoods being output on prematurely terminated search ... NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -205.3829 Parameter estimates: w(0) p(0) w(1) p(1) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) rep 1: 0.049 0.521 0.499 0.479 1.586 3.999 0.04 2.453 3.968 1 Treelengths: TL rep 1: 7.371 Saving final tree from best search rep (#1) to ch.c.M3x2.best.tre Inferring internal state probabilities on best tree... saving to file ch.c.M3x2.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### TREEFILES PASS Running checkpoint test ./check/c.conf Running checkpoint test ./check/c.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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: -195.4001 gen current_lnL precision last_tree_imp 0 -195.4001 0.500 0 10 -195.3555 0.500 0 20 -195.3342 0.500 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 21, seed 950885006, best lnL -195.296 gen current_lnL precision last_tree_imp 21 -195.2958 0.500 0 30 -195.2777 0.500 0 40 -195.2556 0.500 0 50 -195.2139 0.500 0 60 -195.1631 0.500 0 70 -195.0044 0.500 0 80 -194.9480 0.500 0 90 -194.9094 0.500 0 100 -194.9094 0.500 0 NOTE: ****Specified generation limit (100) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 61 (codon data, standard code) One estimated dN/dS ratio (aka omega) = 0.120506 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.637, AG = 5.679, AT = 0.011, CG = 4.174, CT = 2.324, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) 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 : -194.9094 Parameter estimates: w(0) p(0) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) rep 1: 0.121 1.000 1.637 5.679 0.01146 4.174 2.324 1 Treelengths: TL rep 1: 9.255 Saving best tree to bootstrap file ch.c.boot.tre WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/g.dnaBnoZ.conf Running checkpoint test ./check/g.dnaBnoZ.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 -3356.5910 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 0.833 lnL Optimizing branchlengths... improved 0.085 lnL 1100 -3352.7168 0.010 0 1200 -3352.6373 0.010 0 1300 -3352.5144 0.010 0 1400 -3352.4046 0.010 0 1500 -3352.3996 0.010 0 1600 -3352.2933 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 1623, seed 1001019763, best lnL -3352.293 gen current_lnL precision last_tree_imp 1623 -3352.2933 0.010 0 1700 -3352.2857 0.010 0 1800 -3352.2040 0.010 0 1900 -3351.8438 0.010 0 2000 -3351.7704 0.010 0 2100 -3351.6146 0.010 0 2200 -3351.3691 0.010 0 2300 -3351.3430 0.010 0 2400 -3351.3354 0.010 0 2500 -3351.2335 0.010 0 2600 -3351.1680 0.010 0 2700 -3351.1678 0.010 0 2800 -3351.1163 0.010 0 2900 -3351.1148 0.010 0 3000 -3351.1107 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... Current score = -3351.1107 Performing final optimizations... pass 1 : -3351.0504 (branch= 0.0000 alpha= 0.0000 pinv= 0.0227 eq freqs= 0.0001 rel rates= 0.0374 subset rates= 0.0000) pass 2 : -3350.9515 (branch= 0.0000 alpha= 0.0117 pinv= 0.0195 eq freqs= 0.0100 rel rates= 0.0578 subset rates= 0.0000) pass 3 : -3350.8639 (branch= 0.0032 alpha= 0.0186 pinv= 0.0171 eq freqs= 0.0020 rel rates= 0.0467 subset rates= 0.0000) pass 4 : -3350.7872 (branch= 0.0033 alpha= 0.0186 pinv= 0.0153 eq freqs= 0.0000 rel rates= 0.0380 subset rates= 0.0014) pass 5 : -3350.7193 (branch= 0.0062 alpha= 0.0142 pinv= 0.0147 eq freqs= 0.0010 rel rates= 0.0303 subset rates= 0.0016) pass 6 : -3350.6611 (branch= 0.0042 alpha= 0.0129 pinv= 0.0137 eq freqs= 0.0002 rel rates= 0.0271 subset rates= 0.0000) pass 7 : -3350.6090 (branch= 0.0008 alpha= 0.0126 pinv= 0.0124 eq freqs= 0.0002 rel rates= 0.0240 subset rates= 0.0021) pass 8 : -3350.5641 (branch= 0.0022 alpha= 0.0116 pinv= 0.0114 eq freqs= 0.0000 rel rates= 0.0196 subset rates= 0.0000) pass 9 : -3350.5232 (branch= 0.0004 alpha= 0.0105 pinv= 0.0103 eq freqs= 0.0001 rel rates= 0.0181 subset rates= 0.0014) pass 10: -3350.4872 (branch= 0.0014 alpha= 0.0097 pinv= 0.0100 eq freqs= 0.0000 rel rates= 0.0148 subset rates= 0.0000) pass 11: -3350.4563 (branch= 0.0002 alpha= 0.0087 pinv= 0.0085 eq freqs= 0.0000 rel rates= 0.0134 subset rates= 0.0000) pass 12: -3350.4285 (branch= 0.0000 alpha= 0.0083 pinv= 0.0076 eq freqs= 0.0000 rel rates= 0.0118 subset rates= 0.0000) pass 13: -3350.4038 (branch= 0.0000 alpha= 0.0076 pinv= 0.0068 eq freqs= 0.0000 rel rates= 0.0102 subset rates= 0.0000) pass 14: -3350.3810 (branch= 0.0000 alpha= 0.0068 pinv= 0.0061 eq freqs= 0.0000 rel rates= 0.0088 subset rates= 0.0010) pass 15: -3350.3621 (branch= 0.0006 alpha= 0.0058 pinv= 0.0055 eq freqs= 0.0000 rel rates= 0.0070 subset rates= 0.0000) pass 16: -3350.3458 (branch= 0.0001 alpha= 0.0051 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0064 subset rates= 0.0000) pass 17: -3350.3312 (branch= 0.0000 alpha= 0.0047 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0056 subset rates= 0.0000) pass 18: -3350.3181 (branch= 0.0000 alpha= 0.0042 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0050 subset rates= 0.0000) pass 19: -3350.3068 (branch= 0.0000 alpha= 0.0038 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0042 subset rates= 0.0000) pass 20: -3350.2969 (branch= 0.0000 alpha= 0.0033 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0036 subset rates= 0.0000) optimization up to ... pass 30: -3350.2472 (branch= 0.0000 alpha= 0.0167 pinv= 0.0151 eq freqs= 0.0000 rel rates= 0.0178 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= 0.0042 subset rates= 0.0000) optimization up to ... pass 50: -3350.2336 (branch= 0.0000 alpha= 0.0007 pinv= 0.0006 eq freqs= 0.0000 rel rates= 0.0011 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= 0.0002 subset rates= 0.0000) optimization up to ... pass 69: -3350.2330 (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 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 = 10.419, AT = 2.691, CG = 0.001, CT = 21.942, 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 0.3657 Substitution rate categories under this model: rate proportion 0.0000 0.3657 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 2.691 0.001 21.94 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 1.821 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 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 550, seed 1321880065, best lnL -3323.456 gen current_lnL precision last_tree_imp 550 -3323.4558 0.500 1 600 -3323.3460 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 : -3320.2618 (branch= 0.0468 alpha= 0.0000 pinv= 0.0155 eq freqs= 0.0001 rel rates= 0.5580 ins/del rates= 0.0166) pass 2 : -3319.8081 (branch= 0.0688 alpha= 0.0064 pinv= 0.0159 eq freqs= 0.0000 rel rates= 0.3444 ins/del rates= 0.0180) pass 3 : -3319.4760 (branch= 0.0417 alpha= 0.0093 pinv= 0.0157 eq freqs= 0.0000 rel rates= 0.2467 ins/del rates= 0.0187) pass 4 : -3319.2094 (branch= 0.0263 alpha= 0.0091 pinv= 0.0154 eq freqs= 0.0020 rel rates= 0.2036 ins/del rates= 0.0102) pass 5 : -3318.9875 (branch= 0.0185 alpha= 0.0103 pinv= 0.0147 eq freqs= 0.0013 rel rates= 0.1695 ins/del rates= 0.0076) pass 6 : -3318.8026 (branch= 0.0134 alpha= 0.0096 pinv= 0.0138 eq freqs= 0.0013 rel rates= 0.1411 ins/del rates= 0.0057) pass 7 : -3318.6460 (branch= 0.0086 alpha= 0.0103 pinv= 0.0129 eq freqs= 0.0003 rel rates= 0.1208 ins/del rates= 0.0036) pass 8 : -3318.5179 (branch= 0.0056 alpha= 0.0100 pinv= 0.0121 eq freqs= 0.0002 rel rates= 0.0978 ins/del rates= 0.0024) pass 9 : -3318.4102 (branch= 0.0037 alpha= 0.0098 pinv= 0.0112 eq freqs= 0.0002 rel rates= 0.0811 ins/del rates= 0.0016) pass 10: -3318.3188 (branch= 0.0024 alpha= 0.0095 pinv= 0.0109 eq freqs= 0.0002 rel rates= 0.0673 ins/del rates= 0.0010) pass 11: -3318.2440 (branch= 0.0016 alpha= 0.0089 pinv= 0.0094 eq freqs= 0.0002 rel rates= 0.0540 ins/del rates= 0.0007) pass 12: -3318.1805 (branch= 0.0011 alpha= 0.0083 pinv= 0.0086 eq freqs= 0.0001 rel rates= 0.0449 ins/del rates= 0.0005) pass 13: -3318.1264 (branch= 0.0007 alpha= 0.0078 pinv= 0.0078 eq freqs= 0.0001 rel rates= 0.0374 ins/del rates= 0.0003) pass 14: -3318.0803 (branch= 0.0004 alpha= 0.0073 pinv= 0.0071 eq freqs= 0.0001 rel rates= 0.0309 ins/del rates= 0.0002) pass 15: -3318.0412 (branch= 0.0003 alpha= 0.0066 pinv= 0.0064 eq freqs= 0.0001 rel rates= 0.0256 ins/del rates= 0.0001) pass 16: -3318.0076 (branch= 0.0002 alpha= 0.0060 pinv= 0.0058 eq freqs= 0.0001 rel rates= 0.0215 ins/del rates= 0.0001) pass 17: -3317.9782 (branch= 0.0001 alpha= 0.0054 pinv= 0.0052 eq freqs= 0.0001 rel rates= 0.0185 ins/del rates= 0.0000) pass 18: -3317.9528 (branch= 0.0001 alpha= 0.0049 pinv= 0.0046 eq freqs= 0.0000 rel rates= 0.0157 ins/del rates= 0.0000) pass 19: -3317.9308 (branch= 0.0000 alpha= 0.0044 pinv= 0.0041 eq freqs= 0.0000 rel rates= 0.0134 ins/del rates= 0.0000) pass 20: -3317.9117 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0115 ins/del rates= 0.0000) optimization up to ... pass 30: -3317.8164 (branch= 0.0001 alpha= 0.0213 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= 0.0002 ins/del rates= 0.0000) optimization up to ... pass 73: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3317.7871 Time used so far = 0 hours, 0 minutes and 13 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 3.067, AG = 10.272, AT = 2.658, CG = 0.001, CT = 21.556, 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 0.5746 with an invariant (invariable) site category, proportion estimated 0.3612 Substitution rate categories under this model: rate proportion 0.0000 0.3612 0.0479 0.1597 0.2978 0.1597 0.8678 0.1597 2.7865 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: 3.067 10.27 2.658 0.001 21.56 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del rep 1: 0.036 0.158 **ins = proportion of columns that experienced an insertion **del = deletion rate relative to nucleotide substitution rate Treelengths: TL rep 1: 1.419 Saving final tree from best search rep (#1) to ch.g.dnaMix.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/n.G3.conf Running checkpoint test ./check/n.G3.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 -211.1653 0.010 1104 1400 -211.1319 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 -210.8863 0.010 1104 2600 -210.8436 0.010 1104 2800 -210.8250 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 -210.6492 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 -210.5133 0.010 1104 5800 -210.4816 0.010 1104 6000 -210.4626 0.010 1104 6200 -210.4591 0.010 1104 6400 -210.4379 0.010 1104 6600 -210.4141 0.010 1104 6800 -210.3876 0.010 1104 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 6807, seed 343516762, best lnL -210.388 gen current_lnL precision last_tree_imp 6807 -210.3876 0.010 1104 6900 -210.3335 0.010 1104 7000 -210.3298 0.010 1104 7100 -210.3072 0.010 1104 7200 -210.2823 0.010 1104 7300 -210.2573 0.010 1104 7400 -210.2490 0.010 1104 7500 -210.2258 0.010 1104 7600 -210.2188 0.010 1104 7700 -210.1885 0.010 1104 7800 -210.1675 0.010 1104 7900 -210.1664 0.010 1104 8000 -210.1658 0.010 1104 8100 -210.1138 0.010 1104 8200 -210.1029 0.010 1104 8300 -210.0913 0.010 1104 8400 -210.0890 0.010 1104 8500 -210.0862 0.010 1104 8600 -210.0634 0.010 1104 8700 -210.0288 0.010 1104 8800 -210.0035 0.010 8716 8900 -210.0028 0.010 8716 9000 -209.9601 0.010 8716 9100 -209.9395 0.010 8716 9200 -209.9370 0.010 8716 9300 -209.9252 0.010 8716 9400 -209.9226 0.010 8716 9500 -209.9207 0.010 8716 9600 -209.9191 0.010 8716 9700 -209.9035 0.010 8716 9800 -209.8885 0.010 8716 9900 -209.8794 0.010 8716 10000 -209.8437 0.010 8716 Optimizing parameters... improved 0.519 lnL Optimizing branchlengths... improved 0.016 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 = 5.724, AG = 9.823, AT = 0.264, CG = 10.186, CT = 15.625, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2335 0.3288 0.2091 0.2286 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 4.4640 with an invariant (invariable) site category, proportion estimated 0.2923 Substitution rate categories under this model: rate proportion 0.0000 0.2923 0.5336 0.2359 0.9309 0.2359 1.5355 0.2359 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 : -209.3089 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: 5.724 9.823 0.2637 10.19 15.62 1 0.233 0.329 0.209 0.229 4.464 0.292 Treelengths: TL rep 1: 2.261 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 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 0.320 lnL 1000 -167.2068 0.010 843 1200 -167.1476 0.010 843 1400 -167.0487 0.010 843 1600 -166.9641 0.010 843 1800 -166.8222 0.010 843 2000 -166.6788 0.010 843 2200 -166.5887 0.010 843 2400 -166.4579 0.010 843 2600 -166.3862 0.010 843 2800 -166.3657 0.010 843 3000 -166.3070 0.010 843 3200 -166.2787 0.010 843 3400 -166.2099 0.010 843 3600 -166.0618 0.010 843 3800 -165.9521 0.010 843 4000 -165.9340 0.010 843 4200 -165.8876 0.010 843 4400 -165.8800 0.010 843 4600 -165.7809 0.010 843 4800 -165.7682 0.010 843 5000 -165.6807 0.010 843 5200 -165.6629 0.010 843 5400 -165.5966 0.010 843 5600 -165.4767 0.010 843 5800 -165.3754 0.010 843 6000 -165.2856 0.010 843 6200 -165.2442 0.010 6021 6400 -165.1354 0.010 6021 6600 -165.0479 0.010 6021 6800 -165.0428 0.010 6021 7000 -164.8383 0.010 6021 7200 -164.6664 0.010 6021 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 7358, seed 1864093106, best lnL -164.661 gen current_lnL precision last_tree_imp 7358 -164.6613 0.010 6021 7400 -164.6478 0.010 6021 7500 -164.6472 0.010 6021 7600 -164.5352 0.010 7573 7700 -164.4035 0.010 7573 7800 -164.3902 0.010 7573 7900 -164.3595 0.010 7573 8000 -164.3323 0.010 7573 8100 -164.1711 0.010 7573 8200 -164.1537 0.010 7573 8300 -164.0538 0.010 7573 8400 -164.0465 0.010 7573 8500 -164.0049 0.010 7573 8600 -163.9411 0.010 7573 8700 -163.8406 0.010 7573 8800 -163.8133 0.010 7573 8900 -163.8024 0.010 7573 9000 -163.7249 0.010 7573 9100 -163.7136 0.010 7573 9200 -163.7035 0.010 7573 9300 -163.6573 0.010 7573 9400 -163.6398 0.010 7573 9500 -163.5644 0.010 7573 9600 -163.5152 0.010 7573 9700 -163.4697 0.010 7573 9800 -163.4652 0.010 7573 9900 -163.4587 0.010 7573 10000 -163.4575 0.010 7573 Optimizing parameters... improved 1.431 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 = 0.785, AG = 10.721, AT = 2.714, CG = 4.252, CT = 44.709, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1323 0.4184 0.2444 0.2049 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 38.8673 with an invariant (invariable) site category, proportion estimated 0.3493 Substitution rate categories under this model: rate proportion 0.0000 0.3493 0.8041 0.1627 0.9408 0.1627 1.0445 0.1627 1.2106 0.1627 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 : -162.0150 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: 0.7854 10.72 2.714 4.252 44.71 1 0.132 0.418 0.244 0.205 38.867 0.349 Treelengths: TL rep 1: 3.333 Saving best tree to bootstrap file ch.n.G4.boot.tre WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/n.conf Running checkpoint test ./check/n.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./check/n.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.1 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 3.458 lnL 7 8 9 10 11 Initial ln Likelihood: -225.5327 optimizing: starting branch lengths, rel rates, eq freqs... pass 1:+ 7.466 (branch= 0.77 scale= 0.00 freqs= 0.02 rel rates= 6.68) pass 2:+ 0.468 (branch= 0.45 scale= 0.00 freqs= 0.02 rel rates= 0.00) lnL after optimization: -217.5990 gen current_lnL precision last_tree_imp 0 -217.5990 0.500 0 200 -215.8307 0.500 188 400 -214.8938 0.500 276 600 -214.3966 0.500 530 800 -214.1704 0.500 530 1000 -214.0528 0.500 530 Optimization precision reduced Optimizing parameters... improved 0.223 lnL Optimizing branchlengths... improved 0.080 lnL 1200 -213.6191 0.010 530 1400 -213.5800 0.010 530 1600 -213.5575 0.010 530 1800 -213.3951 0.010 530 2000 -213.3646 0.010 530 2200 -213.3318 0.010 530 2400 -213.2446 0.010 530 2600 -213.2282 0.010 530 2800 -213.2194 0.010 530 3000 -213.2002 0.010 530 3200 -213.1946 0.010 530 3400 -213.1682 0.010 530 3600 -213.1582 0.010 530 3800 -213.0252 0.010 3769 4000 -212.9704 0.010 3769 4200 -212.9483 0.010 3769 4400 -212.9234 0.010 3769 4600 -212.8794 0.010 3769 4800 -212.8766 0.010 3769 5000 -212.8761 0.010 3769 5200 -212.8556 0.010 3769 5400 -212.8534 0.010 3769 5600 -212.8186 0.010 3769 5800 -212.7686 0.010 3769 6000 -212.7264 0.010 3769 6200 -212.7248 0.010 3769 6400 -212.7245 0.010 3769 6600 -212.7155 0.010 3769 6800 -212.7057 0.010 3769 7000 -212.7025 0.010 3769 7200 -212.7020 0.010 3769 7400 -212.6750 0.010 3769 7600 -212.6702 0.010 3769 7800 -212.6661 0.010 3769 8000 -212.6646 0.010 3769 8200 -212.6594 0.010 3769 8400 -212.6591 0.010 3769 8600 -212.6390 0.010 3769 8800 -212.5865 0.010 3769 9000 -212.5495 0.010 3769 9200 -212.5341 0.010 3769 9400 -212.5173 0.010 3769 9600 -212.4987 0.010 3769 9800 -212.4933 0.010 3769 10000 -212.4848 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 = 8.254, AG = 15.546, AT = 0.648, CG = 15.522, CT = 10.081, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2186 0.2862 0.1832 0.3120 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.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 : -212.4848 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 8.254 15.55 0.6481 15.52 10.08 1 0.219 0.286 0.183 0.312 Treelengths: TL rep 1: 1.718 Saving final tree from best search rep (#1) to ch.n.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 -212.485 gen current_lnL precision last_tree_imp 10001 -212.4848 0.010 3769 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 8.254, AG = 15.546, AT = 0.648, CG = 15.522, CT = 10.081, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2186 0.2862 0.1832 0.3120 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.n.sitelikes.log ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -212.4848 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 8.254 15.55 0.6481 15.52 10.08 1 0.219 0.286 0.183 0.312 Treelengths: TL rep 1: 1.718 Saving final tree from best search rep (#1) to ch.n.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log ####################################################### TREEFILES PASS Running checkpoint test ./check/n.const.conf Running checkpoint test ./check/n.const.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./check/n.const.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### Loading constraints from file data/z.pos.const.tre Found 6 positively constrained bipartition(s) Bipartition 1: (1,2,3,5,6,7,8,9,10) | (4,11) Bipartition 2: (1,3,5,6,7,8,9,10) | (2,4,11) Bipartition 3: (1,5,6,7,8,9,10) | (2,3,4,11) Bipartition 4: (1,2,3,4,5,8,9,10,11) | (6,7) Bipartition 5: (1,2,3,4,5,8,9,11) | (6,7,10) Bipartition 6: (1,5) | (2,3,4,6,7,8,9,10,11) STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0334 0.2271 0.2519 0.2271 0.8203 0.2271 2.8944 0.2271 Starting with seed=1 creating likelihood stepwise addition starting tree (compatible with constraints)... number of taxa added: 4 5 6 Optimizing parameters... improved 0.006 lnL Optimizing branchlengths... improved 11.173 lnL 7 8 9 10 11 Initial ln Likelihood: -225.0726 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 5.893 (branch= 2.29 scale= 0.89 alpha= 0.00 freqs= 1.20 rel rates= 1.50 pinv= 0.00) pass 2:+ 0.035 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.00) lnL after optimization: -219.1445 gen current_lnL precision last_tree_imp 0 -219.1445 0.500 0 200 -217.4629 0.500 32 400 -216.6525 0.500 363 600 -216.1293 0.500 474 800 -215.4112 0.500 669 1000 -215.0098 0.500 936 1200 -214.3654 0.500 936 1400 -214.0189 0.500 936 Optimization precision reduced Optimizing parameters... improved 1.908 lnL Optimizing branchlengths... improved 0.702 lnL 1600 -211.2006 0.010 1502 1800 -211.0868 0.010 1502 2000 -210.9688 0.010 1502 2200 -210.8961 0.010 1502 2400 -210.8906 0.010 1502 2600 -210.8173 0.010 1502 2800 -210.7848 0.010 1502 3000 -210.7511 0.010 2883 3200 -210.7243 0.010 2883 3400 -210.7006 0.010 2883 3600 -210.6993 0.010 2883 3800 -210.6779 0.010 2883 4000 -210.6776 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 -210.5647 0.010 2883 5200 -210.5368 0.010 2883 5400 -210.5093 0.010 2883 5600 -210.4832 0.010 2883 5800 -210.3736 0.010 2883 6000 -210.3408 0.010 2883 6200 -210.3319 0.010 2883 6400 -210.3259 0.010 2883 6600 -210.2891 0.010 2883 6800 -210.2615 0.010 2883 7000 -210.2579 0.010 2883 7200 -210.2571 0.010 2883 7400 -210.2287 0.010 2883 7600 -210.2174 0.010 2883 7800 -210.1382 0.010 7783 8000 -210.1300 0.010 7783 8200 -210.1282 0.010 7783 8400 -210.1160 0.010 7783 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 8472, seed 1640621176, best lnL -210.081 gen current_lnL precision last_tree_imp 8472 -210.0809 0.010 7783 8500 -210.0806 0.010 7783 8600 -210.0640 0.010 7783 8700 -210.0387 0.010 7783 8800 -209.9972 0.010 7783 8900 -209.9879 0.010 7783 9000 -209.9556 0.010 7783 9100 -209.9410 0.010 7783 9200 -209.9334 0.010 7783 9300 -209.9309 0.010 7783 9400 -209.9300 0.010 7783 9500 -209.9156 0.010 7783 9600 -209.9156 0.010 7783 9700 -209.9019 0.010 7783 9800 -209.8954 0.010 7783 Reached termination condition! last topological improvement at gen 7783 Improvement over last 500 gen = 0.03545 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 2.485, AG = 4.605, AT = 0.214, CG = 4.762, CT = 8.462, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2433 0.3351 0.2122 0.2095 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 2.2903 with an invariant (invariable) site category, proportion estimated 0.2309 Substitution rate categories under this model: rate proportion 0.0000 0.2309 0.3256 0.1923 0.6827 0.1923 1.0758 0.1923 1.9159 0.1923 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 : -209.8954 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: 2.485 4.605 0.214 4.762 8.462 1 0.243 0.335 0.212 0.210 2.290 0.231 Treelengths: TL rep 1: 2.447 Saving final tree from best search rep (#1) to ch.n.const.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.const.internalstates.log ####################################################### TREEFILES PASS Running checkpoint test ./check/p.3diff.conf Running checkpoint test ./check/p.3diff.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./check/p.3diff.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.byPos.11x2178.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful Reading SETS block...storing read block: SETS successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #1 ("1stpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 4 Summary of data: 11 sequences. 441 constant characters. 171 parsimony-informative characters. 113 uninformative variable characters. 725 total characters. 237 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #2 ("2ndpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 5 Summary of data: 11 sequences. 527 constant characters. 90 parsimony-informative characters. 108 uninformative variable characters. 725 total characters. 158 unique patterns in compressed data matrix. GARLI data subset 3 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #3 ("3rdpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 6 Summary of data: 11 sequences. 102 constant characters. 507 parsimony-informative characters. 116 uninformative variable characters. 725 total characters. 548 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 11 MB good approx 10 MB to 9 MB low approx 8 MB to 5 MB very low approx 4 MB to 4 MB the minimum required availablememory is 4 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 16.0 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/p.3diff.start Reading TREES block...storing read block: TREES successful Reading GARLI block...storing read block: GARLI successful STARTING RUN Bootstrap reweighting... Subset 1: Random seed for bootstrap reweighting: 42 Subset 2: Random seed for bootstrap reweighting: 655766889 Subset 3: Random seed for bootstrap reweighting: 486988955 >>>Bootstrap rep 1 (of 1) <<< Obtained starting tree 1 from Nexus Obtained starting or fixed model parameter values from Nexus: MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) AC = 1.000, AG = 10.000, AT = 2.000, CG = 2.000, CT = 0.010, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3150 0.1749 0.3006 0.2095 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.6000 Substitution rate categories under this model: rate proportion 0.0531 0.2500 0.3123 0.2500 0.8813 0.2500 2.7533 0.2500 Model 2 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) AC = 4.000, AG = 4.000, AT = 1.000, CG = 4.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1000 0.2000 0.3000 0.4000 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.4000 Substitution rate categories under this model: rate proportion 0.0167 0.2500 0.1818 0.2500 0.7313 0.2500 3.0702 0.2500 Model 3 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) AC = 1.000, AG = 2.000, AT = 3.000, CG = 5.000, CT = 2.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.4000 0.2000 0.3000 0.1000 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0100 Substitution rate categories under this model: rate proportion 0.0000 0.0100 0.0334 0.2475 0.2519 0.2475 0.8203 0.2475 2.8944 0.2475 Subset rate multipliers: 0.54 0.30 2.16 Starting with seed=1 Initial ln Likelihood: -17331.1409 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates... pass 1:+ 3336.674 (branch=2061.91 scale= 45.13 alpha=125.85 freqs=435.78 rel rates=661.66 pinv= 0.00 subset rates= 6.34) pass 2:+ 338.355 (branch= 41.98 scale= 1.04 alpha= 22.50 freqs=192.29 rel rates= 77.24 pinv= 2.39 subset rates= 0.92) pass 3:+ 222.683 (branch= 0.46 scale= 0.67 alpha= 8.57 freqs= 98.23 rel rates=113.31 pinv= 0.80 subset rates= 0.64) pass 4:+ 44.580 (branch= 0.51 scale= 0.00 alpha= 1.57 freqs= 22.89 rel rates= 19.62 pinv= 0.00 subset rates= 0.00) pass 5:+ 8.682 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 4.12 rel rates= 4.53 pinv= 0.02 subset rates= 0.00) pass 6:+ 1.298 (branch= 0.59 scale= 0.00 alpha= 0.01 freqs= 0.65 rel rates= 0.01 pinv= 0.03 subset rates= 0.00) pass 7:+ 1.354 (branch= 0.00 scale= 0.49 alpha= 0.72 freqs= 0.12 rel rates= 0.02 pinv= 0.01 subset rates= 0.00) pass 8:+ 0.126 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.09 rel rates= 0.02 pinv= 0.01 subset rates= 0.00) lnL after optimization: -13377.3893 gen current_lnL precision last_tree_imp 0 -13377.3893 0.500 0 100 -13375.8793 0.500 0 200 -13373.8435 0.500 0 300 -13372.9677 0.500 0 400 -13371.8985 0.500 0 500 -13371.5864 0.500 0 Optimization precision reduced Optimizing parameters... improved 0.048 lnL Optimizing branchlengths... improved 0.000 lnL 600 -13371.2064 0.402 0 700 -13371.0754 0.402 0 800 -13370.9489 0.402 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 826, seed 1057179346, best lnL -13370.893 gen current_lnL precision last_tree_imp 826 -13370.8929 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 NOTE: ****Specified time limit (1 seconds) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) AC = 1.598, AG = 2.495, AT = 1.210, CG = 1.210, CT = 4.035, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3110 0.1818 0.3061 0.2010 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) 0.2791 0.1777 0.1601 0.3830 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.2460 Substitution rate categories under this model: rate proportion 0.0019 0.2500 0.0638 0.2500 0.4929 0.2500 3.4413 0.2500 Model 3 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) AC = 1.000, AG = 5.347, AT = 4.290, CG = 0.632, CT = 5.347, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1555 0.3460 0.2769 0.2216 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 4.1101 with an invariant (invariable) site category, proportion estimated 0.0486 Substitution rate categories under this model: rate proportion 0.0000 0.0486 0.4603 0.2379 0.7789 0.2379 1.0844 0.2379 1.6764 0.2379 Subset rate multipliers: 0.53 0.29 2.18 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. >>>Terminated Bootstrap rep 1 (of 1) <<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -13370.5606 (TERMINATED PREMATURELY) Parameter estimates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha rep 1: 1.598 2.495 1.21 1.21 4.035 1 0.311 0.182 0.306 0.201 0.364 Partition model subset 2: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha rep 1: 2.627 4.239 0.8212 4.239 2.627 1 0.279 0.178 0.160 0.383 0.246 Partition model subset 3: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 1 5.347 4.29 0.6325 5.347 1 0.156 0.346 0.277 0.222 4.110 0.049 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 1.772 0.530 0.287 2.183 Saving best tree to bootstrap file ch.p.3diff.boot.tre WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mk.ssr.conf Running checkpoint test ./check/p.mk.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./check/p.mk.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, modeled as Standard k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN >>>Search rep 1 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -609.1934 optimizing: starting branch lengths, subset rates... pass 1:+ 130.207 (branch= 124.97 scale= 0.94 subset rates= 4.29) pass 2:+ 9.055 (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:+ 0.304 (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: -467.8138 gen current_lnL precision last_tree_imp 0 -467.8138 0.010 0 100 -467.7847 0.010 76 200 -467.7757 0.010 76 300 -467.7641 0.010 76 400 -467.7601 0.010 76 500 -467.7562 0.010 76 600 -467.7484 0.010 76 700 -467.7453 0.010 76 800 -467.7426 0.010 76 900 -467.7420 0.010 76 1000 -467.7408 0.010 76 1100 -467.7395 0.010 76 1200 -467.7384 0.010 76 1300 -467.7383 0.010 76 1400 -467.7371 0.010 76 1500 -467.7350 0.010 76 1600 -467.7322 0.010 76 1700 -467.7288 0.010 76 1800 -467.7270 0.010 76 1900 -467.7270 0.010 76 2000 -467.7247 0.010 76 2100 -467.7240 0.010 76 2200 -467.7237 0.010 76 2300 -467.7235 0.010 76 2400 -467.7217 0.010 76 2500 -467.7212 0.010 76 2600 -467.7209 0.010 76 2700 -467.7204 0.010 76 2800 -467.7202 0.010 76 2900 -467.7200 0.010 76 3000 -467.7200 0.010 76 3100 -467.7184 0.010 76 3200 -467.7183 0.010 76 3300 -467.7165 0.010 76 3400 -467.7165 0.010 76 3500 -467.7162 0.010 76 3600 -467.7160 0.010 76 3700 -467.7160 0.010 76 3800 -467.7159 0.010 76 Reached termination condition! last topological improvement at gen 76 Improvement over last 500 gen = 0.00059 Current score = -467.7159 Performing final optimizations... pass 1 : -467.7120 (branch= 0.0000 subset rates= 0.0039) pass 2 : -467.6911 (branch= 0.0209 subset rates= 0.0000) pass 3 : -467.6869 (branch= 0.0042 subset rates= 0.0000) pass 4 : -467.6843 (branch= 0.0026 subset rates= 0.0000) pass 5 : -467.6817 (branch= 0.0026 subset rates= 0.0000) pass 6 : -467.6803 (branch= 0.0014 subset rates= 0.0000) pass 7 : -467.6795 (branch= 0.0007 subset rates= 0.0001) pass 8 : -467.6788 (branch= 0.0007 subset rates= 0.0000) pass 9 : -467.6786 (branch= 0.0002 subset rates= 0.0000) pass 10: -467.6784 (branch= 0.0002 subset rates= 0.0000) pass 11: -467.6783 (branch= 0.0001 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 = -467.6782 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 2.18 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. >>>Completed Search rep 1 (of 5)<<< >>>Search rep 2 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1831048457 Initial ln Likelihood: -637.1584 optimizing: starting branch lengths, subset rates... pass 1:+ 151.120 (branch= 144.13 scale= 2.32 subset rates= 4.67) pass 2:+ 14.959 (branch= 13.95 scale= 0.00 subset rates= 1.01) pass 3:+ 2.985 (branch= 2.78 scale= 0.01 subset rates= 0.19) pass 4:+ 0.213 (branch= 0.21 scale= 0.00 subset rates= 0.00) pass 5:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 6:+ 0.025 (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: -467.8409 gen current_lnL precision last_tree_imp 0 -467.8409 0.010 0 100 -467.8006 0.010 88 200 -467.7829 0.010 88 300 -467.7645 0.010 88 400 -467.7572 0.010 88 500 -467.7508 0.010 88 600 -467.7420 0.010 88 700 -467.7377 0.010 88 800 -467.7326 0.010 88 900 -467.7300 0.010 88 1000 -467.7251 0.010 88 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 1036, seed 1879992365, best lnL -467.722 gen current_lnL precision last_tree_imp 1036 -467.7221 0.010 88 1100 -467.7186 0.010 88 1200 -467.7174 0.010 88 1300 -467.7143 0.010 88 1400 -467.7139 0.010 88 1500 -467.7130 0.010 88 1600 -467.7128 0.010 88 1700 -467.7101 0.010 88 1800 -467.7076 0.010 88 1900 -467.7072 0.010 88 2000 -467.7065 0.010 88 2100 -467.7061 0.010 88 2200 -467.7057 0.010 88 2300 -467.7052 0.010 88 2400 -467.7043 0.010 88 2500 -467.7039 0.010 88 2600 -467.7039 0.010 88 2700 -467.7038 0.010 88 2800 -467.7036 0.010 88 2900 -467.7035 0.010 88 Reached termination condition! last topological improvement at gen 88 Improvement over last 500 gen = 0.00077 Current score = -467.7035 Performing final optimizations... pass 1 : -467.7035 (branch= 0.0000 subset rates= 0.0001) pass 2 : -467.6923 (branch= 0.0112 subset rates= 0.0000) pass 3 : -467.6861 (branch= 0.0060 subset rates= 0.0001) pass 4 : -467.6835 (branch= 0.0027 subset rates= 0.0000) pass 5 : -467.6821 (branch= 0.0013 subset rates= 0.0000) pass 6 : -467.6810 (branch= 0.0011 subset rates= 0.0000) pass 7 : -467.6801 (branch= 0.0009 subset rates= 0.0000) pass 8 : -467.6795 (branch= 0.0006 subset rates= 0.0000) pass 9 : -467.6792 (branch= 0.0003 subset rates= 0.0000) pass 10: -467.6789 (branch= 0.0002 subset rates= 0.0001) pass 11: -467.6788 (branch= 0.0002 subset rates= 0.0000) pass 12: -467.6787 (branch= 0.0001 subset rates= 0.0000) pass 13: -467.6787 (branch= 0.0000 subset rates= 0.0000) pass 14: -467.6787 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6787 Time used so far = 0 hours, 0 minutes and 8 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 1.47 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=387765568 Initial ln Likelihood: -629.3844 optimizing: starting branch lengths, subset rates... pass 1:+ 145.913 (branch= 138.38 scale= 3.36 subset rates= 4.18) pass 2:+ 12.537 (branch= 11.64 scale= 0.00 subset rates= 0.90) pass 3:+ 2.852 (branch= 2.62 scale= 0.06 subset rates= 0.18) pass 4:+ 0.211 (branch= 0.21 scale= 0.00 subset rates= 0.00) pass 5:+ 0.034 (branch= 0.03 scale= 0.00 subset rates= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -467.8378 gen current_lnL precision last_tree_imp 0 -467.8378 0.010 0 100 -467.8202 0.010 0 200 -467.7910 0.010 0 300 -467.7852 0.010 0 400 -467.7649 0.010 0 500 -467.7557 0.010 0 600 -467.7482 0.010 0 700 -467.7383 0.010 0 800 -467.7308 0.010 0 900 -467.7283 0.010 0 1000 -467.7269 0.010 0 1100 -467.7258 0.010 0 1200 -467.7235 0.010 0 1300 -467.7213 0.010 0 1400 -467.7173 0.010 0 1500 -467.7162 0.010 0 1600 -467.7145 0.010 0 1700 -467.7136 0.010 0 1800 -467.7115 0.010 0 1900 -467.7100 0.010 0 2000 -467.7098 0.010 0 2100 -467.7097 0.010 0 2200 -467.7095 0.010 0 2300 -467.7095 0.010 0 2400 -467.7094 0.010 0 Reached termination condition! last topological improvement at gen 0 Improvement over last 500 gen = 0.00061 Current score = -467.7094 Performing final optimizations... pass 1 : -467.7094 (branch= 0.0000 subset rates= 0.0000) pass 2 : -467.6977 (branch= 0.0116 subset rates= 0.0001) pass 3 : -467.6920 (branch= 0.0057 subset rates= 0.0000) pass 4 : -467.6870 (branch= 0.0050 subset rates= 0.0000) pass 5 : -467.6847 (branch= 0.0023 subset rates= 0.0000) pass 6 : -467.6819 (branch= 0.0028 subset rates= 0.0000) pass 7 : -467.6797 (branch= 0.0019 subset rates= 0.0003) pass 8 : -467.6790 (branch= 0.0008 subset rates= 0.0000) pass 9 : -467.6786 (branch= 0.0004 subset rates= 0.0000) pass 10: -467.6784 (branch= 0.0002 subset rates= 0.0000) pass 11: -467.6783 (branch= 0.0001 subset rates= 0.0000) pass 12: -467.6783 (branch= 0.0000 subset rates= 0.0000) pass 13: -467.6782 (branch= 0.0000 subset rates= 0.0000) pass 14: -467.6782 (branch= 0.0000 subset rates= 0.0000) pass 15: -467.6782 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6782 Time used so far = 0 hours, 0 minutes and 11 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 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 (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=1057295975 Initial ln Likelihood: -639.3053 optimizing: starting branch lengths, subset rates... pass 1:+ 155.030 (branch= 149.66 scale= 1.11 subset rates= 4.26) pass 2:+ 12.230 (branch= 11.21 scale= 0.06 subset rates= 0.97) pass 3:+ 3.972 (branch= 3.84 scale= 0.00 subset rates= 0.13) pass 4:+ 0.200 (branch= 0.18 scale= 0.02 subset rates= 0.00) pass 5:+ 0.069 (branch= 0.05 scale= 0.01 subset rates= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -467.8049 gen current_lnL precision last_tree_imp 0 -467.8049 0.010 0 100 -467.7812 0.010 0 200 -467.7731 0.010 0 300 -467.7685 0.010 0 400 -467.7534 0.010 301 500 -467.7494 0.010 301 600 -467.7430 0.010 301 NOTE: ****Specified time limit (5 seconds) reached... Current score = -467.7412 Performing final optimizations... pass 1 : -467.7400 (branch= 0.0000 subset rates= 0.0012) pass 2 : -467.7111 (branch= 0.0288 subset rates= 0.0000) pass 3 : -467.6988 (branch= 0.0124 subset rates= 0.0000) pass 4 : -467.6906 (branch= 0.0082 subset rates= 0.0000) pass 5 : -467.6872 (branch= 0.0034 subset rates= 0.0000) pass 6 : -467.6828 (branch= 0.0031 subset rates= 0.0013) pass 7 : -467.6807 (branch= 0.0020 subset rates= 0.0000) pass 8 : -467.6801 (branch= 0.0006 subset rates= 0.0000) pass 9 : -467.6793 (branch= 0.0003 subset rates= 0.0005) pass 10: -467.6791 (branch= 0.0002 subset rates= 0.0000) pass 11: -467.6790 (branch= 0.0001 subset rates= 0.0000) pass 12: -467.6789 (branch= 0.0001 subset rates= 0.0000) pass 13: -467.6789 (branch= 0.0000 subset rates= 0.0000) pass 14: -467.6789 (branch= 0.0000 subset rates= 0.0000) pass 15: -467.6789 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6789 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 2.16 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 : -467.6782 Replicate 2 : -467.6787 (same topology as 1) Replicate 3 : -467.6782 (best) (same topology as 1) Replicate 4 : -467.6789 (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: 3.844 0.786 1.480 2.180 rep 2: 3.839 0.788 1.472 2.178 rep 3: 3.844 0.786 1.480 2.181 rep 4: 3.841 0.787 1.482 2.162 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 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./check/p.mkO.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, modeled as Standard ordered k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN >>>Search rep 1 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -641.9257 optimizing: starting branch lengths, subset rates... pass 1:+ 147.096 (branch= 136.58 scale= 0.83 subset rates= 9.68) pass 2:+ 12.451 (branch= 8.46 scale= 0.00 subset rates= 3.99) pass 3:+ 3.549 (branch= 2.32 scale= 0.03 subset rates= 1.20) pass 4:+ 0.759 (branch= 0.51 scale= 0.00 subset rates= 0.25) pass 5:+ 0.120 (branch= 0.11 scale= 0.00 subset rates= 0.01) pass 6:+ 0.011 (branch= 0.01 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -477.9402 gen current_lnL precision last_tree_imp 0 -477.9402 0.010 0 100 -477.8625 0.010 76 200 -477.8283 0.010 152 300 -477.7511 0.010 215 400 -477.5621 0.010 373 500 -477.5385 0.010 373 600 -477.5298 0.010 373 700 -477.5290 0.010 373 800 -477.5213 0.010 373 900 -477.5166 0.010 373 1000 -477.5163 0.010 373 1100 -477.5124 0.010 373 1200 -477.5109 0.010 373 1300 -477.5098 0.010 373 1400 -477.4981 0.010 373 1500 -477.4922 0.010 373 1600 -477.4850 0.010 373 1700 -477.4817 0.010 373 1800 -477.4773 0.010 373 1900 -477.4761 0.010 373 2000 -477.4748 0.010 373 2100 -477.4739 0.010 373 2200 -477.4732 0.010 373 2300 -477.4729 0.010 373 2400 -477.4726 0.010 373 2500 -477.4723 0.010 373 2600 -477.4711 0.010 373 2700 -477.4707 0.010 373 2800 -477.4706 0.010 373 2900 -477.4705 0.010 373 3000 -477.4702 0.010 373 3100 -477.4701 0.010 373 Reached termination condition! last topological improvement at gen 373 Improvement over last 500 gen = 0.00099 Current score = -477.4701 Performing final optimizations... pass 1 : -477.4701 (branch= 0.0000 subset rates= 0.0000) pass 2 : -477.4430 (branch= 0.0269 subset rates= 0.0002) pass 3 : -477.4394 (branch= 0.0036 subset rates= 0.0000) pass 4 : -477.4366 (branch= 0.0027 subset rates= 0.0000) pass 5 : -477.4354 (branch= 0.0013 subset rates= 0.0000) pass 6 : -477.4347 (branch= 0.0007 subset rates= 0.0000) pass 7 : -477.4334 (branch= 0.0013 subset rates= 0.0000) pass 8 : -477.4324 (branch= 0.0010 subset rates= 0.0000) pass 9 : -477.4321 (branch= 0.0004 subset rates= 0.0000) pass 10: -477.4319 (branch= 0.0002 subset rates= 0.0000) pass 11: -477.4318 (branch= 0.0001 subset rates= 0.0000) pass 12: -477.4316 (branch= 0.0001 subset rates= 0.0001) pass 13: -477.4316 (branch= 0.0000 subset rates= 0.0000) pass 14: -477.4316 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.4316 Time used so far = 0 hours, 0 minutes and 3 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.63 1.92 2.74 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. >>>Completed Search rep 1 (of 5)<<< >>>Search rep 2 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=200420059 Initial ln Likelihood: -656.4902 optimizing: starting branch lengths, subset rates... pass 1:+ 148.906 (branch= 137.62 scale= 1.92 subset rates= 9.37) pass 2:+ 19.722 (branch= 15.83 scale= 0.00 subset rates= 3.89) pass 3:+ 3.562 (branch= 2.11 scale= 0.00 subset rates= 1.45) pass 4:+ 2.460 (branch= 2.02 scale= 0.00 subset rates= 0.44) pass 5:+ 3.227 (branch= 3.23 scale= 0.00 subset rates= 0.00) pass 6:+ 0.745 (branch= 0.71 scale= 0.01 subset rates= 0.02) 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: -477.8527 gen current_lnL precision last_tree_imp 0 -477.8527 0.010 0 100 -477.7879 0.010 74 200 -477.7665 0.010 74 300 -477.7486 0.010 74 400 -477.7424 0.010 74 500 -477.7295 0.010 74 600 -477.7267 0.010 74 700 -477.7205 0.010 74 800 -477.7194 0.010 74 900 -477.7186 0.010 74 1000 -477.7135 0.010 74 1100 -477.7094 0.010 74 1200 -477.7090 0.010 74 1300 -477.7060 0.010 74 1400 -477.7036 0.010 74 1500 -477.7019 0.010 74 1600 -477.7004 0.010 74 1700 -477.6994 0.010 74 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 1766, seed 274794359, best lnL -477.699 gen current_lnL precision last_tree_imp 1766 -477.6991 0.010 74 1800 -477.6984 0.010 74 1900 -477.6977 0.010 74 2000 -477.6953 0.010 74 2100 -477.3774 0.010 2081 2200 -477.3631 0.010 2170 2300 -477.3559 0.010 2170 2400 -477.3497 0.010 2170 2500 -477.3452 0.010 2170 2600 -477.3293 0.010 2170 2700 -477.3261 0.010 2170 2800 -477.3186 0.010 2170 2900 -477.3149 0.010 2170 3000 -477.3144 0.010 2170 3100 -477.3140 0.010 2170 3200 -477.3125 0.010 2170 3300 -477.3125 0.010 2170 3400 -477.3123 0.010 2170 3500 -477.3110 0.010 2170 3600 -477.3109 0.010 2170 3700 -477.3101 0.010 2170 3800 -477.3085 0.010 2170 3900 -477.3085 0.010 2170 4000 -477.3085 0.010 2170 4100 -477.3082 0.010 2170 4200 -477.3082 0.010 2170 4300 -477.3079 0.010 2170 Reached termination condition! last topological improvement at gen 2170 Improvement over last 500 gen = 0.00067 Current score = -477.3079 Performing final optimizations... pass 1 : -477.2447 (branch= 0.0000 subset rates= 0.0632) pass 2 : -477.2336 (branch= 0.0111 subset rates= 0.0000) pass 3 : -477.2150 (branch= 0.0106 subset rates= 0.0080) pass 4 : -477.2129 (branch= 0.0020 subset rates= 0.0000) pass 5 : -477.2082 (branch= 0.0047 subset rates= 0.0000) pass 6 : -477.2060 (branch= 0.0019 subset rates= 0.0003) pass 7 : -477.2056 (branch= 0.0004 subset rates= 0.0000) pass 8 : -477.2049 (branch= 0.0006 subset rates= 0.0001) pass 9 : -477.2047 (branch= 0.0002 subset rates= 0.0000) pass 10: -477.2046 (branch= 0.0001 subset rates= 0.0000) pass 11: -477.2045 (branch= 0.0001 subset rates= 0.0000) pass 12: -477.2045 (branch= 0.0000 subset rates= 0.0000) pass 13: -477.2045 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.2045 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: 0.64 1.93 2.63 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=1602142636 Initial ln Likelihood: -662.4976 optimizing: starting branch lengths, subset rates... pass 1:+ 159.344 (branch= 147.93 scale= 1.33 subset rates= 10.09) pass 2:+ 18.362 (branch= 14.32 scale= 0.01 subset rates= 4.02) pass 3:+ 5.723 (branch= 4.51 scale= 0.00 subset rates= 1.22) pass 4:+ 1.012 (branch= 0.74 scale= 0.00 subset rates= 0.28) pass 5:+ 0.186 (branch= 0.17 scale= 0.00 subset rates= 0.02) pass 6:+ 0.016 (branch= 0.00 scale= 0.02 subset rates= 0.00) pass 7:+ 0.035 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -477.8200 gen current_lnL precision last_tree_imp 0 -477.8200 0.010 0 100 -477.7127 0.010 12 200 -477.6994 0.010 12 300 -477.6923 0.010 12 400 -477.5173 0.010 372 500 -477.5116 0.010 372 600 -477.5057 0.010 372 700 -477.4981 0.010 372 800 -477.4917 0.010 372 900 -477.4851 0.010 372 1000 -477.4827 0.010 372 1100 -477.4798 0.010 372 1200 -477.4747 0.010 372 1300 -477.4729 0.010 372 1400 -477.4704 0.010 372 1500 -477.4686 0.010 372 1600 -477.4673 0.010 372 1700 -477.4649 0.010 372 1800 -477.4647 0.010 372 1900 -477.4633 0.010 372 2000 -477.4630 0.010 372 2100 -477.4621 0.010 372 2200 -477.4620 0.010 372 NOTE: ****Specified time limit (5 seconds) reached... Current score = -477.4604 Performing final optimizations... pass 1 : -477.4592 (branch= 0.0000 subset rates= 0.0013) pass 2 : -477.4450 (branch= 0.0142 subset rates= 0.0000) pass 3 : -477.4386 (branch= 0.0064 subset rates= 0.0000) pass 4 : -477.4380 (branch= 0.0006 subset rates= 0.0000) pass 5 : -477.4358 (branch= 0.0022 subset rates= 0.0000) pass 6 : -477.4342 (branch= 0.0016 subset rates= 0.0000) pass 7 : -477.4328 (branch= 0.0014 subset rates= 0.0000) pass 8 : -477.4323 (branch= 0.0005 subset rates= 0.0000) pass 9 : -477.4318 (branch= 0.0003 subset rates= 0.0001) pass 10: -477.4317 (branch= 0.0001 subset rates= 0.0000) pass 11: -477.4316 (branch= 0.0001 subset rates= 0.0000) pass 12: -477.4316 (branch= 0.0000 subset rates= 0.0000) pass 13: -477.4316 (branch= 0.0000 subset rates= 0.0000) pass 14: -477.4316 (branch= 0.0000 subset rates= 0.0000) pass 15: -477.4316 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.4315 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.63 1.91 2.74 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 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 : -477.4316 Replicate 2 : -477.2045 (best) Replicate 3 : -477.4315 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.930 0.631 1.917 2.740 rep 2: 4.695 0.635 1.931 2.634 rep 3: 4.928 0.632 1.914 2.739 Saving final tree from best search rep (#2) to ch.p.mkO.ssr.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkv.ssr.conf Running checkpoint test ./check/p.mkv.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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= 9.63 scale= 0.00 subset rates= 0.16) pass 3:+ 0.369 (branch= 0.35 scale= 0.00 subset rates= 0.02) pass 4:+ 0.040 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 5:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -439.2244 gen current_lnL precision last_tree_imp 0 -439.2244 0.010 0 100 -430.2535 0.010 92 200 -427.7092 0.010 179 300 -426.9758 0.010 293 400 -425.6931 0.010 365 500 -425.6675 0.010 365 600 -425.6508 0.010 365 700 -425.6316 0.010 365 800 -425.6209 0.010 365 900 -425.6123 0.010 365 1000 -425.6089 0.010 365 1100 -425.6081 0.010 365 1200 -425.6057 0.010 365 1300 -425.6039 0.010 365 1400 -425.6034 0.010 365 1500 -425.6029 0.010 365 1600 -425.6020 0.010 365 1700 -425.6018 0.010 365 1800 -425.6014 0.010 365 1900 -425.6001 0.010 365 2000 -425.5991 0.010 365 2100 -425.5979 0.010 365 2200 -425.5930 0.010 365 2300 -425.5915 0.010 365 2400 -425.5913 0.010 365 2500 -425.5897 0.010 365 2600 -425.5895 0.010 365 2700 -425.5894 0.010 365 2800 -425.5890 0.010 365 2900 -425.5876 0.010 365 3000 -425.5875 0.010 365 3100 -425.5854 0.010 365 3200 -425.5852 0.010 365 3300 -425.5851 0.010 365 3400 -425.5828 0.010 365 3500 -425.5828 0.010 365 3600 -425.5827 0.010 365 3700 -425.5827 0.010 365 3800 -425.5826 0.010 365 3900 -425.5824 0.010 365 Reached termination condition! last topological improvement at gen 365 Improvement over last 500 gen = 0.00046 Current score = -425.5824 Performing final optimizations... pass 1 : -425.5752 (branch= 0.0000 subset rates= 0.0071) pass 2 : -425.5571 (branch= 0.0147 subset rates= 0.0034) pass 3 : -425.5512 (branch= 0.0059 subset rates= 0.0000) pass 4 : -425.5505 (branch= 0.0007 subset rates= 0.0000) pass 5 : -425.5501 (branch= 0.0004 subset rates= 0.0000) pass 6 : -425.5497 (branch= 0.0004 subset rates= 0.0000) pass 7 : -425.5493 (branch= 0.0004 subset rates= 0.0000) pass 8 : -425.5490 (branch= 0.0003 subset rates= 0.0000) pass 9 : -425.5487 (branch= 0.0003 subset rates= 0.0000) pass 10: -425.5487 (branch= 0.0000 subset rates= 0.0000) pass 11: -425.5487 (branch= 0.0000 subset rates= 0.0000) pass 12: -425.5486 (branch= 0.0000 subset rates= 0.0000) pass 13: -425.5486 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.5486 Time used so far = 0 hours, 0 minutes and 4 seconds 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 1 (of 5)<<< >>>Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< Obtained starting tree 1 from Nexus Starting with seed=255600397 Initial ln Likelihood: -577.2924 optimizing: starting branch lengths, subset rates... pass 1:+ 121.000 (branch= 120.23 scale= 0.75 subset rates= 0.02) pass 2:+ 14.984 (branch= 14.74 scale= 0.04 subset rates= 0.20) pass 3:+ 1.951 (branch= 1.90 scale= 0.00 subset rates= 0.05) pass 4:+ 0.046 (branch= 0.05 scale= 0.00 subset rates= 0.00) pass 5:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -439.3118 gen current_lnL precision last_tree_imp 0 -439.3118 0.010 0 100 -428.8361 0.010 97 200 -428.0348 0.010 163 300 -425.9017 0.010 248 400 -425.7902 0.010 327 500 -425.7309 0.010 411 600 -425.6571 0.010 523 700 -425.6380 0.010 523 800 -425.6343 0.010 523 900 -425.6312 0.010 523 1000 -425.6253 0.010 523 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 1074, seed 1502474049, best lnL -425.624 gen current_lnL precision last_tree_imp 1074 -425.6237 0.010 523 1100 -425.6236 0.010 523 1200 -425.6180 0.010 523 1300 -425.6157 0.010 523 1400 -425.6057 0.010 523 1500 -425.6031 0.010 523 1600 -425.5999 0.010 523 1700 -425.5980 0.010 523 1800 -425.5977 0.010 523 1900 -425.5940 0.010 523 2000 -425.5929 0.010 523 2100 -425.5928 0.010 523 2200 -425.5912 0.010 523 2300 -425.5897 0.010 523 2400 -425.5887 0.010 523 2500 -425.5882 0.010 523 2600 -425.5881 0.010 523 2700 -425.5867 0.010 523 2800 -425.5863 0.010 523 2900 -425.5863 0.010 523 3000 -425.5854 0.010 523 3100 -425.5849 0.010 523 3200 -425.5846 0.010 523 3300 -425.5838 0.010 523 3400 -425.5835 0.010 523 3500 -425.5835 0.010 523 3600 -425.5834 0.010 523 3700 -425.5834 0.010 523 3800 -425.5830 0.010 523 Reached termination condition! last topological improvement at gen 523 Improvement over last 500 gen = 0.00079 Current score = -425.5830 Performing final optimizations... pass 1 : -425.5767 (branch= 0.0000 subset rates= 0.0062) pass 2 : -425.5554 (branch= 0.0187 subset rates= 0.0026) pass 3 : -425.5554 (branch= 0.0000 subset rates= 0.0000) pass 4 : -425.5514 (branch= 0.0021 subset rates= 0.0019) pass 5 : -425.5509 (branch= 0.0005 subset rates= 0.0000) pass 6 : -425.5500 (branch= 0.0009 subset rates= 0.0000) pass 7 : -425.5494 (branch= 0.0006 subset rates= 0.0000) pass 8 : -425.5492 (branch= 0.0002 subset rates= 0.0000) pass 9 : -425.5489 (branch= 0.0000 subset rates= 0.0003) pass 10: -425.5488 (branch= 0.0001 subset rates= 0.0000) pass 11: -425.5487 (branch= 0.0000 subset rates= 0.0000) pass 12: -425.5487 (branch= 0.0000 subset rates= 0.0000) pass 13: -425.5487 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.5487 Time used so far = 0 hours, 0 minutes and 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) 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=124386023 Initial ln Likelihood: -667.8582 optimizing: starting branch lengths, subset rates... pass 1:+ 210.703 (branch= 209.92 scale= 0.77 subset rates= 0.01) pass 2:+ 14.697 (branch= 14.50 scale= 0.07 subset rates= 0.12) pass 3:+ 2.972 (branch= 2.91 scale= 0.03 subset rates= 0.04) pass 4:+ 0.250 (branch= 0.24 scale= 0.01 subset rates= 0.00) pass 5:+ 0.035 (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: -439.2013 gen current_lnL precision last_tree_imp 0 -439.2013 0.010 0 100 -429.9526 0.010 95 200 -428.0661 0.010 184 300 -425.6075 0.010 283 400 -425.4842 0.010 312 500 -425.4465 0.010 472 600 -425.4348 0.010 472 700 -425.4277 0.010 472 800 -425.4227 0.010 472 900 -425.3896 0.010 849 1000 -425.3856 0.010 849 1100 -425.3791 0.010 849 1200 -425.3761 0.010 849 1300 -425.3720 0.010 849 1400 -425.3676 0.010 849 1500 -425.3654 0.010 849 1600 -425.3642 0.010 849 1700 -425.3631 0.010 849 1800 -425.3618 0.010 849 1900 -425.3617 0.010 849 2000 -425.3612 0.010 849 2100 -425.3611 0.010 849 2200 -425.3609 0.010 849 NOTE: ****Specified time limit (5 seconds) reached... Current score = -425.3609 Performing final optimizations... pass 1 : -425.3552 (branch= 0.0000 subset rates= 0.0057) pass 2 : -425.3301 (branch= 0.0251 subset rates= 0.0000) pass 3 : -425.3260 (branch= 0.0041 subset rates= 0.0000) pass 4 : -425.3243 (branch= 0.0017 subset rates= 0.0000) pass 5 : -425.3238 (branch= 0.0005 subset rates= 0.0000) pass 6 : -425.3219 (branch= 0.0019 subset rates= 0.0000) pass 7 : -425.3212 (branch= 0.0007 subset rates= 0.0000) pass 8 : -425.3207 (branch= 0.0005 subset rates= 0.0000) pass 9 : -425.3205 (branch= 0.0002 subset rates= 0.0000) pass 10: -425.3205 (branch= 0.0000 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 1.15 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 10 branches were collapsed. >>>Terminated Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 3 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -425.5486 Replicate 2 : -425.5487 (same topology as 1) Replicate 3 : -425.3204 (best) (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: 3.037 0.868 1.530 1.116 rep 2: 3.039 0.869 1.526 1.120 rep 3: 2.980 0.865 1.539 1.149 Saving tree from best search rep (#3) to bootstrap file ch.p.mkv.ssr.boot.tre WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkvO.ssr.conf Running checkpoint test ./check/p.mkvO.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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:+ 1.162 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.156 (branch= 0.12 scale= 0.00 subset rates= 0.03) pass 6:+ 0.044 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 7:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -474.8632 gen current_lnL precision last_tree_imp 0 -474.8632 0.010 0 100 -474.7514 0.010 68 200 -474.7186 0.010 68 300 -474.6982 0.010 68 400 -474.6395 0.010 329 500 -474.1549 0.010 455 600 -474.1345 0.010 560 700 -474.0337 0.010 653 800 -474.0224 0.010 653 900 -474.0129 0.010 653 1000 -474.0072 0.010 653 1100 -474.0048 0.010 653 1200 -474.0017 0.010 653 1300 -473.9998 0.010 653 1400 -473.9960 0.010 653 1500 -473.9930 0.010 653 1600 -473.9888 0.010 653 1700 -473.9875 0.010 653 1800 -473.9857 0.010 653 1900 -473.9846 0.010 653 2000 -473.9839 0.010 653 2100 -473.9834 0.010 653 2200 -473.9820 0.010 653 2300 -473.9814 0.010 653 2400 -473.9804 0.010 653 2500 -473.9804 0.010 653 2600 -473.9801 0.010 653 2700 -473.9793 0.010 653 2800 -473.9779 0.010 653 2900 -473.9777 0.010 653 3000 -473.9777 0.010 653 3100 -473.9773 0.010 653 3200 -473.9772 0.010 653 3300 -473.9770 0.010 653 Reached termination condition! last topological improvement at gen 653 Improvement over last 500 gen = 0.00088 Current score = -473.9770 Performing final optimizations... pass 1 : -473.9770 (branch= 0.0000 subset rates= 0.0000) pass 2 : -473.9587 (branch= 0.0183 subset rates= 0.0000) pass 3 : -473.9587 (branch= 0.0000 subset rates= 0.0000) pass 4 : -473.9562 (branch= 0.0011 subset rates= 0.0014) pass 5 : -473.9537 (branch= 0.0013 subset rates= 0.0013) pass 6 : -473.9523 (branch= 0.0010 subset rates= 0.0003) pass 7 : -473.9516 (branch= 0.0008 subset rates= 0.0000) pass 8 : -473.9511 (branch= 0.0004 subset rates= 0.0001) pass 9 : -473.9509 (branch= 0.0002 subset rates= 0.0000) pass 10: -473.9508 (branch= 0.0000 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: -473.9507 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -473.9507 Time used so far = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.59 2.07 2.80 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. >>>Completed Search rep 1 (of 5)<<< >>>Search rep 2 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=2125680066 Initial ln Likelihood: -649.8224 optimizing: starting branch lengths, subset rates... pass 1:+ 148.288 (branch= 136.88 scale= 0.96 subset rates= 10.45) pass 2:+ 18.126 (branch= 13.41 scale= 0.03 subset rates= 4.69) pass 3:+ 5.650 (branch= 3.93 scale= 0.00 subset rates= 1.72) pass 4:+ 2.345 (branch= 1.67 scale= 0.00 subset rates= 0.67) pass 5:+ 0.473 (branch= 0.43 scale= 0.01 subset rates= 0.03) pass 6:+ 0.134 (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: -474.8071 gen current_lnL precision last_tree_imp 0 -474.8071 0.010 0 100 -474.7912 0.010 0 200 -474.7021 0.010 123 300 -474.5642 0.010 272 400 -474.5190 0.010 272 500 -474.5075 0.010 272 600 -474.5034 0.010 272 700 -474.4997 0.010 272 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Feb 20 2022 10:49:10 using GNU gcc compiler version 12.2.0 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 703, seed 1240733539, best lnL -474.500 gen current_lnL precision last_tree_imp 703 -474.4997 0.010 272 800 -474.4937 0.010 272 900 -474.4913 0.010 272 1000 -474.4880 0.010 272 1100 -474.4855 0.010 272 1200 -474.4847 0.010 272 1300 -474.4838 0.010 272 1400 -474.4822 0.010 272 1500 -474.4804 0.010 272 1600 -474.4798 0.010 272 1700 -474.4795 0.010 272 1800 -474.4790 0.010 272 1900 -474.4786 0.010 272 2000 -474.4786 0.010 272 2100 -474.4782 0.010 272 2200 -474.4775 0.010 272 2300 -474.4768 0.010 272 2400 -474.4764 0.010 272 2500 -474.4764 0.010 272 2600 -474.4747 0.010 272 2700 -474.4736 0.010 272 2800 -474.4720 0.010 272 2900 -474.4720 0.010 272 3000 -474.4652 0.010 272 3100 -474.4597 0.010 272 3200 -474.4561 0.010 272 3300 -474.4551 0.010 272 3400 -474.4539 0.010 272 3500 -474.4525 0.010 272 3600 -474.4521 0.010 272 3700 -474.4507 0.010 272 3800 -474.4505 0.010 272 3900 -474.4503 0.010 272 4000 -474.4502 0.010 272 4100 -474.4501 0.010 272 4200 -474.4492 0.010 272 4300 -474.4491 0.010 272 4400 -474.4486 0.010 272 4500 -474.4484 0.010 272 4600 -474.4483 0.010 272 4700 -474.4474 0.010 272 4800 -474.4471 0.010 272 4900 -474.4464 0.010 272 5000 -474.4464 0.010 272 Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 0.000 lnL NOTE: ****Specified time limit (5 seconds) reached... Current score = -474.4455 Performing final optimizations... pass 1 : -474.4455 (branch= 0.0000 subset rates= 0.0000) pass 2 : -474.4338 (branch= 0.0117 subset rates= 0.0000) pass 3 : -474.4321 (branch= 0.0017 subset rates= 0.0000) pass 4 : -474.4313 (branch= 0.0008 subset rates= 0.0000) pass 5 : -474.4303 (branch= 0.0010 subset rates= 0.0000) pass 6 : -474.4297 (branch= 0.0006 subset rates= 0.0001) pass 7 : -474.4294 (branch= 0.0003 subset rates= 0.0000) pass 8 : -474.4290 (branch= 0.0003 subset rates= 0.0000) pass 9 : -474.4286 (branch= 0.0004 subset rates= 0.0000) pass 10: -474.4283 (branch= 0.0002 subset rates= 0.0000) pass 11: -474.4282 (branch= 0.0001 subset rates= 0.0000) pass 12: -474.4282 (branch= 0.0001 subset rates= 0.0000) pass 13: -474.4282 (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 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.59 2.03 2.92 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. >>>Terminated Search rep 2 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 2 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -473.9507 (best) Replicate 2 : -474.4281 (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: 4.349 0.588 2.066 2.804 rep 2: 4.600 0.588 2.033 2.917 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/garli-2.1/tests' make[3]: Leaving directory '/build/garli-2.1/tests' make[3]: Entering directory '/build/garli-2.1' make[3]: Leaving directory '/build/garli-2.1' make[2]: Leaving directory '/build/garli-2.1' # restore original test dir rm -rf tests mv tests.bak tests make[1]: Leaving directory '/build/garli-2.1' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j3 install DESTDIR=/build/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/garli-2.1' Making install in src make[2]: Entering directory '/build/garli-2.1/src' make[3]: Entering directory '/build/garli-2.1/src' make[3]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/garli-2.1/debian/tmp/usr/bin' /usr/bin/install -c Garli '/build/garli-2.1/debian/tmp/usr/bin' make install-exec-hook make[4]: Entering directory '/build/garli-2.1/src' cd /build/garli-2.1/debian/tmp/usr/bin && \ mv -f Garli Garli-2.1 && \ ln -s Garli-2.1 Garli make[4]: Leaving directory '/build/garli-2.1/src' make[3]: Leaving directory '/build/garli-2.1/src' make[2]: Leaving directory '/build/garli-2.1/src' Making install in tests make[2]: Entering directory '/build/garli-2.1/tests' make[3]: Entering directory '/build/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/garli-2.1/tests' make[2]: Leaving directory '/build/garli-2.1/tests' make[2]: Entering directory '/build/garli-2.1' make[3]: Entering directory '/build/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/garli-2.1' make[2]: Leaving directory '/build/garli-2.1' make[1]: Leaving directory '/build/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 dpkg-shlibdeps: warning: debian/garli/usr/lib/garli/bin/Garli-2.1 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/garli-mpi/usr/lib/garli/bin/Garli-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'garli' in '../garli_2.1-7_armhf.deb'. dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-7_armhf.deb'. dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-7_all.deb'. dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-7_armhf.deb'. dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-7_armhf.deb'. dpkg-genbuildinfo --build=binary -O../garli_2.1-7_armhf.buildinfo dpkg-genchanges --build=binary -O../garli_2.1-7_armhf.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/32726 and its subdirectories I: Current time: Thu May 4 16:39:55 -12 2023 I: pbuilder-time-stamp: 1683261595 Fri May 5 04:41:16 UTC 2023 I: 1st build successful. Starting 2nd build on remote node virt32a-armhf-rb.debian.net. Fri May 5 04:41:16 UTC 2023 I: Preparing to do remote build '2' on virt32a-armhf-rb.debian.net. Fri May 5 05:00:25 UTC 2023 I: Deleting $TMPDIR on virt32a-armhf-rb.debian.net. Fri May 5 05:00:37 UTC 2023 I: garli_2.1-7_armhf.changes: Format: 1.8 Date: Sun, 20 Feb 2022 11:49:10 +0100 Source: garli Binary: garli garli-dbgsym garli-examples garli-mpi garli-mpi-dbgsym Architecture: armhf all Version: 2.1-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss 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 (2.1-7) unstable; urgency=medium . * Team upload. * Set 'bootstrapseed' in tests to further reduce randomness, probably addresses #907905. Checksums-Sha1: eff82e9497f4da496fc34ac690c4910cc21d645d 5009284 garli-dbgsym_2.1-7_armhf.deb 3eaf0596cc836e15aca32438f8129996c5b38712 103072 garli-examples_2.1-7_all.deb 5b2400c370233e59807da81694f72c3244361ce7 5041624 garli-mpi-dbgsym_2.1-7_armhf.deb 403715266a55f673fa3e8251ada3902681d74f29 486964 garli-mpi_2.1-7_armhf.deb 7fe67180f0bf7c51b02f784f3391658616de733b 7554 garli_2.1-7_armhf.buildinfo 90720dfba07537e6b14f2375b01da46f7b324f83 510120 garli_2.1-7_armhf.deb Checksums-Sha256: 2e862f3a47d07307d062e155f348f01ff8da8a3e0434eaa7d1182dd2ed0a3d2d 5009284 garli-dbgsym_2.1-7_armhf.deb 26a43a41a453436972ac432d719332175351ad60e290a173473cf1cb71f3aac5 103072 garli-examples_2.1-7_all.deb 21a2e4be1906d7e479bb9971508ce43f5b34239d8ef96d252b0f85fb5be0f8ca 5041624 garli-mpi-dbgsym_2.1-7_armhf.deb 1e6ff4af1ec8bef92b87856c9db1e6e83e4d0f491f5482cfeb252db99dcc56d4 486964 garli-mpi_2.1-7_armhf.deb 8721b6dd13d24c5041f6ce842fe9a154e8a5d13ff6314514da16ebea9b91bfc3 7554 garli_2.1-7_armhf.buildinfo 24ac0afbd3446599e5510dfe8d69df5ad2c3ac065e5745f668412e1556b369c4 510120 garli_2.1-7_armhf.deb Files: 93c13dd3d7b0eea16c0a47c049a66c9c 5009284 debug optional garli-dbgsym_2.1-7_armhf.deb ad3d560df3733dd689d1d1aa24f48526 103072 science optional garli-examples_2.1-7_all.deb 3adae894d9bc2dfd4048f707df36fab1 5041624 debug optional garli-mpi-dbgsym_2.1-7_armhf.deb c89a30223a6d40e51e2dfa6ec44eb56f 486964 science optional garli-mpi_2.1-7_armhf.deb ba30d2020696b0f26bbfae844b932ed7 7554 science optional garli_2.1-7_armhf.buildinfo d67b433ddad31a393278dda9a0655872 510120 science optional garli_2.1-7_armhf.deb Fri May 5 05:00:38 UTC 2023 I: diffoscope 241 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.q427glx6/garli_2.1-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.q427glx6/garli_2.1-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.q427glx6/garli_2.1-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.q427glx6/b1/garli_2.1-7_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.q427glx6/b2/garli_2.1-7_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.483s) 0.483s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.137s) 0.136s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Fri May 5 05:00:40 UTC 2023 I: diffoscope 241 found no differences in the changes files, and a .buildinfo file also exists. Fri May 5 05:00:40 UTC 2023 I: garli from bookworm built successfully and reproducibly on armhf. Fri May 5 05:00:41 UTC 2023 I: Submitting .buildinfo files to external archives: Fri May 5 05:00:41 UTC 2023 I: Submitting 12K b1/garli_2.1-7_armhf.buildinfo.asc Fri May 5 05:00:41 UTC 2023 I: Submitting 12K b2/garli_2.1-7_armhf.buildinfo.asc Fri May 5 05:00:42 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri May 5 05:00:42 UTC 2023 I: Done submitting .buildinfo files. Fri May 5 05:00:42 UTC 2023 I: Removing signed garli_2.1-7_armhf.buildinfo.asc files: removed './b1/garli_2.1-7_armhf.buildinfo.asc' removed './b2/garli_2.1-7_armhf.buildinfo.asc'