Tue Aug 24 00:00:42 UTC 2021 I: starting to build garli/bullseye/armhf on jenkins on '2021-08-24 00:00' Tue Aug 24 00:00:42 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_10/10248/console.log Tue Aug 24 00:00:42 UTC 2021 I: Downloading source for bullseye/garli=2.1-4 --2021-08-24 00:00:42-- http://cdn-fastly.deb.debian.org/debian/pool/main/g/garli/garli_2.1-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2072 (2.0K) Saving to: ‘garli_2.1-4.dsc’ 0K .. 100% 185M=0s 2021-08-24 00:00:42 (185 MB/s) - ‘garli_2.1-4.dsc’ saved [2072/2072] Tue Aug 24 00:00:42 UTC 2021 I: garli_2.1-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: garli Binary: garli, garli-mpi, garli-examples Architecture: any all Version: 2.1-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/Ashod/garli Standards-Version: 4.5.1 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 15430e6d15f767659cf605a38d4ccf50e8f450ab 4572 garli_2.1-4.debian.tar.xz Checksums-Sha256: 00aa31af5d8ecc2cb9bd276ce93b6580ae6cff93f4f5e1145d95d5fe6359e1b6 1248730 garli_2.1.orig.tar.gz 97414a8a879c0c0028de335dcd301bca53d35540e031197a08ba25c65552cd10 4572 garli_2.1-4.debian.tar.xz Files: 83d6720df816365182291306383d056c 1248730 garli_2.1.orig.tar.gz 2115907a9fe64f51bd9fa277dce9284a 4572 garli_2.1-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl+1KaIRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEvbg//TIxiyh6XalDhZ+RigOUfT/MI0HXDV5YU nApmZMlpDJKPpovn/FibWHWU/cgX4eC8rZMYk2jw+U3qX2CEzZB0irRylJvz29Lu gYX86GepRW4bsYLpnPl8tdaAUP41a27BffB5EUDzEJaAz/8eNKqvpH7u1RCuwnwa yqT+YH2ZY14Z397cnC9RLUgmtwf/0wMU0TqC5xgjKkgYk70NCRwhXDkZ9nqUKuF9 72VbvPqzvcV7sAygUg54j95qGpiD0koT8/vVVy8MaLPxwFztGviE0b79XKd8hbC1 4I8WEqaAAuRSKCJfjJwEJgLcQgTqmsrdgHrnBWsFuatPtszgU4tPm6znQqiPH9ls DqCEwWoY1BfyLYh1WT2CDVmLVxEMMu9utOQL64HPG1j8+ixnK6slVvLIMbeubids iL0INBvMePWLKHiALcdWa9787OXVvuIRdh/I2V1wXoHJ2qBVhOtxRueleTtpqsY4 eFOqeARm40+cVHxaWmvThvHtsWRD19bnu2bj7eL4sjbtpa131k2r/BM6mLuvuHVN a87JVC69QmPS3xKE36WnoZ9v//AQ1CsMhBNng8N1VdviEM7zmyXSxTuDM1UMuKjp XYiSY9yG5S+vRg9lzWAfedyfrqAJFF6idn3aig33kRD0C+9JzTpu/PBAtvn69mM3 RVvL+H20jpI= =qEcl -----END PGP SIGNATURE----- Tue Aug 24 00:00:42 UTC 2021 I: Checking whether the package is not for us Tue Aug 24 00:00:42 UTC 2021 I: Starting 1st build on remote node jtx1b-armhf-rb.debian.net. Tue Aug 24 00:00:42 UTC 2021 I: Preparing to do remote build '1' on jtx1b-armhf-rb.debian.net. Tue Aug 24 00:20:00 UTC 2021 I: Deleting $TMPDIR on jtx1b-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Aug 23 12:00:52 -12 2021 I: pbuilder-time-stamp: 1629763252 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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_2.1-4.dsc] I: copying [./garli_2.1.orig.tar.gz] I: copying [./garli_2.1-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.72Q_3gmw/trustedkeys.kbx': General error gpgv: Signature made Wed Nov 18 02:03:14 2020 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./garli_2.1-4.dsc dpkg-source: info: extracting garli in garli-2.1 dpkg-source: info: unpacking garli_2.1.orig.tar.gz dpkg-source: info: unpacking garli_2.1-4.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4936/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,-fixfilepath parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='a5882269815843e3aff3ed48019875b9' 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='4936' 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/tmp.9BWV4sNWlz/pbuilderrc_OZt4 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.9BWV4sNWlz/b1 --logfile b1/build.log garli_2.1-4.dsc' SUDO_GID='114' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux jtx1b 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux I: ls -l /bin total 3580 -rwxr-xr-x 1 root root 816764 Aug 4 08:25 bash -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 9636 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 26668 Sep 22 2020 cat -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash -rwxr-xr-x 1 root root 75880 Sep 22 2020 date -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd -rwxr-xr-x 1 root root 59912 Sep 22 2020 df -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir -rwxr-xr-x 1 root root 55012 Jul 28 07:09 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 22496 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 47492 Jul 28 07:09 findmnt -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln -rwxr-xr-x 1 root root 35068 Feb 7 2020 login -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls -rwxr-xr-x 1 root root 99940 Jul 28 07:09 lsblk -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 34408 Jul 28 07:09 more -rwsr-xr-x 1 root root 34400 Jul 28 07:09 mount -rwxr-xr-x 1 root root 9824 Jul 28 07:09 mountpoint -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 20 21:28 sh -> dash -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty -rwsr-xr-x 1 root root 46704 Jul 28 07:09 su -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync -rwxr-xr-x 1 root root 340872 Feb 16 2021 tar -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch -rwxr-xr-x 1 root root 22496 Sep 22 2020 true -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 22108 Jul 28 07:09 umount -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir -rwxr-xr-x 1 root root 38512 Jul 28 07:09 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew I: user script /srv/workspace/pbuilder/4936/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 ... 19398 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-10{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcbor0{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-10-dev{a} libgfortran5{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libicu67{a} libjs-jquery{a} libjs-jquery-ui{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libncl-dev{a} libncl2{a} libncurses6{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} libsigsegv2{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 libgpm2 libmail-sendmail-perl lynx wget xauth 0 packages upgraded, 87 newly installed, 0 to remove and 0 not upgraded. Need to get 37.3 MB of archives. After unpacking 127 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-8 [138 kB] Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB] Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB] Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB] Get: 6 http://deb.debian.org/debian bullseye/main armhf readline-common all 8.1-1 [73.7 kB] Get: 7 http://deb.debian.org/debian bullseye/main armhf libreadline8 armhf 8.1-1 [147 kB] Get: 8 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB] Get: 9 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB] Get: 10 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3 [117 kB] Get: 11 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3 [68.1 kB] Get: 12 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB] Get: 13 http://deb.debian.org/debian bullseye/main armhf libmd0 armhf 1.0.3-3 [27.4 kB] Get: 14 http://deb.debian.org/debian bullseye/main armhf libbsd0 armhf 0.11.3-1 [103 kB] Get: 15 http://deb.debian.org/debian bullseye/main armhf libedit2 armhf 3.1-20191231-2+b1 [81.1 kB] Get: 16 http://deb.debian.org/debian bullseye/main armhf libcbor0 armhf 0.5.0+dfsg-2 [19.6 kB] Get: 17 http://deb.debian.org/debian bullseye/main armhf libfido2-1 armhf 1.6.0-2 [48.0 kB] Get: 18 http://deb.debian.org/debian bullseye/main armhf openssh-client armhf 1:8.4p1-5 [842 kB] Get: 19 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB] Get: 20 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB] Get: 21 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB] Get: 22 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 23 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB] Get: 24 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB] Get: 25 http://deb.debian.org/debian bullseye/main armhf libncurses6 armhf 6.2+20201114-2 [80.5 kB] Get: 26 http://deb.debian.org/debian bullseye/main armhf bc armhf 1.07.1-2+b2 [104 kB] Get: 27 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB] Get: 28 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB] Get: 29 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB] Get: 32 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 33 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 34 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB] Get: 35 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB] Get: 36 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB] Get: 37 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [602 kB] Get: 38 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB] Get: 39 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 40 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 41 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] Get: 42 http://deb.debian.org/debian bullseye/main armhf libgfortran5 armhf 10.2.1-6 [237 kB] Get: 43 http://deb.debian.org/debian bullseye/main armhf libgfortran-10-dev armhf 10.2.1-6 [289 kB] Get: 44 http://deb.debian.org/debian bullseye/main armhf gfortran-10 armhf 10.2.1-6 [7123 kB] Get: 45 http://deb.debian.org/debian bullseye/main armhf libnl-3-200 armhf 3.4.0-1+b1 [55.5 kB] Get: 46 http://deb.debian.org/debian bullseye/main armhf libnl-route-3-200 armhf 3.4.0-1+b1 [136 kB] Get: 47 http://deb.debian.org/debian bullseye/main armhf libibverbs1 armhf 33.2-1 [53.0 kB] Get: 48 http://deb.debian.org/debian bullseye/main armhf ibverbs-providers armhf 33.2-1 [25.4 kB] Get: 49 http://deb.debian.org/debian bullseye/main armhf libevent-2.1-7 armhf 2.1.12-stable-1 [169 kB] Get: 50 http://deb.debian.org/debian bullseye/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-1 [127 kB] Get: 51 http://deb.debian.org/debian bullseye/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-1 [101 kB] Get: 52 http://deb.debian.org/debian bullseye/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-1 [56.8 kB] Get: 53 http://deb.debian.org/debian bullseye/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-1 [61.6 kB] Get: 54 http://deb.debian.org/debian bullseye/main armhf libevent-dev armhf 2.1.12-stable-1 [296 kB] Get: 55 http://deb.debian.org/debian bullseye/main armhf librdmacm1 armhf 33.2-1 [60.8 kB] Get: 56 http://deb.debian.org/debian bullseye/main armhf libfabric1 armhf 1.11.0-2 [319 kB] Get: 57 http://deb.debian.org/debian bullseye/main armhf libhwloc15 armhf 2.4.1+dfsg-1 [125 kB] Get: 58 http://deb.debian.org/debian bullseye/main armhf libnuma1 armhf 2.0.12-1+b1 [22.7 kB] Get: 59 http://deb.debian.org/debian bullseye/main armhf libnuma-dev armhf 2.0.12-1+b1 [37.0 kB] Get: 60 http://deb.debian.org/debian bullseye/main armhf libltdl7 armhf 2.4.6-15 [388 kB] Get: 61 http://deb.debian.org/debian bullseye/main armhf libltdl-dev armhf 2.4.6-15 [159 kB] Get: 62 http://deb.debian.org/debian bullseye/main armhf libhwloc-dev armhf 2.4.1+dfsg-1 [208 kB] Get: 63 http://deb.debian.org/debian bullseye/main armhf libpciaccess0 armhf 0.16-1 [51.0 kB] Get: 64 http://deb.debian.org/debian bullseye/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB] Get: 65 http://deb.debian.org/debian bullseye/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 66 http://deb.debian.org/debian bullseye/main armhf libxcb1 armhf 1.14-3 [136 kB] Get: 67 http://deb.debian.org/debian bullseye/main armhf libx11-data all 2:1.7.2-1 [311 kB] Get: 68 http://deb.debian.org/debian bullseye/main armhf libx11-6 armhf 2:1.7.2-1 [713 kB] Get: 69 http://deb.debian.org/debian bullseye/main armhf libxext6 armhf 2:1.3.3-1.1 [47.8 kB] Get: 70 http://deb.debian.org/debian bullseye/main armhf libxnvctrl0 armhf 460.91.03-1 [25.8 kB] Get: 71 http://deb.debian.org/debian bullseye/main armhf ocl-icd-libopencl1 armhf 2.2.14-2 [39.7 kB] Get: 72 http://deb.debian.org/debian bullseye/main armhf libhwloc-plugins armhf 2.4.1+dfsg-1 [19.7 kB] Get: 73 http://deb.debian.org/debian bullseye/main armhf libnl-3-dev armhf 3.4.0-1+b1 [97.1 kB] Get: 74 http://deb.debian.org/debian bullseye/main armhf libnl-route-3-dev armhf 3.4.0-1+b1 [160 kB] Get: 75 http://deb.debian.org/debian bullseye/main armhf libibverbs-dev armhf 33.2-1 [183 kB] Get: 76 http://deb.debian.org/debian bullseye/main armhf libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 77 http://deb.debian.org/debian bullseye/main armhf libjs-jquery-ui all 1.12.1+dfsg-8 [232 kB] Get: 78 http://deb.debian.org/debian bullseye/main armhf libncl2 armhf 2.1.21+git20190531.feceb81-3 [348 kB] Get: 79 http://deb.debian.org/debian bullseye/main armhf libncl-dev armhf 2.1.21+git20190531.feceb81-3 [527 kB] Get: 80 http://deb.debian.org/debian bullseye/main armhf libpmix2 armhf 4.0.0-4.1 [487 kB] Get: 81 http://deb.debian.org/debian bullseye/main armhf libopenmpi3 armhf 4.1.0-10 [1831 kB] Get: 82 http://deb.debian.org/debian bullseye/main armhf openmpi-common all 4.1.0-10 [179 kB] Get: 83 http://deb.debian.org/debian bullseye/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [185 kB] Get: 84 http://deb.debian.org/debian bullseye/main armhf libpmix-dev armhf 4.0.0-4.1 [618 kB] Get: 85 http://deb.debian.org/debian bullseye/main armhf openmpi-bin armhf 4.1.0-10 [206 kB] Get: 86 http://deb.debian.org/debian bullseye/main armhf libopenmpi-dev armhf 4.1.0-10 [1143 kB] Get: 87 http://deb.debian.org/debian bullseye/main armhf ncl-tools armhf 2.1.21+git20190531.feceb81-3 [140 kB] Fetched 37.3 MB in 4s (10.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19398 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_armhf.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../01-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_armhf.deb ... 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Selecting previously unselected package dwz. Preparing to unpack .../34-dwz_0.13+20210201-1_armhf.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:armhf. Preparing to unpack .../35-libicu67_67.1-7_armhf.deb ... Unpacking libicu67:armhf (67.1-7) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../36-libxml2_2.9.10+dfsg-6.7_armhf.deb ... Unpacking libxml2:armhf (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../37-gettext_0.21-4_armhf.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../38-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../39-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../40-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package libgfortran5:armhf. Preparing to unpack .../41-libgfortran5_10.2.1-6_armhf.deb ... Unpacking libgfortran5:armhf (10.2.1-6) ... Selecting previously unselected package libgfortran-10-dev:armhf. Preparing to unpack .../42-libgfortran-10-dev_10.2.1-6_armhf.deb ... Unpacking libgfortran-10-dev:armhf (10.2.1-6) ... Selecting previously unselected package gfortran-10. Preparing to unpack .../43-gfortran-10_10.2.1-6_armhf.deb ... Unpacking gfortran-10 (10.2.1-6) ... Selecting previously unselected package libnl-3-200:armhf. Preparing to unpack .../44-libnl-3-200_3.4.0-1+b1_armhf.deb ... Unpacking libnl-3-200:armhf (3.4.0-1+b1) ... Selecting previously unselected package libnl-route-3-200:armhf. Preparing to unpack .../45-libnl-route-3-200_3.4.0-1+b1_armhf.deb ... Unpacking libnl-route-3-200:armhf (3.4.0-1+b1) ... Selecting previously unselected package libibverbs1:armhf. Preparing to unpack .../46-libibverbs1_33.2-1_armhf.deb ... Unpacking libibverbs1:armhf (33.2-1) ... Selecting previously unselected package ibverbs-providers:armhf. Preparing to unpack .../47-ibverbs-providers_33.2-1_armhf.deb ... Unpacking ibverbs-providers:armhf (33.2-1) ... Selecting previously unselected package libevent-2.1-7:armhf. Preparing to unpack .../48-libevent-2.1-7_2.1.12-stable-1_armhf.deb ... Unpacking libevent-2.1-7:armhf (2.1.12-stable-1) ... Selecting previously unselected package libevent-core-2.1-7:armhf. Preparing to unpack .../49-libevent-core-2.1-7_2.1.12-stable-1_armhf.deb ... Unpacking libevent-core-2.1-7:armhf (2.1.12-stable-1) ... Selecting previously unselected package libevent-extra-2.1-7:armhf. Preparing to unpack .../50-libevent-extra-2.1-7_2.1.12-stable-1_armhf.deb ... Unpacking libevent-extra-2.1-7:armhf (2.1.12-stable-1) ... Selecting previously unselected package libevent-pthreads-2.1-7:armhf. Preparing to unpack .../51-libevent-pthreads-2.1-7_2.1.12-stable-1_armhf.deb ... Unpacking libevent-pthreads-2.1-7:armhf (2.1.12-stable-1) ... Selecting previously unselected package libevent-openssl-2.1-7:armhf. Preparing to unpack .../52-libevent-openssl-2.1-7_2.1.12-stable-1_armhf.deb ... Unpacking libevent-openssl-2.1-7:armhf (2.1.12-stable-1) ... Selecting previously unselected package libevent-dev. Preparing to unpack .../53-libevent-dev_2.1.12-stable-1_armhf.deb ... Unpacking libevent-dev (2.1.12-stable-1) ... Selecting previously unselected package librdmacm1:armhf. Preparing to unpack .../54-librdmacm1_33.2-1_armhf.deb ... Unpacking librdmacm1:armhf (33.2-1) ... Selecting previously unselected package libfabric1. Preparing to unpack .../55-libfabric1_1.11.0-2_armhf.deb ... Unpacking libfabric1 (1.11.0-2) ... Selecting previously unselected package libhwloc15:armhf. Preparing to unpack .../56-libhwloc15_2.4.1+dfsg-1_armhf.deb ... Unpacking libhwloc15:armhf (2.4.1+dfsg-1) ... Selecting previously unselected package libnuma1:armhf. Preparing to unpack .../57-libnuma1_2.0.12-1+b1_armhf.deb ... Unpacking libnuma1:armhf (2.0.12-1+b1) ... Selecting previously unselected package libnuma-dev:armhf. Preparing to unpack .../58-libnuma-dev_2.0.12-1+b1_armhf.deb ... Unpacking libnuma-dev:armhf (2.0.12-1+b1) ... Selecting previously unselected package libltdl7:armhf. Preparing to unpack .../59-libltdl7_2.4.6-15_armhf.deb ... Unpacking libltdl7:armhf (2.4.6-15) ... Selecting previously unselected package libltdl-dev:armhf. Preparing to unpack .../60-libltdl-dev_2.4.6-15_armhf.deb ... Unpacking libltdl-dev:armhf (2.4.6-15) ... Selecting previously unselected package libhwloc-dev:armhf. Preparing to unpack .../61-libhwloc-dev_2.4.1+dfsg-1_armhf.deb ... Unpacking libhwloc-dev:armhf (2.4.1+dfsg-1) ... Selecting previously unselected package libpciaccess0:armhf. Preparing to unpack .../62-libpciaccess0_0.16-1_armhf.deb ... Unpacking libpciaccess0:armhf (0.16-1) ... Selecting previously unselected package libxau6:armhf. Preparing to unpack .../63-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 .../64-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 .../65-libxcb1_1.14-3_armhf.deb ... Unpacking libxcb1:armhf (1.14-3) ... Selecting previously unselected package libx11-data. Preparing to unpack .../66-libx11-data_2%3a1.7.2-1_all.deb ... Unpacking libx11-data (2:1.7.2-1) ... Selecting previously unselected package libx11-6:armhf. Preparing to unpack .../67-libx11-6_2%3a1.7.2-1_armhf.deb ... Unpacking libx11-6:armhf (2:1.7.2-1) ... Selecting previously unselected package libxext6:armhf. Preparing to unpack .../68-libxext6_2%3a1.3.3-1.1_armhf.deb ... Unpacking libxext6:armhf (2:1.3.3-1.1) ... Selecting previously unselected package libxnvctrl0:armhf. Preparing to unpack .../69-libxnvctrl0_460.91.03-1_armhf.deb ... Unpacking libxnvctrl0:armhf (460.91.03-1) ... Selecting previously unselected package ocl-icd-libopencl1:armhf. Preparing to unpack .../70-ocl-icd-libopencl1_2.2.14-2_armhf.deb ... Unpacking ocl-icd-libopencl1:armhf (2.2.14-2) ... Selecting previously unselected package libhwloc-plugins:armhf. Preparing to unpack .../71-libhwloc-plugins_2.4.1+dfsg-1_armhf.deb ... Unpacking libhwloc-plugins:armhf (2.4.1+dfsg-1) ... Selecting previously unselected package libnl-3-dev:armhf. Preparing to unpack .../72-libnl-3-dev_3.4.0-1+b1_armhf.deb ... Unpacking libnl-3-dev:armhf (3.4.0-1+b1) ... Selecting previously unselected package libnl-route-3-dev:armhf. Preparing to unpack .../73-libnl-route-3-dev_3.4.0-1+b1_armhf.deb ... Unpacking libnl-route-3-dev:armhf (3.4.0-1+b1) ... Selecting previously unselected package libibverbs-dev:armhf. Preparing to unpack .../74-libibverbs-dev_33.2-1_armhf.deb ... Unpacking libibverbs-dev:armhf (33.2-1) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../75-libjs-jquery_3.5.1+dfsg+~3.5.5-7_all.deb ... Unpacking libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Selecting previously unselected package libjs-jquery-ui. Preparing to unpack .../76-libjs-jquery-ui_1.12.1+dfsg-8_all.deb ... Unpacking libjs-jquery-ui (1.12.1+dfsg-8) ... Selecting previously unselected package libncl2. Preparing to unpack .../77-libncl2_2.1.21+git20190531.feceb81-3_armhf.deb ... Unpacking libncl2 (2.1.21+git20190531.feceb81-3) ... Selecting previously unselected package libncl-dev. Preparing to unpack .../78-libncl-dev_2.1.21+git20190531.feceb81-3_armhf.deb ... Unpacking libncl-dev (2.1.21+git20190531.feceb81-3) ... Selecting previously unselected package libpmix2:armhf. Preparing to unpack .../79-libpmix2_4.0.0-4.1_armhf.deb ... Unpacking libpmix2:armhf (4.0.0-4.1) ... Selecting previously unselected package libopenmpi3:armhf. Preparing to unpack .../80-libopenmpi3_4.1.0-10_armhf.deb ... Unpacking libopenmpi3:armhf (4.1.0-10) ... Selecting previously unselected package openmpi-common. Preparing to unpack .../81-openmpi-common_4.1.0-10_all.deb ... Unpacking openmpi-common (4.1.0-10) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../82-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ... Selecting previously unselected package libpmix-dev:armhf. Preparing to unpack .../83-libpmix-dev_4.0.0-4.1_armhf.deb ... Unpacking libpmix-dev:armhf (4.0.0-4.1) ... Selecting previously unselected package openmpi-bin. Preparing to unpack .../84-openmpi-bin_4.1.0-10_armhf.deb ... Unpacking openmpi-bin (4.1.0-10) ... Selecting previously unselected package libopenmpi-dev:armhf. 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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_2.1-4_source.changes dpkg-buildpackage: info: source package garli dpkg-buildpackage: info: source version 2.1-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille 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:355: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... configure.ac:355: the top level configure.ac:355: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... configure.ac:355: the top level configure.ac:355: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... configure.ac:355: the top level configure.ac:355: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... configure.ac:355: the top level configure.ac:355: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... configure.ac:355: the top level configure.ac:355: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: 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 thread-safe 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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... 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 we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for ranlib... ranlib checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... 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 stdlib.h... (cached) 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 -fdebug-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 -fdebug-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 -fdebug-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 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 -fdebug-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 configoptions.o configoptions.cpp adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)': adaptation.cpp:271:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 271 | fread((char *) this, 1, scalarSize, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:278:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 278 | fread((char *) improvetotal, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:280:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 280 | fread((char *) randNNI, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:281:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 281 | fread((char *) randNNInum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:283:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 283 | fread((char *) exNNI, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:284:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 284 | fread((char *) exNNInum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:286:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 286 | fread((char *) randSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:287:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 287 | fread((char *) randSPRnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:289:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 289 | fread((char *) limSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:290:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 290 | fread((char *) limSPRnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:292:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 292 | fread((char *) exlimSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:293:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 293 | fread((char *) exlimSPRnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:295:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 295 | fread((char *) randRecom, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:296:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 296 | fread((char *) randRecomnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:298:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 298 | fread((char *) bipartRecom, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:299:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | fread((char *) bipartRecomnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:301:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 301 | fread((char *) onlyBrlen, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:302:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 302 | fread((char *) onlyBrlennum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:304:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 304 | fread((char *) anyModel, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:305:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 305 | fread((char *) anyModelnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fdebug-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 configreader.o configreader.cpp configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': configoptions.cpp:337:26: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 337 | sprintf(modName, "model%d", modelNum); | ^~ configoptions.cpp:337:20: note: directive argument in the range [0, 2147483647] 337 | sprintf(modName, "model%d", modelNum); | ^~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6545, from /usr/include/c++/10/string:55, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/ios:42, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from configoptions.cpp:20: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fdebug-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 datamatr.o datamatr.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-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 funcs.o funcs.cpp configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)': configreader.cpp:602:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 602 | fread(&ch, sizeof(char), 1, file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ configreader.cpp:605:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(&ch, sizeof(char), 1, file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)': datamatr.cpp:1390:8: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1390 | fscanf(inf, "%d %d", &num_taxa, &num_chars); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fdebug-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 garlimain.o garlimain.cpp garlimain.cpp:434:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ garlimain.cpp:434:55: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ 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 -fdebug-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 garlireader.o garlireader.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-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 individual.o individual.cpp garlimain.cpp: In function 'int SubGarliMain(int)': garlimain.cpp:323:28: warning: '%d' directive writing between 2 and 10 bytes into a region of size 6 [-Wformat-overflow=] 323 | else sprintf(temp, ".run%d", rank); | ^~ garlimain.cpp:323:23: note: directive argument in the range [10, 2147483647] 323 | else sprintf(temp, ".run%d", rank); | ^~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6545, from /usr/include/c++/10/string:55, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/ios:42, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from population.h:23, from garlimain.cpp:40: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 15 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ garlimain.cpp:322:38: warning: '%d' directive writing between 1 and 11 bytes into a region of size 5 [-Wformat-overflow=] 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); | ^~ garlimain.cpp:322:32: note: directive argument in the range [-2147483648, 9] 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); | ^~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6545, from /usr/include/c++/10/string:55, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/ios:42, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from population.h:23, from garlimain.cpp:40: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 17 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from population.h:24, from funcs.h:25, from individual.cpp:28: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from population.h:24, from funcs.h:25, from individual.cpp:28: /usr/include/c++/10/bits/stl_vector.h: In member function 'void Individual::RefineStartingConditions(bool, FLOAT_TYPE)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _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 -fdebug-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 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 -fdebug-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 -fdebug-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 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 -fdebug-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 model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': model.cpp:3666:9: 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:3675:9: 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:3677:9: 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:3684:8: 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:3691:9: 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:3692:9: 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:3699:9: 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:3705:8: 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:3710:8: 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:3713:8: 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:4956:9: 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: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)': reconnode.h:388:8: 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:264:8: 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, from individual.h:21, from population.h:31, from population.cpp:45: bipartition.h: In member function 'void Bipartition::BinaryInput(FILE*&)': bipartition.h:518:8: 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:1880:7: 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:1887:7: 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:1896:7: 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fdebug-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 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 -fdebug-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 In file included from /usr/include/c++/10/vector:72, from model.h:28, from model.cpp:25: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from model.h:28, from model.cpp:25: /usr/include/c++/10/bits/stl_vector.h: In constructor 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': population.cpp:3066:22: 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:3066:19: note: directive argument in the range [1, 536870911] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6545, from /usr/include/c++/10/string:55, from population.cpp:25: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 13 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from population.cpp:23: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from model.h:28, from model.cpp:25: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc: In member function 'void Model::CalcSynonymousBranchlengthProportions(std::vector&)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from population.cpp:23: /usr/include/c++/10/bits/stl_vector.h: In member function 'void Population::BetterFinalOptimization()': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void Model::ReadGarliFormattedModelString(std::string&)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function 'void Population::InitialOptimization(Individual*, bool, FLOAT_TYPE)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void ModelPartition::ReadGarliFormattedModelStrings(std::string&)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from model.h:28, from model.cpp:25: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function 'void Model::CreateModelFromSpecification(int)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from model.h:28, from model.cpp:25: /usr/include/c++/10/bits/vector.tcc: In constructor 'ModelPartition::ModelPartition()': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from model.h:28, from model.cpp:25: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from model.h:28, from model.cpp:25: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from population.cpp:23: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, from population.cpp:23: /usr/include/c++/10/bits/stl_vector.h: In member function 'void Population::OptimizeSiteRates()': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from population.cpp:23: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 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 -fdebug-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 -fdebug-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 file included from /usr/include/c++/10/vector:67, from population.cpp:23: /usr/include/c++/10/bits/stl_vector.h: In member function 'void Population::VariableStartingTreeOptimization(bool)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from population.cpp:23: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from population.cpp:23: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from population.cpp:23: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from population.cpp:23: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _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 -fdebug-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 -fdebug-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 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 -fdebug-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:6808:7: 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:6815:7: 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:6816:7: 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:6817:7: 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:6818:7: 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:6819:7: 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:6823:7: 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:6826:7: 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:6829:7: 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:6833:7: 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:6837:7: 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:6841:7: 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:6845:8: 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:6849:8: 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:6855:8: 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:6858:8: 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:6862:8: 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:6865:8: 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:6868:8: 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:6872:8: 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:6878:8: 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:6881:8: 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/c++/10/vector:72, from tree.cpp:21: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from tree.cpp:21: /usr/include/c++/10/bits/stl_vector.h: In member function 'FLOAT_TYPE Tree::OptimizeSubsetRates(FLOAT_TYPE)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ mpic++ -g -O2 -fdebug-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 thread-safe 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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... 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 we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for ranlib... ranlib checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... 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 stdlib.h... (cached) 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 -fdebug-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 -fdebug-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 -fdebug-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 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 -fdebug-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 configoptions.o configoptions.cpp adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)': adaptation.cpp:271:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 271 | fread((char *) this, 1, scalarSize, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:278:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 278 | fread((char *) improvetotal, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:280:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 280 | fread((char *) randNNI, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:281:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 281 | fread((char *) randNNInum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:283:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 283 | fread((char *) exNNI, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:284:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 284 | fread((char *) exNNInum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:286:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 286 | fread((char *) randSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:287:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 287 | fread((char *) randSPRnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:289:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 289 | fread((char *) limSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:290:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 290 | fread((char *) limSPRnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:292:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 292 | fread((char *) exlimSPR, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:293:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 293 | fread((char *) exlimSPRnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:295:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 295 | fread((char *) randRecom, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:296:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 296 | fread((char *) randRecomnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:298:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 298 | fread((char *) bipartRecom, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:299:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | fread((char *) bipartRecomnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:301:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 301 | fread((char *) onlyBrlen, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:302:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 302 | fread((char *) onlyBrlennum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:304:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 304 | fread((char *) anyModel, sizeof(FLOAT_TYPE), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp:305:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 305 | fread((char *) anyModelnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': configoptions.cpp:337:26: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 337 | sprintf(modName, "model%d", modelNum); | ^~ configoptions.cpp:337:20: note: directive argument in the range [0, 2147483647] 337 | sprintf(modName, "model%d", modelNum); | ^~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6545, from /usr/include/c++/10/string:55, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/ios:42, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from configoptions.cpp:20: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fdebug-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 configreader.o configreader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-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 datamatr.o datamatr.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-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 funcs.o funcs.cpp configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)': configreader.cpp:602:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 602 | fread(&ch, sizeof(char), 1, file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ configreader.cpp:605:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(&ch, sizeof(char), 1, file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)': datamatr.cpp:1390:8: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1390 | fscanf(inf, "%d %d", &num_taxa, &num_chars); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-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 garlimain.o garlimain.cpp garlimain.cpp:434:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ garlimain.cpp:434:55: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ 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 -fdebug-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 garlireader.o garlireader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -fdebug-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 individual.o individual.cpp In file included from /usr/include/c++/10/vector:72, from population.h:24, from funcs.h:25, from individual.cpp:28: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from population.h:24, from funcs.h:25, from individual.cpp:28: /usr/include/c++/10/bits/stl_vector.h: In member function 'void Individual::RefineStartingConditions(bool, FLOAT_TYPE)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _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 -fdebug-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 -fdebug-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 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 -fdebug-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 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 -fdebug-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 model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': model.cpp:3666:9: 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:3675:9: 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:3677:9: 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:3684:8: 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:3691:9: 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:3692:9: 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:3699:9: 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:3705:8: 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:3710:8: 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:3713:8: 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:4956:9: 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: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)': reconnode.h:388:8: 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:264:8: 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, from individual.h:21, from population.h:31, from population.cpp:45: bipartition.h: In member function 'void Bipartition::BinaryInput(FILE*&)': bipartition.h:518:8: 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:1880:7: 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:1887:7: 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:1896:7: 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 -fdebug-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 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 -fdebug-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++/10/vector:72, from model.h:28, from model.cpp:25: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from model.h:28, from model.cpp:25: /usr/include/c++/10/bits/stl_vector.h: In constructor 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': population.cpp:3066:22: 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:3066:19: note: directive argument in the range [1, 536870911] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6545, from /usr/include/c++/10/string:55, from population.cpp:25: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 13 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from population.cpp:23: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from model.h:28, from model.cpp:25: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc: In member function 'void Model::CalcSynonymousBranchlengthProportions(std::vector&)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void Model::ReadGarliFormattedModelString(std::string&)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from population.cpp:23: /usr/include/c++/10/bits/stl_vector.h: In member function 'void Population::BetterFinalOptimization()': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function 'void Population::InitialOptimization(Individual*, bool, FLOAT_TYPE)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void ModelPartition::ReadGarliFormattedModelStrings(std::string&)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from model.h:28, from model.cpp:25: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function 'void Model::CreateModelFromSpecification(int)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from model.h:28, from model.cpp:25: /usr/include/c++/10/bits/vector.tcc: In constructor 'ModelPartition::ModelPartition()': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from model.h:28, from model.cpp:25: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from model.h:28, from model.cpp:25: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from population.cpp:23: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, from population.cpp:23: /usr/include/c++/10/bits/stl_vector.h: In member function 'void Population::OptimizeSiteRates()': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from population.cpp:23: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 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 -fdebug-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 -fdebug-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 In file included from /usr/include/c++/10/vector:67, from population.cpp:23: /usr/include/c++/10/bits/stl_vector.h: In member function 'void Population::VariableStartingTreeOptimization(bool)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from population.cpp:23: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from population.cpp:23: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from population.cpp:23: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from population.cpp:23: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _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 -fdebug-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 -fdebug-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 -fdebug-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 tree.cpp: In member function 'void Tree::ReadBinaryFormattedTree(FILE*)': tree.cpp:6808:7: 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:6815:7: 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:6816:7: 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:6817:7: 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:6818:7: 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:6819:7: 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:6823:7: 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:6826:7: 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:6829:7: 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:6833:7: 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:6837:7: 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:6841:7: 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:6845:8: 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:6849:8: 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:6855:8: 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:6858:8: 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:6862:8: 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:6865:8: 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:6868:8: 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:6872:8: 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:6878:8: 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:6881:8: 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/c++/10/vector:72, from tree.cpp:21: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from tree.cpp:21: /usr/include/c++/10/bits/stl_vector.h: In member function 'FLOAT_TYPE Tree::OptimizeSubsetRates(FLOAT_TYPE)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -g -O2 -fdebug-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/' \{\} \; dh_auto_test make -j3 check 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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:+ 77.837 (branch= 2.27 scale= 0.00 alpha= 4.14 freqs= 11.12 rel rates= 3.27 pinv= 0.89 subset rates= 56.14) pass 3:+ 48.839 (branch= 6.87 scale= 0.74 alpha= 4.53 freqs= 1.22 rel rates= 1.34 pinv= 0.01 subset rates= 34.13) pass 4:+ 15.219 (branch= 0.00 scale= 0.77 alpha= 0.64 freqs= 1.21 rel rates= 0.55 pinv= 0.01 subset rates= 12.04) pass 5:+ 5.796 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.10 rel rates= 0.77 pinv= 0.01 subset rates= 4.91) pass 6:+ 0.129 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.09 rel rates= 0.01 pinv= 0.01 subset rates= 0.00) lnL after optimization: -13342.3959 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 25 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 : -3355.4764 (branch= 0.9931 alpha= 0.0078 pinv= 0.0071 eq freqs= 0.1960 rel rates= 1.3028 subset rates= 0.3876) pass 2 : -3354.0482 (branch= 0.5297 alpha= 0.0099 pinv= 0.0115 eq freqs= 0.0231 rel rates= 0.6812 subset rates= 0.1727) pass 3 : -3353.1946 (branch= 0.2772 alpha= 0.0000 pinv= 0.0075 eq freqs= 0.0147 rel rates= 0.4602 subset rates= 0.0939) pass 4 : -3352.5934 (branch= 0.1599 alpha= 0.0032 pinv= 0.0158 eq freqs= 0.0056 rel rates= 0.3608 subset rates= 0.0560) pass 5 : -3352.1469 (branch= 0.0988 alpha= 0.0053 pinv= 0.0164 eq freqs= 0.0017 rel rates= 0.2976 subset rates= 0.0266) pass 6 : -3351.7991 (branch= 0.0531 alpha= 0.0063 pinv= 0.0165 eq freqs= 0.0007 rel rates= 0.2541 subset rates= 0.0172) pass 7 : -3351.5304 (branch= 0.0324 alpha= 0.0091 pinv= 0.0158 eq freqs= 0.0009 rel rates= 0.2001 subset rates= 0.0104) pass 8 : -3351.3153 (branch= 0.0201 alpha= 0.0096 pinv= 0.0150 eq freqs= 0.0005 rel rates= 0.1637 subset rates= 0.0060) pass 9 : -3351.1425 (branch= 0.0106 alpha= 0.0105 pinv= 0.0140 eq freqs= 0.0004 rel rates= 0.1325 subset rates= 0.0048) pass 10: -3351.0011 (branch= 0.0071 alpha= 0.0106 pinv= 0.0138 eq freqs= 0.0004 rel rates= 0.1065 subset rates= 0.0028) pass 11: -3350.8848 (branch= 0.0047 alpha= 0.0103 pinv= 0.0127 eq freqs= 0.0003 rel rates= 0.0865 subset rates= 0.0018) pass 12: -3350.7882 (branch= 0.0032 alpha= 0.0098 pinv= 0.0117 eq freqs= 0.0002 rel rates= 0.0707 subset rates= 0.0011) pass 13: -3350.7085 (branch= 0.0021 alpha= 0.0093 pinv= 0.0106 eq freqs= 0.0002 rel rates= 0.0575 subset rates= 0.0000) pass 14: -3350.6395 (branch= 0.0005 alpha= 0.0090 pinv= 0.0096 eq freqs= 0.0001 rel rates= 0.0485 subset rates= 0.0012) pass 15: -3350.5829 (branch= 0.0010 alpha= 0.0083 pinv= 0.0081 eq freqs= 0.0001 rel rates= 0.0392 subset rates= 0.0000) pass 16: -3350.5343 (branch= 0.0003 alpha= 0.0075 pinv= 0.0073 eq freqs= 0.0001 rel rates= 0.0334 subset rates= 0.0000) pass 17: -3350.4929 (branch= 0.0001 alpha= 0.0072 pinv= 0.0066 eq freqs= 0.0001 rel rates= 0.0275 subset rates= 0.0000) pass 18: -3350.4572 (branch= 0.0000 alpha= 0.0066 pinv= 0.0059 eq freqs= 0.0001 rel rates= 0.0230 subset rates= 0.0000) pass 19: -3350.4265 (branch= 0.0000 alpha= 0.0059 pinv= 0.0053 eq freqs= 0.0001 rel rates= 0.0195 subset rates= 0.0000) pass 20: -3350.4001 (branch= 0.0000 alpha= 0.0052 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0165 subset rates= 0.0000) optimization up to ... pass 30: -3350.2718 (branch= 0.0000 alpha= 0.0276 pinv= 0.0250 eq freqs= 0.0002 rel rates= 0.0754 subset rates= 0.0000) optimization up to ... pass 40: -3350.2422 (branch= 0.0000 alpha= 0.0066 pinv= 0.0061 eq freqs= 0.0000 rel rates= 0.0169 subset rates= 0.0000) optimization up to ... pass 50: -3350.2356 (branch= 0.0000 alpha= 0.0013 pinv= 0.0012 eq freqs= 0.0000 rel rates= 0.0041 subset rates= 0.0000) optimization up to ... pass 60: -3350.2341 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0011 subset rates= 0.0000) optimization up to ... pass 70: -3350.2338 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) optimization up to ... pass 80: -3350.2336 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) Looking for minimum length branches... Final score = -3350.2337 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 : -3350.2337 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 10.4 2.687 0.001 21.85 1 0.333 0.222 0.157 0.288 0.580 0.366 Partition model subset 2: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) rep 1: 0.787 1.820 0.180 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.g.dnaBnoZ.best.all.tre ***********TEST************** ***Score is 3350.23368 ***Expected is 3350.2345 ***SCORE DIFFERENCE IS -.00082 ***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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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:+ 2061.639 (branch=1982.89 scale= 74.28 freqs= 0.89 rel rates= 3.59) pass 2:+ 221.909 (branch= 220.60 scale= 0.00 freqs= 0.86 rel rates= 0.45) pass 3:+ 4.933 (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= 0.03) pass 5:+ 0.068 (branch= 0.07 scale= 0.00 freqs= 0.00 rel rates= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00 freqs= 0.00 rel rates= 0.00) lnL after optimization: -16071.0623 gen current_lnL precision last_tree_imp 0 -16071.0623 0.010 0 100 -14502.0537 0.010 73 200 -14502.0244 0.010 73 300 -14501.0191 0.010 73 400 -14500.3883 0.010 73 500 -14499.9882 0.010 73 600 -14499.5129 0.010 73 700 -14499.2261 0.010 73 800 -14499.0596 0.010 73 900 -14499.0531 0.010 73 1000 -14499.0531 0.010 73 1100 -14498.9756 0.010 73 1200 -14498.9755 0.010 73 1300 -14498.9751 0.010 73 1400 -14498.9751 0.010 73 1500 -14498.9751 0.010 73 1600 -14498.9603 0.010 73 Reached termination condition! last topological improvement at gen 73 Improvement over last 500 gen = 0.01531 Current score = -14498.9603 Performing final optimizations... pass 1 : -14498.9253 (branch= 0.0118 eq freqs= 0.0170 rel rates= 0.0062) pass 2 : -14498.8967 (branch= 0.0212 eq freqs= 0.0030 rel rates= 0.0044) pass 3 : -14498.8929 (branch= 0.0036 eq freqs= 0.0001 rel rates= 0.0001) pass 4 : -14498.8902 (branch= 0.0009 eq freqs= 0.0009 rel rates= 0.0009) pass 5 : -14498.8871 (branch= 0.0009 eq freqs= 0.0008 rel rates= 0.0015) pass 6 : -14498.8866 (branch= 0.0002 eq freqs= 0.0003 rel rates= 0.0001) pass 7 : -14498.8862 (branch= 0.0002 eq freqs= 0.0000 rel rates= 0.0001) pass 8 : -14498.8859 (branch= 0.0001 eq freqs= 0.0000 rel rates= 0.0001) pass 9 : -14498.8857 (branch= 0.0001 eq freqs= 0.0000 rel rates= 0.0001) pass 10: -14498.8856 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) pass 11: -14498.8855 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) pass 12: -14498.8854 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) 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: -14498.8854 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 16: -14498.8854 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 17: -14498.8854 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -14498.8854 Time used = 0 hours, 0 minutes and 8 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.870, AG = 3.674, AT = 1.223, CG = 1.855, 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 : -14498.8854 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 1.87 3.674 1.223 1.855 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 14486.03890 ***Expected is 14486.03829 ***SCORE DIFFERENCE IS .00061 ***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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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:+ 36.659 (branch= 1.45 scale= 0.00 alpha= 0.68 freqs= 18.87 rel rates= 15.00 pinv= 0.00 subset rates= 0.65) pass 5:+ 4.518 (branch= 0.00 scale= 0.00 alpha= 0.02 freqs= 3.51 rel rates= 0.99 pinv= 0.01 subset rates= 0.00) pass 6:+ 0.902 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.10 rel rates= 0.78 pinv= 0.01 subset rates= 0.00) pass 7:+ 0.107 (branch= 0.00 scale= 0.00 alpha= 0.02 freqs= 0.08 rel rates= 0.01 pinv= 0.01 subset rates= 0.00) lnL after optimization: -13315.7940 Current score = -13315.7940 Performing final optimizations... pass 1 : -13309.3736 (branch= 2.8300 alpha= 0.8831 pinv= 0.0159 eq freqs= 0.2323 rel rates= 1.8487 subset rates= 0.6104) pass 2 : -13307.8666 (branch= 0.4306 alpha= 0.1983 pinv= 0.0128 eq freqs= 0.1251 rel rates= 0.6703 subset rates= 0.0699) pass 3 : -13307.2566 (branch= 0.1076 alpha= 0.0596 pinv= 0.0033 eq freqs= 0.0085 rel rates= 0.4228 subset rates= 0.0083) pass 4 : -13306.9006 (branch= 0.0263 alpha= 0.0197 pinv= 0.0028 eq freqs= 0.0084 rel rates= 0.2943 subset rates= 0.0045) pass 5 : -13306.6742 (branch= 0.0056 alpha= 0.0047 pinv= 0.0011 eq freqs= 0.0083 rel rates= 0.2058 subset rates= 0.0011) pass 6 : -13306.5202 (branch= 0.0037 alpha= 0.0018 pinv= 0.0004 eq freqs= 0.0051 rel rates= 0.1424 subset rates= 0.0007) pass 7 : -13306.4174 (branch= 0.0019 alpha= 0.0007 pinv= 0.0002 eq freqs= 0.0032 rel rates= 0.0968 subset rates= 0.0000) pass 8 : -13306.3495 (branch= 0.0011 alpha= 0.0003 pinv= 0.0001 eq freqs= 0.0019 rel rates= 0.0645 subset rates= 0.0000) pass 9 : -13306.3037 (branch= 0.0002 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0016 rel rates= 0.0438 subset rates= 0.0000) pass 10: -13306.2722 (branch= 0.0002 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0011 rel rates= 0.0301 subset rates= 0.0000) pass 11: -13306.2514 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0201 subset rates= 0.0000) pass 12: -13306.2371 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0138 subset rates= 0.0000) pass 13: -13306.2272 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0095 subset rates= 0.0000) pass 14: -13306.2206 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0065 subset rates= 0.0000) pass 15: -13306.2160 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0044 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: -13306.2095 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013 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: -13306.2063 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0013 subset rates= 0.0000) optimization up to ... pass 37: -13306.2062 (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 = -13306.2062 Time used = 0 hours, 0 minutes and 9 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -13306.2062 Parameter estimates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha rep 1: 1.974 2.576 1.414 1.414 3.72 1 0.310 0.177 0.297 0.216 0.407 Partition model subset 2: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha rep 1: 4.372 7.056 1.609 7.056 4.372 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 4.94 3.388 0.4594 4.94 1 0.157 0.354 0.287 0.202 4.032 0.033 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 1.694 0.540 0.300 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 13306.20620 ***Expected is 13306.20608 ***SCORE DIFFERENCE IS .00012 ***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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 Using NCL version 2.1.17 ####################################################### Reading config file ./const/n.neg.const.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### Loading constraints from file data/z.neg.const.tre Found 1 negatively (conversely) constrained bipartition Bipartition 1: (1,2,3,4,5,11) | (6,7,8,9,10) STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0334 0.2271 0.2519 0.2271 0.8203 0.2271 2.8944 0.2271 Starting with seed=1 creating likelihood stepwise addition starting tree (compatible with constraints)... number of taxa added: 4 5 6 Optimizing parameters... improved 0.004 lnL Optimizing branchlengths... improved 0.000 lnL 7 8 9 10 11 Initial ln Likelihood: -227.5619 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 4.671 (branch= 0.06 scale= 0.00 alpha= 0.00 freqs= 2.00 rel rates= 2.60 pinv= 0.00) pass 2:+ 0.025 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.02 rel rates= 0.00 pinv= 0.00) lnL after optimization: -222.8653 gen current_lnL precision last_tree_imp 0 -222.8653 0.500 0 500 -213.0501 0.500 495 1000 -212.5074 0.500 628 Optimization precision reduced Optimizing parameters... improved 1.330 lnL Optimizing branchlengths... improved 0.015 lnL 1500 -210.8784 0.010 1215 2000 -210.6679 0.010 1215 2500 -210.6042 0.010 1215 3000 -210.5104 0.010 1215 3500 -210.4073 0.010 1215 Reached termination condition! last topological improvement at gen 1215 Improvement over last 500 gen = 0.04868 Current score = -210.3681 Performing final optimizations... pass 1 : -210.0052 (branch= 0.0000 alpha= 0.0802 pinv= 0.2367 eq freqs= 0.0000 rel rates= 0.0460) pass 2 : -209.4270 (branch= 0.0069 alpha= 0.3216 pinv= 0.2322 eq freqs= 0.0050 rel rates= 0.0123) pass 3 : -209.2882 (branch= 0.0446 alpha= 0.0682 pinv= 0.0071 eq freqs= 0.0085 rel rates= 0.0106) pass 4 : -209.2345 (branch= 0.0311 alpha= 0.0156 pinv= 0.0010 eq freqs= 0.0010 rel rates= 0.0050) pass 5 : -209.1890 (branch= 0.0296 alpha= 0.0089 pinv= 0.0005 eq freqs= 0.0000 rel rates= 0.0066) pass 6 : -209.1627 (branch= 0.0122 alpha= 0.0046 pinv= 0.0005 eq freqs= 0.0005 rel rates= 0.0084) pass 7 : -209.1415 (branch= 0.0075 alpha= 0.0024 pinv= 0.0002 eq freqs= 0.0007 rel rates= 0.0104) pass 8 : -209.1265 (branch= 0.0040 alpha= 0.0003 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0102) pass 9 : -209.1154 (branch= 0.0014 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0092) pass 10: -209.1062 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0082) pass 11: -209.0984 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0073) pass 12: -209.0914 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0066) pass 13: -209.0851 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0061) pass 14: -209.0792 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0057) pass 15: -209.0738 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0053) pass 16: -209.0686 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0051) pass 17: -209.0639 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) pass 18: -209.0591 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 19: -209.0543 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 20: -209.0491 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) optimization up to ... pass 30: -208.9533 (branch= 0.0162 alpha= 0.0000 pinv= 0.0005 eq freqs= 0.0029 rel rates= 0.0761) optimization up to ... pass 40: -208.7769 (branch= 0.0286 alpha= 0.0000 pinv= 0.0019 eq freqs= 0.0089 rel rates= 0.1370) optimization up to ... pass 50: -208.6663 (branch= 0.0059 alpha= 0.0000 pinv= 0.0008 eq freqs= 0.0032 rel rates= 0.1007) optimization up to ... pass 60: -208.6032 (branch= 0.0007 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0619) optimization up to ... pass 70: -208.5595 (branch= 0.0002 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0433) optimization up to ... pass 80: -208.5271 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0321) optimization up to ... pass 90: -208.5025 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0245) optimization up to ... pass 100: -208.4830 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0193) optimization up to ... pass 110: -208.4672 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0156) optimization up to ... pass 120: -208.4543 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0129) optimization up to ... pass 130: -208.4435 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0107) optimization up to ... pass 140: -208.4344 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0091) optimization up to ... pass 150: -208.4265 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0078) optimization up to ... pass 160: -208.4198 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) optimization up to ... pass 170: -208.4140 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) optimization up to ... pass 180: -208.4089 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0051) optimization up to ... pass 190: -208.4044 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0045) optimization up to ... pass 200: -208.4003 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) optimization up to ... pass 210: -208.3967 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0036) optimization up to ... pass 220: -208.3935 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... pass 230: -208.3906 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) optimization up to ... pass 240: -208.3879 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0027) optimization up to ... pass 250: -208.3855 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... pass 260: -208.3832 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... pass 270: -208.3812 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... pass 280: -208.3793 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 290: -208.3775 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 300: -208.3759 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 310: -208.3744 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... pass 320: -208.3729 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 330: -208.3716 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... pass 340: -208.3704 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 350: -208.3692 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 360: -208.3681 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 370: -208.3671 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 380: -208.3661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 390: -208.3652 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 400: -208.3643 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 410: -208.3635 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 420: -208.3627 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 430: -208.3620 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 440: -208.3613 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 450: -208.3606 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 460: -208.3600 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 470: -208.3594 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 480: -208.3590 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... pass 490: -208.3588 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... Final score = -208.3588 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 = 120.664, AG = 186.216, AT = 6.875, CG = 202.174, CT = 192.375, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2225 0.2906 0.2035 0.2835 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 999.9000 with an invariant (invariable) site category, proportion estimated 0.2781 Substitution rate categories under this model: rate proportion 0.0000 0.2781 0.9601 0.1805 0.9894 0.1805 1.0100 0.1805 1.0405 0.1805 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 2 branches were collapsed. ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -208.3588 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: 120.7 186.2 6.875 202.2 192.4 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL rep 1: 1.881 Saving final tree from best search rep (#1) to con.n.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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 -212.3293 0.010 825 1500 -212.1961 0.010 825 2000 -211.9102 0.010 825 2500 -211.7712 0.010 825 3000 -211.6573 0.010 825 3500 -211.4395 0.010 825 4000 -211.3140 0.010 825 Reached termination condition! last topological improvement at gen 825 Improvement over last 500 gen = 0.03816 Current score = -211.2858 Performing final optimizations... pass 1 : -208.9986 (branch= 0.0000 alpha= 0.7597 pinv= 1.4361 eq freqs= 0.0062 rel rates= 0.0851) pass 2 : -208.6334 (branch= 0.0392 alpha= 0.2794 pinv= 0.0091 eq freqs= 0.0107 rel rates= 0.0269) pass 3 : -208.5093 (branch= 0.0259 alpha= 0.0705 pinv= 0.0000 eq freqs= 0.0020 rel rates= 0.0257) pass 4 : -208.4829 (branch= 0.0031 alpha= 0.0018 pinv= 0.0016 eq freqs= 0.0000 rel rates= 0.0198) pass 5 : -208.4602 (branch= 0.0038 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0184) pass 6 : -208.4428 (branch= 0.0002 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0003 rel rates= 0.0168) pass 7 : -208.4256 (branch= 0.0009 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0163) pass 8 : -208.4103 (branch= 0.0003 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0147) pass 9 : -208.3964 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0137) pass 10: -208.3841 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0122) pass 11: -208.3725 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0115) pass 12: -208.3617 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0107) pass 13: -208.3521 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0096) pass 14: -208.3432 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0089) pass 15: -208.3349 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0082) pass 16: -208.3272 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0077) pass 17: -208.3200 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0072) pass 18: -208.3134 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) pass 19: -208.3070 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0063) pass 20: -208.3012 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) optimization up to ... pass 30: -208.2568 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0442) optimization up to ... pass 40: -208.2294 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0273) optimization up to ... pass 50: -208.2106 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0188) optimization up to ... pass 60: -208.1969 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0136) optimization up to ... pass 70: -208.1866 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0104) optimization up to ... pass 80: -208.1783 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0083) optimization up to ... pass 90: -208.1716 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) optimization up to ... pass 100: -208.1661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0055) optimization up to ... pass 110: -208.1615 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) optimization up to ... pass 120: -208.1575 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0039) optimization up to ... pass 130: -208.1541 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) optimization up to ... pass 140: -208.1511 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0030) optimization up to ... pass 150: -208.1485 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) optimization up to ... pass 160: -208.1461 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... pass 170: -208.1440 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) optimization up to ... pass 180: -208.1421 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 190: -208.1404 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 200: -208.1389 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 210: -208.1374 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 220: -208.1361 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... pass 230: -208.1349 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 240: -208.1338 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 250: -208.1328 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 260: -208.1318 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 270: -208.1309 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 280: -208.1301 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 290: -208.1293 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 300: -208.1285 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 310: -208.1278 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 320: -208.1272 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 330: -208.1265 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 340: -208.1260 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 350: -208.1254 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 360: -208.1249 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) optimization up to ... pass 370: -208.1244 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) optimization up to ... pass 372: -208.1243 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.1243 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 = 22.238, AG = 32.312, AT = 0.001, CG = 36.400, CT = 80.316, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2210 0.3445 0.2161 0.2184 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 999.9000 with an invariant (invariable) site category, proportion estimated 0.3383 Substitution rate categories under this model: rate proportion 0.0000 0.3383 0.9601 0.1654 0.9894 0.1654 1.0100 0.1654 1.0405 0.1654 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -208.1243 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 22.24 32.31 0.001 36.4 80.32 1 0.221 0.344 0.216 0.218 999.900 0.338 Treelengths: TL rep 1: 2.421 Saving final tree from best search rep (#1) to con.n.negBack.const.best.tre ####################################################### TREEFILES PASS Running constraint test n.pos.const Running constraint test n.pos.const Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 -210.7510 0.010 2883 3500 -210.7005 0.010 2883 4000 -210.6775 0.010 2883 4500 -210.6526 0.010 2883 5000 -210.5940 0.010 4692 5500 -210.5367 0.010 5207 6000 -210.4081 0.010 5812 6500 -210.3701 0.010 5812 7000 -210.3450 0.010 5812 7500 -210.3290 0.010 5812 8000 -210.1893 0.010 7789 8500 -210.0964 0.010 7789 9000 -210.0080 0.010 7789 9500 -209.9339 0.010 7789 Reached termination condition! last topological improvement at gen 7789 Improvement over last 500 gen = 0.04494 Current score = -209.9271 Performing final optimizations... pass 1 : -209.4421 (branch= 0.0000 alpha= 0.1471 pinv= 0.2741 eq freqs= 0.0000 rel rates= 0.0638) pass 2 : -209.3055 (branch= 0.0127 alpha= 0.0938 pinv= 0.0161 eq freqs= 0.0000 rel rates= 0.0141) pass 3 : -209.2298 (branch= 0.0405 alpha= 0.0220 pinv= 0.0028 eq freqs= 0.0059 rel rates= 0.0045) pass 4 : -209.1644 (branch= 0.0419 alpha= 0.0176 pinv= 0.0013 eq freqs= 0.0008 rel rates= 0.0038) pass 5 : -209.1063 (branch= 0.0352 alpha= 0.0144 pinv= 0.0009 eq freqs= 0.0021 rel rates= 0.0057) pass 6 : -209.0754 (branch= 0.0142 alpha= 0.0061 pinv= 0.0000 eq freqs= 0.0016 rel rates= 0.0090) pass 7 : -209.0608 (branch= 0.0053 alpha= 0.0010 pinv= 0.0000 eq freqs= 0.0013 rel rates= 0.0071) pass 8 : -209.0532 (branch= 0.0012 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0058) pass 9 : -209.0466 (branch= 0.0009 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0055) pass 10: -209.0398 (branch= 0.0010 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0056) pass 11: -209.0325 (branch= 0.0011 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0059) pass 12: -209.0245 (branch= 0.0014 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0063) pass 13: -209.0156 (branch= 0.0017 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0069) pass 14: -209.0054 (branch= 0.0021 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0076) pass 15: -208.9941 (branch= 0.0025 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0004 rel rates= 0.0084) pass 16: -208.9815 (branch= 0.0028 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0005 rel rates= 0.0092) pass 17: -208.9676 (branch= 0.0030 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0006 rel rates= 0.0101) pass 18: -208.9527 (branch= 0.0032 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0007 rel rates= 0.0109) pass 19: -208.9367 (branch= 0.0033 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0008 rel rates= 0.0117) pass 20: -208.9198 (branch= 0.0033 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0009 rel rates= 0.0125) optimization up to ... pass 30: -208.7457 (branch= 0.0247 alpha= 0.0000 pinv= 0.0020 eq freqs= 0.0087 rel rates= 0.1387) optimization up to ... pass 40: -208.6504 (branch= 0.0033 alpha= 0.0000 pinv= 0.0005 eq freqs= 0.0019 rel rates= 0.0896) optimization up to ... pass 50: -208.5925 (branch= 0.0005 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0570) optimization up to ... pass 60: -208.5515 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0406) optimization up to ... pass 70: -208.5209 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0303) optimization up to ... pass 80: -208.4974 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0233) optimization up to ... pass 90: -208.4788 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0185) optimization up to ... pass 100: -208.4637 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0150) optimization up to ... pass 110: -208.4512 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0124) optimization up to ... pass 120: -208.4408 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0104) optimization up to ... pass 130: -208.4319 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0089) optimization up to ... pass 140: -208.4243 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0076) optimization up to ... pass 150: -208.4177 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0065) optimization up to ... pass 160: -208.4120 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0057) optimization up to ... pass 170: -208.4070 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) optimization up to ... pass 180: -208.4027 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0044) optimization up to ... pass 190: -208.3988 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0039) optimization up to ... pass 200: -208.3953 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0035) optimization up to ... pass 210: -208.3921 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... pass 220: -208.3892 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) optimization up to ... pass 230: -208.3866 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) optimization up to ... pass 240: -208.3842 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... pass 250: -208.3820 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... pass 260: -208.3799 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... pass 270: -208.3781 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 280: -208.3763 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 290: -208.3747 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 300: -208.3732 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... pass 310: -208.3718 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 320: -208.3705 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... pass 330: -208.3693 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 340: -208.3682 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 350: -208.3671 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 360: -208.3661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 370: -208.3651 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 380: -208.3642 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 390: -208.3633 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 400: -208.3625 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 410: -208.3618 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 420: -208.3610 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 430: -208.3603 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 440: -208.3597 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 450: -208.3591 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) optimization up to ... pass 460: -208.3588 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... pass 470: -208.3585 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... pass 480: -208.3582 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... pass 490: -208.3579 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... pass 496: -208.3578 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... Final score = -208.3578 Time used = 0 hours, 0 minutes and 9 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 121.356, AG = 187.750, AT = 6.914, CG = 203.540, CT = 193.592, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2225 0.2906 0.2034 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) 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. ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -208.3578 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: 121.4 187.8 6.914 203.5 193.6 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL rep 1: 1.881 Saving final tree from best search rep (#1) to con.n.pos.const.best.tre ####################################################### TREEFILES PASS Running constraint test n.posBack.const Running constraint test n.posBack.const Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 -210.7768 0.010 1230 2500 -210.6533 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 : -210.1947 (branch= 0.0000 alpha= 0.1301 pinv= 0.2110 eq freqs= 0.0000 rel rates= 0.0608) pass 2 : -209.5813 (branch= 0.0039 alpha= 0.3412 pinv= 0.2326 eq freqs= 0.0032 rel rates= 0.0325) pass 3 : -209.3378 (branch= 0.0520 alpha= 0.1491 pinv= 0.0227 eq freqs= 0.0088 rel rates= 0.0108) pass 4 : -209.2553 (branch= 0.0519 alpha= 0.0228 pinv= 0.0016 eq freqs= 0.0022 rel rates= 0.0040) pass 5 : -209.2051 (branch= 0.0347 alpha= 0.0093 pinv= 0.0010 eq freqs= 0.0004 rel rates= 0.0048) pass 6 : -209.1745 (branch= 0.0174 alpha= 0.0054 pinv= 0.0003 eq freqs= 0.0006 rel rates= 0.0069) pass 7 : -209.1480 (branch= 0.0106 alpha= 0.0034 pinv= 0.0002 eq freqs= 0.0012 rel rates= 0.0110) pass 8 : -209.1257 (branch= 0.0071 alpha= 0.0024 pinv= 0.0000 eq freqs= 0.0011 rel rates= 0.0117) pass 9 : -209.1113 (branch= 0.0035 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0009 rel rates= 0.0099) pass 10: -209.1008 (branch= 0.0012 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0086) pass 11: -209.0924 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0075) pass 12: -209.0853 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0066) pass 13: -209.0790 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0059) pass 14: -209.0734 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0054) pass 15: -209.0682 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0051) pass 16: -209.0633 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 17: -209.0585 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 18: -209.0536 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) pass 19: -209.0483 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) pass 20: -209.0426 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0052) optimization up to ... pass 30: -208.9337 (branch= 0.0197 alpha= 0.0000 pinv= 0.0007 eq freqs= 0.0039 rel rates= 0.0846) optimization up to ... pass 40: -208.7577 (branch= 0.0267 alpha= 0.0000 pinv= 0.0020 eq freqs= 0.0087 rel rates= 0.1386) optimization up to ... pass 50: -208.6568 (branch= 0.0042 alpha= 0.0000 pinv= 0.0006 eq freqs= 0.0023 rel rates= 0.0938) optimization up to ... pass 60: -208.5970 (branch= 0.0005 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0589) optimization up to ... pass 70: -208.5550 (branch= 0.0002 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0416) optimization up to ... pass 80: -208.5238 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0309) optimization up to ... pass 90: -208.4999 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0237) optimization up to ... pass 100: -208.4809 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0188) optimization up to ... pass 110: -208.4655 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0153) optimization up to ... pass 120: -208.4529 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0126) optimization up to ... pass 130: -208.4424 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0104) optimization up to ... pass 140: -208.4333 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0090) optimization up to ... pass 150: -208.4256 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0077) optimization up to ... pass 160: -208.4189 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0066) optimization up to ... pass 170: -208.4132 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0057) optimization up to ... pass 180: -208.4082 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) optimization up to ... pass 190: -208.4038 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0044) optimization up to ... pass 200: -208.3998 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0039) optimization up to ... pass 210: -208.3963 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0035) optimization up to ... pass 220: -208.3931 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... pass 230: -208.3902 (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: -208.3851 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... pass 260: -208.3829 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... pass 270: -208.3809 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... pass 280: -208.3790 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 290: -208.3773 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 300: -208.3757 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 310: -208.3742 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... pass 320: -208.3727 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 330: -208.3714 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... pass 340: -208.3702 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 350: -208.3691 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 360: -208.3680 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 370: -208.3669 (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: -208.3642 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 410: -208.3634 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 420: -208.3626 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 430: -208.3619 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 440: -208.3612 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 450: -208.3605 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 460: -208.3599 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 470: -208.3593 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 480: -208.3587 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 490: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) optimization up to ... pass 492: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.3584 Time used = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 122.573, AG = 189.142, AT = 6.992, CG = 205.361, CT = 195.393, 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 0.2780 Substitution rate categories under this model: rate proportion 0.0000 0.2780 0.9601 0.1805 0.9894 0.1805 1.0100 0.1805 1.0405 0.1805 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 2 branches were collapsed. NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with a positive constraint, it is possible for a constrained branch itself to be collapsed. If you care, be careful to check whether this has happened or turn off branch collapsing. ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -208.3584 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 122.6 189.1 6.992 205.4 195.4 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL rep 1: 1.881 Saving final tree from best search rep (#1) to con.n.posBack.const.best.tre ####################################################### TREEFILES PASS ************************** Running output tests ... ************************** Running output test a.G3 Running output test a.G3 Running GARLI Version 2.1. () ->Single processor version for 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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:+ 77.837 (branch= 2.27 scale= 0.00 alpha= 4.14 freqs= 11.12 rel rates= 3.27 pinv= 0.89 subset rates= 56.14) pass 3:+ 48.839 (branch= 6.87 scale= 0.74 alpha= 4.53 freqs= 1.22 rel rates= 1.34 pinv= 0.01 subset rates= 34.13) pass 4:+ 15.219 (branch= 0.00 scale= 0.77 alpha= 0.64 freqs= 1.21 rel rates= 0.55 pinv= 0.01 subset rates= 12.04) pass 5:+ 5.796 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.10 rel rates= 0.77 pinv= 0.01 subset rates= 4.91) pass 6:+ 0.129 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.09 rel rates= 0.01 pinv= 0.01 subset rates= 0.00) lnL after optimization: -13342.3959 gen current_lnL precision last_tree_imp 0 -13342.3959 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 = 2.515, CG = 0.379, CT = 4.110, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1592 0.3524 0.2839 0.2045 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 4.1127 with an invariant (invariable) site category, proportion estimated 0.0274 Substitution rate categories under this model: rate proportion 0.0000 0.0274 0.4604 0.2432 0.7790 0.2432 1.0844 0.2432 1.6762 0.2432 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 : -13324.0948 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 2.515 0.3786 4.11 1 0.159 0.352 0.284 0.204 4.113 0.027 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 1.695 0.538 0.326 2.136 Saving final tree from best search rep (#1) to out.p.3diff.best.tre Inferring internal state probabilities on best tree... saving to file out.p.3diff.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.p.3diff.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: SETS storing read block: ASSUMPTIONS storing read block: TREES TREEFILES PASS Running output test p.mkvO.ssr Running output test p.mkvO.ssr Running GARLI Version 2.1. () ->Single processor version for 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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: 1 >>>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 0.077 lnL 7 8 9 10 11 Initial ln Likelihood: -105.0557 optimizing: starting branch lengths, alpha shape, prop. invar... pass 1:+ 1.547 (branch= 1.55 scale= 0.00 alpha= 0.00 pinv= 0.00) pass 2:+ 0.271 (branch= 0.27 scale= 0.00 alpha= 0.00 pinv= 0.00) lnL after optimization: -103.2377 gen current_lnL precision last_tree_imp 0 -103.2377 0.500 0 100 -102.5786 0.500 81 200 -100.8816 0.500 183 300 -100.5813 0.500 183 400 -100.3300 0.500 183 500 -100.0135 0.500 183 600 -99.2983 0.500 549 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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: 1 Restarting from checkpoint... Bootstrap rep 1 (of 1) generation 634, seed 276364763, best lnL -99.264 gen current_lnL precision last_tree_imp 634 -99.2638 0.500 549 700 -99.1955 0.500 549 800 -99.0437 0.500 783 900 -99.0045 0.500 783 1000 -98.8740 0.500 949 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 0.6652 with an invariant (invariable) site category, proportion estimated 0.0626 Substitution rate categories under this model: rate proportion 0.0000 0.0626 0.1054 0.3125 0.5916 0.3125 2.3030 0.3125 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 : -98.8740 Parameter estimates: alpha pinv rep 1: 0.665 0.063 Treelengths: TL rep 1: 1.521 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 418, seed 1667153938, best lnL -112.048 gen current_lnL precision last_tree_imp 418 -112.0477 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 Using NCL version 2.1.17 ####################################################### Reading config file ./check/a.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 11 sequences. 3 constant characters. 6 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.2 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 2 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0165 0.0083 0.0496 0.0909 0.0909 0.0083 0.0744 0.0083 0.0083 0.1074 0.1157 0.0248 0.1240 0.0331 0.0083 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 0.121 lnL 7 8 9 10 11 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -117.7533 optimizing: starting branch lengths... pass 1:+ 0.632 (branch= 0.63 scale= 0.00) pass 2:+ 0.134 (branch= 0.13 scale= 0.00) lnL after optimization: -116.9881 gen current_lnL precision last_tree_imp 0 -116.9881 0.500 0 100 -113.6842 0.500 91 200 -112.5462 0.500 160 300 -112.1250 0.500 160 400 -111.8851 0.500 160 500 -111.7755 0.500 160 600 -111.6975 0.500 563 700 -111.6876 0.500 563 800 -111.6844 0.500 563 900 -111.6835 0.500 563 1000 -111.6829 0.500 563 1100 -111.6827 0.500 563 Optimization precision reduced Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 0.000 lnL 1200 -111.6824 0.010 563 1300 -111.6822 0.010 563 1400 -111.6821 0.010 563 1500 -111.6819 0.010 563 1600 -111.6818 0.010 563 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 1618, seed 598468670, best lnL -111.682 gen current_lnL precision last_tree_imp 1618 -111.6818 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 : -111.6818 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 25, seed 2069048048, best lnL -205.650 gen current_lnL precision last_tree_imp 25 -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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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: 1 >>>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 0.004 lnL Optimizing branchlengths... improved 1.386 lnL 7 8 9 10 11 Initial ln Likelihood: -215.6208 optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters... pass 1:+ 11.345 (branch= 1.56 scale= 0.00 omega= 0.58 rel rates= 9.21) pass 2:+ 0.537 (branch= 0.07 scale= 0.00 omega= 0.00 rel rates= 0.46) pass 3:+ 0.103 (branch= 0.01 scale= 0.00 omega= 0.00 rel rates= 0.09) lnL after optimization: -203.6354 gen current_lnL precision last_tree_imp 0 -203.6354 0.500 0 10 -200.0495 0.500 7 20 -198.2138 0.500 20 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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: 1 Restarting from checkpoint... Bootstrap rep 1 (of 1) generation 20, seed 268317158, best lnL -198.214 gen current_lnL precision last_tree_imp 20 -198.2138 0.500 20 30 -198.1347 0.500 20 40 -197.7953 0.500 33 50 -197.7548 0.500 33 60 -197.7423 0.500 33 70 -197.7423 0.500 33 80 -197.6855 0.500 33 90 -197.6756 0.500 33 100 -197.6654 0.500 33 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) = 0.154177 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 2.497, AG = 4.006, AT = 0.007, CG = 2.679, CT = 2.184, 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 : -197.6654 Parameter estimates: w(0) p(0) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) rep 1: 0.154 1.000 2.497 4.006 0.00742 2.679 2.184 1 Treelengths: TL rep 1: 7.277 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 0.834 lnL Optimizing branchlengths... improved 0.086 lnL 1100 -3352.7118 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 1184, seed 506006923, best lnL -3352.650 gen current_lnL precision last_tree_imp 1184 -3352.6500 0.010 0 1200 -3352.6304 0.010 0 1300 -3352.5083 0.010 0 1400 -3352.3976 0.010 0 1500 -3352.3929 0.010 0 1600 -3352.2848 0.010 0 1700 -3352.2769 0.010 0 1800 -3352.1985 0.010 0 1900 -3351.8445 0.010 0 2000 -3351.7633 0.010 0 2100 -3351.6181 0.010 0 2200 -3351.3705 0.010 0 2300 -3351.3467 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... Current score = -3351.3446 Performing final optimizations... pass 1 : -3351.2188 (branch= 0.0084 alpha= 0.0000 pinv= 0.0155 eq freqs= 0.0268 rel rates= 0.0735 subset rates= 0.0017) pass 2 : -3351.0857 (branch= 0.0120 alpha= 0.0129 pinv= 0.0189 eq freqs= 0.0035 rel rates= 0.0848 subset rates= 0.0010) pass 3 : -3350.9802 (branch= 0.0085 alpha= 0.0144 pinv= 0.0173 eq freqs= 0.0000 rel rates= 0.0643 subset rates= 0.0010) pass 4 : -3350.8810 (branch= 0.0107 alpha= 0.0148 pinv= 0.0162 eq freqs= 0.0018 rel rates= 0.0545 subset rates= 0.0013) pass 5 : -3350.7990 (branch= 0.0051 alpha= 0.0149 pinv= 0.0148 eq freqs= 0.0000 rel rates= 0.0461 subset rates= 0.0011) pass 6 : -3350.7298 (branch= 0.0033 alpha= 0.0133 pinv= 0.0137 eq freqs= 0.0005 rel rates= 0.0384 subset rates= 0.0000) pass 7 : -3350.6670 (branch= 0.0016 alpha= 0.0123 pinv= 0.0126 eq freqs= 0.0001 rel rates= 0.0347 subset rates= 0.0017) pass 8 : -3350.6134 (branch= 0.0019 alpha= 0.0117 pinv= 0.0115 eq freqs= 0.0001 rel rates= 0.0284 subset rates= 0.0000) pass 9 : -3350.5665 (branch= 0.0004 alpha= 0.0107 pinv= 0.0105 eq freqs= 0.0000 rel rates= 0.0254 subset rates= 0.0000) pass 10: -3350.5225 (branch= 0.0002 alpha= 0.0104 pinv= 0.0102 eq freqs= 0.0000 rel rates= 0.0218 subset rates= 0.0013) pass 11: -3350.4856 (branch= 0.0012 alpha= 0.0091 pinv= 0.0092 eq freqs= 0.0001 rel rates= 0.0175 subset rates= 0.0000) pass 12: -3350.4541 (branch= 0.0002 alpha= 0.0079 pinv= 0.0077 eq freqs= 0.0000 rel rates= 0.0156 subset rates= 0.0000) pass 13: -3350.4258 (branch= 0.0001 alpha= 0.0076 pinv= 0.0069 eq freqs= 0.0000 rel rates= 0.0137 subset rates= 0.0000) pass 14: -3350.4008 (branch= 0.0000 alpha= 0.0069 pinv= 0.0062 eq freqs= 0.0000 rel rates= 0.0118 subset rates= 0.0000) pass 15: -3350.3790 (branch= 0.0000 alpha= 0.0062 pinv= 0.0055 eq freqs= 0.0000 rel rates= 0.0100 subset rates= 0.0000) pass 16: -3350.3599 (branch= 0.0000 alpha= 0.0056 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0086 subset rates= 0.0000) pass 17: -3350.3431 (branch= 0.0000 alpha= 0.0049 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0074 subset rates= 0.0000) pass 18: -3350.3285 (branch= 0.0000 alpha= 0.0044 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0063 subset rates= 0.0000) pass 19: -3350.3158 (branch= 0.0000 alpha= 0.0039 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0054 subset rates= 0.0000) pass 20: -3350.3047 (branch= 0.0000 alpha= 0.0034 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0047 subset rates= 0.0000) optimization up to ... pass 30: -3350.2494 (branch= 0.0000 alpha= 0.0172 pinv= 0.0155 eq freqs= 0.0001 rel rates= 0.0225 subset rates= 0.0000) optimization up to ... pass 40: -3350.2367 (branch= 0.0000 alpha= 0.0038 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0053 subset rates= 0.0000) optimization up to ... pass 50: -3350.2340 (branch= 0.0000 alpha= 0.0007 pinv= 0.0007 eq freqs= 0.0000 rel rates= 0.0013 subset rates= 0.0000) optimization up to ... pass 60: -3350.2335 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0003 subset rates= 0.0000) optimization up to ... pass 69: -3350.2333 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) Looking for minimum length branches... Final score = -3350.2334 Time used so far = 0 hours, 0 minutes and 13 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 3.116, AG = 10.413, AT = 2.690, CG = 0.001, CT = 21.902, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3329 0.2222 0.1567 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5782 with an invariant (invariable) site category, proportion estimated 0.3659 Substitution rate categories under this model: rate proportion 0.0000 0.3659 0.0486 0.1585 0.2999 0.1585 0.8698 0.1585 2.7816 0.1585 Model 2 Number of states = 2 (binary data) Character change matrix: Binary, no all-zero columns (2-state symmetric one rate model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.82 0.18 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. >>>Terminated Search rep 1 (of 2)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 2). Results: Replicate 1 : -3350.2334 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 3.116 10.41 2.69 0.001 21.9 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: 0.788 1.820 0.180 Saving final tree from best search rep (#1) to ch.g.dnaBnoZ.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/g.dnaMix.conf Running checkpoint test ./check/g.dnaMix.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 Using NCL version 2.1.17 ####################################################### Reading config file ./check/g.dnaMix.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/dnaGap.8x1K.nex ... Reading TAXA block...storing read block: TAXA successful Reading CHARACTERS block...storing read block: CHARACTERS found dna data... successful Reading CHARACTERS block...storing read block: CHARACTERS found standard data... successful Reading TREES block...storing read block: TREES successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1GapsAsMissing") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 8 sequences. 428 constant characters. 129 parsimony-informative characters. 100 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 239 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #2 ("Untitled DATA Block 1GapsAsBinary") Data read as Gap-coded data, oriented with respect to time, modeled as Gap-coded data, oriented with respect to time Summary of data: 8 sequences. 502 constant characters. 39 parsimony-informative characters. 116 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 24 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 2 MB good approx 2 MB to 2 MB low approx 2 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 3.2 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### WARNING - specified outgroup (1) being ignored due to inference of a rooted true ####################################################### STARTING RUN >>>Search rep 1 (of 2)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3220 0.2180 0.1602 0.2999 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.1629 Substitution rate categories under this model: rate proportion 0.0000 0.1629 0.0334 0.2093 0.2519 0.2093 0.8203 0.2093 2.8944 0.2093 Model 2 Number of states = 2 (0/1 coding of gaps) Character change matrix: irreversible matrix deletion rate parameter only estimated if using a partitioned model without subset rates deletion rate = 1.000 Equilibrium State Frequencies: proportion of inserted sites parameter insert proportion = 0.500 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 Initial ln Likelihood: -4257.0961 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, ins rate, del rate... pass 1:+ 640.405 (branch= 431.06 scale= 2.03 alpha= 9.92 freqs= 3.07 rel rates= 7.29 pinv= 0.00 ins/del=187.03) pass 2:+ 169.102 (branch= 75.12 scale= 1.32 alpha= 0.88 freqs= 0.65 rel rates= 0.01 pinv= 0.00 ins/del= 91.12) pass 3:+ 55.144 (branch= 7.14 scale= 1.85 alpha= 1.09 freqs= 0.05 rel rates= 0.90 pinv= 0.00 ins/del= 44.12) pass 4:+ 25.231 (branch= 7.02 scale= 1.52 alpha= 0.69 freqs= 0.06 rel rates= 0.01 pinv= 0.00 ins/del= 15.94) pass 5:+ 14.361 (branch= 7.97 scale= 1.87 alpha= 0.01 freqs= 0.05 rel rates= 2.45 pinv= 0.00 ins/del= 2.01) pass 6:+ 10.438 (branch= 7.36 scale= 2.34 alpha= 0.01 freqs= 0.07 rel rates= 0.00 pinv= 0.00 ins/del= 0.66) pass 7:+ 6.158 (branch= 5.23 scale= 0.83 alpha= 0.01 freqs= 0.06 rel rates= 0.00 pinv= 0.00 ins/del= 0.03) pass 8:+ 3.640 (branch= 2.31 scale= 0.00 alpha= 0.00 freqs= 0.05 rel rates= 0.60 pinv= 0.00 ins/del= 0.67) pass 9:+ 0.148 (branch= 0.08 scale= 0.00 alpha= 0.00 freqs= 0.06 rel rates= 0.00 pinv= 0.00 ins/del= 0.00) lnL after optimization: -3332.4700 gen current_lnL precision last_tree_imp 0 -3332.4700 0.500 0 100 -3324.9856 0.500 1 200 -3324.7543 0.500 1 300 -3324.3007 0.500 1 400 -3323.9848 0.500 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 453, seed 922520793, best lnL -3323.716 gen current_lnL precision last_tree_imp 453 -3323.7158 0.500 1 500 -3323.6818 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 NOTE: ****Specified time limit (5 seconds) reached... Current score = -3320.9773 Performing final optimizations... pass 1 : -3320.2915 (branch= 0.0904 alpha= 0.0000 pinv= 0.0166 eq freqs= 0.0001 rel rates= 0.5599 ins/del rates= 0.0188) pass 2 : -3319.8397 (branch= 0.0587 alpha= 0.0068 pinv= 0.0160 eq freqs= 0.0000 rel rates= 0.3543 ins/del rates= 0.0159) pass 3 : -3319.4954 (branch= 0.0434 alpha= 0.0093 pinv= 0.0154 eq freqs= 0.0000 rel rates= 0.2576 ins/del rates= 0.0185) pass 4 : -3319.2238 (branch= 0.0275 alpha= 0.0096 pinv= 0.0153 eq freqs= 0.0020 rel rates= 0.2070 ins/del rates= 0.0102) pass 5 : -3318.9992 (branch= 0.0194 alpha= 0.0100 pinv= 0.0146 eq freqs= 0.0011 rel rates= 0.1719 ins/del rates= 0.0076) pass 6 : -3318.8110 (branch= 0.0122 alpha= 0.0103 pinv= 0.0138 eq freqs= 0.0013 rel rates= 0.1457 ins/del rates= 0.0050) pass 7 : -3318.6535 (branch= 0.0089 alpha= 0.0098 pinv= 0.0130 eq freqs= 0.0002 rel rates= 0.1218 ins/del rates= 0.0038) pass 8 : -3318.5258 (branch= 0.0054 alpha= 0.0106 pinv= 0.0121 eq freqs= 0.0004 rel rates= 0.0969 ins/del rates= 0.0023) pass 9 : -3318.4171 (branch= 0.0039 alpha= 0.0095 pinv= 0.0112 eq freqs= 0.0002 rel rates= 0.0822 ins/del rates= 0.0016) pass 10: -3318.3244 (branch= 0.0026 alpha= 0.0095 pinv= 0.0109 eq freqs= 0.0002 rel rates= 0.0684 ins/del rates= 0.0011) pass 11: -3318.2486 (branch= 0.0017 alpha= 0.0089 pinv= 0.0094 eq freqs= 0.0002 rel rates= 0.0549 ins/del rates= 0.0007) pass 12: -3318.1843 (branch= 0.0011 alpha= 0.0083 pinv= 0.0086 eq freqs= 0.0001 rel rates= 0.0457 ins/del rates= 0.0005) pass 13: -3318.1295 (branch= 0.0007 alpha= 0.0078 pinv= 0.0078 eq freqs= 0.0001 rel rates= 0.0381 ins/del rates= 0.0003) pass 14: -3318.0826 (branch= 0.0005 alpha= 0.0072 pinv= 0.0071 eq freqs= 0.0001 rel rates= 0.0319 ins/del rates= 0.0002) pass 15: -3318.0431 (branch= 0.0003 alpha= 0.0067 pinv= 0.0064 eq freqs= 0.0001 rel rates= 0.0259 ins/del rates= 0.0001) pass 16: -3318.0090 (branch= 0.0002 alpha= 0.0060 pinv= 0.0058 eq freqs= 0.0001 rel rates= 0.0220 ins/del rates= 0.0001) pass 17: -3317.9795 (branch= 0.0001 alpha= 0.0054 pinv= 0.0052 eq freqs= 0.0000 rel rates= 0.0187 ins/del rates= 0.0000) pass 18: -3317.9539 (branch= 0.0001 alpha= 0.0049 pinv= 0.0046 eq freqs= 0.0000 rel rates= 0.0159 ins/del rates= 0.0000) pass 19: -3317.9317 (branch= 0.0000 alpha= 0.0044 pinv= 0.0041 eq freqs= 0.0000 rel rates= 0.0136 ins/del rates= 0.0000) pass 20: -3317.9124 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0116 ins/del rates= 0.0000) optimization up to ... pass 30: -3317.8166 (branch= 0.0001 alpha= 0.0213 pinv= 0.0196 eq freqs= 0.0001 rel rates= 0.0548 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= 0.0126 ins/del rates= 0.0000) optimization up to ... pass 50: -3317.7885 (branch= 0.0000 alpha= 0.0011 pinv= 0.0010 eq freqs= 0.0000 rel rates= 0.0030 ins/del rates= 0.0000) optimization up to ... pass 60: -3317.7874 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0007 ins/del rates= 0.0000) optimization up to ... pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) optimization up to ... pass 76: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3317.7871 Time used so far = 0 hours, 0 minutes and 13 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 3.066, AG = 10.265, AT = 2.657, CG = 0.001, CT = 21.541, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3328 0.2223 0.1567 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5749 with an invariant (invariable) site category, proportion estimated 0.3614 Substitution rate categories under this model: rate proportion 0.0000 0.3614 0.0480 0.1596 0.2981 0.1596 0.8680 0.1596 2.7860 0.1596 Model 2 Number of states = 2 (0/1 coding of gaps) Character change matrix: irreversible matrix deletion rate parameter only estimated if using a partitioned model without subset rates deletion rate = 0.158 Equilibrium State Frequencies: proportion of inserted sites parameter insert proportion = 0.036 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. >>>Terminated Search rep 1 (of 2)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 2). Results: Replicate 1 : -3317.7871 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 3.066 10.26 2.657 0.001 21.54 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del rep 1: 0.036 0.158 **ins = proportion of columns that experienced an insertion **del = deletion rate relative to nucleotide substitution rate Treelengths: TL rep 1: 1.418 Saving final tree from best search rep (#1) to ch.g.dnaMix.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/n.G3.conf Running checkpoint test ./check/n.G3.conf Running GARLI Version 2.1. () ->Single processor version for 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 -211.1654 0.010 1104 1400 -211.1320 0.010 1104 1600 -211.0218 0.010 1104 1800 -210.9998 0.010 1104 2000 -210.9460 0.010 1104 2200 -210.8945 0.010 1104 2400 -210.8864 0.010 1104 2600 -210.8436 0.010 1104 2800 -210.8250 0.010 1104 3000 -210.8189 0.010 1104 3200 -210.7905 0.010 1104 3400 -210.7553 0.010 1104 3600 -210.7287 0.010 1104 3800 -210.7084 0.010 1104 4000 -210.6947 0.010 1104 4200 -210.6741 0.010 1104 4400 -210.6493 0.010 1104 4600 -210.6257 0.010 1104 4800 -210.5949 0.010 1104 5000 -210.5740 0.010 1104 5200 -210.5694 0.010 1104 5400 -210.5451 0.010 1104 5600 -210.5083 0.010 1104 5800 -210.4709 0.010 1104 6000 -210.4363 0.010 1104 6200 -210.4333 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 6205, seed 805740742, best lnL -210.433 gen current_lnL precision last_tree_imp 6205 -210.4333 0.010 1104 6300 -210.3894 0.010 1104 6400 -210.3828 0.010 1104 6500 -210.3682 0.010 1104 6600 -210.3672 0.010 1104 6700 -210.3649 0.010 1104 6800 -210.3388 0.010 1104 6900 -210.2789 0.010 1104 7000 -210.2678 0.010 1104 7100 -210.2669 0.010 1104 7200 -210.2658 0.010 1104 7300 -210.2112 0.010 1104 7400 -210.2005 0.010 1104 7500 -210.1759 0.010 1104 7600 -210.1719 0.010 1104 7700 -210.1248 0.010 1104 7800 -210.1109 0.010 1104 7900 -210.1075 0.010 1104 8000 -210.1051 0.010 1104 8100 -210.0631 0.010 1104 8200 -210.0542 0.010 1104 8300 -210.0443 0.010 1104 8400 -210.0362 0.010 1104 8500 -210.0345 0.010 1104 8600 -210.0072 0.010 1104 8700 -209.9622 0.010 1104 8800 -209.9561 0.010 1104 8900 -209.9495 0.010 1104 9000 -209.9142 0.010 1104 9100 -209.9062 0.010 1104 9200 -209.9044 0.010 1104 9300 -209.8883 0.010 1104 9400 -209.8881 0.010 1104 9500 -209.8846 0.010 1104 Reached termination condition! last topological improvement at gen 1104 Improvement over last 500 gen = 0.02958 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 4.463, AG = 7.646, AT = 0.194, CG = 8.002, CT = 13.103, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2355 0.3330 0.2090 0.2224 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 2.0184 with an invariant (invariable) site category, proportion estimated 0.2338 Substitution rate categories under this model: rate proportion 0.0000 0.2338 0.3565 0.2554 0.8504 0.2554 1.7931 0.2554 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. Saving site likelihoods to file ch.n.G3.sitelikes.log ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -209.8846 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: 4.463 7.646 0.1943 8.002 13.1 1 0.236 0.333 0.209 0.222 2.018 0.234 Treelengths: TL rep 1: 2.364 Saving final tree from best search rep (#1) to ch.n.G3.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.G3.internalstates.log ####################################################### TREEFILES PASS Running checkpoint test ./check/n.G4.conf Running checkpoint test ./check/n.G4.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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: 1 >>>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 0.748 lnL Optimizing branchlengths... improved 0.000 lnL 7 8 9 10 11 Initial ln Likelihood: -219.9437 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 11.531 (branch= 2.29 scale= 0.00 alpha= 1.06 freqs= 2.85 rel rates= 5.33 pinv= 0.00) pass 2:+ 1.732 (branch= 0.06 scale= 0.00 alpha= 0.66 freqs= 0.61 rel rates= 0.40 pinv= 0.00) pass 3:+ 0.479 (branch= 0.00 scale= 0.39 alpha= 0.00 freqs= 0.04 rel rates= 0.04 pinv= 0.00) lnL after optimization: -206.2017 gen current_lnL precision last_tree_imp 0 -206.2017 0.500 0 200 -195.8582 0.500 189 400 -194.6871 0.500 189 600 -194.1186 0.500 189 800 -193.5549 0.500 694 1000 -193.2220 0.500 694 1200 -193.1176 0.500 694 Optimization precision reduced Optimizing parameters... improved 1.295 lnL Optimizing branchlengths... improved 0.177 lnL 1400 -191.5429 0.010 1238 1600 -191.4262 0.010 1238 1800 -191.2927 0.010 1238 2000 -191.1581 0.010 1979 2200 -191.0939 0.010 1979 2400 -190.9583 0.010 1979 2600 -190.9305 0.010 1979 2800 -190.8936 0.010 1979 3000 -190.8746 0.010 1979 3200 -190.8648 0.010 1979 3400 -190.8494 0.010 1979 3600 -190.8372 0.010 1979 3800 -190.7695 0.010 1979 4000 -190.7609 0.010 1979 4200 -190.7108 0.010 1979 4400 -190.6941 0.010 1979 4600 -190.6596 0.010 1979 4800 -190.6553 0.010 1979 5000 -190.6512 0.010 1979 5200 -190.6443 0.010 1979 5400 -190.6435 0.010 1979 5600 -190.6010 0.010 1979 5800 -190.5523 0.010 1979 6000 -190.5495 0.010 1979 6200 -190.5464 0.010 1979 6400 -190.5268 0.010 1979 6600 -190.5081 0.010 1979 6800 -190.5071 0.010 1979 7000 -190.5058 0.010 1979 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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: 1 Restarting from checkpoint... Bootstrap rep 1 (of 1) generation 7057, seed 301406992, best lnL -190.500 gen current_lnL precision last_tree_imp 7057 -190.5002 0.010 1979 7100 -190.4949 0.010 1979 Reached termination condition! last topological improvement at gen 1979 Improvement over last 500 gen = 0.01314 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 0.654, AG = 1.342, AT = 0.009, CG = 2.993, CT = 14.463, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3161 0.3192 0.2594 0.1053 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 6.7629 with an invariant (invariable) site category, proportion estimated 0.1389 Substitution rate categories under this model: rate proportion 0.0000 0.1389 0.5621 0.2153 0.8368 0.2153 1.0795 0.2153 1.5216 0.2153 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -190.4949 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: 0.6542 1.342 0.008904 2.993 14.46 1 0.316 0.319 0.259 0.105 6.763 0.139 Treelengths: TL rep 1: 2.315 Saving best tree to bootstrap file ch.n.G4.boot.tre >>>Completed Bootstrap rep 1<<< ####################################################### TREEFILES PASS Running checkpoint test ./check/n.conf Running checkpoint test ./check/n.conf Running GARLI Version 2.1. () ->Single processor version for 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 Using NCL version 2.1.17 ####################################################### Reading config file ./check/n.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.1 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 3.458 lnL 7 8 9 10 11 Initial ln Likelihood: -225.5327 optimizing: starting branch lengths, rel rates, eq freqs... pass 1:+ 7.466 (branch= 0.77 scale= 0.00 freqs= 0.02 rel rates= 6.68) pass 2:+ 0.468 (branch= 0.45 scale= 0.00 freqs= 0.02 rel rates= 0.00) lnL after optimization: -217.5990 gen current_lnL precision last_tree_imp 0 -217.5990 0.500 0 200 -215.8307 0.500 188 400 -214.8938 0.500 276 600 -214.3966 0.500 530 800 -214.1704 0.500 530 1000 -214.0528 0.500 530 Optimization precision reduced Optimizing parameters... improved 0.223 lnL Optimizing branchlengths... improved 0.080 lnL 1200 -213.6190 0.010 530 1400 -213.5798 0.010 530 1600 -213.5574 0.010 530 1800 -213.3950 0.010 530 2000 -213.3645 0.010 530 2200 -213.3317 0.010 530 2400 -213.2445 0.010 530 2600 -213.2282 0.010 530 2800 -213.2194 0.010 530 3000 -213.2002 0.010 530 3200 -213.1946 0.010 530 3400 -213.1682 0.010 530 3600 -213.1581 0.010 530 3800 -213.0251 0.010 3769 4000 -212.9704 0.010 3769 4200 -212.9482 0.010 3769 4400 -212.9233 0.010 3769 4600 -212.8794 0.010 3769 4800 -212.8766 0.010 3769 5000 -212.8761 0.010 3769 5200 -212.8556 0.010 3769 5400 -212.8533 0.010 3769 5600 -212.8185 0.010 3769 5800 -212.7686 0.010 3769 6000 -212.7263 0.010 3769 6200 -212.7248 0.010 3769 6400 -212.7244 0.010 3769 6600 -212.7154 0.010 3769 6800 -212.7057 0.010 3769 7000 -212.7025 0.010 3769 7200 -212.7020 0.010 3769 7400 -212.6750 0.010 3769 7600 -212.6701 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 = 8.255, AG = 15.546, AT = 0.648, CG = 15.522, CT = 10.080, 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 : -212.4847 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 8.255 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 -212.4847 0.010 3769 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 8.255, AG = 15.546, AT = 0.648, CG = 15.522, CT = 10.080, 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 : -212.4847 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 8.255 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 -210.8172 0.010 1502 2800 -210.7847 0.010 1502 3000 -210.7510 0.010 2883 3200 -210.7243 0.010 2883 3400 -210.7005 0.010 2883 3600 -210.6993 0.010 2883 3800 -210.6778 0.010 2883 4000 -210.6775 0.010 2883 4200 -210.6761 0.010 2883 4400 -210.6526 0.010 2883 4600 -210.6396 0.010 2883 4800 -210.6026 0.010 4692 5000 -210.5940 0.010 4692 5200 -210.5720 0.010 4692 5400 -210.5439 0.010 5207 5600 -210.5367 0.010 5207 5800 -210.4677 0.010 5207 6000 -210.4081 0.010 5812 6200 -210.4005 0.010 5812 6400 -210.3714 0.010 5812 6600 -210.3661 0.010 5812 6800 -210.3533 0.010 5812 7000 -210.3450 0.010 5812 7200 -210.3444 0.010 5812 7400 -210.3290 0.010 5812 7600 -210.3233 0.010 5812 7800 -210.2350 0.010 7789 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 7994, seed 1910171639, best lnL -210.189 gen current_lnL precision last_tree_imp 7994 -210.1893 0.010 7789 8000 -210.1893 0.010 7789 8100 -210.1876 0.010 7789 8200 -210.1873 0.010 7789 8300 -210.1797 0.010 7789 8400 -210.1348 0.010 7789 8500 -210.0964 0.010 7789 8600 -210.0952 0.010 7789 8700 -210.0821 0.010 7789 8800 -210.0512 0.010 7789 8900 -210.0377 0.010 7789 9000 -210.0080 0.010 7789 9100 -209.9968 0.010 7789 9200 -209.9885 0.010 7789 9300 -209.9721 0.010 7789 9400 -209.9480 0.010 7789 9500 -209.9339 0.010 7789 9600 -209.9336 0.010 7789 9700 -209.9330 0.010 7789 9800 -209.9271 0.010 7789 Reached termination condition! last topological improvement at gen 7789 Improvement over last 500 gen = 0.04494 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 2.658, AG = 4.801, AT = 0.220, CG = 4.939, CT = 8.706, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2422 0.3327 0.2114 0.2137 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 2.1330 with an invariant (invariable) site category, proportion estimated 0.2263 Substitution rate categories under this model: rate proportion 0.0000 0.2263 0.3087 0.1934 0.6685 0.1934 1.0730 0.1934 1.9499 0.1934 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with a positive constraint, it is possible for a constrained branch itself to be collapsed. If you care, be careful to check whether this has happened or turn off branch collapsing. Saving site likelihoods to file ch.n.const.sitelikes.log ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -209.9271 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 2.658 4.801 0.2199 4.939 8.706 1 0.242 0.333 0.211 0.214 2.133 0.226 Treelengths: TL rep 1: 2.428 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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: 1 Subset 2: Random seed for bootstrap reweighting: 1396138699 Subset 3: Random seed for bootstrap reweighting: 1903425807 >>>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: -16991.3142 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates... pass 1:+ 3314.864 (branch=2093.63 scale= 34.07 alpha=147.40 freqs=371.50 rel rates=663.20 pinv= 0.00 subset rates= 5.06) pass 2:+ 305.509 (branch= 40.11 scale= 0.00 alpha= 22.26 freqs=173.91 rel rates= 68.13 pinv= 1.10 subset rates= 0.00) pass 3:+ 157.341 (branch= 1.60 scale= 0.00 alpha= 3.94 freqs= 72.25 rel rates= 77.88 pinv= 0.00 subset rates= 1.67) pass 4:+ 23.271 (branch= 3.93 scale= 0.00 alpha= 0.01 freqs= 12.11 rel rates= 7.21 pinv= 0.01 subset rates= 0.00) pass 5:+ 2.276 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 1.09 rel rates= 0.68 pinv= 0.50 subset rates= 0.00) pass 6:+ 0.297 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.28 rel rates= 0.01 pinv= 0.00 subset rates= 0.00) lnL after optimization: -13187.7578 gen current_lnL precision last_tree_imp 0 -13187.7578 0.500 0 100 -13185.0341 0.500 1 200 -13183.9652 0.500 1 300 -13183.5099 0.500 1 400 -13182.4431 0.500 1 500 -13182.2598 0.500 1 600 -13181.9021 0.500 1 Optimization precision reduced Optimizing parameters... improved 0.055 lnL Optimizing branchlengths... improved 0.000 lnL 700 -13181.7193 0.402 1 800 -13181.6899 0.402 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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: 1 Subset 2: Random seed for bootstrap reweighting: 1396138699 Subset 3: Random seed for bootstrap reweighting: 1903425807 Restarting from checkpoint... Bootstrap rep 1 (of 1) generation 867, seed 1800452886, best lnL -13181.607 gen current_lnL precision last_tree_imp 867 -13181.6070 0.402 1 900 -13181.6040 0.402 1 1000 -13181.4970 0.402 1 1100 -13181.4426 0.402 1 Optimization precision reduced Optimizing parameters... improved 0.019 lnL Optimizing branchlengths... improved 0.000 lnL 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 = 2.015, AG = 3.173, AT = 1.167, CG = 1.167, CT = 2.631, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3054 0.1867 0.2740 0.2339 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.3876 Substitution rate categories under this model: rate proportion 0.0150 0.2500 0.1724 0.2500 0.7175 0.2500 3.0952 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 = 3.906, AG = 4.801, AT = 0.742, CG = 4.801, CT = 3.906, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2514 0.1562 0.1902 0.4022 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.4487 Substitution rate categories under this model: rate proportion 0.0243 0.2500 0.2171 0.2500 0.7790 0.2500 2.9796 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 = 7.157, AT = 5.571, CG = 1.050, CT = 7.157, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1612 0.3397 0.2962 0.2030 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 4.5458 with an invariant (invariable) site category, proportion estimated 0.0111 Substitution rate categories under this model: rate proportion 0.0000 0.0111 0.4820 0.2472 0.7922 0.2472 1.0840 0.2472 1.6418 0.2472 Subset rate multipliers: 0.53 0.28 2.20 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 : -13181.4112 (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: 2.015 3.173 1.167 1.167 2.631 1 0.305 0.187 0.274 0.234 0.388 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: 3.906 4.801 0.7415 4.801 3.906 1 0.251 0.156 0.190 0.402 0.449 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 7.157 5.571 1.05 7.157 1 0.161 0.340 0.296 0.203 4.546 0.011 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 1.673 0.526 0.278 2.196 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 5 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.79 1.48 2.18 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. >>>Completed Search rep 1 (of 5)<<< >>>Search rep 2 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=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 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 483, seed 1667434309, best lnL -467.753 gen current_lnL precision last_tree_imp 483 -467.7525 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 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 9 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.79 1.47 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 NOTE: ****Specified time limit (5 seconds) reached... Current score = -467.7095 Performing final optimizations... pass 1 : -467.7084 (branch= 0.0000 subset rates= 0.0011) pass 2 : -467.6965 (branch= 0.0118 subset rates= 0.0001) pass 3 : -467.6923 (branch= 0.0038 subset rates= 0.0005) pass 4 : -467.6881 (branch= 0.0040 subset rates= 0.0001) pass 5 : -467.6848 (branch= 0.0034 subset rates= 0.0000) pass 6 : -467.6818 (branch= 0.0030 subset rates= 0.0000) pass 7 : -467.6801 (branch= 0.0017 subset rates= 0.0000) pass 8 : -467.6794 (branch= 0.0007 subset rates= 0.0000) pass 9 : -467.6789 (branch= 0.0004 subset rates= 0.0001) pass 10: -467.6786 (branch= 0.0002 subset rates= 0.0000) pass 11: -467.6785 (branch= 0.0002 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: -467.6783 (branch= 0.0000 subset rates= 0.0000) pass 15: -467.6782 (branch= 0.0000 subset rates= 0.0001) Looking for minimum length branches... Final score = -467.6782 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.79 1.48 2.19 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. >>>Terminated Search rep 3 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 3 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -467.6782 Replicate 2 : -467.6787 (same topology as 1) Replicate 3 : -467.6782 (best) (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 3.844 0.786 1.480 2.180 rep 2: 3.839 0.788 1.472 2.178 rep 3: 3.844 0.786 1.477 2.188 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.63 1.92 2.74 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 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 1110, seed 1892573554, best lnL -477.709 gen current_lnL precision last_tree_imp 1110 -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 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 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.64 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 NOTE: ****Specified time limit (5 seconds) reached... Current score = -477.4747 Performing final optimizations... pass 1 : -477.4747 (branch= 0.0000 subset rates= 0.0000) pass 2 : -477.4598 (branch= 0.0148 subset rates= 0.0001) pass 3 : -477.4461 (branch= 0.0137 subset rates= 0.0000) pass 4 : -477.4414 (branch= 0.0042 subset rates= 0.0005) pass 5 : -477.4386 (branch= 0.0028 subset rates= 0.0000) pass 6 : -477.4354 (branch= 0.0032 subset rates= 0.0000) pass 7 : -477.4341 (branch= 0.0013 subset rates= 0.0000) pass 8 : -477.4329 (branch= 0.0013 subset rates= 0.0000) pass 9 : -477.4324 (branch= 0.0004 subset rates= 0.0000) pass 10: -477.4322 (branch= 0.0003 subset rates= 0.0000) pass 11: -477.4320 (branch= 0.0002 subset rates= 0.0000) pass 12: -477.4319 (branch= 0.0001 subset rates= 0.0000) pass 13: -477.4319 (branch= 0.0001 subset rates= 0.0000) pass 14: -477.4318 (branch= 0.0000 subset rates= 0.0000) pass 15: -477.4318 (branch= 0.0000 subset rates= 0.0000) pass 16: -477.4318 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.4318 Time used so far = 0 hours, 0 minutes and 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 : -477.4318 (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: 4.925 0.633 1.909 2.740 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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: 1 Subset 2: Random seed for bootstrap reweighting: 2128236579 Subset 3: Random seed for bootstrap reweighting: 585640194 >>>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: -670.4532 optimizing: starting branch lengths, subset rates... pass 1:+ 152.607 (branch= 142.18 scale= 1.18 subset rates= 9.25) pass 2:+ 18.856 (branch= 15.06 scale= 0.00 subset rates= 3.80) pass 3:+ 2.161 (branch= 1.20 scale= 0.00 subset rates= 0.97) pass 4:+ 0.235 (branch= 0.07 scale= 0.00 subset rates= 0.16) pass 5:+ 0.020 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -496.5747 gen current_lnL precision last_tree_imp 0 -496.5747 0.010 0 100 -493.2457 0.010 95 200 -486.5900 0.010 191 300 -486.5307 0.010 248 400 -486.5130 0.010 248 500 -486.5055 0.010 248 600 -485.9534 0.010 590 700 -484.6559 0.010 661 800 -484.6467 0.010 661 900 -484.6405 0.010 661 1000 -484.6308 0.010 661 1100 -484.6230 0.010 661 1200 -484.6200 0.010 661 1300 -484.6151 0.010 661 1400 -484.6083 0.010 661 1500 -484.6061 0.010 661 1600 -484.6042 0.010 661 1700 -484.6009 0.010 661 1800 -484.5977 0.010 661 1900 -484.5941 0.010 661 2000 -484.5901 0.010 661 2100 -484.5884 0.010 661 2200 -484.5881 0.010 661 2300 -484.5861 0.010 661 2400 -484.5846 0.010 661 2500 -484.5845 0.010 661 2600 -484.5838 0.010 661 2700 -484.5830 0.010 661 2800 -484.5823 0.010 661 2900 -484.5822 0.010 661 3000 -484.5818 0.010 661 3100 -484.5812 0.010 661 3200 -484.5805 0.010 661 3300 -484.5794 0.010 661 3400 -484.5791 0.010 661 3500 -484.5745 0.010 661 3600 -484.5745 0.010 661 3700 -484.5745 0.010 661 3800 -484.5745 0.010 661 3900 -484.5741 0.010 661 4000 -484.5740 0.010 661 Reached termination condition! last topological improvement at gen 661 Improvement over last 500 gen = 0.00055 Current score = -484.5740 Performing final optimizations... pass 1 : -484.5688 (branch= 0.0049 subset rates= 0.0003) pass 2 : -484.5554 (branch= 0.0134 subset rates= 0.0000) pass 3 : -484.5488 (branch= 0.0067 subset rates= 0.0000) pass 4 : -484.5460 (branch= 0.0027 subset rates= 0.0000) pass 5 : -484.5448 (branch= 0.0012 subset rates= 0.0000) pass 6 : -484.5440 (branch= 0.0008 subset rates= 0.0000) pass 7 : -484.5436 (branch= 0.0005 subset rates= 0.0000) pass 8 : -484.5430 (branch= 0.0006 subset rates= 0.0000) pass 9 : -484.5430 (branch= 0.0001 subset rates= 0.0000) pass 10: -484.5429 (branch= 0.0001 subset rates= 0.0000) pass 11: -484.5429 (branch= 0.0000 subset rates= 0.0000) pass 12: -484.5428 (branch= 0.0000 subset rates= 0.0000) pass 13: -484.5428 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -484.5428 Time used so far = 0 hours, 0 minutes and 5 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.66 2.00 2.95 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 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=1418804583 Initial ln Likelihood: -694.9819 optimizing: starting branch lengths, subset rates... pass 1:+ 174.392 (branch= 164.34 scale= 0.02 subset rates= 10.04) pass 2:+ 9.231 (branch= 5.66 scale= 0.05 subset rates= 3.52) pass 3:+ 4.898 (branch= 3.30 scale= 0.00 subset rates= 1.59) pass 4:+ 9.221 (branch= 8.95 scale= 0.00 subset rates= 0.27) pass 5:+ 0.626 (branch= 0.62 scale= 0.00 subset rates= 0.01) pass 6:+ 0.018 (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: -496.5963 gen current_lnL precision last_tree_imp 0 -496.5963 0.010 0 100 -496.1522 0.010 56 200 -493.1251 0.010 188 300 -489.5913 0.010 276 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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: 1 Subset 2: Random seed for bootstrap reweighting: 2128236579 Subset 3: Random seed for bootstrap reweighting: 585640194 Restarting from checkpoint... Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 313, seed 1644352132, best lnL -486.385 gen current_lnL precision last_tree_imp 313 -486.3847 0.010 301 400 -485.3399 0.010 377 500 -484.8544 0.010 500 600 -484.8310 0.010 577 700 -484.6771 0.010 682 800 -484.6429 0.010 728 900 -484.6380 0.010 728 1000 -484.6310 0.010 728 1100 -484.6267 0.010 728 1200 -484.6197 0.010 728 1300 -484.6177 0.010 728 1400 -484.6124 0.010 728 1500 -484.6118 0.010 728 1600 -484.6080 0.010 728 1700 -484.6059 0.010 728 1800 -484.6058 0.010 728 1900 -484.6038 0.010 728 2000 -484.6033 0.010 728 2100 -484.6025 0.010 728 2200 -484.6021 0.010 728 2300 -484.6015 0.010 728 2400 -484.6007 0.010 728 2500 -484.6002 0.010 728 2600 -484.5988 0.010 728 2700 -484.5983 0.010 728 2800 -484.5979 0.010 728 2900 -484.5969 0.010 728 3000 -484.5963 0.010 728 3100 -484.5962 0.010 728 3200 -484.5952 0.010 728 3300 -484.5950 0.010 728 3400 -484.5950 0.010 728 3500 -484.5930 0.010 728 3600 -484.5930 0.010 728 3700 -484.5922 0.010 728 3800 -484.5918 0.010 728 3900 -484.5905 0.010 728 4000 -484.5899 0.010 728 4100 -484.5893 0.010 728 4200 -484.5881 0.010 728 4300 -484.5864 0.010 728 4400 -484.5862 0.010 728 4500 -484.5860 0.010 728 4600 -484.5850 0.010 728 4700 -484.5850 0.010 728 4800 -484.5844 0.010 728 4900 -484.5838 0.010 728 NOTE: ****Specified time limit (5 seconds) reached... Current score = -484.5837 Performing final optimizations... pass 1 : -484.5732 (branch= 0.0102 subset rates= 0.0002) pass 2 : -484.5529 (branch= 0.0202 subset rates= 0.0002) pass 3 : -484.5495 (branch= 0.0015 subset rates= 0.0020) pass 4 : -484.5470 (branch= 0.0025 subset rates= 0.0000) pass 5 : -484.5455 (branch= 0.0014 subset rates= 0.0000) pass 6 : -484.5444 (branch= 0.0012 subset rates= 0.0000) pass 7 : -484.5438 (branch= 0.0006 subset rates= 0.0000) pass 8 : -484.5437 (branch= 0.0001 subset rates= 0.0000) pass 9 : -484.5435 (branch= 0.0002 subset rates= 0.0001) pass 10: -484.5433 (branch= 0.0001 subset rates= 0.0000) pass 11: -484.5433 (branch= 0.0000 subset rates= 0.0000) pass 12: -484.5433 (branch= 0.0000 subset rates= 0.0000) pass 13: -484.5433 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -484.5433 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: 0.66 2.00 2.95 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. >>>Terminated Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 2 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -484.5428 (best) Replicate 2 : -484.5433 (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: 3.520 0.660 2.002 2.951 rep 2: 3.519 0.661 1.999 2.951 Saving tree from best search rep (#1) to bootstrap file ch.p.mkv.ssr.boot.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkvO.ssr.conf Running checkpoint test ./check/p.mkvO.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 5 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.59 2.07 2.80 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 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 Nov 18 2020 13:05:54 using GNU gcc compiler version 10.2.1 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 384, seed 582863206, best lnL -474.519 gen current_lnL precision last_tree_imp 384 -474.5190 0.010 272 400 -474.5190 0.010 272 500 -474.5075 0.010 272 600 -474.5034 0.010 272 700 -474.4997 0.010 272 800 -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 NOTE: ****Specified time limit (5 seconds) reached... Current score = -474.4484 Performing final optimizations... pass 1 : -474.4484 (branch= 0.0000 subset rates= 0.0000) pass 2 : -474.4367 (branch= 0.0117 subset rates= 0.0000) pass 3 : -474.4325 (branch= 0.0041 subset rates= 0.0000) pass 4 : -474.4311 (branch= 0.0014 subset rates= 0.0000) pass 5 : -474.4307 (branch= 0.0004 subset rates= 0.0000) pass 6 : -474.4298 (branch= 0.0009 subset rates= 0.0000) pass 7 : -474.4292 (branch= 0.0006 subset rates= 0.0000) pass 8 : -474.4287 (branch= 0.0004 subset rates= 0.0000) pass 9 : -474.4285 (branch= 0.0003 subset rates= 0.0000) pass 10: -474.4283 (branch= 0.0001 subset rates= 0.0000) pass 11: -474.4283 (branch= 0.0001 subset rates= 0.0000) pass 12: -474.4282 (branch= 0.0000 subset rates= 0.0000) pass 13: -474.4282 (branch= 0.0000 subset rates= 0.0000) pass 14: -474.4282 (branch= 0.0000 subset rates= 0.0000) pass 15: -474.4282 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -474.4282 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.59 2.03 2.93 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 : -474.4282 (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.349 0.588 2.066 2.804 rep 2: 4.601 0.588 2.030 2.926 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-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 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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-4_all.deb'. dpkg-deb: building package 'garli' in '../garli_2.1-4_armhf.deb'. dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-4_armhf.deb'. dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-4_armhf.deb'. dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-4_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../garli_2.1-4_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/4936 and its subdirectories I: Current time: Mon Aug 23 12:19:15 -12 2021 I: pbuilder-time-stamp: 1629764355 Tue Aug 24 00:20:03 UTC 2021 I: 1st build successful. Starting 2nd build on remote node virt32a-armhf-rb.debian.net. Tue Aug 24 00:20:03 UTC 2021 I: Preparing to do remote build '2' on virt32a-armhf-rb.debian.net. Tue Aug 24 00:39:44 UTC 2021 I: Deleting $TMPDIR on virt32a-armhf-rb.debian.net. Tue Aug 24 00:39:47 UTC 2021 I: garli_2.1-4_armhf.changes: Format: 1.8 Date: Wed, 18 Nov 2020 14:05:54 +0100 Source: garli Binary: garli garli-dbgsym garli-examples garli-mpi garli-mpi-dbgsym Architecture: armhf all Version: 2.1-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille 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 (2.1-4) unstable; urgency=medium . * Standards-Version: 4.5.1 (routine-update) * debhelper-compat 13 (routine-update) * Secure URI in copyright format (routine-update) * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit. * watch file standard 4 (routine-update) Checksums-Sha1: 5072b2d0d178990489530b48afa4b3ad89453124 5116000 garli-dbgsym_2.1-4_armhf.deb 8ef00687e1b4bc9de805a031ec5c74208a373652 103392 garli-examples_2.1-4_all.deb 736bbf6fcadeef5c5c7a9f9d7d98674ee6453dd2 5170152 garli-mpi-dbgsym_2.1-4_armhf.deb 9f11824fe00d847500ab3cf5f3ae4bee579f944a 478292 garli-mpi_2.1-4_armhf.deb 9e5b9a38b4a0385c631491511995186f95669321 7360 garli_2.1-4_armhf.buildinfo 5b987c11d48cf3351124997036b872dc76589b18 502496 garli_2.1-4_armhf.deb Checksums-Sha256: abcb29f8b39ed1e816fca360461533d5ec99f52961ae356aa6888909905d44c3 5116000 garli-dbgsym_2.1-4_armhf.deb cc4e048245fa0d64d876dcce3f639459c46b218067bdb6e0e110537f22167239 103392 garli-examples_2.1-4_all.deb 933ef4a55b85458eb2ff7cd961413c694a6df203881f93202e1cee9b12a079b2 5170152 garli-mpi-dbgsym_2.1-4_armhf.deb 9269f0839937431aac1fdb7be355c92d33f1f4c95a3dbbb4e4f21a09acf20924 478292 garli-mpi_2.1-4_armhf.deb a1bec4a21dad424179134689c044b482ac831ffe5f631bfba40f0e6a252f1d24 7360 garli_2.1-4_armhf.buildinfo b2f8126f3aca32a703ee3403649f7cee5545c794f2b8c302c380f53ff2441c46 502496 garli_2.1-4_armhf.deb Files: 894d6704f405e2e78b20d974193d2c72 5116000 debug optional garli-dbgsym_2.1-4_armhf.deb a6a7d80854639946d393e13e89fa64a0 103392 science optional garli-examples_2.1-4_all.deb 5bc57d95d531aa98fab70d48c8fcbad3 5170152 debug optional garli-mpi-dbgsym_2.1-4_armhf.deb 6a93efbc68f1a9115884ccbd4b222a13 478292 science optional garli-mpi_2.1-4_armhf.deb 816183c76f77fbf73c0134619769ee0c 7360 science optional garli_2.1-4_armhf.buildinfo d9524b1a15e618f6a8c907adf1cb68b6 502496 science optional garli_2.1-4_armhf.deb Tue Aug 24 00:39:48 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.9BWV4sNWlz/garli_2.1-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.9BWV4sNWlz/garli_2.1-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.9BWV4sNWlz/garli_2.1-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.9BWV4sNWlz/b1/garli_2.1-4_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.9BWV4sNWlz/b2/garli_2.1-4_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: 0.319s) 0.319s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.115s) 0.114s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Tue Aug 24 00:39:50 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Tue Aug 24 00:39:50 UTC 2021 I: garli from bullseye built successfully and reproducibly on armhf. Tue Aug 24 00:39:51 UTC 2021 I: Submitting .buildinfo files to external archives: Tue Aug 24 00:39:51 UTC 2021 I: Submitting 12K b1/garli_2.1-4_armhf.buildinfo.asc Tue Aug 24 00:39:52 UTC 2021 I: Submitting 12K b2/garli_2.1-4_armhf.buildinfo.asc Tue Aug 24 00:39:53 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Aug 24 00:39:53 UTC 2021 I: Done submitting .buildinfo files. Tue Aug 24 00:39:53 UTC 2021 I: Removing signed garli_2.1-4_armhf.buildinfo.asc files: removed './b1/garli_2.1-4_armhf.buildinfo.asc' removed './b2/garli_2.1-4_armhf.buildinfo.asc'