Sun Nov 10 05:08:27 UTC 2024 I: starting to build garli/unstable/amd64 on jenkins on '2024-11-10 05:08' Sun Nov 10 05:08:27 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_9/22654/console.log Sun Nov 10 05:08:27 UTC 2024 I: Downloading source for unstable/garli=2.1-8 --2024-11-10 05:08:27-- http://deb.debian.org/debian/pool/main/g/garli/garli_2.1-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2186 (2.1K) [text/prs.lines.tag] Saving to: ‘garli_2.1-8.dsc’ 0K .. 100% 304M=0s 2024-11-10 05:08:27 (304 MB/s) - ‘garli_2.1-8.dsc’ saved [2186/2186] Sun Nov 10 05:08:27 UTC 2024 I: garli_2.1-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: garli Binary: garli, garli-mpi, garli-examples Architecture: any all Version: 2.1-8 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/Ashod/garli Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/garli Vcs-Git: https://salsa.debian.org/med-team/garli.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libncl-dev, mpi-default-dev, ncl-tools, bc Package-List: garli deb science optional arch=any garli-examples deb science optional arch=all garli-mpi deb science optional arch=any Checksums-Sha1: a7a5cb81f92ed19672324b5aacf8c7da1f6a2df3 1248730 garli_2.1.orig.tar.gz 814a8022142225579f0cbfa76b78f9593da39808 4912 garli_2.1-8.debian.tar.xz Checksums-Sha256: 00aa31af5d8ecc2cb9bd276ce93b6580ae6cff93f4f5e1145d95d5fe6359e1b6 1248730 garli_2.1.orig.tar.gz cefd24a1fd4eea484b2b0df5da32eb85047d6962aa15179b716f0bed8008c825 4912 garli_2.1-8.debian.tar.xz Files: 83d6720df816365182291306383d056c 1248730 garli_2.1.orig.tar.gz 921292b575a872b1945eb69ac7e8bb33 4912 garli_2.1-8.debian.tar.xz Dgit: f961cd430e58057b663aab8b268b7ad398dd9348 debian archive/debian/2.1-8 https://git.dgit.debian.org/garli -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmcv7gAUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdo1vhAAopSdbSxr0xlXxjYVZKMBv44SC5JW /nF8pEf3vck0UEmr62ulUuxsnVtmkHFtXi1ceXG4TTmtINLYfq0wxbRZgSioHDLx 3y5gMO6BNu3q00kTxjXs72JmdW8raP9JtgRCVINyMnDaz0EjvqmvVdFSOVjpF/nn JvxwJQGdmXFcBtrG/CvjyF6D5bZw3ey/FFwK+l4cLeGhNw6ejln3CSQrdN3PiYVj DuZpMTfNFMazGUUKOANBXjD6/D0YTv0cQPoDhc1qx8Xil1Qotx001+AkPlvJbdLz FzZVpErElr3jyx/55UX2qFcHW9as1OI4Lh0X5BCe4BPmrU17Ge5hblQqhvqKE/6Y b9bwWbGg66+tmq+ILNHjQ9IhmYwkRg7/oUefvdfX0GC1xhTeOAQovJJg76v7xv11 yhWJL3/3KHjyZXCoWFOGtP56UnRo5TkcqjEc4VCef5YMCy1B+AjHAuqI3CKlAyvJ OUYKtJ6pJbdsWwUOMKM4JBsvrFtOW+4ImQVv1eFEYshgFKvkQ8+33ojmcbT+wDG2 Cbn/XnPmjNb65MbuIl8qP/b3WIifhYOtOjIZhZGc5EME19awQ0uLf0VfK9M5PlLL hYVxmtCdNXVcfa6qGxHT+35QQOYTQD/KvkzDYeFLYy5/kNgbTrkeTEeJQMKaUxUB iffI2fqQZ9DxfDk= =8fm1 -----END PGP SIGNATURE----- Sun Nov 10 05:08:27 UTC 2024 I: Checking whether the package is not for us Sun Nov 10 05:08:28 UTC 2024 I: Starting 1st build on remote node ionos1-amd64.debian.net. Sun Nov 10 05:08:28 UTC 2024 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Sun Nov 10 05:33:11 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Nov 9 17:08:31 -12 2024 I: pbuilder-time-stamp: 1731215311 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [garli_2.1-8.dsc] I: copying [./garli_2.1.orig.tar.gz] I: copying [./garli_2.1-8.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Nov 9 23:19:28 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./garli_2.1-8.dsc: no acceptable signature found dpkg-source: info: extracting garli in garli-2.1 dpkg-source: info: unpacking garli_2.1.orig.tar.gz dpkg-source: info: unpacking garli_2.1-8.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/229569/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='47c41f7a2bc34582876e0fc58c8e6dd3' 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='229569' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.N2DF4RH9/pbuilderrc_Sfub --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.N2DF4RH9/b1 --logfile b1/build.log garli_2.1-8.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/229569/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libncl-dev, mpi-default-dev, ncl-tools, bc dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19970 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libncl-dev; however: Package libncl-dev is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-dev; however: Package mpi-default-dev is not installed. pbuilder-satisfydepends-dummy depends on ncl-tools; however: Package ncl-tools is not installed. pbuilder-satisfydepends-dummy depends on bc; however: Package bc is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bc{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran-14{a} gfortran-14-x86-64-linux-gnu{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libcbor0.10{a} libcom-err2{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libgssapi-krb5-2{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{a} libibverbs-dev{a} libibverbs1{a} libicu72{a} libjs-jquery{a} libjs-jquery-ui{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libllvm17t64{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmunge2{a} libncl-dev{a} libncl2{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi3t64{a} libpciaccess0{a} libpipeline1{a} libpmix-dev{a} libpmix2t64{a} libpsm-infinipath1{a} libpsm2-2{a} librdmacm1t64{a} libreadline8t64{a} libtool{a} libuchardet0{a} libucx0{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} libz3-4{a} m4{a} man-db{a} mpi-default-dev{a} ncl-tools{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} po-debconf{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libmail-sendmail-perl lynx wget xauth 0 packages upgraded, 105 newly installed, 0 to remove and 0 not upgraded. Need to get 108 MB of archives. After unpacking 438 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-10 [97.2 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.15.0-1+b1 [78.7 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 19 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:9.9p1-3 [991 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 bc amd64 1.07.1-4 [103 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 35 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libgfortran-14-dev amd64 14.2.0-8 [878 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-8 [11.7 MB] Get: 46 http://deb.debian.org/debian unstable/main amd64 gfortran-14 amd64 14.2.0-8 [12.2 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.7.0-0.3+b1 [59.4 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.7.0-0.3+b1 [182 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 52.0-2+b1 [62.2 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 52.0-2+b1 [343 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-18 [23.6 MB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get: 55 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libhsakmt1 amd64 6.1.2+ds-1 [59.8 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 6.1.2-2 [535 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libamdhip64-5 amd64 5.7.1-5 [8877 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b1 [108 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b1 [61.1 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-10+b1 [305 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 52.0-2+b1 [70.4 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 1.17.0-3.1 [631 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.11.2-1 [164 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.18-1+b1 [36.6 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.4.7-8 [393 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.4.7-8 [165 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.11.2-1 [254 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b2 [51.9 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b2 [24.4 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1+b1 [14.2 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b2 [40.2 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.11.2-1 [18.1 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 52.0-2+b1 [28.2 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 52.0-2+b1 [43.4 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.7.0-0.3+b1 [100 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.7.0-0.3+b1 [200 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 52.0-2+b1 [636 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.15-4+b1 [20.0 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libncl2 amd64 2.1.21+git20210811.b1213a7-6 [383 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libncl-dev amd64 2.1.21+git20210811.b1213a7-6 [599 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 5.0.3-2+b1 [662 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.17.0+ds-3 [1130 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libopenmpi3t64 amd64 5.0.5-3 [2007 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 5.0.5-3 [95.0 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libpmix-dev amd64 5.0.3-2+b1 [3958 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 5.0.5-3 [168 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 5.0.5-3 [1087 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.17 [3148 B] Get: 105 http://deb.debian.org/debian unstable/main amd64 ncl-tools amd64 2.1.21+git20210811.b1213a7-6 [190 kB] Fetched 108 MB in 8s (13.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19970 files and directories currently installed.) Preparing to unpack .../000-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package bc. Preparing to unpack .../027-bc_1.07.1-4_amd64.deb ... Unpacking bc (1.07.1-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../028-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../029-libtool_2.4.7-8_all.deb ... 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Selecting previously unselected package libnl-route-3-200:amd64. Preparing to unpack .../047-libnl-route-3-200_3.7.0-0.3+b1_amd64.deb ... Unpacking libnl-route-3-200:amd64 (3.7.0-0.3+b1) ... Selecting previously unselected package libibverbs1:amd64. Preparing to unpack .../048-libibverbs1_52.0-2+b1_amd64.deb ... Unpacking libibverbs1:amd64 (52.0-2+b1) ... Selecting previously unselected package ibverbs-providers:amd64. Preparing to unpack .../049-ibverbs-providers_52.0-2+b1_amd64.deb ... Unpacking ibverbs-providers:amd64 (52.0-2+b1) ... Selecting previously unselected package libz3-4:amd64. Preparing to unpack .../050-libz3-4_4.13.3-1_amd64.deb ... Unpacking libz3-4:amd64 (4.13.3-1) ... Selecting previously unselected package libllvm17t64:amd64. Preparing to unpack .../051-libllvm17t64_1%3a17.0.6-18_amd64.deb ... Unpacking libllvm17t64:amd64 (1:17.0.6-18) ... Selecting previously unselected package libamd-comgr2:amd64. Preparing to unpack .../052-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3+b2_amd64.deb ... Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Selecting previously unselected package libdrm-common. Preparing to unpack .../053-libdrm-common_2.4.123-1_all.deb ... Unpacking libdrm-common (2.4.123-1) ... Selecting previously unselected package libdrm2:amd64. Preparing to unpack .../054-libdrm2_2.4.123-1_amd64.deb ... Unpacking libdrm2:amd64 (2.4.123-1) ... Selecting previously unselected package libdrm-amdgpu1:amd64. Preparing to unpack .../055-libdrm-amdgpu1_2.4.123-1_amd64.deb ... Unpacking libdrm-amdgpu1:amd64 (2.4.123-1) ... Selecting previously unselected package libnuma1:amd64. Preparing to unpack .../056-libnuma1_2.0.18-1+b1_amd64.deb ... Unpacking libnuma1:amd64 (2.0.18-1+b1) ... Selecting previously unselected package libhsakmt1:amd64. Preparing to unpack .../057-libhsakmt1_6.1.2+ds-1_amd64.deb ... Unpacking libhsakmt1:amd64 (6.1.2+ds-1) ... Selecting previously unselected package libhsa-runtime64-1:amd64. Preparing to unpack .../058-libhsa-runtime64-1_6.1.2-2_amd64.deb ... Unpacking libhsa-runtime64-1:amd64 (6.1.2-2) ... Selecting previously unselected package libamdhip64-5. Preparing to unpack .../059-libamdhip64-5_5.7.1-5_amd64.deb ... Unpacking libamdhip64-5 (5.7.1-5) ... Selecting previously unselected package libevent-2.1-7t64:amd64. Preparing to unpack .../060-libevent-2.1-7t64_2.1.12-stable-10+b1_amd64.deb ... Unpacking libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libevent-core-2.1-7t64:amd64. Preparing to unpack .../061-libevent-core-2.1-7t64_2.1.12-stable-10+b1_amd64.deb ... Unpacking libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libevent-extra-2.1-7t64:amd64. Preparing to unpack .../062-libevent-extra-2.1-7t64_2.1.12-stable-10+b1_amd64.deb ... Unpacking libevent-extra-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64. Preparing to unpack .../063-libevent-pthreads-2.1-7t64_2.1.12-stable-10+b1_amd64.deb ... Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libevent-openssl-2.1-7t64:amd64. Preparing to unpack .../064-libevent-openssl-2.1-7t64_2.1.12-stable-10+b1_amd64.deb ... Unpacking libevent-openssl-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libevent-dev. Preparing to unpack .../065-libevent-dev_2.1.12-stable-10+b1_amd64.deb ... Unpacking libevent-dev (2.1.12-stable-10+b1) ... Selecting previously unselected package libpsm-infinipath1. Preparing to unpack .../066-libpsm-infinipath1_3.3+20.604758e7-6.3_amd64.deb ... Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3) ... Selecting previously unselected package libpsm2-2. Preparing to unpack .../067-libpsm2-2_11.2.185-2.1_amd64.deb ... Unpacking libpsm2-2 (11.2.185-2.1) ... Selecting previously unselected package librdmacm1t64:amd64. Preparing to unpack .../068-librdmacm1t64_52.0-2+b1_amd64.deb ... Unpacking librdmacm1t64:amd64 (52.0-2+b1) ... Selecting previously unselected package libfabric1:amd64. Preparing to unpack .../069-libfabric1_1.17.0-3.1_amd64.deb ... Unpacking libfabric1:amd64 (1.17.0-3.1) ... Selecting previously unselected package libhwloc15:amd64. Preparing to unpack .../070-libhwloc15_2.11.2-1_amd64.deb ... Unpacking libhwloc15:amd64 (2.11.2-1) ... Selecting previously unselected package libnuma-dev:amd64. Preparing to unpack .../071-libnuma-dev_2.0.18-1+b1_amd64.deb ... Unpacking libnuma-dev:amd64 (2.0.18-1+b1) ... Selecting previously unselected package libltdl7:amd64. Preparing to unpack .../072-libltdl7_2.4.7-8_amd64.deb ... Unpacking libltdl7:amd64 (2.4.7-8) ... Selecting previously unselected package libltdl-dev:amd64. Preparing to unpack .../073-libltdl-dev_2.4.7-8_amd64.deb ... Unpacking libltdl-dev:amd64 (2.4.7-8) ... Selecting previously unselected package libhwloc-dev:amd64. Preparing to unpack .../074-libhwloc-dev_2.11.2-1_amd64.deb ... Unpacking libhwloc-dev:amd64 (2.11.2-1) ... Selecting previously unselected package libpciaccess0:amd64. Preparing to unpack .../075-libpciaccess0_0.17-3+b2_amd64.deb ... Unpacking libpciaccess0:amd64 (0.17-3+b2) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../076-libxau6_1%3a1.0.11-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../077-libxdmcp6_1%3a1.1.2-3+b2_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3+b2) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../078-libxcb1_1.17.0-2+b1_amd64.deb ... Unpacking libxcb1:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../079-libx11-data_2%3a1.8.10-2_all.deb ... Unpacking libx11-data (2:1.8.10-2) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../080-libx11-6_2%3a1.8.10-2_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.10-2) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../081-libxext6_2%3a1.3.4-1+b2_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1+b2) ... Selecting previously unselected package libxnvctrl0:amd64. Preparing to unpack .../082-libxnvctrl0_535.171.04-1+b1_amd64.deb ... Unpacking libxnvctrl0:amd64 (535.171.04-1+b1) ... Selecting previously unselected package ocl-icd-libopencl1:amd64. Preparing to unpack .../083-ocl-icd-libopencl1_2.3.2-1+b2_amd64.deb ... Unpacking ocl-icd-libopencl1:amd64 (2.3.2-1+b2) ... Selecting previously unselected package libhwloc-plugins:amd64. Preparing to unpack .../084-libhwloc-plugins_2.11.2-1_amd64.deb ... Unpacking libhwloc-plugins:amd64 (2.11.2-1) ... Selecting previously unselected package libibumad3:amd64. Preparing to unpack .../085-libibumad3_52.0-2+b1_amd64.deb ... 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Setting up libedit2:amd64 (3.1-20240808-1) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up libibumad3:amd64 (52.0-2+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libibmad5:amd64 (52.0-2+b1) ... Setting up libcom-err2:amd64 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libncl2:amd64 (2.1.21+git20210811.b1213a7-6) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libncl-dev:amd64 (2.1.21+git20210811.b1213a7-6) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libmunge2:amd64 (0.5.15-4+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libhwloc15:amd64 (2.11.2-1) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libltdl7:amd64 (2.4.7-8) ... Setting up libgfortran5:amd64 (14.2.0-8) ... 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Setting up libnl-route-3-dev:amd64 (3.7.0-0.3+b1) ... Setting up libevent-dev (2.1.12-stable-10+b1) ... Setting up libpmix2t64:amd64 (5.0.3-2+b1) ... Setting up librdmacm1t64:amd64 (52.0-2+b1) ... Setting up libpmix-dev:amd64 (5.0.3-2+b1) ... Setting up libhsakmt1:amd64 (6.1.2+ds-1) ... Setting up libfabric1:amd64 (1.17.0-3.1) ... Setting up debhelper (13.20) ... Setting up libibverbs-dev:amd64 (52.0-2+b1) ... Setting up libhsa-runtime64-1:amd64 (6.1.2-2) ... Setting up libamdhip64-5 (5.7.1-5) ... Setting up libucx0:amd64 (1.17.0+ds-3) ... Setting up libopenmpi3t64:amd64 (5.0.5-3) ... Setting up openmpi-bin (5.0.5-3) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/mpirun.1.gz because associated file /usr/share/man/man1/mpirun.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:amd64 (5.0.5-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up mpi-default-dev (1.17) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/garli-2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../garli_2.1-8_source.changes dpkg-buildpackage: info: source package garli dpkg-buildpackage: info: source version 2.1-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf aclocal: warning: couldn't open directory 'config/m4': No such file or directory configure.ac:8: warning: The macro 'AC_CONFIG_HEADER' is obsolete. configure.ac:8: You should run autoupdate. ./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from... configure.ac:8: the top level configure.ac:47: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.ac:47: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.ac:47: the top level configure.ac:64: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:64: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:64: the top level configure.ac:68: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:68: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:68: the top level configure.ac:80: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:80: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:80: the top level configure.ac:92: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:92: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:92: the top level configure.ac:104: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:104: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:104: the top level configure.ac:113: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:113: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:113: the top level configure.ac:122: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:122: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:122: the top level configure.ac:131: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:131: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:131: the top level configure.ac:140: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:140: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:140: the top level configure.ac:224: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.ac:224: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... config/acx_mpi.m4:74: ACX_MPI is expanded from... configure.ac:224: the top level configure.ac:249: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:249: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:249: the top level configure.ac:280: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:280: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:280: the top level configure.ac:339: warning: The macro 'AC_TRY_LINK' is obsolete. configure.ac:339: You should run autoupdate. ./lib/autoconf/general.m4:2918: AC_TRY_LINK is expanded from... configure.ac:339: the top level configure.ac:349: warning: The macro 'AC_TRY_LINK' is obsolete. configure.ac:349: You should run autoupdate. ./lib/autoconf/general.m4:2918: AC_TRY_LINK is expanded from... configure.ac:349: the top level configure.ac:355: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ./lib/autoconf/lang.m4:199: AC_LANG_CONFTEST is expanded from... ./lib/autoconf/general.m4:2821: _AC_COMPILE_IFELSE is expanded from... ./lib/autoconf/general.m4:2837: AC_COMPILE_IFELSE is expanded from... configure.ac:355: the top level configure.ac:25: warning: support for distribution archives compressed with legacy program 'compress' is deprecated. configure.ac:25: It will be removed in Automake 2.0 debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/garli-2.1' # First build MPI version of Garli dh_auto_configure -- --with-ncl=/usr --enable-mpi ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-ncl=/usr --enable-mpi checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '1111' is supported by ustar format... yes checking whether GID '1111' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking for ranlib... ranlib checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for float.h... yes checking for malloc.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for sys/time.h... yes checking for _Bool... yes checking for stdbool.h that conforms to C99 or later... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for error_at_line... yes checking for GNU libc compatible malloc... yes checking for working strtod... yes checking for floor... no checking for memmove... yes checking for memset... yes checking for pow... no checking for sqrt... no checking for strchr... yes checking for strdup... yes checking for strtol... yes configure: *** NOTE: compiling MPI run distributing version checking for mpic++... mpic++ checking for MPI_Init... yes checking for mpi.h... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating tests/Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build make -j20 make[2]: Entering directory '/build/reproducible-path/garli-2.1' make all-recursive make[3]: Entering directory '/build/reproducible-path/garli-2.1' Making all in src make[4]: Entering directory '/build/reproducible-path/garli-2.1/src' mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o adaptation.o adaptation.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o bipartition.o bipartition.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o condlike.o condlike.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configoptions.o configoptions.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configreader.o configreader.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o datamatr.o datamatr.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o funcs.o funcs.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlimain.o garlimain.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlireader.o garlireader.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o individual.o individual.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)': linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1322 | register int nsq = n * n; | ^~~ garlimain.cpp:434:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ garlimain.cpp:434:76: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ In file included from bipartition.cpp:20: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from bipartition.h:23, from bipartition.cpp:19: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from configoptions.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from tree.h:35, from optimization.cpp:19: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from tree.h:24: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from optimization.cpp:21: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/iomanip:42, from individual.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from population.cpp:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from population.cpp:49: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from model.cpp:26: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from model.cpp:17: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from garlimain.cpp:46: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from tree.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, from funcs.cpp:30: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from configreader.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, from mpitrick.cpp:27: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from mpitrick.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from adaptation.cpp:18: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)': datamatr.cpp:1390:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1390 | fscanf(inf, "%d %d", &num_taxa, &num_chars); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;idlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6845:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6845 | fread(&dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6849:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6849 | fread(&dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6855:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6855 | fread(&dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6858:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6858 | fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6862:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6862 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6865:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6865 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6868:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6868 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6872:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6872 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6878:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6878 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6881 | fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from translatetable.h:24, from translatetable.cpp:19: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from rng.h:36, from tree.h:30: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from treenode.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from model.h:25, from clamanager.h:25, from condlike.cpp:22: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from datamatr.h:23, from sequencedata.h:27, from sequencedata.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from datamatr.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from configreader.cpp:18: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/ncl/ncl.h:27, from garlireader.cpp:41: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from population.cpp:25: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from datamatr.h:23, from sequencedata.h:27, from tree.cpp:31: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] garlimain.cpp: In function 'int SubGarliMain(int)': garlimain.cpp:323:49: warning: '%d' directive writing between 2 and 10 bytes into a region of size 6 [-Wformat-overflow=] 323 | else sprintf(temp, ".run%d", rank); | ^~ garlimain.cpp:323:44: note: directive argument in the range [10, 2147483647] 323 | else sprintf(temp, ".run%d", rank); | ^~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int SubGarliMain(int)' at garlimain.cpp:323:16: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 15 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ garlimain.cpp: In function 'int SubGarliMain(int)': garlimain.cpp:322:59: warning: '%d' directive writing between 1 and 11 bytes into a region of size 5 [-Wformat-overflow=] 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); | ^~ garlimain.cpp:322:53: note: directive argument in the range [-2147483648, 9] 322 | if(rank < 10) sprintf(temp, ".run0%d", rank); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int SubGarliMain(int)' at garlimain.cpp:322:25: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 17 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': population.cpp:3066:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~ population.cpp:3066:47: note: directive argument in the range [1, 2147483647] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mpic++ -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-z,relro -Wl,-z,now -L/usr/lib -o Garli adaptation.o bipartition.o condlike.o configoptions.o configreader.o datamatr.o funcs.o garlimain.o garlireader.o individual.o linalg.o model.o optimization.o population.o rng.o sequencedata.o set.o translatetable.o tree.o treenode.o mpitrick.o -lncl -lncl make[4]: Leaving directory '/build/reproducible-path/garli-2.1/src' Making all in tests make[4]: Entering directory '/build/reproducible-path/garli-2.1/tests' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/garli-2.1/tests' make[4]: Entering directory '/build/reproducible-path/garli-2.1' make[4]: Leaving directory '/build/reproducible-path/garli-2.1' make[3]: Leaving directory '/build/reproducible-path/garli-2.1' make[2]: Leaving directory '/build/reproducible-path/garli-2.1' mkdir -p debian/mpi mv src/Garli debian/mpi/Garli-mpi make distclean make[2]: Entering directory '/build/reproducible-path/garli-2.1' Making distclean in src make[3]: Entering directory '/build/reproducible-path/garli-2.1/src' 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/reproducible-path/garli-2.1/src' Making distclean in tests make[3]: Entering directory '/build/reproducible-path/garli-2.1/tests' test -z "" || rm -f test . = "." || test -z "" || rm -f rm -f Makefile make[3]: Leaving directory '/build/reproducible-path/garli-2.1/tests' make[3]: Entering directory '/build/reproducible-path/garli-2.1' 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/reproducible-path/garli-2.1' rm -f config.status config.cache config.log configure.lineno config.status.lineno rm -f Makefile make[2]: Leaving directory '/build/reproducible-path/garli-2.1' # Now build single processor binary dh_auto_configure -- --with-ncl=/usr ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-ncl=/usr checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '1111' is supported by ustar format... yes checking whether GID '1111' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking for ranlib... ranlib checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for float.h... yes checking for malloc.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for sys/time.h... yes checking for _Bool... yes checking for stdbool.h that conforms to C99 or later... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for error_at_line... yes checking for GNU libc compatible malloc... yes checking for working strtod... yes checking for floor... no checking for memmove... yes checking for memset... yes checking for pow... no checking for sqrt... no checking for strchr... yes checking for strdup... yes checking for strtol... yes checking for mpic++... mpic++ checking for MPI_Init... yes checking for mpi.h... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating tests/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/reproducible-path/garli-2.1' dh_auto_build make -j20 make[1]: Entering directory '/build/reproducible-path/garli-2.1' make all-recursive make[2]: Entering directory '/build/reproducible-path/garli-2.1' Making all in src make[3]: Entering directory '/build/reproducible-path/garli-2.1/src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o adaptation.o adaptation.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o bipartition.o bipartition.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o condlike.o condlike.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configoptions.o configoptions.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configreader.o configreader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o datamatr.o datamatr.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o funcs.o funcs.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlimain.o garlimain.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlireader.o garlireader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o individual.o individual.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp garlimain.cpp:434:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ garlimain.cpp:434:76: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)': linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1322 | register int nsq = n * n; | ^~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from configoptions.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': configoptions.cpp:337:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 337 | sprintf(modName, "model%d", modelNum); | ^~ configoptions.cpp:337:34: note: directive argument in the range [0, 2147483647] 337 | sprintf(modName, "model%d", modelNum); | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)' at configoptions.cpp:337:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from bipartition.cpp:20: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from bipartition.h:23, from bipartition.cpp:19: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, from adaptation.cpp:25: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from adaptation.cpp:18: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from model.cpp:17: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from tree.h:35, from optimization.cpp:19: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from tree.h:24: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from garlimain.cpp:40: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from optimization.cpp:21: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from population.cpp:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from garlimain.cpp:46: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/iomanip:42, from individual.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, from funcs.cpp:30: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from population.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from population.cpp:49: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from configreader.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from tree.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)': reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; | ~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;idlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6845:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6845 | fread(&dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6849:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6849 | fread(&dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6855:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6855 | fread(&dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6858:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6858 | fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6862:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6862 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6865:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6865 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6868:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6868 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6872:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6872 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6878:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6878 | fread((char*) &dum, sizeof(dum), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6881 | fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from translatetable.h:24, from translatetable.cpp:19: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from model.h:25, from clamanager.h:25, from condlike.cpp:22: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from treenode.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from datamatr.h:23, from sequencedata.h:27, from sequencedata.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from rng.h:36, from tree.h:30: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/ncl/ncl.h:27, from garlireader.cpp:41: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from configreader.cpp:18: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from datamatr.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from datamatr.h:23, from sequencedata.h:27, from tree.cpp:31: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from population.cpp:25: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': population.cpp:3066:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~ population.cpp:3066:47: note: directive argument in the range [1, 2147483647] 3066 | sprintf(oStr, "R(%d)", d + 1); | ^~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-z,relro -Wl,-z,now -L/usr/lib -o Garli adaptation.o bipartition.o condlike.o configoptions.o configreader.o datamatr.o funcs.o garlimain.o garlireader.o individual.o linalg.o model.o optimization.o population.o rng.o sequencedata.o set.o translatetable.o tree.o treenode.o mpitrick.o -lncl -lncl make[3]: Leaving directory '/build/reproducible-path/garli-2.1/src' Making all in tests make[3]: Entering directory '/build/reproducible-path/garli-2.1/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/garli-2.1/tests' make[3]: Entering directory '/build/reproducible-path/garli-2.1' make[3]: Leaving directory '/build/reproducible-path/garli-2.1' make[2]: Leaving directory '/build/reproducible-path/garli-2.1' make[1]: Leaving directory '/build/reproducible-path/garli-2.1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/garli-2.1' cp -a tests tests.bak # get (mostly!) reproducible test results and avoid failures as described in bug #907905 find tests -name "*.conf" -exec sed -i~ 's/randseed *= *-1/randseed = 1\nbootstrapseed = 42/' \{\} \; dh_auto_test make -j20 check "TESTSUITEFLAGS=-j20 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/garli-2.1' Making check in src make[3]: Entering directory '/build/reproducible-path/garli-2.1/src' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/garli-2.1/src' Making check in tests make[3]: Entering directory '/build/reproducible-path/garli-2.1/tests' make check-local make[4]: Entering directory '/build/reproducible-path/garli-2.1/tests' ./runtests.sh . ../src/Garli /usr/bin/NEXUSvalidator Linking to data .... data folder already exists ************************** Running internal tests ... ************************** Running internal test ./internal/a.G3.conf Running internal test ./internal/a.G3.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/a.G3.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/moore.matK90-120.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 86 sequences. 2 constant characters. 6 parsimony-informative characters. 2 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 5 MB good approx 4 MB to 2 MB low approx 2 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 5.8 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/moore.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0088 0.0022 0.0131 0.3020 0.0985 0.0088 0.0109 0.0284 0.0810 0.0503 0.1794 0.0022 0.0044 0.1575 0.0109 0.0109 0.0044 0.0044 0.0022 0.0197 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0500 Substitution rate categories under this model: rate proportion 0.0000 0.0500 0.0603 0.3167 0.4894 0.3167 2.4503 0.3167 Starting with seed=1 WARNING: Polytomies found in start tree. These were arbitrarily resolved. Initial ln Likelihood: -534.6163 optimizing: starting branch lengths, alpha shape, prop. invar... pass 1:+ 97.093 (branch= 90.61 scale= 6.48 alpha= 0.00 pinv= 0.00) pass 2:+ 26.504 (branch= 20.56 scale= 5.94 alpha= 0.00 pinv= 0.00) pass 3:+ 7.183 (branch= 6.27 scale= 0.91 alpha= 0.00 pinv= 0.00) pass 4:+ 2.513 (branch= 1.73 scale= 0.78 alpha= 0.00 pinv= 0.00) pass 5:+ 1.030 (branch= 0.48 scale= 0.55 alpha= 0.00 pinv= 0.00) pass 6:+ 0.375 (branch= 0.37 scale= 0.00 alpha= 0.00 pinv= 0.00) lnL after optimization: -399.9190 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/a.G4.conf Running internal test ./internal/a.G4.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/a.G4.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/moore.matK90-120.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 86 sequences. 2 constant characters. 6 parsimony-informative characters. 2 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 6 MB good approx 5 MB to 4 MB low approx 3 MB to 2 MB very low approx 2 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 7.7 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/moore.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0088 0.0022 0.0131 0.3020 0.0985 0.0088 0.0109 0.0284 0.0810 0.0503 0.1794 0.0022 0.0044 0.1575 0.0109 0.0109 0.0044 0.0044 0.0022 0.0197 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0500 Substitution rate categories under this model: rate proportion 0.0000 0.0500 0.0334 0.2375 0.2519 0.2375 0.8203 0.2375 2.8944 0.2375 Starting with seed=1 WARNING: Polytomies found in start tree. These were arbitrarily resolved. Initial ln Likelihood: -532.4673 optimizing: starting branch lengths, alpha shape, prop. invar... pass 1:+ 92.949 (branch= 88.74 scale= 4.20 alpha= 0.00 pinv= 0.00) pass 2:+ 25.801 (branch= 20.07 scale= 5.73 alpha= 0.00 pinv= 0.00) pass 3:+ 9.142 (branch= 7.26 scale= 1.88 alpha= 0.00 pinv= 0.00) pass 4:+ 3.445 (branch= 2.67 scale= 0.78 alpha= 0.00 pinv= 0.00) pass 5:+ 0.802 (branch= 0.25 scale= 0.55 alpha= 0.00 pinv= 0.00) pass 6:+ 0.294 (branch= 0.29 scale= 0.00 alpha= 0.00 pinv= 0.00) lnL after optimization: -400.0333 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/a.conf Running internal test ./internal/a.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/a.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/moore.matK90-120.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 86 sequences. 2 constant characters. 6 parsimony-informative characters. 2 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 2 MB good approx 2 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 2.0 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/moore.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0088 0.0022 0.0131 0.3020 0.0985 0.0088 0.0109 0.0284 0.0810 0.0503 0.1794 0.0022 0.0044 0.1575 0.0109 0.0109 0.0044 0.0044 0.0022 0.0197 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 WARNING: Polytomies found in start tree. These were arbitrarily resolved. NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -567.2416 optimizing: starting branch lengths... pass 1:+ 135.572 (branch= 118.31 scale= 17.26) pass 2:+ 21.497 (branch= 16.34 scale= 5.15) pass 3:+ 6.821 (branch= 6.09 scale= 0.73) pass 4:+ 2.066 (branch= 1.47 scale= 0.59) pass 5:+ 1.595 (branch= 1.59 scale= 0.00) pass 6:+ 1.322 (branch= 0.81 scale= 0.51) pass 7:+ 0.354 (branch= 0.35 scale= 0.00) lnL after optimization: -398.0145 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/c.M3x2.conf Running internal test ./internal/c.M3x2.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/c.M3x2.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x30.stop.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Codon data Warning: stop codon TAA found at codon site 11 (nuc site 31) in taxon MorNa6. Treating as missing data because ignorestopcodons = 1 is set in configuration file. Warning: stop codon TAA found at codon site 11 (nuc site 31) in taxon ClownNa6. Treating as missing data because ignorestopcodons = 1 is set in configuration file. Base usage at codon positions: A C G T pos 1 0.27184 0.35922 0.21359 0.15534 pos 2 0.32039 0.20388 0.07767 0.39806 pos 3 0.12621 0.37864 0.26214 0.23301 all pos 0.23948 0.31392 0.18447 0.26214 Summary of data: 11 sequences. 0 constant characters. 9 parsimony-informative characters. 1 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 10 total characters (11 before removing empty columns). 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 1.3 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### STARTING RUN starting internal tests... MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0112 0.0337 0.0233 0.0207 0.0071 0.0214 0.0148 0.0132 0.0027 0.0082 0.0057 0.0050 0.0139 0.0418 0.0290 0.0258 0.0148 0.0445 0.0308 0.0274 0.0094 0.0283 0.0196 0.0174 0.0036 0.0108 0.0075 0.0066 0.0184 0.0553 0.0383 0.0340 0.0088 0.0265 0.0183 0.0163 0.0056 0.0168 0.0117 0.0104 0.0021 0.0064 0.0044 0.0039 0.0110 0.0329 0.0228 0.0202 0.0192 0.0118 0.0041 0.0122 0.0085 0.0075 0.0047 0.0032 0.0029 0.0080 0.0239 0.0166 0.0147 Rate Heterogeneity Model: 2 nonsynonymous rate categories, rate and proportion of each estimated (this is effectively the M3 model of PAML) dN/dS Proportion 0.2500 0.5000 0.5000 0.5000 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 4.421 lnL Optimizing branchlengths... improved 0.690 lnL 7 8 9 10 11 Initial ln Likelihood: -215.5693 optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters... pass 1:+ 6.143 (branch= 0.00 scale= 0.00 omega= 0.01 rel rates= 6.13) pass 2:+ 0.420 (branch= 0.00 scale= 0.00 omega= 0.01 rel rates= 0.41) lnL after optimization: -209.0069 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/c.conf Running internal test ./internal/c.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/c.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Codon data Base usage at codon positions: A C G T pos 1 0.27723 0.36634 0.21782 0.13861 pos 2 0.30693 0.20792 0.07921 0.40594 pos 3 0.10891 0.38614 0.26733 0.23762 all pos 0.23102 0.32013 0.18812 0.26073 Summary of data: 11 sequences. 0 constant characters. 9 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### STARTING RUN starting internal tests... MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 61 (codon data, standard code) One estimated dN/dS ratio (aka omega) = 0.250000 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0094 0.0334 0.0231 0.0206 0.0064 0.0226 0.0157 0.0139 0.0024 0.0086 0.0060 0.0053 0.0125 0.0442 0.0306 0.0272 0.0125 0.0442 0.0306 0.0272 0.0084 0.0299 0.0207 0.0184 0.0032 0.0114 0.0079 0.0070 0.0165 0.0584 0.0405 0.0360 0.0074 0.0263 0.0182 0.0162 0.0050 0.0178 0.0123 0.0110 0.0019 0.0068 0.0047 0.0042 0.0098 0.0347 0.0241 0.0214 0.0167 0.0103 0.0032 0.0113 0.0078 0.0070 0.0043 0.0030 0.0027 0.0062 0.0221 0.0153 0.0136 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.001 lnL Optimizing branchlengths... improved 0.000 lnL 7 8 9 10 11 Initial ln Likelihood: -225.6424 optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters... pass 1:+ 10.931 (branch= 2.26 scale= 0.50 omega= 0.00 rel rates= 8.17) pass 2:+ 0.924 (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: -213.0383 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/n.G3.conf Running internal test ./internal/n.G3.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/n.G3.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/moore.matK90-120.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 86 sequences. 10 constant characters. 13 parsimony-informative characters. 7 uninformative variable characters. 30 total characters. 24 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 2 MB good approx 2 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 2.9 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN starting internal tests... MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.4638 0.0976 0.2304 0.2082 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0833 Substitution rate categories under this model: rate proportion 0.0000 0.0833 0.0603 0.3056 0.4894 0.3056 2.4503 0.3056 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 Optimizing parameters... improved 2.070 lnL Optimizing branchlengths... improved 1.544 lnL 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 Initial ln Likelihood: -351.3160 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 11.635 (branch= 3.88 scale= 0.50 alpha= 0.97 freqs= 0.05 rel rates= 6.23 pinv= 0.01) pass 2:+ 1.385 (branch= 0.93 scale= 0.41 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.01) pass 3:+ 0.338 (branch= 0.30 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.01) lnL after optimization: -337.9573 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/n.G4.conf Running internal test ./internal/n.G4.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/n.G4.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/moore.matK90-120.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 86 sequences. 10 constant characters. 13 parsimony-informative characters. 7 uninformative variable characters. 30 total characters. 24 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 4 MB good approx 3 MB to 2 MB low approx 2 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 3.8 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN starting internal tests... MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.4638 0.0976 0.2304 0.2082 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0833 Substitution rate categories under this model: rate proportion 0.0000 0.0833 0.0334 0.2292 0.2519 0.2292 0.8203 0.2292 2.8944 0.2292 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 Optimizing parameters... improved 2.099 lnL Optimizing branchlengths... improved 1.492 lnL 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 Initial ln Likelihood: -363.1701 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 13.147 (branch= 2.38 scale= 2.97 alpha= 0.67 freqs= 1.24 rel rates= 5.88 pinv= 0.01) pass 2:+ 2.663 (branch= 2.63 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.00) pass 3:+ 0.035 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.00) lnL after optimization: -347.3249 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/n.conf Running internal test ./internal/n.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/n.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/moore.matK90-120.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 86 sequences. 10 constant characters. 13 parsimony-informative characters. 7 uninformative variable characters. 30 total characters. 24 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 1.0 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN starting internal tests... MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 1 rate Equilibrium State Frequencies: estimated (ACGT) 0.4638 0.0976 0.2304 0.2082 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 2.038 lnL 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 Initial ln Likelihood: -371.0442 optimizing: starting branch lengths, eq freqs... pass 1:+ 3.897 (branch= 2.20 scale= 0.00 freqs= 1.70) pass 2:+ 0.641 (branch= 0.60 scale= 0.00 freqs= 0.04) pass 3:+ 0.073 (branch= 0.03 scale= 0.00 freqs= 0.04) lnL after optimization: -366.4339 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.3diff.conf Running internal test ./internal/p.3diff.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/p.3diff.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.byPos.11x2178.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful Reading SETS block...storing read block: SETS successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #1 ("1stpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 4 Summary of data: 11 sequences. 441 constant characters. 171 parsimony-informative characters. 113 uninformative variable characters. 725 total characters. 237 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #2 ("2ndpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 5 Summary of data: 11 sequences. 527 constant characters. 90 parsimony-informative characters. 108 uninformative variable characters. 725 total characters. 158 unique patterns in compressed data matrix. GARLI data subset 3 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #3 ("3rdpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 6 Summary of data: 11 sequences. 102 constant characters. 507 parsimony-informative characters. 116 uninformative variable characters. 725 total characters. 548 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 11 MB good approx 10 MB to 9 MB low approx 8 MB to 5 MB very low approx 4 MB to 4 MB the minimum required availablememory is 4 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 16.0 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### STARTING RUN starting internal tests... MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3150 0.1749 0.3006 0.2095 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 Substitution rate categories under this model: rate proportion 0.0334 0.2500 0.2519 0.2500 0.8203 0.2500 2.8944 0.2500 Model 2 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) AC = 4.000, AG = 4.000, AT = 1.000, CG = 4.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2706 0.1568 0.1630 0.4096 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 Substitution rate categories under this model: rate proportion 0.0334 0.2500 0.2519 0.2500 0.8203 0.2500 2.8944 0.2500 Model 3 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1462 0.3614 0.2906 0.2018 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0352 Substitution rate categories under this model: rate proportion 0.0000 0.0352 0.0334 0.2412 0.2519 0.2412 0.8203 0.2412 2.8944 0.2412 Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 168.526 lnL Optimizing branchlengths... improved 66.084 lnL 7 8 9 10 11 Initial ln Likelihood: -13699.7841 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates... pass 1:+ 209.508 (branch= 7.95 scale= 0.00 alpha= 35.56 freqs= 28.90 rel rates= 62.03 pinv= 0.19 subset rates= 74.88) pass 2:+ 77.016 (branch= 1.74 scale= 0.00 alpha= 4.25 freqs= 11.29 rel rates= 3.50 pinv= 0.68 subset rates= 55.55) pass 3:+ 50.073 (branch= 8.13 scale= 0.55 alpha= 4.79 freqs= 1.15 rel rates= 1.36 pinv= 0.01 subset rates= 34.08) pass 4:+ 16.647 (branch= 1.54 scale= 0.00 alpha= 0.63 freqs= 1.21 rel rates= 1.36 pinv= 0.01 subset rates= 11.89) pass 5:+ 6.281 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.12 rel rates= 1.30 pinv= 0.01 subset rates= 4.84) pass 6:+ 0.125 (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: -13340.1342 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mk.conf Running internal test ./internal/p.mk.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/p.mk.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, modeled as Standard k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -609.1934 optimizing: starting branch lengths... pass 1:+ 125.912 (branch= 124.97 scale= 0.94) pass 2:+ 7.205 (branch= 7.20 scale= 0.00) pass 3:+ 1.518 (branch= 1.48 scale= 0.03) pass 4:+ 0.225 (branch= 0.22 scale= 0.00) pass 5:+ 0.014 (branch= 0.01 scale= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -474.3188 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mk.ssr.conf Running internal test ./internal/p.mk.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/p.mk.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, modeled as Standard k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -609.1934 optimizing: starting branch lengths, subset rates... pass 1:+ 130.207 (branch= 124.97 scale= 0.94 subset rates= 4.30) pass 2:+ 9.055 (branch= 8.14 scale= 0.00 subset rates= 0.91) pass 3:+ 1.801 (branch= 1.66 scale= 0.02 subset rates= 0.12) pass 4:+ 0.303 (branch= 0.30 scale= 0.00 subset rates= 0.00) pass 5:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -467.8152 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mkO.conf Running internal test ./internal/p.mkO.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/p.mkO.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, modeled as Standard ordered k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -641.9257 optimizing: starting branch lengths... pass 1:+ 137.411 (branch= 136.58 scale= 0.83) pass 2:+ 7.774 (branch= 7.77 scale= 0.00) pass 3:+ 1.542 (branch= 1.52 scale= 0.02) pass 4:+ 0.091 (branch= 0.09 scale= 0.00) pass 5:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -495.1076 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mkO.ssr.conf Running internal test ./internal/p.mkO.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/p.mkO.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, modeled as Standard ordered k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -641.9257 optimizing: starting branch lengths, subset rates... pass 1:+ 147.096 (branch= 136.58 scale= 0.83 subset rates= 9.68) pass 2:+ 12.450 (branch= 8.46 scale= 0.00 subset rates= 3.99) pass 3:+ 3.552 (branch= 2.32 scale= 0.03 subset rates= 1.21) pass 4:+ 0.757 (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: -477.9409 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mkv.conf Running internal test ./internal/p.mkv.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/p.mkv.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, variable only, modeled as Standard k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -605.5989 optimizing: starting branch lengths... pass 1:+ 124.584 (branch= 123.99 scale= 0.59) pass 2:+ 6.980 (branch= 6.98 scale= 0.00) pass 3:+ 1.324 (branch= 1.31 scale= 0.02) pass 4:+ 0.161 (branch= 0.16 scale= 0.00) pass 5:+ 0.013 (branch= 0.01 scale= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -472.5370 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mkv.ssr.conf Running internal test ./internal/p.mkv.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/p.mkv.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, variable only, modeled as Standard k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -605.5989 optimizing: starting branch lengths, subset rates... pass 1:+ 129.564 (branch= 123.99 scale= 0.59 subset rates= 4.98) pass 2:+ 9.273 (branch= 7.97 scale= 0.00 subset rates= 1.30) pass 3:+ 1.739 (branch= 1.57 scale= 0.00 subset rates= 0.17) pass 4:+ 0.312 (branch= 0.31 scale= 0.00 subset rates= 0.00) pass 5:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -464.7108 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mkvO.conf Running internal test ./internal/p.mkvO.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/p.mkvO.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, variable only, modeled as Standard ordered k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -637.9212 optimizing: starting branch lengths... pass 1:+ 134.883 (branch= 134.40 scale= 0.48) pass 2:+ 7.290 (branch= 7.29 scale= 0.00) pass 3:+ 1.758 (branch= 1.73 scale= 0.03) pass 4:+ 0.187 (branch= 0.19 scale= 0.00) pass 5:+ 0.011 (branch= 0.01 scale= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -493.7915 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** Running internal test ./internal/p.mkvO.ssr.conf Running internal test ./internal/p.mkvO.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./internal/p.mkvO.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, variable only, modeled as Standard ordered k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN starting internal tests... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -637.9212 optimizing: starting branch lengths, subset rates... pass 1:+ 144.867 (branch= 134.40 scale= 0.48 subset rates= 9.98) pass 2:+ 12.967 (branch= 8.30 scale= 0.00 subset rates= 4.67) pass 3:+ 3.846 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.161 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.157 (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: -474.8624 WARNING: You are running internal tests with NDEBUG defined! It should not be defined for full error checking. ******Successfully completed tests.****** ************************** Running scoring tests ... ************************** Running scoring test ./scoring/a.G3.conf Running scoring test ./scoring/a.G3.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/a.G3.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x2178.AA.nex ... Reading TAXA block...storing read block: TAXA successful Reading CHARACTERS block...storing read block: CHARACTERS found protein data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful Reading CODONS block...storing read block: CODONS successful Reading MESQUITECHARMODELS block...storing read block: MESQUITECHARMODELS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Protein translation of Character Matrix") Data read as Amino acid data, modeled as Amino acid data Found wtset "equal" with data, applying... Summary of data: 11 sequences. 389 constant characters. 190 parsimony-informative characters. 147 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 726 total characters (727 before removing empty columns). 343 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 13 MB good approx 12 MB to 9 MB low approx 8 MB to 5 MB very low approx 4 MB to 2 MB the minimum required availablememory is 2 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 5 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 18.0 MB of memory ####################################################### Found outgroup specification: 1 2 ####################################################### Loading starting model and/or tree from file data/a.G3.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus Obtained starting or fixed model parameter values from configuration file: MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: WAG Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0500 0.0252 0.0458 0.0579 0.0750 0.0561 0.0078 0.0882 0.0489 0.1128 0.0438 0.0500 0.0296 0.0252 0.0373 0.0552 0.0444 0.0906 0.0217 0.0346 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.4368 Substitution rate categories under this model: rate proportion 0.0437 0.3333 0.4372 0.3333 2.5190 0.3333 Starting with seed=1 Initial ln Likelihood: -6242.8631 optimizing: starting branch lengths, alpha shape... pass 1:+ 0.000 (branch= 0.00 scale= 0.00 alpha= 0.00) lnL after optimization: -6242.8629 Current score = -6242.8629 Performing final optimizations... pass 1 : -6242.8629 (branch= 0.0000 alpha= 0.0000) pass 2 : -6242.8595 (branch= 0.0034 alpha= 0.0000) pass 3 : -6242.8595 (branch= 0.0000 alpha= 0.0000) pass 4 : -6242.8595 (branch= 0.0000 alpha= 0.0000) pass 5 : -6242.8591 (branch= 0.0004 alpha= 0.0000) pass 6 : -6242.8586 (branch= 0.0005 alpha= 0.0000) pass 7 : -6242.8585 (branch= 0.0001 alpha= 0.0000) pass 8 : -6242.8583 (branch= 0.0002 alpha= 0.0000) pass 9 : -6242.8582 (branch= 0.0001 alpha= 0.0000) pass 10: -6242.8581 (branch= 0.0001 alpha= 0.0000) pass 11: -6242.8580 (branch= 0.0000 alpha= 0.0000) pass 12: -6242.8580 (branch= 0.0000 alpha= 0.0000) pass 13: -6242.8580 (branch= 0.0000 alpha= 0.0000) Looking for minimum length branches... Final score = -6242.8580 Time used = 0 hours, 0 minutes and 3 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -6242.8580 Parameter estimates: alpha rep 1: 0.436 Treelengths: TL rep 1: 1.345 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.a.G3.best.all.tre ***********TEST************** ***Score is 6242.85802 ***Expected is 6242.85802 ***SCORE DIFFERENCE IS 0 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/a.G3.conf *** Running scoring test ./scoring/a.G4.conf Running scoring test ./scoring/a.G4.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/a.G4.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x2178.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data Some sites treated as missing data for taxon SterNa6 due to ambiguity in translation. Aminoacids coded as missing for that taxon: 708 Summary of data: 11 sequences. 389 constant characters. 190 parsimony-informative characters. 147 uninformative variable characters. 726 total characters. 343 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 17 MB good approx 16 MB to 13 MB low approx 12 MB to 6 MB very low approx 5 MB to 3 MB the minimum required availablememory is 3 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 6 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 23.9 MB of memory ####################################################### Found outgroup specification: 1-5 ####################################################### Loading starting model and/or tree from file data/a.G4.start Reading TREES block...storing read block: TREES successful Reading GARLI block...storing read block: GARLI successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus Obtained starting or fixed model parameter values from Nexus: MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: values specified by user (fixed) Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0500 0.0252 0.0458 0.0579 0.0750 0.0561 0.0078 0.0882 0.0489 0.1128 0.0438 0.0500 0.0296 0.0252 0.0373 0.0552 0.0444 0.0906 0.0217 0.0346 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.4616 Substitution rate categories under this model: rate proportion 0.0265 0.2500 0.2261 0.2500 0.7902 0.2500 2.9572 0.2500 Starting with seed=1 Initial ln Likelihood: -6249.1664 optimizing: starting branch lengths, alpha shape... pass 1:+ 1.482 (branch= 0.00 scale= 1.47 alpha= 0.01) pass 2:+ 0.010 (branch= 0.00 scale= 0.00 alpha= 0.01) lnL after optimization: -6247.6743 Current score = -6247.6743 Performing final optimizations... pass 1 : -6247.0539 (branch= 0.2066 alpha= 0.4138) pass 2 : -6247.0347 (branch= 0.0192 alpha= 0.0000) pass 3 : -6247.0279 (branch= 0.0068 alpha= 0.0000) pass 4 : -6247.0255 (branch= 0.0023 alpha= 0.0000) pass 5 : -6247.0234 (branch= 0.0022 alpha= 0.0000) pass 6 : -6247.0228 (branch= 0.0005 alpha= 0.0000) pass 7 : -6247.0226 (branch= 0.0002 alpha= 0.0000) pass 8 : -6247.0223 (branch= 0.0002 alpha= 0.0000) pass 9 : -6247.0222 (branch= 0.0001 alpha= 0.0000) pass 10: -6247.0222 (branch= 0.0000 alpha= 0.0000) Looking for minimum length branches... Final score = -6247.0222 Time used = 0 hours, 0 minutes and 3 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -6247.0222 Parameter estimates: alpha rep 1: 0.423 Treelengths: TL rep 1: 1.467 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.a.G4.best.all.tre ***********TEST************** ***Score is 6247.02222 ***Expected is 6247.02222 ***SCORE DIFFERENCE IS 0 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/a.G4.conf *** Running scoring test ./scoring/a.conf Running scoring test ./scoring/a.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/a.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x2178.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data Some sites treated as missing data for taxon SterNa6 due to ambiguity in translation. Aminoacids coded as missing for that taxon: 708 Summary of data: 11 sequences. 389 constant characters. 190 parsimony-informative characters. 147 uninformative variable characters. 726 total characters. 343 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 4 MB good approx 3 MB to 3 MB low approx 2 MB to 2 MB very low approx 1 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 2 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 6.1 MB of memory ####################################################### Found outgroup specification: 1 ####################################################### Loading starting model and/or tree from file data/a.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: WAG Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0500 0.0252 0.0458 0.0579 0.0750 0.0561 0.0078 0.0882 0.0489 0.1128 0.0438 0.0500 0.0296 0.0252 0.0373 0.0552 0.0444 0.0906 0.0217 0.0346 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -6434.5146 optimizing: starting branch lengths... pass 1:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -6434.5146 Current score = -6434.5146 Performing final optimizations... pass 1 : -6434.5146 (branch= 0.0000) pass 2 : -6434.5101 (branch= 0.0045) pass 3 : -6434.5101 (branch= 0.0000) pass 4 : -6434.5101 (branch= 0.0000) pass 5 : -6434.5101 (branch= 0.0000) pass 6 : -6434.5092 (branch= 0.0009) pass 7 : -6434.5092 (branch= 0.0000) pass 8 : -6434.5092 (branch= 0.0000) pass 9 : -6434.5092 (branch= 0.0000) pass 10: -6434.5092 (branch= 0.0000) pass 11: -6434.5092 (branch= 0.0000) Looking for minimum length branches... Final score = -6434.5092 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -6434.5092 Parameter estimates: Model contains no estimated parameters Treelengths: TL rep 1: 1.143 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.a.best.all.tre ***********TEST************** ***Score is 6434.50916 ***Expected is 6434.50916 ***SCORE DIFFERENCE IS 0 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/a.conf *** Running scoring test ./scoring/c.M3x2.conf Running scoring test ./scoring/c.M3x2.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/c.M3x2.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x2178.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Codon data Gaps or ambiguity codes found within codon for taxon SterNa6. Codons coded as missing for that taxon: 708 Gaps or ambiguity codes found within codon for taxon PinniNa6. Codons coded as missing for that taxon: 513 646 Summary of data: 11 sequences. 72 constant characters. 527 parsimony-informative characters. 127 uninformative variable characters. 726 total characters. 668 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 47 MB good approx 46 MB to 36 MB low approx 35 MB to 18 MB very low approx 17 MB to 7 MB the minimum required availablememory is 7 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 15 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 70.8 MB of memory ####################################################### Found outgroup specification: 1 2 ####################################################### Loading starting model and/or tree from file data/c.M3x2.start Reading TREES block...storing read block: TREES successful Reading GARLI block...storing read block: GARLI successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus Obtained starting or fixed model parameter values from Nexus: MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates Values specified by user (fixed) AC = 1.260, AG = 2.449, AT = 1.259, CG = 0.687, CT = 1.396, GT = 1.000 Equilibrium State Frequencies: empirical (observed) values, fixed: (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0179 0.0349 0.0309 0.0152 0.0114 0.0181 0.0065 0.0084 0.0095 0.0122 0.0083 0.0104 0.0094 0.0507 0.0438 0.0281 0.0078 0.0049 0.0174 0.0029 0.0087 0.0102 0.0023 0.0085 0.0034 0.0080 0.0029 0.0051 0.0072 0.0286 0.0417 0.0152 0.0204 0.0307 0.0375 0.0151 0.0119 0.0221 0.0043 0.0118 0.0166 0.0168 0.0134 0.0093 0.0080 0.0260 0.0435 0.0130 0.0220 0.0127 0.0077 0.0130 0.0034 0.0085 0.0159 0.0217 0.0093 0.0061 0.0469 0.0139 0.0281 Rate Heterogeneity Model: 2 nonsynonymous rate categories, rate and proportion of each estimated (this is effectively the M3 model of PAML) dN/dS Proportion 0.0200 0.6965 0.2936 0.3035 Starting with seed=1 Initial ln Likelihood: -12956.1235 Current score = -12956.1235 Performing final optimizations... pass 1 : -12956.1235 (branch= 0.0000 omega= 0.0000) pass 2 : -12956.1235 (branch= 0.0000 omega= 0.0000) pass 3 : -12956.1235 (branch= 0.0000 omega= 0.0000) pass 4 : -12956.1235 (branch= 0.0000 omega= 0.0000) pass 5 : -12956.1235 (branch= 0.0000 omega= 0.0000) pass 6 : -12956.1235 (branch= 0.0000 omega= 0.0000) pass 7 : -12956.1235 (branch= 0.0000 omega= 0.0000) pass 8 : -12956.1235 (branch= 0.0000 omega= 0.0000) pass 9 : -12956.1235 (branch= 0.0000 omega= 0.0000) pass 10: -12956.1235 (branch= 0.0000 omega= 0.0000) Looking for minimum length branches... Final score = -12956.1235 Time used = 0 hours, 1 minutes and 11 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -12956.1235 Parameter estimates: w(0) p(0) w(1) p(1) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) rep 1: 0.020 0.696 0.294 0.304 1.26 2.449 1.259 0.6866 1.396 1 Treelengths: TL rep 1: 5.371 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.c.M3x2.best.all.tre ***********TEST************** ***Score is 12956.12351 ***Expected is 12956.1235 ***SCORE DIFFERENCE IS .00001 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/c.M3x2.conf *** Running scoring test ./scoring/c.conf Running scoring test ./scoring/c.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/c.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x2178.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Codon data Gaps or ambiguity codes found within codon for taxon SterNa6. Codons coded as missing for that taxon: 708 Gaps or ambiguity codes found within codon for taxon PinniNa6. Codons coded as missing for that taxon: 513 646 Summary of data: 11 sequences. 72 constant characters. 527 parsimony-informative characters. 127 uninformative variable characters. 726 total characters. 668 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 24 MB good approx 23 MB to 18 MB low approx 17 MB to 9 MB very low approx 8 MB to 4 MB the minimum required availablememory is 4 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 8 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 35.5 MB of memory ####################################################### Found outgroup specification: 1 2 ####################################################### Loading starting model and/or tree from file data/c.start Reading TREES block...storing read block: TREES successful Reading GARLI block...storing read block: GARLI successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus Obtained starting or fixed model parameter values from Nexus: MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 61 (codon data, standard code) One dN/dS ratio (aka omega). Value provided by user (fixed) = 0.087400 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.265, AG = 2.362, AT = 1.151, CG = 0.706, CT = 1.402, GT = 1.000 Equilibrium State Frequencies: empirical (observed) values, fixed: (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0179 0.0349 0.0309 0.0152 0.0114 0.0181 0.0065 0.0084 0.0095 0.0122 0.0083 0.0104 0.0094 0.0507 0.0438 0.0281 0.0078 0.0049 0.0174 0.0029 0.0087 0.0102 0.0023 0.0085 0.0034 0.0080 0.0029 0.0051 0.0072 0.0286 0.0417 0.0152 0.0204 0.0307 0.0375 0.0151 0.0119 0.0221 0.0043 0.0118 0.0166 0.0168 0.0134 0.0093 0.0080 0.0260 0.0435 0.0130 0.0220 0.0127 0.0077 0.0130 0.0034 0.0085 0.0159 0.0217 0.0093 0.0061 0.0469 0.0139 0.0281 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 Initial ln Likelihood: -13269.2298 Current score = -13269.2298 Performing final optimizations... pass 1 : -13269.2298 (branch= 0.0000 rel rates= 0.0000) pass 2 : -13269.2298 (branch= 0.0000 rel rates= 0.0000) pass 3 : -13269.2298 (branch= 0.0000 rel rates= 0.0000) pass 4 : -13269.2298 (branch= 0.0000 rel rates= 0.0000) pass 5 : -13269.2298 (branch= 0.0000 rel rates= 0.0000) pass 6 : -13269.2298 (branch= 0.0000 rel rates= 0.0000) pass 7 : -13269.2298 (branch= 0.0000 rel rates= 0.0000) pass 8 : -13269.2298 (branch= 0.0000 rel rates= 0.0000) pass 9 : -13269.2298 (branch= 0.0000 rel rates= 0.0000) pass 10: -13269.2298 (branch= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13269.2298 Time used = 0 hours, 0 minutes and 49 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -13269.2298 Parameter estimates: w(0) p(0) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) rep 1: 0.087 1.000 1.265 2.362 1.151 0.7058 1.402 1 Treelengths: TL rep 1: 5.169 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.c.best.all.tre ***********TEST************** ***Score is 13269.22979 ***Expected is 13269.229793 ***SCORE DIFFERENCE IS -.000003 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/c.conf *** Running scoring test ./scoring/g.dnaBnoZ.conf Running scoring test ./scoring/g.dnaBnoZ.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/g.dnaBnoZ.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/dnaGap.8x1K.nex ... Reading TAXA block...storing read block: TAXA successful Reading CHARACTERS block...storing read block: CHARACTERS found dna data... successful Reading CHARACTERS block...storing read block: CHARACTERS found standard data... successful Reading TREES block...storing read block: TREES successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1GapsAsMissing") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 8 sequences. 428 constant characters. 129 parsimony-informative characters. 100 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 239 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #2 ("Untitled DATA Block 1GapsAsBinary") Data read as Binary data, no constant state 0 chars, modeled as Binary data, no constant state 0 chars NOTE: entirely missing characters removed from matrix: 1 25 29-34 36 37 52-54 61 67-69 84 85 87 95 96 99 106 110-116 125 138-145 163-165 167 169-177 188 197-199 202-210 213 216-218 228-231 233-236 238-240 247 249 256 257 260 266-270 \ 2 271-277 281-285 290-294 298-300 311 312 322 325 331 332 336-338 344 359 369 373-378 397 404-406 413 416 417 420-426 439-442 450-454 \ 2 455-460 462 471 474-479 487-490 492 494 495 497 502-506 510 521-526 532 533 538-541 544 547 551-553 562 570-572 577 579 609 610 614 615 622 624-626 639 640 647-650 653 655-660 667 668 673-676 679 680 685 695 696 701-705 708-713 716 717 731 742-749 751-755 762 763 770 771 783 788 791-793 804 806-808 813 821-825 827 830-832 840 842 843 845 850 851 856-865 886-894 896 897 903-905 913 914 924 927 948-956 963-971 976-981 991-993 996 Subset of data with 2 states: chars 1-1000 Summary of data: 8 sequences. 502 constant characters. 39 parsimony-informative characters. 116 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 24 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 2 MB good approx 1 MB to 2 MB low approx 1 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 2.3 MB of memory ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3220 0.2180 0.1602 0.2999 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.1629 Substitution rate categories under this model: rate proportion 0.0000 0.1629 0.0334 0.2093 0.2519 0.2093 0.8203 0.2093 2.8944 0.2093 Model 2 Number of states = 2 (binary data) Character change matrix: Binary, no all-zero columns (2-state symmetric one rate model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -4043.7391 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates... pass 1:+ 532.047 (branch= 438.84 scale= 6.77 alpha= 15.79 freqs= 3.30 rel rates= 8.48 pinv= 0.00 subset rates= 58.86) pass 2:+ 88.209 (branch= 42.39 scale= 0.83 alpha= 0.82 freqs= 0.72 rel rates= 0.01 pinv= 0.00 subset rates= 43.45) pass 3:+ 34.899 (branch= 0.70 scale= 2.02 alpha= 1.89 freqs= 0.04 rel rates= 0.72 pinv= 0.00 subset rates= 29.52) pass 4:+ 17.437 (branch= 4.66 scale= 2.38 alpha= 1.70 freqs= 0.05 rel rates= 0.01 pinv= 0.00 subset rates= 8.64) pass 5:+ 10.201 (branch= 4.19 scale= 1.64 alpha= 0.69 freqs= 0.05 rel rates= 2.14 pinv= 0.00 subset rates= 1.49) pass 6:+ 1.986 (branch= 0.00 scale= 1.92 alpha= 0.00 freqs= 0.06 rel rates= 0.01 pinv= 0.00 subset rates= 0.00) pass 7:+ 0.532 (branch= 0.47 scale= 0.00 alpha= 0.00 freqs= 0.06 rel rates= 0.01 pinv= 0.00 subset rates= 0.00) pass 8:+ 0.057 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.05 rel rates= 0.01 pinv= 0.00 subset rates= 0.00) lnL after optimization: -3358.3708 Current score = -3358.3708 Performing final optimizations... pass 1 : -3355.4759 (branch= 0.9931 alpha= 0.0078 pinv= 0.0071 eq freqs= 0.1960 rel rates= 1.3047 subset rates= 0.3862) pass 2 : -3354.0563 (branch= 0.5298 alpha= 0.0091 pinv= 0.0117 eq freqs= 0.0207 rel rates= 0.6834 subset rates= 0.1648) pass 3 : -3353.1967 (branch= 0.2868 alpha= 0.0000 pinv= 0.0083 eq freqs= 0.0152 rel rates= 0.4605 subset rates= 0.0888) pass 4 : -3352.5812 (branch= 0.1724 alpha= 0.0025 pinv= 0.0159 eq freqs= 0.0063 rel rates= 0.3678 subset rates= 0.0506) pass 5 : -3352.1335 (branch= 0.0836 alpha= 0.0059 pinv= 0.0162 eq freqs= 0.0020 rel rates= 0.3069 subset rates= 0.0331) pass 6 : -3351.7942 (branch= 0.0548 alpha= 0.0068 pinv= 0.0164 eq freqs= 0.0009 rel rates= 0.2446 subset rates= 0.0158) pass 7 : -3351.5261 (branch= 0.0336 alpha= 0.0083 pinv= 0.0159 eq freqs= 0.0005 rel rates= 0.2003 subset rates= 0.0095) pass 8 : -3351.3125 (branch= 0.0179 alpha= 0.0100 pinv= 0.0150 eq freqs= 0.0007 rel rates= 0.1629 subset rates= 0.0071) pass 9 : -3351.1406 (branch= 0.0111 alpha= 0.0103 pinv= 0.0140 eq freqs= 0.0006 rel rates= 0.1316 subset rates= 0.0044) pass 10: -3351.0000 (branch= 0.0073 alpha= 0.0105 pinv= 0.0138 eq freqs= 0.0004 rel rates= 0.1059 subset rates= 0.0027) pass 11: -3350.8841 (branch= 0.0049 alpha= 0.0102 pinv= 0.0127 eq freqs= 0.0003 rel rates= 0.0862 subset rates= 0.0016) pass 12: -3350.7874 (branch= 0.0028 alpha= 0.0098 pinv= 0.0116 eq freqs= 0.0002 rel rates= 0.0710 subset rates= 0.0013) pass 13: -3350.7077 (branch= 0.0020 alpha= 0.0094 pinv= 0.0106 eq freqs= 0.0002 rel rates= 0.0576 subset rates= 0.0000) pass 14: -3350.6388 (branch= 0.0005 alpha= 0.0090 pinv= 0.0096 eq freqs= 0.0001 rel rates= 0.0485 subset rates= 0.0013) pass 15: -3350.5822 (branch= 0.0010 alpha= 0.0082 pinv= 0.0081 eq freqs= 0.0001 rel rates= 0.0391 subset rates= 0.0000) pass 16: -3350.5338 (branch= 0.0003 alpha= 0.0075 pinv= 0.0073 eq freqs= 0.0001 rel rates= 0.0333 subset rates= 0.0000) pass 17: -3350.4924 (branch= 0.0001 alpha= 0.0072 pinv= 0.0066 eq freqs= 0.0001 rel rates= 0.0274 subset rates= 0.0000) pass 18: -3350.4568 (branch= 0.0000 alpha= 0.0066 pinv= 0.0059 eq freqs= 0.0001 rel rates= 0.0230 subset rates= 0.0000) pass 19: -3350.4263 (branch= 0.0000 alpha= 0.0059 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0193 subset rates= 0.0000) pass 20: -3350.3999 (branch= 0.0000 alpha= 0.0052 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0164 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= 0.0753 subset rates= 0.0000) optimization up to ... pass 40: -3350.2423 (branch= 0.0000 alpha= 0.0066 pinv= 0.0061 eq freqs= 0.0001 rel rates= 0.0168 subset rates= 0.0000) optimization up to ... pass 50: -3350.2357 (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: -3350.2339 (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 78: -3350.2337 (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 = -3350.2338 Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -3350.2338 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: 3.108 10.39 2.682 0.001 21.82 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 3350.23377 ***Expected is 3350.2345 ***SCORE DIFFERENCE IS -.00073 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/g.dnaBnoZ.conf *** Running scoring test ./scoring/g.dnaMix.conf Running scoring test ./scoring/g.dnaMix.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/g.dnaMix.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/dnaGap.8x1K.nex ... Reading TAXA block...storing read block: TAXA successful Reading CHARACTERS block...storing read block: CHARACTERS found dna data... successful Reading CHARACTERS block...storing read block: CHARACTERS found standard data... successful Reading TREES block...storing read block: TREES successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1GapsAsMissing") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 8 sequences. 428 constant characters. 129 parsimony-informative characters. 100 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 239 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #2 ("Untitled DATA Block 1GapsAsBinary") Data read as Gap-coded data, oriented with respect to time, modeled as Gap-coded data, oriented with respect to time Summary of data: 8 sequences. 502 constant characters. 39 parsimony-informative characters. 116 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 24 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 2 MB good approx 1 MB to 2 MB low approx 1 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 2.7 MB of memory ####################################################### WARNING - specified outgroup (1) being ignored due to inference of a rooted true ####################################################### STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3220 0.2180 0.1602 0.2999 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.1629 Substitution rate categories under this model: rate proportion 0.0000 0.1629 0.0334 0.2093 0.2519 0.2093 0.8203 0.2093 2.8944 0.2093 Model 2 Number of states = 2 (0/1 coding of gaps) Character change matrix: irreversible matrix deletion rate parameter only estimated if using a partitioned model without subset rates deletion rate = 1.000 Equilibrium State Frequencies: proportion of inserted sites parameter insert proportion = 0.500 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 Initial ln Likelihood: -4257.0961 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, ins rate, del rate... pass 1:+ 640.405 (branch= 431.06 scale= 2.03 alpha= 9.92 freqs= 3.07 rel rates= 7.29 pinv= 0.00 ins/del=187.03) pass 2:+ 169.102 (branch= 75.12 scale= 1.32 alpha= 0.88 freqs= 0.65 rel rates= 0.01 pinv= 0.00 ins/del= 91.12) pass 3:+ 55.144 (branch= 7.14 scale= 1.85 alpha= 1.09 freqs= 0.05 rel rates= 0.90 pinv= 0.00 ins/del= 44.12) pass 4:+ 25.231 (branch= 7.02 scale= 1.52 alpha= 0.69 freqs= 0.06 rel rates= 0.01 pinv= 0.00 ins/del= 15.94) pass 5:+ 14.361 (branch= 7.97 scale= 1.87 alpha= 0.01 freqs= 0.05 rel rates= 2.45 pinv= 0.00 ins/del= 2.01) pass 6:+ 10.438 (branch= 7.36 scale= 2.34 alpha= 0.01 freqs= 0.07 rel rates= 0.00 pinv= 0.00 ins/del= 0.66) pass 7:+ 6.158 (branch= 5.23 scale= 0.83 alpha= 0.01 freqs= 0.06 rel rates= 0.00 pinv= 0.00 ins/del= 0.03) pass 8:+ 3.640 (branch= 2.31 scale= 0.00 alpha= 0.00 freqs= 0.05 rel rates= 0.60 pinv= 0.00 ins/del= 0.67) pass 9:+ 0.148 (branch= 0.08 scale= 0.00 alpha= 0.00 freqs= 0.06 rel rates= 0.00 pinv= 0.00 ins/del= 0.00) lnL after optimization: -3332.4700 Current score = -3332.4700 Performing final optimizations... pass 1 : -3329.9920 (branch= 1.3745 alpha= 0.0217 pinv= 0.0099 eq freqs= 0.2403 rel rates= 0.7561 ins/del rates= 0.0754) pass 2 : -3329.0411 (branch= 0.3511 alpha= 0.0000 pinv= 0.0096 eq freqs= 0.0000 rel rates= 0.5271 ins/del rates= 0.0631) pass 3 : -3328.4259 (branch= 0.1466 alpha= 0.0039 pinv= 0.0146 eq freqs= 0.0186 rel rates= 0.3891 ins/del rates= 0.0424) pass 4 : -3327.9681 (branch= 0.0854 alpha= 0.0069 pinv= 0.0148 eq freqs= 0.0031 rel rates= 0.3185 ins/del rates= 0.0290) pass 5 : -3327.6151 (branch= 0.0531 alpha= 0.0079 pinv= 0.0147 eq freqs= 0.0016 rel rates= 0.2576 ins/del rates= 0.0180) pass 6 : -3327.3302 (branch= 0.0345 alpha= 0.0079 pinv= 0.0146 eq freqs= 0.0008 rel rates= 0.2156 ins/del rates= 0.0116) pass 7 : -3327.1087 (branch= 0.0219 alpha= 0.0095 pinv= 0.0140 eq freqs= 0.0008 rel rates= 0.1676 ins/del rates= 0.0077) pass 8 : -3326.9280 (branch= 0.0143 alpha= 0.0097 pinv= 0.0133 eq freqs= 0.0006 rel rates= 0.1378 ins/del rates= 0.0051) pass 9 : -3326.7821 (branch= 0.0094 alpha= 0.0098 pinv= 0.0125 eq freqs= 0.0004 rel rates= 0.1105 ins/del rates= 0.0034) pass 10: -3326.6617 (branch= 0.0063 alpha= 0.0097 pinv= 0.0123 eq freqs= 0.0003 rel rates= 0.0895 ins/del rates= 0.0023) pass 11: -3326.5618 (branch= 0.0042 alpha= 0.0094 pinv= 0.0114 eq freqs= 0.0002 rel rates= 0.0731 ins/del rates= 0.0016) pass 12: -3326.4795 (branch= 0.0028 alpha= 0.0090 pinv= 0.0099 eq freqs= 0.0002 rel rates= 0.0593 ins/del rates= 0.0010) pass 13: -3326.4105 (branch= 0.0019 alpha= 0.0085 pinv= 0.0091 eq freqs= 0.0001 rel rates= 0.0488 ins/del rates= 0.0007) pass 14: -3326.3518 (branch= 0.0013 alpha= 0.0079 pinv= 0.0083 eq freqs= 0.0001 rel rates= 0.0405 ins/del rates= 0.0005) pass 15: -3326.3015 (branch= 0.0009 alpha= 0.0074 pinv= 0.0076 eq freqs= 0.0001 rel rates= 0.0340 ins/del rates= 0.0003) pass 16: -3326.2590 (branch= 0.0005 alpha= 0.0070 pinv= 0.0068 eq freqs= 0.0001 rel rates= 0.0278 ins/del rates= 0.0002) pass 17: -3326.2225 (branch= 0.0004 alpha= 0.0063 pinv= 0.0062 eq freqs= 0.0001 rel rates= 0.0234 ins/del rates= 0.0001) pass 18: -3326.1908 (branch= 0.0002 alpha= 0.0057 pinv= 0.0056 eq freqs= 0.0000 rel rates= 0.0200 ins/del rates= 0.0001) pass 19: -3326.1633 (branch= 0.0002 alpha= 0.0052 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0171 ins/del rates= 0.0000) pass 20: -3326.1394 (branch= 0.0001 alpha= 0.0047 pinv= 0.0045 eq freqs= 0.0000 rel rates= 0.0145 ins/del rates= 0.0000) optimization up to ... pass 30: -3326.0197 (branch= 0.0002 alpha= 0.0262 pinv= 0.0243 eq freqs= 0.0002 rel rates= 0.0687 ins/del rates= 0.0000) optimization up to ... pass 40: -3325.9908 (branch= 0.0001 alpha= 0.0068 pinv= 0.0063 eq freqs= 0.0000 rel rates= 0.0157 ins/del rates= 0.0000) optimization up to ... pass 50: -3325.9841 (branch= 0.0000 alpha= 0.0015 pinv= 0.0014 eq freqs= 0.0000 rel rates= 0.0037 ins/del rates= 0.0000) optimization up to ... pass 60: -3325.9826 (branch= 0.0000 alpha= 0.0003 pinv= 0.0003 eq freqs= 0.0000 rel rates= 0.0009 ins/del rates= 0.0000) optimization up to ... pass 70: -3325.9823 (branch= 0.0000 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 ins/del rates= 0.0000) optimization up to ... pass 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 5 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -3325.9822 Parameter estimates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 3.061 10.26 2.655 0.001 21.52 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del rep 1: 0.053 0.145 **ins = proportion of columns that experienced an insertion **del = deletion rate relative to nucleotide substitution rate Treelengths: TL rep 1: 1.417 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.g.dnaMix.best.all.tre ***********TEST************** ***Score is 3325.98219 ***Expected is 3325.98222 ***SCORE DIFFERENCE IS -.00003 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/g.dnaMix.conf *** Running scoring test ./scoring/n.G4.conf Running scoring test ./scoring/n.G4.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/n.G4.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x2178.wtset.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 816 1012 1019 1022 1995 2180 Found wtset "compensate" with data, applying... Summary of data: 11 sequences. 1072 constant characters. 768 parsimony-informative characters. 338 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 2178 total characters (2179 before removing empty columns). 845 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 8 MB good approx 7 MB to 6 MB low approx 5 MB to 3 MB very low approx 2 MB to 2 MB the minimum required availablememory is 2 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 4 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 12.1 MB of memory ####################################################### Found outgroup specification: 2 ####################################################### Loading starting model and/or tree from file data/n.G4.start Reading TREES block...storing read block: TREES successful Reading PAUP block...storing read block: PAUP successful Reading GARLI block...storing read block: GARLI successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus Obtained starting or fixed model parameter values from Nexus: MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.532, AG = 3.880, AT = 1.559, CG = 1.283, CT = 4.738, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2442 0.2425 0.2497 0.2635 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 1.2505 with an invariant (invariable) site category, proportion estimated 0.3018 Substitution rate categories under this model: rate proportion 0.0000 0.3018 0.1841 0.1746 0.5410 0.1746 1.0317 0.1746 2.2433 0.1746 Starting with seed=1 Initial ln Likelihood: -13930.5181 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 0.000 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.00 rel rates= 0.00 pinv= 0.00) lnL after optimization: -13930.5181 Current score = -13930.5181 Performing final optimizations... pass 1 : -13930.5181 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 2 : -13930.5181 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 3 : -13930.5181 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 4 : -13930.5181 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 5 : -13930.5180 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 6 : -13930.5180 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 7 : -13930.5180 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 8 : -13930.5180 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 9 : -13930.5180 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 10: -13930.5180 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13930.5180 Time used = 0 hours, 0 minutes and 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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/n.G5.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x2178.wtset.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 816 1012 1019 1022 1995 2180 Found wtset "compensate" with data, applying... Summary of data: 11 sequences. 1072 constant characters. 768 parsimony-informative characters. 338 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 2178 total characters (2179 before removing empty columns). 845 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 10 MB good approx 10 MB to 8 MB low approx 7 MB to 4 MB very low approx 3 MB to 2 MB the minimum required availablememory is 2 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 4 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 15.0 MB of memory ####################################################### Found outgroup specification: 1 ####################################################### Loading starting model and/or tree from file data/n.G5.start Reading TREES block...storing read block: TREES successful Reading GARLI block...storing read block: GARLI successful Reading PAUP block...storing read block: PAUP successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus Obtained starting or fixed model parameter values from Nexus: MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.530, AG = 3.881, AT = 1.553, CG = 1.285, CT = 4.742, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2445 0.2424 0.2496 0.2636 Rate Heterogeneity Model: 5 discrete gamma distributed rate categories, alpha param estimated 1.3438 with an invariant (invariable) site category, proportion estimated 0.3098 Substitution rate categories under this model: rate proportion 0.0000 0.3098 0.1655 0.1380 0.4459 0.1380 0.7709 0.1380 1.2349 0.1380 2.3828 0.1380 Starting with seed=1 Initial ln Likelihood: -13931.0233 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 0.000 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.00 rel rates= 0.00 pinv= 0.00) lnL after optimization: -13931.0233 Current score = -13931.0233 Performing final optimizations... pass 1 : -13931.0233 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 2 : -13931.0233 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 3 : -13931.0233 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 4 : -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 5 : -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 6 : -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 7 : -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 8 : -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 9 : -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 10: -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13931.0232 Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -13931.0232 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 1.53 3.88 1.552 1.284 4.739 1 0.244 0.242 0.250 0.264 1.346 0.310 Treelengths: TL rep 1: 1.581 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.n.G5.best.all.tre ***********TEST************** ***Score is 13918.08407 ***Expected is 13918.08407 ***SCORE DIFFERENCE IS 0 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/n.G5.conf *** Running scoring test ./scoring/n.conf Running scoring test ./scoring/n.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/n.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x2178.wtset.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 816 1012 1019 1022 1995 2180 Found wtset "compensate" with data, applying... Summary of data: 11 sequences. 1072 constant characters. 768 parsimony-informative characters. 338 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 2178 total characters (2179 before removing empty columns). 845 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 4 MB good approx 3 MB to 2 MB low approx 2 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 3.9 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1-3 ####################################################### Loading starting model and/or tree from file data/n.start Reading GARLI block...storing read block: GARLI successful STARTING RUN Obtained starting or fixed model parameter values from Nexus: MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.869, AG = 3.671, AT = 1.221, CG = 1.853, CT = 4.414, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2554 0.2086 0.2382 0.2978 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating random starting tree... Initial ln Likelihood: -18359.9501 optimizing: starting branch lengths, rel rates, eq freqs... pass 1:+ 2061.639 (branch=1982.89 scale= 74.28 freqs= 0.89 rel rates= 3.59) pass 2:+ 221.911 (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:+ 0.338 (branch= 0.30 scale= 0.00 freqs= 0.00 rel rates= 0.03) pass 5:+ 0.068 (branch= 0.07 scale= 0.00 freqs= 0.00 rel rates= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00 freqs= 0.00 rel rates= 0.00) lnL after optimization: -16071.0612 gen current_lnL precision last_tree_imp 0 -16071.0612 0.010 0 100 -14502.0532 0.010 73 200 -14502.0253 0.010 73 300 -14501.0213 0.010 73 400 -14500.3918 0.010 73 500 -14499.9898 0.010 73 600 -14499.5149 0.010 73 700 -14499.2258 0.010 73 800 -14499.0579 0.010 73 900 -14499.0514 0.010 73 1000 -14499.0514 0.010 73 1100 -14498.9758 0.010 73 1200 -14498.9756 0.010 73 1300 -14498.9754 0.010 73 1400 -14498.9754 0.010 73 1500 -14498.9754 0.010 73 1600 -14498.9606 0.010 73 Reached termination condition! last topological improvement at gen 73 Improvement over last 500 gen = 0.01516 Current score = -14498.9606 Performing final optimizations... pass 1 : -14498.9271 (branch= 0.0118 eq freqs= 0.0156 rel rates= 0.0061) pass 2 : -14498.8998 (branch= 0.0172 eq freqs= 0.0063 rel rates= 0.0038) pass 3 : -14498.8933 (branch= 0.0062 eq freqs= 0.0001 rel rates= 0.0002) pass 4 : -14498.8887 (branch= 0.0009 eq freqs= 0.0014 rel rates= 0.0024) pass 5 : -14498.8879 (branch= 0.0006 eq freqs= 0.0001 rel rates= 0.0001) pass 6 : -14498.8868 (branch= 0.0004 eq freqs= 0.0004 rel rates= 0.0003) pass 7 : -14498.8861 (branch= 0.0003 eq freqs= 0.0002 rel rates= 0.0001) pass 8 : -14498.8859 (branch= 0.0001 eq freqs= 0.0000 rel rates= 0.0001) pass 9 : -14498.8857 (branch= 0.0001 eq freqs= 0.0000 rel rates= 0.0001) pass 10: -14498.8856 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) pass 11: -14498.8855 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) pass 12: -14498.8854 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) pass 13: -14498.8854 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 14: -14498.8854 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 15: -14498.8854 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) pass 16: -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 23 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 = 1.222, CG = 1.855, CT = 4.418, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2554 0.2085 0.2382 0.2978 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file scr.n.sitelikes.log ... WARNING: Site likelihoods are being output when wtset compensate is in effect. Sites with weight > 1 will only be output once! ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -14498.8854 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 1.87 3.674 1.222 1.855 4.418 1 0.255 0.209 0.238 0.298 Treelengths: TL rep 1: 1.298 Saving final tree from best search rep (#1) to scr.n.best.tre ####################################################### ***********TEST************** ***Score is 14486.03891 ***Expected is 14486.03829 ***SCORE DIFFERENCE IS .00062 ***ALLOWED ERROR IS 0.01 ***Scoring OK for ./scoring/n.conf *** Running scoring test ./scoring/p.3diff.conf Running scoring test ./scoring/p.3diff.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/p.3diff.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.byPos.11x2178.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful Reading SETS block...storing read block: SETS successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #1 ("1stpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 4 Summary of data: 11 sequences. 441 constant characters. 171 parsimony-informative characters. 113 uninformative variable characters. 725 total characters. 237 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #2 ("2ndpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 5 Summary of data: 11 sequences. 527 constant characters. 90 parsimony-informative characters. 108 uninformative variable characters. 725 total characters. 158 unique patterns in compressed data matrix. GARLI data subset 3 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #3 ("3rdpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 6 Summary of data: 11 sequences. 102 constant characters. 507 parsimony-informative characters. 116 uninformative variable characters. 725 total characters. 548 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 9 MB good approx 8 MB to 7 MB low approx 6 MB to 4 MB very low approx 3 MB to 2 MB the minimum required availablememory is 2 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 4 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 13.5 MB of memory ####################################################### Loading starting model and/or tree from file data/p.3diff.start Reading TREES block...storing read block: TREES successful Reading GARLI block...storing read block: GARLI successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus Obtained starting or fixed model parameter values from Nexus: MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) AC = 1.000, AG = 10.000, AT = 2.000, CG = 2.000, CT = 0.010, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3150 0.1749 0.3006 0.2095 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.6000 Substitution rate categories under this model: rate proportion 0.0531 0.2500 0.3123 0.2500 0.8813 0.2500 2.7533 0.2500 Model 2 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) AC = 4.000, AG = 4.000, AT = 1.000, CG = 4.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1000 0.2000 0.3000 0.4000 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.4000 Substitution rate categories under this model: rate proportion 0.0167 0.2500 0.1818 0.2500 0.7313 0.2500 3.0702 0.2500 Model 3 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) AC = 1.000, AG = 2.000, AT = 3.000, CG = 5.000, CT = 2.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.4000 0.2000 0.3000 0.1000 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0100 Substitution rate categories under this model: rate proportion 0.0000 0.0100 0.0334 0.2475 0.2519 0.2475 0.8203 0.2475 2.8944 0.2475 Subset rate multipliers: 0.54 0.30 2.16 Starting with seed=1 Initial ln Likelihood: -17270.1042 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates... pass 1:+ 3387.561 (branch=2073.05 scale= 39.85 alpha=118.40 freqs=413.09 rel rates=737.83 pinv= 0.00 subset rates= 5.33) pass 2:+ 327.989 (branch= 41.53 scale= 0.00 alpha= 19.91 freqs=187.33 rel rates= 77.79 pinv= 0.74 subset rates= 0.69) pass 3:+ 196.574 (branch= 1.56 scale= 1.04 alpha= 7.14 freqs= 83.86 rel rates=102.19 pinv= 0.01 subset rates= 0.77) pass 4:+ 36.659 (branch= 1.45 scale= 0.00 alpha= 0.68 freqs= 18.87 rel rates= 15.00 pinv= 0.00 subset rates= 0.65) pass 5:+ 4.518 (branch= 0.00 scale= 0.00 alpha= 0.02 freqs= 3.51 rel rates= 0.99 pinv= 0.01 subset rates= 0.00) pass 6:+ 0.902 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.10 rel rates= 0.78 pinv= 0.01 subset rates= 0.00) pass 7:+ 0.107 (branch= 0.00 scale= 0.00 alpha= 0.02 freqs= 0.08 rel rates= 0.01 pinv= 0.01 subset rates= 0.00) lnL after optimization: -13315.7939 Current score = -13315.7939 Performing final optimizations... pass 1 : -13309.3701 (branch= 2.8300 alpha= 0.8831 pinv= 0.0157 eq freqs= 0.2323 rel rates= 1.8499 subset rates= 0.6129) pass 2 : -13307.8643 (branch= 0.4301 alpha= 0.1996 pinv= 0.0131 eq freqs= 0.1261 rel rates= 0.6707 subset rates= 0.0662) pass 3 : -13307.2553 (branch= 0.1056 alpha= 0.0573 pinv= 0.0031 eq freqs= 0.0091 rel rates= 0.4215 subset rates= 0.0124) pass 4 : -13306.8903 (branch= 0.0281 alpha= 0.0207 pinv= 0.0029 eq freqs= 0.0100 rel rates= 0.3008 subset rates= 0.0025) pass 5 : -13306.6718 (branch= 0.0048 alpha= 0.0050 pinv= 0.0011 eq freqs= 0.0057 rel rates= 0.2008 subset rates= 0.0011) pass 6 : -13306.5187 (branch= 0.0045 alpha= 0.0014 pinv= 0.0003 eq freqs= 0.0050 rel rates= 0.1405 subset rates= 0.0014) pass 7 : -13306.4183 (branch= 0.0012 alpha= 0.0008 pinv= 0.0001 eq freqs= 0.0027 rel rates= 0.0954 subset rates= 0.0000) pass 8 : -13306.3501 (branch= 0.0006 alpha= 0.0002 pinv= 0.0000 eq freqs= 0.0022 rel rates= 0.0651 subset rates= 0.0000) pass 9 : -13306.3046 (branch= 0.0003 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0014 rel rates= 0.0437 subset rates= 0.0000) pass 10: -13306.2736 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0010 rel rates= 0.0299 subset rates= 0.0000) pass 11: -13306.2525 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0203 subset rates= 0.0000) pass 12: -13306.2383 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0137 subset rates= 0.0000) pass 13: -13306.2284 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0095 subset rates= 0.0000) pass 14: -13306.2217 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0064 subset rates= 0.0001) pass 15: -13306.2173 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0043 subset rates= 0.0000) pass 16: -13306.2135 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0029 subset rates= 0.0008) pass 17: -13306.2111 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0022 subset rates= 0.0000) pass 18: -13306.2094 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0015 subset rates= 0.0001) 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= 0.0014 subset rates= 0.0000) optimization up to ... pass 38: -13306.2060 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0001) Looking for minimum length branches... Final score = -13306.2060 Time used = 0 hours, 0 minutes and 22 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -13306.2060 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: 1.975 2.577 1.414 1.414 3.721 1 0.309 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: 4.374 7.059 1.609 7.059 4.374 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 4.936 3.385 0.4592 4.936 1 0.157 0.354 0.287 0.202 4.037 0.033 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 1.694 0.540 0.301 2.159 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.p.3diff.best.all.tre ***********TEST************** ***Score is 13306.20604 ***Expected is 13306.20608 ***SCORE DIFFERENCE IS -.00004 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.3diff.conf *** Running scoring test ./scoring/p.mk.conf Running scoring test ./scoring/p.mk.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/p.mk.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, modeled as Standard k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -609.1934 optimizing: starting branch lengths... pass 1:+ 125.912 (branch= 124.97 scale= 0.94) pass 2:+ 7.205 (branch= 7.20 scale= 0.00) pass 3:+ 1.518 (branch= 1.48 scale= 0.03) pass 4:+ 0.225 (branch= 0.22 scale= 0.00) pass 5:+ 0.014 (branch= 0.01 scale= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -474.3188 Current score = -474.3188 Performing final optimizations... pass 1 : -474.2925 (branch= 0.0264) pass 2 : -474.2170 (branch= 0.0755) pass 3 : -474.1996 (branch= 0.0173) pass 4 : -474.1939 (branch= 0.0057) pass 5 : -474.1908 (branch= 0.0031) pass 6 : -474.1886 (branch= 0.0022) pass 7 : -474.1872 (branch= 0.0014) pass 8 : -474.1869 (branch= 0.0003) pass 9 : -474.1867 (branch= 0.0002) pass 10: -474.1865 (branch= 0.0002) pass 11: -474.1864 (branch= 0.0001) pass 12: -474.1864 (branch= 0.0000) pass 13: -474.1864 (branch= 0.0000) pass 14: -474.1864 (branch= 0.0000) Looking for minimum length branches... Final score = -474.1864 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -474.1864 Parameter estimates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths: TL rep 1: 3.854 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.p.mk.best.all.tre ***********TEST************** ***Score is 474.18638 ***Expected is 474.1864 ***SCORE DIFFERENCE IS -.00002 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mk.conf *** Running scoring test ./scoring/p.mk.ssr.conf Running scoring test ./scoring/p.mk.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/p.mk.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, modeled as Standard k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -609.1934 optimizing: starting branch lengths, subset rates... pass 1:+ 130.207 (branch= 124.97 scale= 0.94 subset rates= 4.30) pass 2:+ 9.055 (branch= 8.14 scale= 0.00 subset rates= 0.91) pass 3:+ 1.801 (branch= 1.66 scale= 0.02 subset rates= 0.12) pass 4:+ 0.303 (branch= 0.30 scale= 0.00 subset rates= 0.00) pass 5:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -467.8152 Current score = -467.8152 Performing final optimizations... pass 1 : -467.7873 (branch= 0.0213 subset rates= 0.0066) pass 2 : -467.7197 (branch= 0.0649 subset rates= 0.0027) pass 3 : -467.6968 (branch= 0.0229 subset rates= 0.0000) pass 4 : -467.6869 (branch= 0.0099 subset rates= 0.0000) pass 5 : -467.6823 (branch= 0.0046 subset rates= 0.0000) pass 6 : -467.6802 (branch= 0.0020 subset rates= 0.0000) pass 7 : -467.6793 (branch= 0.0009 subset rates= 0.0000) pass 8 : -467.6790 (branch= 0.0003 subset rates= 0.0000) pass 9 : -467.6788 (branch= 0.0003 subset rates= 0.0000) pass 10: -467.6787 (branch= 0.0001 subset rates= 0.0000) pass 11: -467.6786 (branch= 0.0001 subset rates= 0.0000) pass 12: -467.6785 (branch= 0.0000 subset rates= 0.0000) pass 13: -467.6783 (branch= 0.0002 subset rates= 0.0000) pass 14: -467.6783 (branch= 0.0000 subset rates= 0.0000) pass 15: -467.6783 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6783 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -467.6783 Parameter estimates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 3.842 0.786 1.480 2.178 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 467.67826 ***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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/p.mkO.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, modeled as Standard ordered k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -641.9257 optimizing: starting branch lengths... pass 1:+ 137.411 (branch= 136.58 scale= 0.83) pass 2:+ 7.774 (branch= 7.77 scale= 0.00) pass 3:+ 1.542 (branch= 1.52 scale= 0.02) pass 4:+ 0.091 (branch= 0.09 scale= 0.00) pass 5:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -495.1076 Current score = -495.1076 Performing final optimizations... pass 1 : -495.0677 (branch= 0.0399) pass 2 : -494.9999 (branch= 0.0678) pass 3 : -494.9820 (branch= 0.0179) pass 4 : -494.9768 (branch= 0.0051) pass 5 : -494.9724 (branch= 0.0044) pass 6 : -494.9711 (branch= 0.0013) pass 7 : -494.9709 (branch= 0.0002) pass 8 : -494.9703 (branch= 0.0006) pass 9 : -494.9702 (branch= 0.0001) pass 10: -494.9701 (branch= 0.0001) pass 11: -494.9701 (branch= 0.0000) pass 12: -494.9700 (branch= 0.0000) pass 13: -494.9700 (branch= 0.0000) Looking for minimum length branches... Final score = -494.9700 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -494.9700 Parameter estimates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths: TL rep 1: 4.503 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.p.mkO.best.all.tre ***********TEST************** ***Score is 494.97003 ***Expected is 494.9700 ***SCORE DIFFERENCE IS .00003 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mkO.conf *** Running scoring test ./scoring/p.mkO.ssr.conf Running scoring test ./scoring/p.mkO.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/p.mkO.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, modeled as Standard ordered k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -641.9257 optimizing: starting branch lengths, subset rates... pass 1:+ 147.096 (branch= 136.58 scale= 0.83 subset rates= 9.68) pass 2:+ 12.450 (branch= 8.46 scale= 0.00 subset rates= 3.99) pass 3:+ 3.552 (branch= 2.32 scale= 0.03 subset rates= 1.21) pass 4:+ 0.757 (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: -477.9409 Current score = -477.9409 Performing final optimizations... pass 1 : -477.8563 (branch= 0.0846 subset rates= 0.0000) pass 2 : -477.7629 (branch= 0.0915 subset rates= 0.0020) pass 3 : -477.7298 (branch= 0.0331 subset rates= 0.0000) pass 4 : -477.7113 (branch= 0.0185 subset rates= 0.0000) pass 5 : -477.6980 (branch= 0.0096 subset rates= 0.0037) pass 6 : -477.6925 (branch= 0.0055 subset rates= 0.0000) pass 7 : -477.6901 (branch= 0.0024 subset rates= 0.0000) pass 8 : -477.6886 (branch= 0.0015 subset rates= 0.0000) pass 9 : -477.6879 (branch= 0.0008 subset rates= 0.0000) pass 10: -477.6875 (branch= 0.0004 subset rates= 0.0000) pass 11: -477.6869 (branch= 0.0002 subset rates= 0.0004) pass 12: -477.6852 (branch= 0.0010 subset rates= 0.0007) pass 13: -477.6849 (branch= 0.0003 subset rates= 0.0000) pass 14: -477.6847 (branch= 0.0001 subset rates= 0.0000) pass 15: -477.6847 (branch= 0.0001 subset rates= 0.0000) pass 16: -477.6846 (branch= 0.0000 subset rates= 0.0000) pass 17: -477.6846 (branch= 0.0000 subset rates= 0.0000) pass 18: -477.6846 (branch= 0.0000 subset rates= 0.0000) pass 19: -477.6846 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.6846 Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -477.6846 Parameter estimates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.915 0.630 1.899 2.808 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 477.68460 ***Expected is 477.6848 ***SCORE DIFFERENCE IS -.00020 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mkO.ssr.conf *** Running scoring test ./scoring/p.mkv.conf Running scoring test ./scoring/p.mkv.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/p.mkv.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, variable only, modeled as Standard k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -605.5989 optimizing: starting branch lengths... pass 1:+ 124.584 (branch= 123.99 scale= 0.59) pass 2:+ 6.980 (branch= 6.98 scale= 0.00) pass 3:+ 1.324 (branch= 1.31 scale= 0.02) pass 4:+ 0.161 (branch= 0.16 scale= 0.00) pass 5:+ 0.013 (branch= 0.01 scale= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -472.5370 Current score = -472.5370 Performing final optimizations... pass 1 : -472.4890 (branch= 0.0480) pass 2 : -472.4195 (branch= 0.0694) pass 3 : -472.4053 (branch= 0.0142) pass 4 : -472.3958 (branch= 0.0095) pass 5 : -472.3935 (branch= 0.0024) pass 6 : -472.3921 (branch= 0.0013) pass 7 : -472.3917 (branch= 0.0005) pass 8 : -472.3912 (branch= 0.0004) pass 9 : -472.3908 (branch= 0.0004) pass 10: -472.3907 (branch= 0.0001) pass 11: -472.3906 (branch= 0.0001) pass 12: -472.3906 (branch= 0.0000) pass 13: -472.3906 (branch= 0.0000) pass 14: -472.3906 (branch= 0.0000) Looking for minimum length branches... Final score = -472.3906 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -472.3906 Parameter estimates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths: TL rep 1: 3.621 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.p.mkv.best.all.tre ***********TEST************** ***Score is 472.39058 ***Expected is 472.3906 ***SCORE DIFFERENCE IS -.00002 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mkv.conf *** Running scoring test ./scoring/p.mkv.ssr.conf Running scoring test ./scoring/p.mkv.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/p.mkv.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, variable only, modeled as Standard k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -605.5989 optimizing: starting branch lengths, subset rates... pass 1:+ 129.564 (branch= 123.99 scale= 0.59 subset rates= 4.98) pass 2:+ 9.273 (branch= 7.97 scale= 0.00 subset rates= 1.30) pass 3:+ 1.739 (branch= 1.57 scale= 0.00 subset rates= 0.17) pass 4:+ 0.312 (branch= 0.31 scale= 0.00 subset rates= 0.00) pass 5:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -464.7108 Current score = -464.7108 Performing final optimizations... pass 1 : -464.6721 (branch= 0.0277 subset rates= 0.0109) pass 2 : -464.5845 (branch= 0.0864 subset rates= 0.0012) pass 3 : -464.5684 (branch= 0.0157 subset rates= 0.0005) pass 4 : -464.5555 (branch= 0.0128 subset rates= 0.0000) pass 5 : -464.5518 (branch= 0.0035 subset rates= 0.0002) pass 6 : -464.5497 (branch= 0.0020 subset rates= 0.0000) pass 7 : -464.5492 (branch= 0.0005 subset rates= 0.0000) pass 8 : -464.5484 (branch= 0.0008 subset rates= 0.0000) pass 9 : -464.5481 (branch= 0.0003 subset rates= 0.0000) pass 10: -464.5480 (branch= 0.0001 subset rates= 0.0000) pass 11: -464.5480 (branch= 0.0001 subset rates= 0.0000) pass 12: -464.5479 (branch= 0.0000 subset rates= 0.0000) pass 13: -464.5479 (branch= 0.0000 subset rates= 0.0000) pass 14: -464.5479 (branch= 0.0000 subset rates= 0.0000) pass 15: -464.5479 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -464.5479 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 : -464.5479 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: 3.399 0.773 1.638 2.446 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 464.54789 ***Expected is 464.5473 ***SCORE DIFFERENCE IS .00059 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mkv.ssr.conf *** Running scoring test ./scoring/p.mkvO.conf Running scoring test ./scoring/p.mkvO.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/p.mkvO.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, variable only, modeled as Standard ordered k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -637.9212 optimizing: starting branch lengths... pass 1:+ 134.883 (branch= 134.40 scale= 0.48) pass 2:+ 7.290 (branch= 7.29 scale= 0.00) pass 3:+ 1.758 (branch= 1.73 scale= 0.03) pass 4:+ 0.187 (branch= 0.19 scale= 0.00) pass 5:+ 0.011 (branch= 0.01 scale= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00) lnL after optimization: -493.7915 Current score = -493.7915 Performing final optimizations... pass 1 : -493.7599 (branch= 0.0316) pass 2 : -493.6921 (branch= 0.0678) pass 3 : -493.6791 (branch= 0.0130) pass 4 : -493.6729 (branch= 0.0062) pass 5 : -493.6703 (branch= 0.0026) pass 6 : -493.6691 (branch= 0.0012) pass 7 : -493.6680 (branch= 0.0011) pass 8 : -493.6679 (branch= 0.0001) pass 9 : -493.6678 (branch= 0.0001) pass 10: -493.6677 (branch= 0.0000) pass 11: -493.6677 (branch= 0.0001) pass 12: -493.6676 (branch= 0.0000) pass 13: -493.6676 (branch= 0.0000) Looking for minimum length branches... Final score = -493.6676 Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -493.6676 Parameter estimates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths: TL rep 1: 4.301 NOTE: collapsebranches setting ignored when writing and comparing optimized trees... Writing optimized trees and models to scr.p.mkvO.best.all.tre ***********TEST************** ***Score is 493.66764 ***Expected is 493.667 ***SCORE DIFFERENCE IS .00064 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mkvO.conf *** Running scoring test ./scoring/p.mkvO.ssr.conf Running scoring test ./scoring/p.mkvO.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./scoring/p.mkvO.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, variable only, modeled as Standard ordered k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB NOTE: Less memory is required when scoring or optimizing fixed trees. minimum of 1 availablememory would be required to search You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Optimizing tree 1 ... Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -637.9212 optimizing: starting branch lengths, subset rates... pass 1:+ 144.867 (branch= 134.40 scale= 0.48 subset rates= 9.98) pass 2:+ 12.967 (branch= 8.30 scale= 0.00 subset rates= 4.67) pass 3:+ 3.846 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.161 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.157 (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: -474.8624 Current score = -474.8624 Performing final optimizations... pass 1 : -474.7936 (branch= 0.0575 subset rates= 0.0113) pass 2 : -474.6948 (branch= 0.0955 subset rates= 0.0033) pass 3 : -474.6697 (branch= 0.0251 subset rates= 0.0000) pass 4 : -474.6594 (branch= 0.0104 subset rates= 0.0000) pass 5 : -474.6525 (branch= 0.0054 subset rates= 0.0015) pass 6 : -474.6494 (branch= 0.0031 subset rates= 0.0000) pass 7 : -474.6473 (branch= 0.0021 subset rates= 0.0000) pass 8 : -474.6466 (branch= 0.0006 subset rates= 0.0000) pass 9 : -474.6462 (branch= 0.0004 subset rates= 0.0000) pass 10: -474.6460 (branch= 0.0002 subset rates= 0.0000) pass 11: -474.6459 (branch= 0.0001 subset rates= 0.0000) pass 12: -474.6458 (branch= 0.0001 subset rates= 0.0000) pass 13: -474.6458 (branch= 0.0000 subset rates= 0.0000) pass 14: -474.6458 (branch= 0.0000 subset rates= 0.0000) pass 15: -474.6456 (branch= 0.0000 subset rates= 0.0001) 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: 4.582 0.587 2.016 2.988 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 474.64560 ***Expected is 474.6455633 ***SCORE DIFFERENCE IS .0000367 ***ALLOWED ERROR IS 0.05 ***Scoring OK for ./scoring/p.mkvO.ssr.conf *** ************************** Running constraint tests ... ************************** Running constraint test n.neg.const Running constraint test n.neg.const Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./const/n.neg.const.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### Loading constraints from file data/z.neg.const.tre Found 1 negatively (conversely) constrained bipartition Bipartition 1: (1,2,3,4,5,11) | (6,7,8,9,10) STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0334 0.2271 0.2519 0.2271 0.8203 0.2271 2.8944 0.2271 Starting with seed=1 creating likelihood stepwise addition starting tree (compatible with constraints)... number of taxa added: 4 5 6 Optimizing parameters... improved 0.004 lnL Optimizing branchlengths... improved 0.000 lnL 7 8 9 10 11 Initial ln Likelihood: -227.5619 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 4.671 (branch= 0.06 scale= 0.00 alpha= 0.00 freqs= 2.00 rel rates= 2.60 pinv= 0.00) pass 2:+ 0.025 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.02 rel rates= 0.00 pinv= 0.00) lnL after optimization: -222.8653 gen current_lnL precision last_tree_imp 0 -222.8653 0.500 0 500 -213.0501 0.500 495 1000 -212.5074 0.500 628 Optimization precision reduced Optimizing parameters... improved 1.330 lnL Optimizing branchlengths... improved 0.015 lnL 1500 -210.8785 0.010 1215 2000 -210.6585 0.010 1215 2500 -210.6112 0.010 1215 3000 -210.5162 0.010 1215 Reached termination condition! last topological improvement at gen 1215 Improvement over last 500 gen = 0.03350 Current score = -210.5119 Performing final optimizations... pass 1 : -210.1434 (branch= 0.0000 alpha= 0.0976 pinv= 0.2247 eq freqs= 0.0000 rel rates= 0.0461) pass 2 : -209.5389 (branch= 0.0000 alpha= 0.3281 pinv= 0.2512 eq freqs= 0.0028 rel rates= 0.0225) pass 3 : -209.3295 (branch= 0.0347 alpha= 0.1440 pinv= 0.0168 eq freqs= 0.0070 rel rates= 0.0070) pass 4 : -209.2576 (branch= 0.0482 alpha= 0.0145 pinv= 0.0019 eq freqs= 0.0011 rel rates= 0.0062) pass 5 : -209.2201 (branch= 0.0237 alpha= 0.0068 pinv= 0.0003 eq freqs= 0.0000 rel rates= 0.0067) pass 6 : -209.1969 (branch= 0.0107 alpha= 0.0029 pinv= 0.0003 eq freqs= 0.0002 rel rates= 0.0091) pass 7 : -209.1773 (branch= 0.0068 alpha= 0.0021 pinv= 0.0001 eq freqs= 0.0004 rel rates= 0.0103) pass 8 : -209.1596 (branch= 0.0043 alpha= 0.0010 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0116) pass 9 : -209.1458 (branch= 0.0022 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0005 rel rates= 0.0111) pass 10: -209.1346 (branch= 0.0009 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0099) pass 11: -209.1249 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0089) pass 12: -209.1163 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0081) pass 13: -209.1085 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0075) pass 14: -209.1014 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0069) pass 15: -209.0947 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0065) pass 16: -209.0885 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0061) pass 17: -209.0826 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0058) pass 18: -209.0771 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0054) pass 19: -209.0718 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0052) pass 20: -209.0670 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0048) optimization up to ... pass 30: -208.9996 (branch= 0.0075 alpha= 0.0000 pinv= 0.0003 eq freqs= 0.0012 rel rates= 0.0584) optimization up to ... pass 40: -208.8388 (branch= 0.0297 alpha= 0.0000 pinv= 0.0015 eq freqs= 0.0076 rel rates= 0.1219) optimization up to ... pass 50: -208.6967 (branch= 0.0133 alpha= 0.0000 pinv= 0.0014 eq freqs= 0.0057 rel rates= 0.1216) optimization up to ... pass 60: -208.6227 (branch= 0.0012 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0007 rel rates= 0.0719) optimization up to ... pass 70: -208.5735 (branch= 0.0003 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0487) optimization up to ... pass 80: -208.5377 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0354) optimization up to ... pass 90: -208.5106 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0269) optimization up to ... pass 100: -208.4894 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0210) optimization up to ... pass 110: -208.4724 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0169) optimization up to ... pass 120: -208.4586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0138) optimization up to ... pass 130: -208.4472 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0114) optimization up to ... pass 140: -208.4374 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0097) optimization up to ... pass 150: -208.4292 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0082) optimization up to ... pass 160: -208.4221 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0070) optimization up to ... pass 170: -208.4160 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0061) optimization up to ... pass 180: -208.4107 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0053) optimization up to ... pass 190: -208.4059 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) optimization up to ... pass 200: -208.4018 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0041) optimization up to ... pass 210: -208.3981 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0037) optimization up to ... pass 220: -208.3947 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0033) optimization up to ... pass 230: -208.3916 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0031) optimization up to ... pass 240: -208.3888 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0028) optimization up to ... pass 250: -208.3863 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0025) optimization up to ... pass 260: -208.3840 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0023) optimization up to ... pass 270: -208.3819 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) optimization up to ... pass 280: -208.3799 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 290: -208.3781 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) optimization up to ... pass 300: -208.3764 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 310: -208.3749 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 320: -208.3734 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 330: -208.3721 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... pass 340: -208.3708 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... pass 350: -208.3696 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 360: -208.3685 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 370: -208.3674 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 380: -208.3665 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 390: -208.3655 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 400: -208.3646 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 410: -208.3638 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 420: -208.3630 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 430: -208.3622 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 440: -208.3615 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 450: -208.3608 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 460: -208.3602 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 470: -208.3596 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 480: -208.3590 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 490: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0004) optimization up to ... pass 497: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... Final score = -208.3584 Time used = 0 hours, 0 minutes and 21 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 122.591, AG = 189.174, AT = 6.994, CG = 205.391, CT = 195.428, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2225 0.2906 0.2035 0.2835 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 999.8998 with an invariant (invariable) site category, proportion estimated 0.2781 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 : -208.3584 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: 122.6 189.2 6.994 205.4 195.4 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.neg.const.best.tre ####################################################### TREEFILES PASS Running constraint test n.negBack.const Running constraint test n.negBack.const Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./const/n.negBack.const.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1-3 ####################################################### Loading constraints from file data/z.negBack.const.tre All constraints are backbone All constraints involve the same backbone set of taxa Found 1 negatively (conversely) constrained bipartition Bipartition 1 (backbone): (1,2,3,5,8,9,10) | (4,11) STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0334 0.2271 0.2519 0.2271 0.8203 0.2271 2.8944 0.2271 Starting with seed=1 creating likelihood stepwise addition starting tree (compatible with constraints)... number of taxa added: 4 5 6 Optimizing parameters... improved 0.005 lnL Optimizing branchlengths... improved 0.292 lnL 7 8 9 10 11 Initial ln Likelihood: -238.2863 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 6.219 (branch= 2.07 scale= 0.00 alpha= 0.00 freqs= 1.61 rel rates= 2.53 pinv= 0.00) pass 2:+ 1.027 (branch= 0.47 scale= 0.00 alpha= 0.00 freqs= 0.55 rel rates= 0.00 pinv= 0.00) pass 3:+ 0.029 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.02 rel rates= 0.00 pinv= 0.00) lnL after optimization: -231.0119 gen current_lnL precision last_tree_imp 0 -231.0119 0.500 0 500 -214.6598 0.500 276 Optimization precision reduced Optimizing parameters... improved 1.751 lnL Optimizing branchlengths... improved 0.106 lnL 1000 -212.3290 0.010 825 1500 -212.1958 0.010 825 2000 -211.9100 0.010 825 2500 -211.7710 0.010 825 3000 -211.6571 0.010 825 3500 -211.4394 0.010 825 4000 -211.3130 0.010 825 Reached termination condition! last topological improvement at gen 825 Improvement over last 500 gen = 0.03748 Current score = -211.2888 Performing final optimizations... pass 1 : -209.0567 (branch= 0.0000 alpha= 0.7586 pinv= 1.3876 eq freqs= 0.0053 rel rates= 0.0806) pass 2 : -208.6461 (branch= 0.0502 alpha= 0.3118 pinv= 0.0090 eq freqs= 0.0114 rel rates= 0.0282) pass 3 : -208.5218 (branch= 0.0332 alpha= 0.0623 pinv= 0.0020 eq freqs= 0.0021 rel rates= 0.0247) pass 4 : -208.4912 (branch= 0.0069 alpha= 0.0008 pinv= 0.0000 eq freqs= 0.0011 rel rates= 0.0218) pass 5 : -208.4694 (branch= 0.0013 alpha= 0.0000 pinv= 0.0005 eq freqs= 0.0003 rel rates= 0.0197) pass 6 : -208.4487 (branch= 0.0013 alpha= 0.0006 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0186) pass 7 : -208.4319 (branch= 0.0004 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0163) pass 8 : -208.4157 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0157) pass 9 : -208.4011 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0144) pass 10: -208.3880 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0129) pass 11: -208.3761 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0119) pass 12: -208.3650 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0109) pass 13: -208.3552 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0098) pass 14: -208.3461 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0091) pass 15: -208.3376 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0085) pass 16: -208.3297 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0078) pass 17: -208.3223 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0074) pass 18: -208.3156 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) pass 19: -208.3091 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0065) pass 20: -208.3031 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0059) optimization up to ... pass 30: -208.2580 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0450) optimization up to ... pass 40: -208.2301 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0278) optimization up to ... pass 50: -208.2111 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0189) optimization up to ... pass 60: -208.1973 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0137) optimization up to ... pass 70: -208.1869 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0104) optimization up to ... pass 80: -208.1786 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0083) optimization up to ... pass 90: -208.1719 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0067) optimization up to ... pass 100: -208.1664 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0055) optimization up to ... pass 110: -208.1617 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0046) optimization up to ... pass 120: -208.1577 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) optimization up to ... pass 130: -208.1543 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0034) optimization up to ... pass 140: -208.1513 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0030) optimization up to ... pass 150: -208.1486 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0027) optimization up to ... pass 160: -208.1462 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... pass 170: -208.1441 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) optimization up to ... pass 180: -208.1422 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 190: -208.1405 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 200: -208.1389 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 210: -208.1375 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 220: -208.1362 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... pass 230: -208.1350 (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: -208.1286 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 310: -208.1279 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 320: -208.1272 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 330: -208.1266 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 340: -208.1260 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 350: -208.1254 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 360: -208.1249 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) optimization up to ... pass 370: -208.1244 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0005) optimization up to ... pass 372: -208.1244 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.1244 Time used = 0 hours, 0 minutes and 20 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 22.224, AG = 32.291, AT = 0.001, CG = 36.376, CT = 80.264, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2210 0.3445 0.2161 0.2184 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 999.9000 with an invariant (invariable) site category, proportion estimated 0.3383 Substitution rate categories under this model: rate proportion 0.0000 0.3383 0.9601 0.1654 0.9894 0.1654 1.0100 0.1654 1.0405 0.1654 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -208.1244 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 22.22 32.29 0.001 36.38 80.26 1 0.221 0.344 0.216 0.218 999.900 0.338 Treelengths: TL rep 1: 2.421 Saving final tree from best search rep (#1) to con.n.negBack.const.best.tre ####################################################### TREEFILES PASS Running constraint test n.pos.const Running constraint test n.pos.const Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./const/n.pos.const.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1-5 ####################################################### Loading constraints from file data/z.pos.const.tre Found 6 positively constrained bipartition(s) Bipartition 1: (1,2,3,5,6,7,8,9,10) | (4,11) Bipartition 2: (1,3,5,6,7,8,9,10) | (2,4,11) Bipartition 3: (1,5,6,7,8,9,10) | (2,3,4,11) Bipartition 4: (1,2,3,4,5,8,9,10,11) | (6,7) Bipartition 5: (1,2,3,4,5,8,9,11) | (6,7,10) Bipartition 6: (1,5) | (2,3,4,6,7,8,9,10,11) STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0334 0.2271 0.2519 0.2271 0.8203 0.2271 2.8944 0.2271 Starting with seed=1 creating likelihood stepwise addition starting tree (compatible with constraints)... number of taxa added: 4 5 6 Optimizing parameters... improved 0.006 lnL Optimizing branchlengths... improved 11.173 lnL 7 8 9 10 11 Initial ln Likelihood: -225.0726 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 5.893 (branch= 2.29 scale= 0.89 alpha= 0.00 freqs= 1.20 rel rates= 1.50 pinv= 0.00) pass 2:+ 0.035 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.00) lnL after optimization: -219.1444 gen current_lnL precision last_tree_imp 0 -219.1444 0.500 0 500 -216.3490 0.500 474 1000 -215.0097 0.500 936 1500 -213.9531 0.500 936 Optimization precision reduced Optimizing parameters... improved 1.908 lnL Optimizing branchlengths... improved 0.702 lnL 2000 -210.9748 0.010 1986 2500 -210.8645 0.010 1986 3000 -210.7259 0.010 1986 3500 -210.6567 0.010 1986 4000 -210.6358 0.010 1986 Reached termination condition! last topological improvement at gen 1986 Improvement over last 500 gen = 0.02085 Current score = -210.6358 Performing final optimizations... pass 1 : -210.1101 (branch= 0.0000 alpha= 0.1171 pinv= 0.2670 eq freqs= 0.0000 rel rates= 0.1416) pass 2 : -209.4779 (branch= 0.0153 alpha= 0.3684 pinv= 0.2099 eq freqs= 0.0103 rel rates= 0.0282) pass 3 : -209.3226 (branch= 0.0490 alpha= 0.0860 pinv= 0.0099 eq freqs= 0.0024 rel rates= 0.0079) pass 4 : -209.2696 (branch= 0.0318 alpha= 0.0104 pinv= 0.0011 eq freqs= 0.0023 rel rates= 0.0074) pass 5 : -209.2429 (branch= 0.0112 alpha= 0.0054 pinv= 0.0000 eq freqs= 0.0013 rel rates= 0.0088) pass 6 : -209.2170 (branch= 0.0097 alpha= 0.0041 pinv= 0.0000 eq freqs= 0.0009 rel rates= 0.0112) pass 7 : -209.1934 (branch= 0.0086 alpha= 0.0024 pinv= 0.0002 eq freqs= 0.0011 rel rates= 0.0112) pass 8 : -209.1711 (branch= 0.0062 alpha= 0.0022 pinv= 0.0001 eq freqs= 0.0010 rel rates= 0.0129) pass 9 : -209.1529 (branch= 0.0054 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0008 rel rates= 0.0121) pass 10: -209.1396 (branch= 0.0019 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0006 rel rates= 0.0108) pass 11: -209.1288 (branch= 0.0008 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0096) pass 12: -209.1194 (branch= 0.0004 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0087) pass 13: -209.1112 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0078) pass 14: -209.1038 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0071) pass 15: -209.0969 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0067) pass 16: -209.0905 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0062) pass 17: -209.0845 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0059) pass 18: -209.0788 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0056) pass 19: -209.0735 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0052) pass 20: -209.0685 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) optimization up to ... pass 30: -209.0028 (branch= 0.0069 alpha= 0.0000 pinv= 0.0003 eq freqs= 0.0011 rel rates= 0.0574) optimization up to ... pass 40: -208.8446 (branch= 0.0294 alpha= 0.0000 pinv= 0.0015 eq freqs= 0.0073 rel rates= 0.1200) optimization up to ... pass 50: -208.6998 (branch= 0.0142 alpha= 0.0000 pinv= 0.0014 eq freqs= 0.0061 rel rates= 0.1231) optimization up to ... pass 60: -208.6244 (branch= 0.0013 alpha= 0.0000 pinv= 0.0002 eq freqs= 0.0008 rel rates= 0.0732) optimization up to ... pass 70: -208.5748 (branch= 0.0003 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0002 rel rates= 0.0490) optimization up to ... pass 80: -208.5387 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0358) optimization up to ... pass 90: -208.5113 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0272) optimization up to ... pass 100: -208.4900 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0212) optimization up to ... pass 110: -208.4730 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0169) optimization up to ... pass 120: -208.4590 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0138) optimization up to ... pass 130: -208.4475 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0115) optimization up to ... pass 140: -208.4377 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0097) optimization up to ... pass 150: -208.4294 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0083) optimization up to ... pass 160: -208.4223 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0071) optimization up to ... pass 170: -208.4161 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0061) optimization up to ... pass 180: -208.4108 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0053) optimization up to ... pass 190: -208.4061 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0047) optimization up to ... pass 200: -208.4019 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0042) optimization up to ... pass 210: -208.3982 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0037) optimization up to ... pass 220: -208.3948 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0033) optimization up to ... pass 230: -208.3918 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0030) optimization up to ... pass 240: -208.3890 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0028) optimization up to ... pass 250: -208.3865 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0025) optimization up to ... pass 260: -208.3842 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0023) optimization up to ... pass 270: -208.3820 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0021) optimization up to ... pass 280: -208.3801 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... pass 290: -208.3783 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0018) optimization up to ... pass 300: -208.3766 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 310: -208.3750 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 320: -208.3735 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... pass 330: -208.3721 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 340: -208.3709 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... pass 350: -208.3697 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 360: -208.3685 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 370: -208.3675 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 380: -208.3665 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 390: -208.3656 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 400: -208.3647 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 410: -208.3638 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 420: -208.3631 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 430: -208.3623 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 440: -208.3616 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 450: -208.3609 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 460: -208.3602 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 470: -208.3596 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 480: -208.3590 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 490: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0004) optimization up to ... pass 494: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... Final score = -208.3586 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 = 121.695, AG = 187.809, AT = 6.943, CG = 203.906, CT = 194.017, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2225 0.2906 0.2035 0.2835 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 999.9000 with an invariant (invariable) site category, proportion estimated 0.2781 Substitution rate categories under this model: rate proportion 0.0000 0.2781 0.9601 0.1805 0.9894 0.1805 1.0100 0.1805 1.0405 0.1805 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 2 branches were collapsed. NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with a positive constraint, it is possible for a constrained branch itself to be collapsed. If you care, be careful to check whether this has happened or turn off branch collapsing. ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -208.3586 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 121.7 187.8 6.943 203.9 194 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL rep 1: 1.881 Saving final tree from best search rep (#1) to con.n.pos.const.best.tre ####################################################### TREEFILES PASS Running constraint test n.posBack.const Running constraint test n.posBack.const Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./const/n.posBack.const.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 2 ####################################################### Loading constraints from file data/z.posBack.const.tre All constraints are backbone All constraints involve the same backbone set of taxa Found 4 positively constrained bipartition(s) Bipartition 1 (backbone): (1,2,3,5,8,9,10) | (4,11) Bipartition 2 (backbone): (1,3,5,8,9,10) | (2,4,11) Bipartition 3 (backbone): (1,5,8,9,10) | (2,3,4,11) Bipartition 4 (backbone): (1,5) | (2,3,4,8,9,10,11) STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0334 0.2271 0.2519 0.2271 0.8203 0.2271 2.8944 0.2271 Starting with seed=1 creating likelihood stepwise addition starting tree (compatible with constraints)... number of taxa added: 4 5 6 Optimizing parameters... improved 0.006 lnL Optimizing branchlengths... improved 11.173 lnL 7 8 9 10 11 Initial ln Likelihood: -221.7983 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 5.406 (branch= 2.03 scale= 0.00 alpha= 0.00 freqs= 1.20 rel rates= 2.17 pinv= 0.00) pass 2:+ 0.072 (branch= 0.04 scale= 0.00 alpha= 0.00 freqs= 0.02 rel rates= 0.00 pinv= 0.00) lnL after optimization: -216.3203 gen current_lnL precision last_tree_imp 0 -216.3203 0.500 0 500 -213.9944 0.500 208 1000 -213.0248 0.500 547 Optimization precision reduced Optimizing parameters... improved 1.494 lnL Optimizing branchlengths... improved 0.350 lnL 1500 -210.9424 0.010 1230 2000 -210.7781 0.010 1230 2500 -210.6534 0.010 1230 3000 -210.6000 0.010 1230 Reached termination condition! last topological improvement at gen 1230 Improvement over last 500 gen = 0.04762 Current score = -210.5885 Performing final optimizations... pass 1 : -210.1851 (branch= 0.0000 alpha= 0.1346 pinv= 0.1999 eq freqs= 0.0000 rel rates= 0.0689) pass 2 : -209.5873 (branch= 0.0031 alpha= 0.3060 pinv= 0.2468 eq freqs= 0.0032 rel rates= 0.0387) pass 3 : -209.3473 (branch= 0.0521 alpha= 0.1554 pinv= 0.0219 eq freqs= 0.0070 rel rates= 0.0037) pass 4 : -209.2635 (branch= 0.0535 alpha= 0.0235 pinv= 0.0010 eq freqs= 0.0016 rel rates= 0.0042) pass 5 : -209.2109 (branch= 0.0340 alpha= 0.0091 pinv= 0.0016 eq freqs= 0.0011 rel rates= 0.0068) pass 6 : -209.1745 (branch= 0.0208 alpha= 0.0063 pinv= 0.0003 eq freqs= 0.0014 rel rates= 0.0075) pass 7 : -209.1476 (branch= 0.0103 alpha= 0.0038 pinv= 0.0002 eq freqs= 0.0015 rel rates= 0.0111) pass 8 : -209.1244 (branch= 0.0077 alpha= 0.0027 pinv= 0.0000 eq freqs= 0.0012 rel rates= 0.0116) pass 9 : -209.1092 (branch= 0.0041 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0010 rel rates= 0.0100) pass 10: -209.0986 (branch= 0.0014 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0007 rel rates= 0.0086) pass 11: -209.0902 (branch= 0.0006 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0004 rel rates= 0.0074) pass 12: -209.0831 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0003 rel rates= 0.0065) pass 13: -209.0769 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0002 rel rates= 0.0059) pass 14: -209.0714 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0053) pass 15: -209.0662 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0050) pass 16: -209.0612 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0049) pass 17: -209.0560 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0049) pass 18: -209.0506 (branch= 0.0003 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) pass 19: -209.0447 (branch= 0.0005 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0054) pass 20: -209.0381 (branch= 0.0007 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0058) optimization up to ... pass 30: -208.9192 (branch= 0.0216 alpha= 0.0000 pinv= 0.0008 eq freqs= 0.0045 rel rates= 0.0920) optimization up to ... pass 40: -208.7470 (branch= 0.0241 alpha= 0.0000 pinv= 0.0019 eq freqs= 0.0083 rel rates= 0.1378) optimization up to ... pass 50: -208.6513 (branch= 0.0034 alpha= 0.0000 pinv= 0.0005 eq freqs= 0.0020 rel rates= 0.0899) optimization up to ... pass 60: -208.5930 (branch= 0.0005 alpha= 0.0000 pinv= 0.0001 eq freqs= 0.0003 rel rates= 0.0575) optimization up to ... pass 70: -208.5520 (branch= 0.0002 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0406) optimization up to ... pass 80: -208.5213 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0304) optimization up to ... pass 90: -208.4976 (branch= 0.0001 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.0235) optimization up to ... pass 100: -208.4790 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0185) optimization up to ... pass 110: -208.4638 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0150) optimization up to ... pass 120: -208.4515 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0123) optimization up to ... pass 130: -208.4410 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0105) optimization up to ... pass 140: -208.4321 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0088) optimization up to ... pass 150: -208.4245 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0076) optimization up to ... pass 160: -208.4179 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0065) optimization up to ... pass 170: -208.4122 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0057) optimization up to ... pass 180: -208.4072 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0050) optimization up to ... pass 190: -208.4029 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0044) optimization up to ... pass 200: -208.3989 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0040) optimization up to ... pass 210: -208.3953 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0035) optimization up to ... pass 220: -208.3922 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0032) optimization up to ... pass 230: -208.3893 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0029) optimization up to ... pass 240: -208.3866 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0026) optimization up to ... pass 250: -208.3842 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0024) optimization up to ... pass 260: -208.3820 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0022) optimization up to ... pass 270: -208.3800 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0020) optimization up to ... pass 280: -208.3781 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0019) optimization up to ... pass 290: -208.3764 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0017) optimization up to ... pass 300: -208.3748 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0016) optimization up to ... pass 310: -208.3733 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0015) optimization up to ... pass 320: -208.3719 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0014) optimization up to ... pass 330: -208.3706 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0013) optimization up to ... pass 340: -208.3693 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0012) optimization up to ... pass 350: -208.3682 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 360: -208.3671 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0011) optimization up to ... pass 370: -208.3661 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0010) optimization up to ... pass 380: -208.3651 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 390: -208.3642 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 400: -208.3634 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0009) optimization up to ... pass 410: -208.3626 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 420: -208.3618 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0008) optimization up to ... pass 430: -208.3610 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 440: -208.3603 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 450: -208.3597 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0007) optimization up to ... pass 460: -208.3590 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0006) optimization up to ... pass 470: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0004) optimization up to ... pass 480: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... pass 490: -208.3580 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... pass 500: -208.3577 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0003) optimization up to ... pass 503: -208.3577 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.3577 Time used = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 122.162, AG = 188.510, AT = 6.957, CG = 204.705, CT = 194.795, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2225 0.2906 0.2035 0.2834 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 999.9000 with an invariant (invariable) site category, proportion estimated 0.2781 Substitution rate categories under this model: rate proportion 0.0000 0.2781 0.9601 0.1805 0.9894 0.1805 1.0100 0.1805 1.0405 0.1805 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 2 branches were collapsed. NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with a positive constraint, it is possible for a constrained branch itself to be collapsed. If you care, be careful to check whether this has happened or turn off branch collapsing. ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -208.3577 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: 122.2 188.5 6.957 204.7 194.8 1 0.223 0.291 0.203 0.283 999.900 0.278 Treelengths: TL rep 1: 1.881 Saving final tree from best search rep (#1) to con.n.posBack.const.best.tre ####################################################### TREEFILES PASS ************************** Running output tests ... ************************** Running output test a.G3 Running output test a.G3 Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./output/a.G3.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 11 sequences. 3 constant characters. 6 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0165 0.0083 0.0496 0.0909 0.0909 0.0083 0.0744 0.0083 0.0083 0.1074 0.1157 0.0248 0.1240 0.0331 0.0083 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0750 Substitution rate categories under this model: rate proportion 0.0000 0.0750 0.0603 0.3083 0.4894 0.3083 2.4503 0.3083 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.002 lnL Optimizing branchlengths... improved 0.000 lnL 7 8 9 10 11 Initial ln Likelihood: -116.5267 optimizing: starting branch lengths, alpha shape, prop. invar... pass 1:+ 0.949 (branch= 0.95 scale= 0.00 alpha= 0.00 pinv= 0.00) pass 2:+ 0.099 (branch= 0.10 scale= 0.00 alpha= 0.00 pinv= 0.00) lnL after optimization: -115.4785 gen current_lnL precision last_tree_imp 0 -115.4785 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0165 0.0083 0.0496 0.0909 0.0909 0.0083 0.0744 0.0083 0.0083 0.1074 0.1157 0.0248 0.1240 0.0331 0.0083 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.5015 with an invariant (invariable) site category, proportion estimated 0.0735 Substitution rate categories under this model: rate proportion 0.0000 0.0735 0.0607 0.3088 0.4905 0.3088 2.4487 0.3088 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.a.G3.sitelikes.log ... WARNING: Site likelihoods being output on prematurely terminated search ... NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -114.0488 Parameter estimates: alpha pinv rep 1: 0.501 0.073 Treelengths: TL rep 1: 1.377 Saving final tree from best search rep (#1) to out.a.G3.best.tre Inferring internal state probabilities on best tree... saving to file out.a.G3.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.a.G3.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found 11 instead at line 1, column (approximately) 4 (file position 3) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 16, column (approximately) 1 (file position 470) storing implied block: TAXA storing read block: TREES TREEFILES PASS Running output test a.G4 Running output test a.G4 Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./output/a.G4.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 11 sequences. 3 constant characters. 6 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.8 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 2 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0165 0.0083 0.0496 0.0909 0.0909 0.0083 0.0744 0.0083 0.0083 0.1074 0.1157 0.0248 0.1240 0.0331 0.0083 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0750 Substitution rate categories under this model: rate proportion 0.0000 0.0750 0.0334 0.2313 0.2519 0.2313 0.8203 0.2313 2.8944 0.2313 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.001 lnL Optimizing branchlengths... improved 0.006 lnL 7 8 9 10 11 Initial ln Likelihood: -117.7431 optimizing: starting branch lengths, alpha shape, prop. invar... pass 1:+ 1.466 (branch= 1.13 scale= 0.33 alpha= 0.00 pinv= 0.00) pass 2:+ 0.134 (branch= 0.13 scale= 0.00 alpha= 0.00 pinv= 0.00) lnL after optimization: -116.1434 gen current_lnL precision last_tree_imp 0 -116.1434 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0165 0.0083 0.0496 0.0909 0.0909 0.0083 0.0744 0.0083 0.0083 0.1074 0.1157 0.0248 0.1240 0.0331 0.0083 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5015 with an invariant (invariable) site category, proportion estimated 0.0735 Substitution rate categories under this model: rate proportion 0.0000 0.0735 0.0337 0.2316 0.2529 0.2316 0.8214 0.2316 2.8921 0.2316 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.a.G4.sitelikes.log ... WARNING: Site likelihoods being output on prematurely terminated search ... NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -114.3787 Parameter estimates: alpha pinv rep 1: 0.501 0.073 Treelengths: TL rep 1: 1.339 Saving final tree from best search rep (#1) to out.a.G4.best.tre Inferring internal state probabilities on best tree... saving to file out.a.G4.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.a.G4.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found 11 instead at line 1, column (approximately) 4 (file position 3) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 16, column (approximately) 1 (file position 470) storing implied block: TAXA storing read block: TREES TREEFILES PASS Running output test a Running output test a Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./output/a.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.AA.fas as Fasta amino acid format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Amino acid data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 11 sequences. 3 constant characters. 6 parsimony-informative characters. 1 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 10 total characters (11 before removing empty columns). 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.2 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1-3 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0165 0.0083 0.0496 0.0909 0.0909 0.0083 0.0744 0.0083 0.0083 0.1074 0.1157 0.0248 0.1240 0.0331 0.0083 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 0.121 lnL 7 8 9 10 11 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -117.7533 optimizing: starting branch lengths... pass 1:+ 0.632 (branch= 0.63 scale= 0.00) pass 2:+ 0.134 (branch= 0.13 scale= 0.00) lnL after optimization: -116.9881 gen current_lnL precision last_tree_imp 0 -116.9881 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0165 0.0083 0.0496 0.0909 0.0909 0.0083 0.0744 0.0083 0.0083 0.1074 0.1157 0.0248 0.1240 0.0331 0.0083 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.a.sitelikes.log ... WARNING: Site likelihoods being output on prematurely terminated search ... NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -115.6197 Parameter estimates: Model contains no estimated parameters Treelengths: TL rep 1: 2.324 Saving final tree from best search rep (#1) to out.a.best.tre Inferring internal state probabilities on best tree... saving to file out.a.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.a.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found > instead at line 1, column (approximately) 2 (file position 1) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 26, column (approximately) 1 (file position 310) storing implied block: TAXA storing read block: TREES TREEFILES PASS Running output test c.M3x2 Running output test c.M3x2 Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./output/c.M3x2.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Codon data Base usage at codon positions: A C G T pos 1 0.27723 0.36634 0.21782 0.13861 pos 2 0.30693 0.20792 0.07921 0.40594 pos 3 0.10891 0.38614 0.26733 0.23762 all pos 0.23102 0.32013 0.18812 0.26073 Summary of data: 11 sequences. 0 constant characters. 9 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 1.3 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1-5 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0094 0.0334 0.0231 0.0206 0.0064 0.0226 0.0157 0.0139 0.0024 0.0086 0.0060 0.0053 0.0125 0.0442 0.0306 0.0272 0.0125 0.0442 0.0306 0.0272 0.0084 0.0299 0.0207 0.0184 0.0032 0.0114 0.0079 0.0070 0.0165 0.0584 0.0405 0.0360 0.0074 0.0263 0.0182 0.0162 0.0050 0.0178 0.0123 0.0110 0.0019 0.0068 0.0047 0.0042 0.0098 0.0347 0.0241 0.0214 0.0167 0.0103 0.0032 0.0113 0.0078 0.0070 0.0043 0.0030 0.0027 0.0062 0.0221 0.0153 0.0136 Rate Heterogeneity Model: 2 nonsynonymous rate categories, rate and proportion of each estimated (this is effectively the M3 model of PAML) dN/dS Proportion 0.2500 0.5000 0.5000 0.5000 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 4.461 lnL Optimizing branchlengths... improved 0.701 lnL 7 8 9 10 11 Initial ln Likelihood: -215.8071 optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters... pass 1:+ 6.388 (branch= 0.00 scale= 0.44 omega= 0.01 rel rates= 5.93) pass 2:+ 0.434 (branch= 0.00 scale= 0.00 omega= 0.01 rel rates= 0.42) lnL after optimization: -208.9856 gen current_lnL precision last_tree_imp 0 -208.9856 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.586, AG = 3.999, AT = 0.040, CG = 2.453, CT = 3.999, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0094 0.0334 0.0231 0.0206 0.0064 0.0226 0.0157 0.0139 0.0024 0.0086 0.0060 0.0053 0.0125 0.0442 0.0306 0.0272 0.0125 0.0442 0.0306 0.0272 0.0084 0.0299 0.0207 0.0184 0.0032 0.0114 0.0079 0.0070 0.0165 0.0584 0.0405 0.0360 0.0074 0.0263 0.0182 0.0162 0.0050 0.0178 0.0123 0.0110 0.0019 0.0068 0.0047 0.0042 0.0098 0.0347 0.0241 0.0214 0.0167 0.0103 0.0032 0.0113 0.0078 0.0070 0.0043 0.0030 0.0027 0.0062 0.0221 0.0153 0.0136 Rate Heterogeneity Model: 2 nonsynonymous rate categories, rate and proportion of each estimated (this is effectively the M3 model of PAML) dN/dS Proportion 0.0490 0.5030 0.4995 0.4970 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.c.M3x2.sitelikes.log ... WARNING: Site likelihoods being output on prematurely terminated search ... NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -208.2373 Parameter estimates: w(0) p(0) w(1) p(1) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) rep 1: 0.049 0.503 0.499 0.497 1.586 3.999 0.04 2.453 3.999 1 Treelengths: TL rep 1: 9.626 Saving final tree from best search rep (#1) to out.c.M3x2.best.tre Inferring internal state probabilities on best tree... saving to file out.c.M3x2.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.c.M3x2.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found 11 instead at line 1, column (approximately) 4 (file position 3) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 16, column (approximately) 1 (file position 470) storing implied block: TAXA storing read block: TREES TREEFILES PASS Running output test c Running output test c Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./output/c.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Codon data Base usage at codon positions: A C G T pos 1 0.27723 0.36634 0.21782 0.13861 pos 2 0.30693 0.20792 0.07921 0.40594 pos 3 0.10891 0.38614 0.26733 0.23762 all pos 0.23102 0.32013 0.18812 0.26073 Summary of data: 11 sequences. 0 constant characters. 9 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 5 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 61 (codon data, standard code) One estimated dN/dS ratio (aka omega) = 0.250000 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0094 0.0334 0.0231 0.0206 0.0064 0.0226 0.0157 0.0139 0.0024 0.0086 0.0060 0.0053 0.0125 0.0442 0.0306 0.0272 0.0125 0.0442 0.0306 0.0272 0.0084 0.0299 0.0207 0.0184 0.0032 0.0114 0.0079 0.0070 0.0165 0.0584 0.0405 0.0360 0.0074 0.0263 0.0182 0.0162 0.0050 0.0178 0.0123 0.0110 0.0019 0.0068 0.0047 0.0042 0.0098 0.0347 0.0241 0.0214 0.0167 0.0103 0.0032 0.0113 0.0078 0.0070 0.0043 0.0030 0.0027 0.0062 0.0221 0.0153 0.0136 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.001 lnL Optimizing branchlengths... improved 0.000 lnL 7 8 9 10 11 Initial ln Likelihood: -225.6424 optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters... pass 1:+ 10.931 (branch= 2.26 scale= 0.50 omega= 0.00 rel rates= 8.17) pass 2:+ 0.924 (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: -213.0383 gen current_lnL precision last_tree_imp 0 -213.0383 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) = 0.130420 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 2.468, AG = 4.008, AT = 0.588, CG = 2.683, CT = 2.282, 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 : -210.2322 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 2.282 1 Treelengths: TL rep 1: 8.650 Saving final tree from best search rep (#1) to out.c.best.tre Inferring internal state probabilities on best tree... saving to file out.c.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.c.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found 11 instead at line 1, column (approximately) 4 (file position 3) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 16, column (approximately) 1 (file position 470) storing implied block: TAXA storing read block: TREES TREEFILES PASS Running output test n.G3 Running output test n.G3 Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./output/n.G3.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.3 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0603 0.3028 0.4894 0.3028 2.4503 0.3028 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.004 lnL Optimizing branchlengths... improved 0.000 lnL 7 8 9 10 11 Initial ln Likelihood: -226.8217 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 3.951 (branch= 0.75 scale= 0.00 alpha= 0.00 freqs= 1.76 rel rates= 1.44 pinv= 0.00) pass 2:+ 0.586 (branch= 0.56 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.00) pass 3:+ 1.297 (branch= 0.66 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.61 pinv= 0.00) pass 4:+ 0.021 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.02 rel rates= 0.00 pinv= 0.00) lnL after optimization: -220.9660 gen current_lnL precision last_tree_imp 0 -220.9660 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.002, AG = 3.998, AT = 0.998, CG = 2.322, CT = 3.998, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2184 0.3566 0.2049 0.2201 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.5025 with an invariant (invariable) site category, proportion estimated 0.0892 Substitution rate categories under this model: rate proportion 0.0000 0.0892 0.0610 0.3036 0.4913 0.3036 2.4477 0.3036 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.n.G3.sitelikes.log ... WARNING: Site likelihoods being output on prematurely terminated search ... NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -220.9571 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 1.002 3.998 0.998 2.322 3.998 1 0.218 0.357 0.205 0.220 0.502 0.089 Treelengths: TL rep 1: 2.169 Saving final tree from best search rep (#1) to out.n.G3.best.tre Inferring internal state probabilities on best tree... saving to file out.n.G3.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.n.G3.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found 11 instead at line 1, column (approximately) 4 (file position 3) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 16, column (approximately) 1 (file position 470) storing implied block: TAXA storing read block: TREES storing read block: PAUP TREEFILES PASS Running output test n.G4 Running output test n.G4 Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./output/n.G4.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1-4 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0334 0.2271 0.2519 0.2271 0.8203 0.2271 2.8944 0.2271 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.005 lnL Optimizing branchlengths... improved 0.292 lnL 7 8 9 10 11 Initial ln Likelihood: -226.2799 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 5.831 (branch= 2.05 scale= 0.00 alpha= 0.00 freqs= 1.45 rel rates= 2.33 pinv= 0.00) pass 2:+ 0.107 (branch= 0.07 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.00) lnL after optimization: -220.3414 gen current_lnL precision last_tree_imp 0 -220.3414 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.001, AG = 2.400, AT = 0.589, CG = 1.512, CT = 4.001, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2259 0.3629 0.1852 0.2261 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5015 with an invariant (invariable) site category, proportion estimated 0.0902 Substitution rate categories under this model: rate proportion 0.0000 0.0902 0.0337 0.2275 0.2529 0.2275 0.8214 0.2275 2.8921 0.2275 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.n.G4.sitelikes.log ... WARNING: Site likelihoods being output on prematurely terminated search ... NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -217.4380 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 1.001 2.4 0.589 1.512 4.001 1 0.226 0.363 0.185 0.226 0.501 0.090 Treelengths: TL rep 1: 1.694 Saving final tree from best search rep (#1) to out.n.G4.best.tre Inferring internal state probabilities on best tree... saving to file out.n.G4.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.n.G4.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found 11 instead at line 1, column (approximately) 4 (file position 3) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 16, column (approximately) 1 (file position 470) storing implied block: TAXA storing read block: TREES storing read block: PAUP TREEFILES PASS Running output test n Running output test n Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./output/n.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.1 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 2 3 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 3.458 lnL 7 8 9 10 11 Initial ln Likelihood: -225.5327 optimizing: starting branch lengths, rel rates, eq freqs... pass 1:+ 7.466 (branch= 0.77 scale= 0.00 freqs= 0.02 rel rates= 6.68) pass 2:+ 0.468 (branch= 0.45 scale= 0.00 freqs= 0.02 rel rates= 0.00) lnL after optimization: -217.5990 gen current_lnL precision last_tree_imp 0 -217.5990 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.511, AG = 3.999, AT = 0.200, CG = 2.619, CT = 2.047, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2300 0.3205 0.1884 0.2611 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.n.sitelikes.log ... WARNING: Site likelihoods being output on prematurely terminated search ... NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -217.2394 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 1.511 3.999 0.1995 2.619 2.047 1 0.230 0.321 0.188 0.261 Treelengths: TL rep 1: 1.686 Saving final tree from best search rep (#1) to out.n.best.tre Inferring internal state probabilities on best tree... saving to file out.n.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.n.nex ] Executing Warning: Expecting #NEXUS to be the first token in the file, but found 11 instead at line 1, column (approximately) 4 (file position 3) Warning: A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. at line 16, column (approximately) 1 (file position 470) storing implied block: TAXA storing read block: TREES storing read block: PAUP TREEFILES PASS Running output test n.wackyNames Running output test n.wackyNames Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./output/n.wackyNames.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x30.wackyNames.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.1 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 3.458 lnL 7 8 9 10 11 Initial ln Likelihood: -225.5327 optimizing: starting branch lengths, rel rates, eq freqs... pass 1:+ 7.466 (branch= 0.77 scale= 0.00 freqs= 0.02 rel rates= 6.68) pass 2:+ 0.468 (branch= 0.45 scale= 0.00 freqs= 0.02 rel rates= 0.00) lnL after optimization: -217.5990 gen current_lnL precision last_tree_imp 0 -217.5990 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.511, AG = 3.999, AT = 0.200, CG = 2.619, CT = 2.047, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2300 0.3205 0.1884 0.2611 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. Saving site likelihoods to file out.n.sitelikes.log ... WARNING: Site likelihoods being output on prematurely terminated search ... NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -217.2394 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 1.511 3.999 0.1995 2.619 2.047 1 0.230 0.321 0.188 0.261 Treelengths: TL rep 1: 1.686 Saving final tree from best search rep (#1) to out.n.best.tre ####################################################### cat: out.n.wackyNames.best.tre: No such file or directory [Reading test.out.n.wackyNames.nex ] Executing storing implied block: TAXA storing read block: DATA TREEFILES PASS Running output test p.3diff Running output test p.3diff Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./output/p.3diff.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.byPos.11x2178.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful Reading SETS block...storing read block: SETS successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #1 ("1stpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 4 Summary of data: 11 sequences. 441 constant characters. 171 parsimony-informative characters. 113 uninformative variable characters. 725 total characters. 237 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #2 ("2ndpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 5 Summary of data: 11 sequences. 527 constant characters. 90 parsimony-informative characters. 108 uninformative variable characters. 725 total characters. 158 unique patterns in compressed data matrix. GARLI data subset 3 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #3 ("3rdpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 6 Summary of data: 11 sequences. 102 constant characters. 507 parsimony-informative characters. 116 uninformative variable characters. 725 total characters. 548 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 11 MB good approx 10 MB to 9 MB low approx 8 MB to 5 MB very low approx 4 MB to 4 MB the minimum required availablememory is 4 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 16.0 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 2 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3150 0.1749 0.3006 0.2095 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 Substitution rate categories under this model: rate proportion 0.0334 0.2500 0.2519 0.2500 0.8203 0.2500 2.8944 0.2500 Model 2 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) AC = 4.000, AG = 4.000, AT = 1.000, CG = 4.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2706 0.1568 0.1630 0.4096 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 Substitution rate categories under this model: rate proportion 0.0334 0.2500 0.2519 0.2500 0.8203 0.2500 2.8944 0.2500 Model 3 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1462 0.3614 0.2906 0.2018 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0352 Substitution rate categories under this model: rate proportion 0.0000 0.0352 0.0334 0.2412 0.2519 0.2412 0.8203 0.2412 2.8944 0.2412 Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 168.526 lnL Optimizing branchlengths... improved 66.084 lnL 7 8 9 10 11 Initial ln Likelihood: -13699.7841 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates... pass 1:+ 209.508 (branch= 7.95 scale= 0.00 alpha= 35.56 freqs= 28.90 rel rates= 62.03 pinv= 0.19 subset rates= 74.88) pass 2:+ 77.016 (branch= 1.74 scale= 0.00 alpha= 4.25 freqs= 11.29 rel rates= 3.50 pinv= 0.68 subset rates= 55.55) pass 3:+ 50.073 (branch= 8.13 scale= 0.55 alpha= 4.79 freqs= 1.15 rel rates= 1.36 pinv= 0.01 subset rates= 34.08) pass 4:+ 16.647 (branch= 1.54 scale= 0.00 alpha= 0.63 freqs= 1.21 rel rates= 1.36 pinv= 0.01 subset rates= 11.89) pass 5:+ 6.281 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.12 rel rates= 1.30 pinv= 0.01 subset rates= 4.84) pass 6:+ 0.125 (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: -13340.1342 gen current_lnL precision last_tree_imp 0 -13340.1342 0.500 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) AC = 1.951, AG = 2.401, AT = 1.337, CG = 1.337, CT = 3.999, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3133 0.1756 0.2989 0.2122 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.3651 Substitution rate categories under this model: rate proportion 0.0120 0.2500 0.1552 0.2500 0.6905 0.2500 3.1423 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 = 4.002, AG = 6.112, AT = 1.224, CG = 6.112, CT = 4.002, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2815 0.1660 0.1576 0.3948 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.3377 Substitution rate categories under this model: rate proportion 0.0088 0.2500 0.1340 0.2500 0.6540 0.2500 3.2032 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 = 4.475, AT = 2.816, CG = 0.436, CT = 4.475, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1595 0.3510 0.2837 0.2058 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 4.2180 with an invariant (invariable) site category, proportion estimated 0.0301 Substitution rate categories under this model: rate proportion 0.0000 0.0301 0.4660 0.2425 0.7824 0.2425 1.0843 0.2425 1.6673 0.2425 Subset rate multipliers: 0.54 0.32 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 : -13322.8959 Parameter estimates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha rep 1: 1.951 2.401 1.337 1.337 3.999 1 0.313 0.176 0.299 0.212 0.365 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: 4.002 6.112 1.224 6.112 4.002 1 0.282 0.166 0.158 0.395 0.338 Partition model subset 3: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 1 4.475 2.816 0.4357 4.475 1 0.160 0.351 0.284 0.206 4.218 0.030 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 1.721 0.537 0.325 2.139 Saving final tree from best search rep (#1) to out.p.3diff.best.tre Inferring internal state probabilities on best tree... saving to file out.p.3diff.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### [Reading test.out.p.3diff.nex ] Executing storing implied block: TAXA storing read block: DATA storing read block: SETS storing read block: ASSUMPTIONS storing read block: TREES TREEFILES PASS Running output test p.mkvO.ssr Running output test p.mkvO.ssr Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./output/p.mkvO.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, variable only, modeled as Standard ordered k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 5 ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN >>>Search rep 1 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -637.9212 optimizing: starting branch lengths, subset rates... pass 1:+ 144.867 (branch= 134.40 scale= 0.48 subset rates= 9.98) pass 2:+ 12.967 (branch= 8.30 scale= 0.00 subset rates= 4.67) pass 3:+ 3.846 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.161 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.157 (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: -474.8624 gen current_lnL precision last_tree_imp 0 -474.8624 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 : -474.8616 (best) Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.474 0.599 2.019 2.819 Saving final tree from best search rep (#1) to out.p.mkvO.ssr.best.tre ####################################################### >>>Search rep 2 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1351934195 Initial ln Likelihood: -668.6258 optimizing: starting branch lengths, subset rates... pass 1:+ 167.892 (branch= 157.14 scale= 1.13 subset rates= 9.62) pass 2:+ 19.859 (branch= 15.03 scale= 0.02 subset rates= 4.81) pass 3:+ 5.106 (branch= 3.29 scale= 0.00 subset rates= 1.82) pass 4:+ 0.827 (branch= 0.20 scale= 0.00 subset rates= 0.62) pass 5:+ 0.064 (branch= 0.04 scale= 0.00 subset rates= 0.03) pass 6:+ 0.027 (branch= 0.03 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -474.8512 gen current_lnL precision last_tree_imp 0 -474.8512 0.010 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.60 2.01 2.84 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 6 branches were collapsed. NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 2 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -474.8616 Replicate 2 : -474.8505 (best) Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.474 0.599 2.019 2.819 rep 2: 4.516 0.599 2.014 2.839 Saving final trees from all search reps to out.p.mkvO.ssr.best.all.tre Saving final tree from best search rep (#2) to out.p.mkvO.ssr.best.tre ####################################################### >>>Search rep 3 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=290145159 Initial ln Likelihood: -605.1903 optimizing: starting branch lengths, subset rates... pass 1:+ 116.111 (branch= 105.75 scale= 0.22 subset rates= 10.14) pass 2:+ 10.329 (branch= 5.57 scale= 0.02 subset rates= 4.75) pass 3:+ 2.693 (branch= 1.07 scale= 0.00 subset rates= 1.62) pass 4:+ 0.940 (branch= 0.38 scale= 0.00 subset rates= 0.56) pass 5:+ 0.206 (branch= 0.17 scale= 0.00 subset rates= 0.04) pass 6:+ 0.019 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -474.8928 gen current_lnL precision last_tree_imp 0 -474.8928 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 : -474.8616 Replicate 2 : -474.8505 (best) Replicate 3 : -474.8835 Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.474 0.599 2.019 2.819 rep 2: 4.516 0.599 2.014 2.839 rep 3: 4.460 0.600 2.011 2.835 Saving final trees from all search reps to out.p.mkvO.ssr.best.all.tre Saving final tree from best search rep (#2) to out.p.mkvO.ssr.best.tre ####################################################### >>>Search rep 4 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=2044747317 Initial ln Likelihood: -652.1691 optimizing: starting branch lengths, subset rates... pass 1:+ 155.944 (branch= 145.32 scale= 0.58 subset rates= 10.04) pass 2:+ 15.207 (branch= 10.68 scale= 0.00 subset rates= 4.52) pass 3:+ 3.710 (branch= 2.16 scale= 0.00 subset rates= 1.55) pass 4:+ 1.983 (branch= 1.40 scale= 0.00 subset rates= 0.58) pass 5:+ 0.364 (branch= 0.33 scale= 0.00 subset rates= 0.03) pass 6:+ 0.111 (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: -474.8511 gen current_lnL precision last_tree_imp 0 -474.8511 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 : -474.8616 Replicate 2 : -474.8505 Replicate 3 : -474.8835 Replicate 4 : -474.8497 (best) Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.474 0.599 2.019 2.819 rep 2: 4.516 0.599 2.014 2.839 rep 3: 4.460 0.600 2.011 2.835 rep 4: 4.504 0.598 2.009 2.857 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: -474.9109 gen current_lnL precision last_tree_imp 0 -474.9109 0.010 0 NOTE: ****Specified generation limit (5) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.60 2.02 2.84 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 4 branches were collapsed. NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 5 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -474.8616 Replicate 2 : -474.8505 Replicate 3 : -474.8835 Replicate 4 : -474.8497 (best) Replicate 5 : -474.9076 Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.474 0.599 2.019 2.819 rep 2: 4.516 0.599 2.014 2.839 rep 3: 4.460 0.600 2.011 2.835 rep 4: 4.504 0.598 2.009 2.857 rep 5: 4.499 0.597 2.020 2.841 Saving final trees from all search reps to out.p.mkvO.ssr.best.all.tre Saving final tree from best search rep (#4) to out.p.mkvO.ssr.best.tre ####################################################### [Reading test.out.p.mkvO.ssr.nex ] Executing Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS storing read block: ASSUMPTIONS storing read block: TREES TREEFILES PASS ************************** Running checkpoint tests ... ************************** Running checkpoint test ./check/a.G3.conf Running checkpoint test ./check/a.G3.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./check/a.G3.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x30.stop.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data Warning: stop codon TAA found at codon site 11 (nuc site 31) in taxon MorNa6. Treating as missing data because ignorestopcodons = 1 is set in configuration file. Some sites treated as missing data for taxon MorNa6 due to ambiguity in translation. Aminoacids coded as missing for that taxon: 11 Warning: stop codon TAA found at codon site 11 (nuc site 31) in taxon ClownNa6. Treating as missing data because ignorestopcodons = 1 is set in configuration file. Some sites treated as missing data for taxon ClownNa6 due to ambiguity in translation. Aminoacids coded as missing for that taxon: 11 WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 11 sequences. 3 constant characters. 6 parsimony-informative characters. 1 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 10 total characters (11 before removing empty columns). 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 2 ####################################################### STARTING RUN Bootstrap reweighting... Subset 1: Random seed for bootstrap reweighting: 42 >>>Bootstrap rep 1 (of 1) <<< MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0165 0.0083 0.0496 0.0909 0.0909 0.0083 0.0744 0.0083 0.0083 0.1074 0.1157 0.0248 0.1240 0.0331 0.0083 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0750 Substitution rate categories under this model: rate proportion 0.0000 0.0750 0.0603 0.3083 0.4894 0.3083 2.4503 0.3083 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.001 lnL Optimizing branchlengths... improved 0.178 lnL 7 8 9 10 11 Initial ln Likelihood: -94.5491 optimizing: starting branch lengths, alpha shape, prop. invar... pass 1:+ 1.029 (branch= 1.03 scale= 0.00 alpha= 0.00 pinv= 0.00) pass 2:+ 0.113 (branch= 0.11 scale= 0.00 alpha= 0.00 pinv= 0.00) lnL after optimization: -93.4068 gen current_lnL precision last_tree_imp 0 -93.4068 0.500 0 100 -93.0240 0.500 0 200 -91.3705 0.500 199 300 -90.7565 0.500 215 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./restart/a.G3.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.11x30.stop.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data Warning: stop codon TAA found at codon site 11 (nuc site 31) in taxon MorNa6. Treating as missing data because ignorestopcodons = 1 is set in configuration file. Some sites treated as missing data for taxon MorNa6 due to ambiguity in translation. Aminoacids coded as missing for that taxon: 11 Warning: stop codon TAA found at codon site 11 (nuc site 31) in taxon ClownNa6. Treating as missing data because ignorestopcodons = 1 is set in configuration file. Some sites treated as missing data for taxon ClownNa6 due to ambiguity in translation. Aminoacids coded as missing for that taxon: 11 WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 11 sequences. 3 constant characters. 6 parsimony-informative characters. 1 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 10 total characters (11 before removing empty columns). 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 2 ####################################################### STARTING RUN Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... Bootstrap rep 1 (of 1) generation 357, seed 802776076, best lnL -90.634 gen current_lnL precision last_tree_imp 357 -90.6343 0.500 215 400 -90.4959 0.500 215 500 -90.3850 0.500 215 600 -90.2906 0.500 215 700 -90.2169 0.500 215 800 -90.1648 0.500 215 Optimization precision reduced Optimizing parameters... improved 0.159 lnL Optimizing branchlengths... improved 0.317 lnL 900 -88.9507 0.010 879 1000 -88.8871 0.010 879 NOTE: ****Specified generation limit (1000) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0165 0.0083 0.0496 0.0909 0.0909 0.0083 0.0744 0.0083 0.0083 0.1074 0.1157 0.0248 0.1240 0.0331 0.0083 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.9045 with an invariant (invariable) site category, proportion estimated 0.1355 Substitution rate categories under this model: rate proportion 0.0000 0.1355 0.1669 0.2882 0.6855 0.2882 2.1476 0.2882 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -88.8871 Parameter estimates: alpha pinv rep 1: 0.904 0.136 Treelengths: TL rep 1: 2.441 Saving best tree to bootstrap file ch.a.G3.boot.tre WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/a.G4.conf Running checkpoint test ./check/a.G4.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./check/a.G4.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.AA.fas as Fasta amino acid format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Amino acid data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 11 sequences. 3 constant characters. 6 parsimony-informative characters. 1 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 10 total characters (11 before removing empty columns). 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.8 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 2 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0165 0.0083 0.0496 0.0909 0.0909 0.0083 0.0744 0.0083 0.0083 0.1074 0.1157 0.0248 0.1240 0.0331 0.0083 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0750 Substitution rate categories under this model: rate proportion 0.0000 0.0750 0.0334 0.2313 0.2519 0.2313 0.8203 0.2313 2.8944 0.2313 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.001 lnL Optimizing branchlengths... improved 0.006 lnL 7 8 9 10 11 Initial ln Likelihood: -117.7431 optimizing: starting branch lengths, alpha shape, prop. invar... pass 1:+ 1.466 (branch= 1.13 scale= 0.33 alpha= 0.00 pinv= 0.00) pass 2:+ 0.134 (branch= 0.13 scale= 0.00 alpha= 0.00 pinv= 0.00) lnL after optimization: -116.1434 gen current_lnL precision last_tree_imp 0 -116.1434 0.500 0 100 -112.9555 0.500 84 200 -112.4964 0.500 84 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./restart/a.G4.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.AA.fas as Fasta amino acid format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Amino acid data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 11 sequences. 3 constant characters. 6 parsimony-informative characters. 1 uninformative variable characters. 1 characters were completely missing or ambiguous (removed). 10 total characters (11 before removing empty columns). 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.8 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 2 ####################################################### STARTING RUN Restarting from checkpoint... generation 219, seed 1338654090, best lnL -112.488 gen current_lnL precision last_tree_imp 219 -112.4878 0.500 84 300 -112.3224 0.500 84 400 -112.1061 0.500 84 500 -111.8129 0.500 84 600 -111.7788 0.500 84 Optimization precision reduced Optimizing parameters... improved 0.386 lnL Optimizing branchlengths... improved 0.390 lnL 700 -110.8142 0.010 615 800 -110.5642 0.010 707 900 -110.5555 0.010 707 1000 -110.5066 0.010 707 NOTE: ****Specified generation limit (1000) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0165 0.0083 0.0496 0.0909 0.0909 0.0083 0.0744 0.0083 0.0083 0.1074 0.1157 0.0248 0.1240 0.0331 0.0083 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 1.3049 with an invariant (invariable) site category, proportion estimated 0.0988 Substitution rate categories under this model: rate proportion 0.0000 0.0988 0.1935 0.2253 0.5525 0.2253 1.0366 0.2253 2.2174 0.2253 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. Saving site likelihoods to file ch.a.G4.sitelikes.log ... WARNING: Site likelihoods being output on prematurely terminated search ... NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -110.5066 Parameter estimates: alpha pinv rep 1: 1.305 0.099 Treelengths: TL rep 1: 2.534 Saving final tree from best search rep (#1) to ch.a.G4.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.G4.internalstates.log WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### TREEFILES PASS Running checkpoint test ./check/a.conf Running checkpoint test ./check/a.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./check/a.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 11 sequences. 3 constant characters. 6 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.2 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 2 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones Equilibrium State Frequencies: empirical (observed) values (+F) (ACDEFGHIKLMNPQRSTVWY) 0.0165 0.0083 0.0496 0.0909 0.0909 0.0083 0.0744 0.0083 0.0083 0.1074 0.1157 0.0248 0.1240 0.0331 0.0083 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 0.121 lnL 7 8 9 10 11 NOTE: Model contains no mutable parameters! Setting model mutation weight to zero. Initial ln Likelihood: -117.7533 optimizing: starting branch lengths... pass 1:+ 0.632 (branch= 0.63 scale= 0.00) pass 2:+ 0.134 (branch= 0.13 scale= 0.00) lnL after optimization: -116.9881 gen current_lnL precision last_tree_imp 0 -116.9881 0.500 0 100 -113.6842 0.500 91 200 -112.5462 0.500 160 300 -112.1250 0.500 160 400 -111.8851 0.500 160 500 -111.7755 0.500 160 600 -111.6975 0.500 563 700 -111.6876 0.500 563 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./restart/a.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Amino acid data WARNING: Not all amino acids were observed in this dataset. One pseudo-count will be added to each amino acid for calculation of the empirical frequencies. You should probably use a statefrequencies setting other than emprical. Summary of data: 11 sequences. 3 constant characters. 6 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.2 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 2 ####################################################### STARTING RUN Restarting from checkpoint... generation 797, seed 887566533, best lnL -111.684 gen current_lnL precision last_tree_imp 797 -111.6844 0.500 563 800 -111.6844 0.500 563 900 -111.6835 0.500 563 1000 -111.6829 0.500 563 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: 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 ... 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 : -111.6829 Parameter estimates: Model contains no estimated parameters Treelengths: TL rep 1: 2.616 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 WARNING: Internal states inferred on tree from prematurely terminated search ####################################################### TREEFILES PASS Running checkpoint test ./check/c.M3x2.conf Running checkpoint test ./check/c.M3x2.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./check/c.M3x2.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Codon data Base usage at codon positions: A C G T pos 1 0.27723 0.36634 0.21782 0.13861 pos 2 0.30693 0.20792 0.07921 0.40594 pos 3 0.10891 0.38614 0.26733 0.23762 all pos 0.23102 0.32013 0.18812 0.26073 Summary of data: 11 sequences. 0 constant characters. 9 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 1.3 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0094 0.0334 0.0231 0.0206 0.0064 0.0226 0.0157 0.0139 0.0024 0.0086 0.0060 0.0053 0.0125 0.0442 0.0306 0.0272 0.0125 0.0442 0.0306 0.0272 0.0084 0.0299 0.0207 0.0184 0.0032 0.0114 0.0079 0.0070 0.0165 0.0584 0.0405 0.0360 0.0074 0.0263 0.0182 0.0162 0.0050 0.0178 0.0123 0.0110 0.0019 0.0068 0.0047 0.0042 0.0098 0.0347 0.0241 0.0214 0.0167 0.0103 0.0032 0.0113 0.0078 0.0070 0.0043 0.0030 0.0027 0.0062 0.0221 0.0153 0.0136 Rate Heterogeneity Model: 2 nonsynonymous rate categories, rate and proportion of each estimated (this is effectively the M3 model of PAML) dN/dS Proportion 0.2500 0.5000 0.5000 0.5000 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 4.461 lnL Optimizing branchlengths... improved 0.701 lnL 7 8 9 10 11 Initial ln Likelihood: -215.8071 optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters... pass 1:+ 6.388 (branch= 0.00 scale= 0.44 omega= 0.01 rel rates= 5.93) pass 2:+ 0.434 (branch= 0.00 scale= 0.00 omega= 0.01 rel rates= 0.42) lnL after optimization: -208.9856 gen current_lnL precision last_tree_imp 0 -208.9856 0.500 0 10 -207.1401 0.500 10 20 -205.6892 0.500 18 NOTE: ****Specified time limit (10 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./restart/c.M3x2.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Codon data Base usage at codon positions: A C G T pos 1 0.27723 0.36634 0.21782 0.13861 pos 2 0.30693 0.20792 0.07921 0.40594 pos 3 0.10891 0.38614 0.26733 0.23762 all pos 0.23102 0.32013 0.18812 0.26073 Summary of data: 11 sequences. 0 constant characters. 9 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 1.3 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN Restarting from checkpoint... generation 21, seed 950885006, best lnL -205.650 gen current_lnL precision last_tree_imp 21 -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 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./check/c.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Codon data Base usage at codon positions: A C G T pos 1 0.27723 0.36634 0.21782 0.13861 pos 2 0.30693 0.20792 0.07921 0.40594 pos 3 0.10891 0.38614 0.26733 0.23762 all pos 0.23102 0.32013 0.18812 0.26073 Summary of data: 11 sequences. 0 constant characters. 9 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 2 ####################################################### STARTING RUN Bootstrap reweighting... Subset 1: Random seed for bootstrap reweighting: 42 >>>Bootstrap rep 1 (of 1) <<< MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 61 (codon data, standard code) One estimated dN/dS ratio (aka omega) = 0.250000 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0094 0.0334 0.0231 0.0206 0.0064 0.0226 0.0157 0.0139 0.0024 0.0086 0.0060 0.0053 0.0125 0.0442 0.0306 0.0272 0.0125 0.0442 0.0306 0.0272 0.0084 0.0299 0.0207 0.0184 0.0032 0.0114 0.0079 0.0070 0.0165 0.0584 0.0405 0.0360 0.0074 0.0263 0.0182 0.0162 0.0050 0.0178 0.0123 0.0110 0.0019 0.0068 0.0047 0.0042 0.0098 0.0347 0.0241 0.0214 0.0167 0.0103 0.0032 0.0113 0.0078 0.0070 0.0043 0.0030 0.0027 0.0062 0.0221 0.0153 0.0136 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.353 lnL Optimizing branchlengths... improved 0.746 lnL 7 8 9 10 11 Initial ln Likelihood: -208.5106 optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters... pass 1:+ 10.487 (branch= 0.90 scale= 0.55 omega= 0.01 rel rates= 9.03) pass 2:+ 2.529 (branch= 2.19 scale= 0.00 omega= 0.00 rel rates= 0.34) pass 3:+ 0.095 (branch= 0.02 scale= 0.00 omega= 0.00 rel rates= 0.07) lnL after optimization: -195.3999 gen current_lnL precision last_tree_imp 0 -195.3999 0.500 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./restart/c.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Codon data Base usage at codon positions: A C G T pos 1 0.27723 0.36634 0.21782 0.13861 pos 2 0.30693 0.20792 0.07921 0.40594 pos 3 0.10891 0.38614 0.26733 0.23762 all pos 0.23102 0.32013 0.18812 0.26073 Summary of data: 11 sequences. 0 constant characters. 9 parsimony-informative characters. 1 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 2 ####################################################### STARTING RUN Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... Bootstrap rep 1 (of 1) generation 6, seed 897054849, best lnL -195.400 gen current_lnL precision last_tree_imp 6 -195.3999 0.500 0 10 -195.3553 0.500 0 20 -195.3340 0.500 0 30 -195.2776 0.500 0 40 -195.2554 0.500 0 50 -195.2137 0.500 0 60 -195.1629 0.500 0 70 -195.0042 0.500 0 80 -194.9478 0.500 0 90 -194.9092 0.500 0 100 -194.9092 0.500 0 NOTE: ****Specified generation limit (100) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 61 (codon data, standard code) One estimated dN/dS ratio (aka omega) = 0.120507 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates AC = 1.637, AG = 5.680, AT = 0.011, CG = 4.174, CT = 2.324, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) 0.0094 0.0334 0.0231 0.0206 0.0064 0.0226 0.0157 0.0139 0.0024 0.0086 0.0060 0.0053 0.0125 0.0442 0.0306 0.0272 0.0125 0.0442 0.0306 0.0272 0.0084 0.0299 0.0207 0.0184 0.0032 0.0114 0.0079 0.0070 0.0165 0.0584 0.0405 0.0360 0.0074 0.0263 0.0182 0.0162 0.0050 0.0178 0.0123 0.0110 0.0019 0.0068 0.0047 0.0042 0.0098 0.0347 0.0241 0.0214 0.0167 0.0103 0.0032 0.0113 0.0078 0.0070 0.0043 0.0030 0.0027 0.0062 0.0221 0.0153 0.0136 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -194.9092 Parameter estimates: w(0) p(0) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) rep 1: 0.121 1.000 1.637 5.68 0.01146 4.174 2.324 1 Treelengths: TL rep 1: 9.255 Saving best tree to bootstrap file ch.c.boot.tre WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/g.dnaBnoZ.conf Running checkpoint test ./check/g.dnaBnoZ.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./check/g.dnaBnoZ.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/dnaGap.8x1K.nex ... Reading TAXA block...storing read block: TAXA successful Reading CHARACTERS block...storing read block: CHARACTERS found dna data... successful Reading CHARACTERS block...storing read block: CHARACTERS found standard data... successful Reading TREES block...storing read block: TREES successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1GapsAsMissing") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 8 sequences. 428 constant characters. 129 parsimony-informative characters. 100 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 239 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #2 ("Untitled DATA Block 1GapsAsBinary") Data read as Binary data, no constant state 0 chars, modeled as Binary data, no constant state 0 chars NOTE: entirely missing characters removed from matrix: 1 25 29-34 36 37 52-54 61 67-69 84 85 87 95 96 99 106 110-116 125 138-145 163-165 167 169-177 188 197-199 202-210 213 216-218 228-231 233-236 238-240 247 249 256 257 260 266-270 \ 2 271-277 281-285 290-294 298-300 311 312 322 325 331 332 336-338 344 359 369 373-378 397 404-406 413 416 417 420-426 439-442 450-454 \ 2 455-460 462 471 474-479 487-490 492 494 495 497 502-506 510 521-526 532 533 538-541 544 547 551-553 562 570-572 577 579 609 610 614 615 622 624-626 639 640 647-650 653 655-660 667 668 673-676 679 680 685 695 696 701-705 708-713 716 717 731 742-749 751-755 762 763 770 771 783 788 791-793 804 806-808 813 821-825 827 830-832 840 842 843 845 850 851 856-865 886-894 896 897 903-905 913 914 924 927 948-956 963-971 976-981 991-993 996 Subset of data with 2 states: chars 1-1000 Summary of data: 8 sequences. 502 constant characters. 39 parsimony-informative characters. 116 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 24 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 2 MB good approx 2 MB to 2 MB low approx 2 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 2.8 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN >>>Search rep 1 (of 2)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3220 0.2180 0.1602 0.2999 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.1629 Substitution rate categories under this model: rate proportion 0.0000 0.1629 0.0334 0.2093 0.2519 0.2093 0.8203 0.2093 2.8944 0.2093 Model 2 Number of states = 2 (binary data) Character change matrix: Binary, no all-zero columns (2-state symmetric one rate model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -4043.7391 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates... pass 1:+ 532.047 (branch= 438.84 scale= 6.77 alpha= 15.79 freqs= 3.30 rel rates= 8.48 pinv= 0.00 subset rates= 58.86) pass 2:+ 88.209 (branch= 42.39 scale= 0.83 alpha= 0.82 freqs= 0.72 rel rates= 0.01 pinv= 0.00 subset rates= 43.45) pass 3:+ 34.899 (branch= 0.70 scale= 2.02 alpha= 1.89 freqs= 0.04 rel rates= 0.72 pinv= 0.00 subset rates= 29.52) pass 4:+ 17.437 (branch= 4.66 scale= 2.38 alpha= 1.70 freqs= 0.05 rel rates= 0.01 pinv= 0.00 subset rates= 8.64) pass 5:+ 10.201 (branch= 4.19 scale= 1.64 alpha= 0.69 freqs= 0.05 rel rates= 2.14 pinv= 0.00 subset rates= 1.49) pass 6:+ 1.986 (branch= 0.00 scale= 1.92 alpha= 0.00 freqs= 0.06 rel rates= 0.01 pinv= 0.00 subset rates= 0.00) pass 7:+ 0.532 (branch= 0.47 scale= 0.00 alpha= 0.00 freqs= 0.06 rel rates= 0.01 pinv= 0.00 subset rates= 0.00) pass 8:+ 0.057 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.05 rel rates= 0.01 pinv= 0.00 subset rates= 0.00) lnL after optimization: -3358.3708 gen current_lnL precision last_tree_imp 0 -3358.3708 0.500 0 100 -3357.1202 0.500 0 200 -3356.8081 0.500 0 300 -3356.5910 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 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./restart/g.dnaBnoZ.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/dnaGap.8x1K.nex ... Reading TAXA block...storing read block: TAXA successful Reading CHARACTERS block...storing read block: CHARACTERS found dna data... successful Reading CHARACTERS block...storing read block: CHARACTERS found standard data... successful Reading TREES block...storing read block: TREES successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1GapsAsMissing") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 8 sequences. 428 constant characters. 129 parsimony-informative characters. 100 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 239 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #2 ("Untitled DATA Block 1GapsAsBinary") Data read as Binary data, no constant state 0 chars, modeled as Binary data, no constant state 0 chars NOTE: entirely missing characters removed from matrix: 1 25 29-34 36 37 52-54 61 67-69 84 85 87 95 96 99 106 110-116 125 138-145 163-165 167 169-177 188 197-199 202-210 213 216-218 228-231 233-236 238-240 247 249 256 257 260 266-270 \ 2 271-277 281-285 290-294 298-300 311 312 322 325 331 332 336-338 344 359 369 373-378 397 404-406 413 416 417 420-426 439-442 450-454 \ 2 455-460 462 471 474-479 487-490 492 494 495 497 502-506 510 521-526 532 533 538-541 544 547 551-553 562 570-572 577 579 609 610 614 615 622 624-626 639 640 647-650 653 655-660 667 668 673-676 679 680 685 695 696 701-705 708-713 716 717 731 742-749 751-755 762 763 770 771 783 788 791-793 804 806-808 813 821-825 827 830-832 840 842 843 845 850 851 856-865 886-894 896 897 903-905 913 914 924 927 948-956 963-971 976-981 991-993 996 Subset of data with 2 states: chars 1-1000 Summary of data: 8 sequences. 502 constant characters. 39 parsimony-informative characters. 116 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 24 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 2 MB good approx 2 MB to 2 MB low approx 2 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 2.8 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN Restarting from checkpoint... Search rep 1 (of 2) generation 654, seed 362564633, best lnL -3354.418 gen current_lnL precision last_tree_imp 654 -3354.4176 0.255 0 700 -3354.3974 0.255 0 800 -3354.0880 0.255 0 900 -3353.8939 0.255 0 1000 -3353.6942 0.255 0 Optimization precision reduced Optimizing parameters... improved 0.831 lnL Optimizing branchlengths... improved 0.084 lnL 1100 -3352.7241 0.010 0 1200 -3352.6772 0.010 0 1300 -3352.5555 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... Current score = -3352.5544 Performing final optimizations... pass 1 : -3352.1856 (branch= 0.0078 alpha= 0.0000 pinv= 0.0100 eq freqs= 0.0148 rel rates= 0.3138 subset rates= 0.0223) pass 2 : -3351.8766 (branch= 0.0307 alpha= 0.0159 pinv= 0.0186 eq freqs= 0.0118 rel rates= 0.2279 subset rates= 0.0041) pass 3 : -3351.6298 (branch= 0.0178 alpha= 0.0139 pinv= 0.0172 eq freqs= 0.0022 rel rates= 0.1914 subset rates= 0.0044) pass 4 : -3351.4195 (branch= 0.0196 alpha= 0.0140 pinv= 0.0164 eq freqs= 0.0007 rel rates= 0.1554 subset rates= 0.0041) pass 5 : -3351.2433 (branch= 0.0139 alpha= 0.0127 pinv= 0.0158 eq freqs= 0.0011 rel rates= 0.1285 subset rates= 0.0041) pass 6 : -3351.0988 (branch= 0.0092 alpha= 0.0115 pinv= 0.0148 eq freqs= 0.0008 rel rates= 0.1061 subset rates= 0.0022) pass 7 : -3350.9729 (branch= 0.0049 alpha= 0.0119 pinv= 0.0136 eq freqs= 0.0004 rel rates= 0.0936 subset rates= 0.0014) pass 8 : -3350.8693 (branch= 0.0036 alpha= 0.0113 pinv= 0.0126 eq freqs= 0.0004 rel rates= 0.0758 subset rates= 0.0000) pass 9 : -3350.7778 (branch= 0.0006 alpha= 0.0107 pinv= 0.0114 eq freqs= 0.0002 rel rates= 0.0668 subset rates= 0.0017) pass 10: -3350.7004 (branch= 0.0017 alpha= 0.0107 pinv= 0.0111 eq freqs= 0.0002 rel rates= 0.0537 subset rates= 0.0000) pass 11: -3350.6336 (branch= 0.0003 alpha= 0.0097 pinv= 0.0100 eq freqs= 0.0001 rel rates= 0.0456 subset rates= 0.0012) pass 12: -3350.5783 (branch= 0.0009 alpha= 0.0088 pinv= 0.0085 eq freqs= 0.0001 rel rates= 0.0369 subset rates= 0.0000) pass 13: -3350.5311 (branch= 0.0001 alpha= 0.0080 pinv= 0.0077 eq freqs= 0.0001 rel rates= 0.0314 subset rates= 0.0000) pass 14: -3350.4905 (branch= 0.0000 alpha= 0.0076 pinv= 0.0069 eq freqs= 0.0001 rel rates= 0.0259 subset rates= 0.0000) pass 15: -3350.4557 (branch= 0.0000 alpha= 0.0069 pinv= 0.0062 eq freqs= 0.0001 rel rates= 0.0217 subset rates= 0.0000) pass 16: -3350.4255 (branch= 0.0000 alpha= 0.0062 pinv= 0.0055 eq freqs= 0.0000 rel rates= 0.0184 subset rates= 0.0000) pass 17: -3350.3995 (branch= 0.0000 alpha= 0.0055 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0155 subset rates= 0.0000) pass 18: -3350.3770 (branch= 0.0000 alpha= 0.0049 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0132 subset rates= 0.0000) pass 19: -3350.3576 (branch= 0.0000 alpha= 0.0043 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0112 subset rates= 0.0000) pass 20: -3350.3408 (branch= 0.0000 alpha= 0.0038 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0095 subset rates= 0.0000) optimization up to ... pass 30: -3350.2582 (branch= 0.0000 alpha= 0.0196 pinv= 0.0178 eq freqs= 0.0001 rel rates= 0.0450 subset rates= 0.0000) optimization up to ... pass 40: -3350.2392 (branch= 0.0000 alpha= 0.0044 pinv= 0.0041 eq freqs= 0.0000 rel rates= 0.0104 subset rates= 0.0000) optimization up to ... pass 50: -3350.2350 (branch= 0.0000 alpha= 0.0008 pinv= 0.0008 eq freqs= 0.0000 rel rates= 0.0026 subset rates= 0.0000) optimization up to ... pass 60: -3350.2340 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0007 subset rates= 0.0000) optimization up to ... pass 68: -3350.2338 (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 = -3350.2338 Time used so far = 0 hours, 0 minutes and 14 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 3.107, AG = 10.379, AT = 2.679, CG = 0.001, CT = 21.805, 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 0.5790 with an invariant (invariable) site category, proportion estimated 0.3660 Substitution rate categories under this model: rate proportion 0.0000 0.3660 0.0488 0.1585 0.3004 0.1585 0.8702 0.1585 2.7806 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 : -3350.2338 (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: 3.107 10.38 2.679 0.001 21.81 1 0.333 0.222 0.157 0.288 0.579 0.366 Partition model subset 2: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) rep 1: 0.787 1.820 0.180 Saving final tree from best search rep (#1) to ch.g.dnaBnoZ.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/g.dnaMix.conf Running checkpoint test ./check/g.dnaMix.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./check/g.dnaMix.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/dnaGap.8x1K.nex ... Reading TAXA block...storing read block: TAXA successful Reading CHARACTERS block...storing read block: CHARACTERS found dna data... successful Reading CHARACTERS block...storing read block: CHARACTERS found standard data... successful Reading TREES block...storing read block: TREES successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1GapsAsMissing") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 8 sequences. 428 constant characters. 129 parsimony-informative characters. 100 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 239 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #2 ("Untitled DATA Block 1GapsAsBinary") Data read as Gap-coded data, oriented with respect to time, modeled as Gap-coded data, oriented with respect to time Summary of data: 8 sequences. 502 constant characters. 39 parsimony-informative characters. 116 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 24 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 2 MB good approx 2 MB to 2 MB low approx 2 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 3.2 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### WARNING - specified outgroup (1) being ignored due to inference of a rooted true ####################################################### STARTING RUN >>>Search rep 1 (of 2)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3220 0.2180 0.1602 0.2999 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.1629 Substitution rate categories under this model: rate proportion 0.0000 0.1629 0.0334 0.2093 0.2519 0.2093 0.8203 0.2093 2.8944 0.2093 Model 2 Number of states = 2 (0/1 coding of gaps) Character change matrix: irreversible matrix deletion rate parameter only estimated if using a partitioned model without subset rates deletion rate = 1.000 Equilibrium State Frequencies: proportion of inserted sites parameter insert proportion = 0.500 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 Initial ln Likelihood: -4257.0961 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, ins rate, del rate... pass 1:+ 640.405 (branch= 431.06 scale= 2.03 alpha= 9.92 freqs= 3.07 rel rates= 7.29 pinv= 0.00 ins/del=187.03) pass 2:+ 169.102 (branch= 75.12 scale= 1.32 alpha= 0.88 freqs= 0.65 rel rates= 0.01 pinv= 0.00 ins/del= 91.12) pass 3:+ 55.144 (branch= 7.14 scale= 1.85 alpha= 1.09 freqs= 0.05 rel rates= 0.90 pinv= 0.00 ins/del= 44.12) pass 4:+ 25.231 (branch= 7.02 scale= 1.52 alpha= 0.69 freqs= 0.06 rel rates= 0.01 pinv= 0.00 ins/del= 15.94) pass 5:+ 14.361 (branch= 7.97 scale= 1.87 alpha= 0.01 freqs= 0.05 rel rates= 2.45 pinv= 0.00 ins/del= 2.01) pass 6:+ 10.438 (branch= 7.36 scale= 2.34 alpha= 0.01 freqs= 0.07 rel rates= 0.00 pinv= 0.00 ins/del= 0.66) pass 7:+ 6.158 (branch= 5.23 scale= 0.83 alpha= 0.01 freqs= 0.06 rel rates= 0.00 pinv= 0.00 ins/del= 0.03) pass 8:+ 3.640 (branch= 2.31 scale= 0.00 alpha= 0.00 freqs= 0.05 rel rates= 0.60 pinv= 0.00 ins/del= 0.67) pass 9:+ 0.148 (branch= 0.08 scale= 0.00 alpha= 0.00 freqs= 0.06 rel rates= 0.00 pinv= 0.00 ins/del= 0.00) lnL after optimization: -3332.4700 gen current_lnL precision last_tree_imp 0 -3332.4700 0.500 0 100 -3324.9856 0.500 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./restart/g.dnaMix.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/dnaGap.8x1K.nex ... Reading TAXA block...storing read block: TAXA successful Reading CHARACTERS block...storing read block: CHARACTERS found dna data... successful Reading CHARACTERS block...storing read block: CHARACTERS found standard data... successful Reading TREES block...storing read block: TREES successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1GapsAsMissing") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 8 sequences. 428 constant characters. 129 parsimony-informative characters. 100 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 239 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #2 ("Untitled DATA Block 1GapsAsBinary") Data read as Gap-coded data, oriented with respect to time, modeled as Gap-coded data, oriented with respect to time Summary of data: 8 sequences. 502 constant characters. 39 parsimony-informative characters. 116 uninformative variable characters. 343 characters were completely missing or ambiguous (removed). 657 total characters (1000 before removing empty columns). 24 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 2 MB good approx 2 MB to 2 MB low approx 2 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 3.2 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### WARNING - specified outgroup (1) being ignored due to inference of a rooted true ####################################################### STARTING RUN Restarting from checkpoint... Search rep 1 (of 2) generation 152, seed 1087693397, best lnL -3324.837 gen current_lnL precision last_tree_imp 152 -3324.8374 0.500 1 200 -3324.7543 0.500 1 300 -3324.3007 0.500 1 NOTE: ****Specified time limit (5 seconds) reached... Current score = -3324.0406 Performing final optimizations... pass 1 : -3321.5103 (branch= 0.3894 alpha= 0.0227 pinv= 0.0147 eq freqs= 0.0550 rel rates= 0.7183 ins/del rates= 1.3302) pass 2 : -3320.5615 (branch= 0.2916 alpha= 0.0000 pinv= 0.0324 eq freqs= 0.0340 rel rates= 0.5564 ins/del rates= 0.0344) pass 3 : -3320.0064 (branch= 0.0851 alpha= 0.0070 pinv= 0.0162 eq freqs= 0.0091 rel rates= 0.4150 ins/del rates= 0.0227) pass 4 : -3319.5848 (branch= 0.0378 alpha= 0.0101 pinv= 0.0153 eq freqs= 0.0036 rel rates= 0.3418 ins/del rates= 0.0131) pass 5 : -3319.2611 (branch= 0.0238 alpha= 0.0099 pinv= 0.0149 eq freqs= 0.0012 rel rates= 0.2641 ins/del rates= 0.0098) pass 6 : -3319.0086 (branch= 0.0148 alpha= 0.0102 pinv= 0.0141 eq freqs= 0.0009 rel rates= 0.2064 ins/del rates= 0.0061) pass 7 : -3318.8082 (branch= 0.0095 alpha= 0.0105 pinv= 0.0133 eq freqs= 0.0007 rel rates= 0.1623 ins/del rates= 0.0041) pass 8 : -3318.6444 (branch= 0.0060 alpha= 0.0104 pinv= 0.0124 eq freqs= 0.0005 rel rates= 0.1319 ins/del rates= 0.0026) pass 9 : -3318.5117 (branch= 0.0037 alpha= 0.0104 pinv= 0.0115 eq freqs= 0.0004 rel rates= 0.1050 ins/del rates= 0.0016) pass 10: -3318.4012 (branch= 0.0026 alpha= 0.0096 pinv= 0.0113 eq freqs= 0.0003 rel rates= 0.0856 ins/del rates= 0.0011) pass 11: -3318.3095 (branch= 0.0018 alpha= 0.0092 pinv= 0.0103 eq freqs= 0.0002 rel rates= 0.0695 ins/del rates= 0.0008) pass 12: -3318.2347 (branch= 0.0012 alpha= 0.0086 pinv= 0.0089 eq freqs= 0.0002 rel rates= 0.0555 ins/del rates= 0.0005) pass 13: -3318.1714 (branch= 0.0008 alpha= 0.0079 pinv= 0.0081 eq freqs= 0.0001 rel rates= 0.0460 ins/del rates= 0.0003) pass 14: -3318.1178 (branch= 0.0005 alpha= 0.0074 pinv= 0.0073 eq freqs= 0.0001 rel rates= 0.0381 ins/del rates= 0.0002) pass 15: -3318.0719 (branch= 0.0003 alpha= 0.0068 pinv= 0.0066 eq freqs= 0.0001 rel rates= 0.0318 ins/del rates= 0.0001) pass 16: -3318.0333 (branch= 0.0002 alpha= 0.0063 pinv= 0.0060 eq freqs= 0.0001 rel rates= 0.0259 ins/del rates= 0.0001) pass 17: -3318.0003 (branch= 0.0001 alpha= 0.0057 pinv= 0.0054 eq freqs= 0.0001 rel rates= 0.0217 ins/del rates= 0.0000) pass 18: -3317.9716 (branch= 0.0001 alpha= 0.0051 pinv= 0.0048 eq freqs= 0.0001 rel rates= 0.0186 ins/del rates= 0.0000) pass 19: -3317.9470 (branch= 0.0001 alpha= 0.0046 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0157 ins/del rates= 0.0000) pass 20: -3317.9255 (branch= 0.0000 alpha= 0.0041 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0135 ins/del rates= 0.0000) optimization up to ... pass 30: -3317.8195 (branch= 0.0001 alpha= 0.0222 pinv= 0.0205 eq freqs= 0.0001 rel rates= 0.0630 ins/del rates= 0.0000) optimization up to ... pass 40: -3317.7944 (branch= 0.0001 alpha= 0.0055 pinv= 0.0051 eq freqs= 0.0000 rel rates= 0.0143 ins/del rates= 0.0000) optimization up to ... pass 50: -3317.7887 (branch= 0.0000 alpha= 0.0012 pinv= 0.0011 eq freqs= 0.0000 rel rates= 0.0034 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= 0.0009 ins/del rates= 0.0000) optimization up to ... pass 70: -3317.7871 (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 73: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3317.7871 Time used so far = 0 hours, 0 minutes and 15 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 3.065, AG = 10.258, AT = 2.653, CG = 0.001, CT = 21.526, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3328 0.2223 0.1566 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5748 with an invariant (invariable) site category, proportion estimated 0.3613 Substitution rate categories under this model: rate proportion 0.0000 0.3613 0.0480 0.1597 0.2980 0.1597 0.8679 0.1597 2.7862 0.1597 Model 2 Number of states = 2 (0/1 coding of gaps) Character change matrix: irreversible matrix deletion rate parameter only estimated if using a partitioned model without subset rates deletion rate = 0.158 Equilibrium State Frequencies: proportion of inserted sites parameter insert proportion = 0.036 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. >>>Terminated Search rep 1 (of 2)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 2). Results: Replicate 1 : -3317.7871 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 3.065 10.26 2.653 0.001 21.53 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del rep 1: 0.036 0.158 **ins = proportion of columns that experienced an insertion **del = deletion rate relative to nucleotide substitution rate Treelengths: TL rep 1: 1.419 Saving final tree from best search rep (#1) to ch.g.dnaMix.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/n.G3.conf Running checkpoint test ./check/n.G3.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./check/n.G3.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.3 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0603 0.3028 0.4894 0.3028 2.4503 0.3028 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.004 lnL Optimizing branchlengths... improved 0.000 lnL 7 8 9 10 11 Initial ln Likelihood: -226.8217 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 3.951 (branch= 0.75 scale= 0.00 alpha= 0.00 freqs= 1.76 rel rates= 1.44 pinv= 0.00) pass 2:+ 0.586 (branch= 0.56 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.00) pass 3:+ 1.297 (branch= 0.66 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.61 pinv= 0.00) pass 4:+ 0.021 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.02 rel rates= 0.00 pinv= 0.00) lnL after optimization: -220.9660 gen current_lnL precision last_tree_imp 0 -220.9660 0.500 0 200 -214.6292 0.500 192 400 -213.8826 0.500 231 600 -213.2669 0.500 572 800 -213.0149 0.500 572 1000 -212.8168 0.500 572 Optimization precision reduced Optimizing parameters... improved 1.264 lnL Optimizing branchlengths... improved 0.275 lnL 1200 -211.1652 0.010 1104 1400 -211.1318 0.010 1104 1600 -211.0218 0.010 1104 1800 -210.9997 0.010 1104 2000 -210.9460 0.010 1104 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./restart/n.G3.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.3 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN Restarting from checkpoint... generation 2176, seed 1442498373, best lnL -210.918 gen current_lnL precision last_tree_imp 2176 -210.9177 0.010 1104 2200 -210.8946 0.010 1104 2300 -210.8921 0.010 1104 2400 -210.8864 0.010 1104 2500 -210.8674 0.010 1104 2600 -210.8436 0.010 1104 2700 -210.8339 0.010 1104 2800 -210.8249 0.010 1104 2900 -210.8228 0.010 1104 3000 -210.8188 0.010 1104 3100 -210.8049 0.010 1104 3200 -210.7905 0.010 1104 Reached termination condition! last topological improvement at gen 1104 Improvement over last 500 gen = 0.04342 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 2.253, AG = 4.315, AT = 0.229, CG = 3.799, CT = 6.515, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2299 0.3376 0.2132 0.2194 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated 1.1008 with an invariant (invariable) site category, proportion estimated 0.1053 Substitution rate categories under this model: rate proportion 0.0000 0.1053 0.2110 0.2982 0.7362 0.2982 2.0528 0.2982 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. Saving site likelihoods to file ch.n.G3.sitelikes.log ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -210.7905 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: 2.253 4.315 0.2288 3.799 6.515 1 0.230 0.338 0.213 0.219 1.101 0.105 Treelengths: TL rep 1: 2.237 Saving final tree from best search rep (#1) to ch.n.G3.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.G3.internalstates.log ####################################################### TREEFILES PASS Running checkpoint test ./check/n.G4.conf Running checkpoint test ./check/n.G4.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./check/n.G4.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN Bootstrap reweighting... Subset 1: Random seed for bootstrap reweighting: 42 >>>Bootstrap rep 1 (of 1) <<< MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0334 0.2271 0.2519 0.2271 0.8203 0.2271 2.8944 0.2271 Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.004 lnL Optimizing branchlengths... improved 0.786 lnL 7 8 9 10 11 Initial ln Likelihood: -178.2162 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 5.336 (branch= 0.56 scale= 1.69 alpha= 0.00 freqs= 1.38 rel rates= 1.70 pinv= 0.00) pass 2:+ 0.075 (branch= 0.04 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.00) lnL after optimization: -172.8046 gen current_lnL precision last_tree_imp 0 -172.8046 0.500 0 200 -171.4789 0.500 172 400 -170.7806 0.500 296 600 -170.2707 0.500 296 800 -169.9099 0.500 296 Optimization precision reduced Optimizing parameters... improved 2.192 lnL Optimizing branchlengths... improved 0.320 lnL 1000 -167.2067 0.010 843 1200 -167.1474 0.010 843 1400 -167.0485 0.010 843 1600 -166.9639 0.010 843 1800 -166.8221 0.010 843 2000 -166.6786 0.010 843 2200 -166.5885 0.010 843 2400 -166.4577 0.010 843 2600 -166.3860 0.010 843 2800 -166.3655 0.010 843 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./restart/n.G4.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... Bootstrap rep 1 (of 1) generation 2976, seed 1061359276, best lnL -166.317 gen current_lnL precision last_tree_imp 2976 -166.3171 0.010 843 3000 -166.3068 0.010 843 3100 -166.2828 0.010 843 3200 -166.2785 0.010 843 3300 -166.2761 0.010 843 3400 -166.2097 0.010 843 3500 -166.0930 0.010 843 3600 -166.0616 0.010 843 3700 -166.0202 0.010 843 3800 -165.9519 0.010 843 3900 -165.9403 0.010 843 4000 -165.9338 0.010 843 4100 -165.9076 0.010 843 4200 -165.8874 0.010 843 4300 -165.8810 0.010 843 4400 -165.8798 0.010 843 4500 -165.8543 0.010 843 4600 -165.7807 0.010 843 4700 -165.7797 0.010 843 4800 -165.7680 0.010 843 4900 -165.6825 0.010 843 5000 -165.6805 0.010 843 5100 -165.6630 0.010 843 5200 -165.6627 0.010 843 5300 -165.6247 0.010 843 5400 -165.5964 0.010 843 5500 -165.5254 0.010 843 5600 -165.4765 0.010 843 5700 -165.4332 0.010 843 5800 -165.3752 0.010 843 NOTE: ****Specified time limit (5 seconds) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 0.610, AG = 7.488, AT = 1.180, CG = 2.828, CT = 13.765, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1302 0.4096 0.2306 0.2295 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 2.2066 with an invariant (invariable) site category, proportion estimated 0.2588 Substitution rate categories under this model: rate proportion 0.0000 0.2588 0.3167 0.1853 0.6753 0.1853 1.0744 0.1853 1.9335 0.1853 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 2 branches were collapsed. >>>Terminated Bootstrap rep 1 (of 1) <<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -165.3700 (TERMINATED PREMATURELY) Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 0.6103 7.488 1.18 2.828 13.76 1 0.130 0.410 0.231 0.229 2.207 0.259 Treelengths: TL rep 1: 2.197 Saving best tree to bootstrap file ch.n.G4.boot.tre WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/n.conf Running checkpoint test ./check/n.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./check/n.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.1 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: no rate heterogeneity Starting with seed=1 creating likelihood stepwise addition starting tree... number of taxa added: 4 5 6 Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 3.458 lnL 7 8 9 10 11 Initial ln Likelihood: -225.5327 optimizing: starting branch lengths, rel rates, eq freqs... pass 1:+ 7.466 (branch= 0.77 scale= 0.00 freqs= 0.02 rel rates= 6.68) pass 2:+ 0.468 (branch= 0.45 scale= 0.00 freqs= 0.02 rel rates= 0.00) lnL after optimization: -217.5990 gen current_lnL precision last_tree_imp 0 -217.5990 0.500 0 200 -215.8307 0.500 188 400 -214.8938 0.500 276 600 -214.3966 0.500 530 800 -214.1704 0.500 530 1000 -214.0528 0.500 530 Optimization precision reduced Optimizing parameters... improved 0.223 lnL Optimizing branchlengths... improved 0.080 lnL 1200 -213.6189 0.010 530 1400 -213.5798 0.010 530 1600 -213.5574 0.010 530 1800 -213.3950 0.010 530 2000 -213.3636 0.010 530 2200 -213.3210 0.010 530 2400 -213.2330 0.010 530 2600 -213.2163 0.010 530 2800 -213.2053 0.010 530 3000 -213.1864 0.010 530 3200 -213.1790 0.010 530 3400 -213.1579 0.010 530 3600 -213.1518 0.010 530 3800 -212.9970 0.010 530 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./restart/n.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.1 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### STARTING RUN Restarting from checkpoint... generation 3859, seed 280993830, best lnL -212.996 gen current_lnL precision last_tree_imp 3859 -212.9959 0.010 530 3900 -212.9717 0.010 530 4000 -212.9591 0.010 530 4100 -212.9590 0.010 530 4200 -212.9296 0.010 530 4300 -212.9108 0.010 530 4400 -212.9046 0.010 530 4500 -212.8562 0.010 530 4600 -212.8454 0.010 530 4700 -212.8360 0.010 530 4800 -212.8357 0.010 530 4900 -212.8350 0.010 530 5000 -212.8350 0.010 530 Reached termination condition! last topological improvement at gen 530 Improvement over last 500 gen = 0.02114 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 4.195, AG = 8.259, AT = 0.325, CG = 8.113, CT = 5.263, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2223 0.2935 0.1809 0.3033 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 : -212.8350 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) rep 1: 4.195 8.259 0.3247 8.113 5.263 1 0.222 0.294 0.181 0.303 Treelengths: TL rep 1: 1.732 Saving final tree from best search rep (#1) to ch.n.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log ####################################################### TREEFILES PASS Running checkpoint test ./check/n.const.conf Running checkpoint test ./check/n.const.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./check/n.const.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### Loading constraints from file data/z.pos.const.tre Found 6 positively constrained bipartition(s) Bipartition 1: (1,2,3,5,6,7,8,9,10) | (4,11) Bipartition 2: (1,3,5,6,7,8,9,10) | (2,4,11) Bipartition 3: (1,5,6,7,8,9,10) | (2,3,4,11) Bipartition 4: (1,2,3,4,5,8,9,10,11) | (6,7) Bipartition 5: (1,2,3,4,5,8,9,11) | (6,7,10) Bipartition 6: (1,5) | (2,3,4,6,7,8,9,10,11) STARTING RUN MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2310 0.3201 0.1881 0.2607 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0917 Substitution rate categories under this model: rate proportion 0.0000 0.0917 0.0334 0.2271 0.2519 0.2271 0.8203 0.2271 2.8944 0.2271 Starting with seed=1 creating likelihood stepwise addition starting tree (compatible with constraints)... number of taxa added: 4 5 6 Optimizing parameters... improved 0.006 lnL Optimizing branchlengths... improved 11.173 lnL 7 8 9 10 11 Initial ln Likelihood: -225.0726 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs... pass 1:+ 5.893 (branch= 2.29 scale= 0.89 alpha= 0.00 freqs= 1.20 rel rates= 1.50 pinv= 0.00) pass 2:+ 0.035 (branch= 0.00 scale= 0.00 alpha= 0.00 freqs= 0.03 rel rates= 0.00 pinv= 0.00) lnL after optimization: -219.1444 gen current_lnL precision last_tree_imp 0 -219.1444 0.500 0 200 -217.4629 0.500 32 400 -216.6525 0.500 363 600 -216.1292 0.500 474 800 -215.4112 0.500 669 1000 -215.0097 0.500 936 1200 -214.3653 0.500 936 1400 -214.0189 0.500 936 Optimization precision reduced Optimizing parameters... improved 1.908 lnL Optimizing branchlengths... improved 0.702 lnL 1600 -211.2007 0.010 1502 1800 -211.0869 0.010 1502 2000 -210.9748 0.010 1986 2200 -210.9049 0.010 1986 2400 -210.8867 0.010 1986 2600 -210.8079 0.010 1986 2800 -210.7641 0.010 1986 3000 -210.7259 0.010 1986 3200 -210.6946 0.010 1986 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./restart/n.const.conf ################################################### READING OF DATA Attempting to read data file data/z.11x30.phy as relaxed Phylip DNA format (using NCL) ... storing implied block: TAXA storing read block: DATA Data read successfully. ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") Data read as Nucleotide data, modeled as Nucleotide data Summary of data: 11 sequences. 11 constant characters. 17 parsimony-informative characters. 2 uninformative variable characters. 30 total characters. 25 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.4 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Found outgroup specification: 1 ####################################################### Loading constraints from file data/z.pos.const.tre Found 6 positively constrained bipartition(s) Bipartition 1: (1,2,3,5,6,7,8,9,10) | (4,11) Bipartition 2: (1,3,5,6,7,8,9,10) | (2,4,11) Bipartition 3: (1,5,6,7,8,9,10) | (2,3,4,11) Bipartition 4: (1,2,3,4,5,8,9,10,11) | (6,7) Bipartition 5: (1,2,3,4,5,8,9,11) | (6,7,10) Bipartition 6: (1,5) | (2,3,4,6,7,8,9,10,11) STARTING RUN Restarting from checkpoint... generation 3248, seed 2141288047, best lnL -210.694 gen current_lnL precision last_tree_imp 3248 -210.6938 0.010 1986 3300 -210.6709 0.010 1986 3400 -210.6598 0.010 1986 3500 -210.6567 0.010 1986 3600 -210.6566 0.010 1986 3700 -210.6372 0.010 1986 3800 -210.6363 0.010 1986 3900 -210.6358 0.010 1986 4000 -210.6358 0.010 1986 Reached termination condition! last topological improvement at gen 1986 Improvement over last 500 gen = 0.02085 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates AC = 1.745, AG = 3.199, AT = 0.210, CG = 2.841, CT = 5.925, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2410 0.3439 0.2146 0.2005 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 1.2504 with an invariant (invariable) site category, proportion estimated 0.1701 Substitution rate categories under this model: rate proportion 0.0000 0.1701 0.1841 0.2075 0.5410 0.2075 1.0317 0.2075 2.2433 0.2075 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with a positive constraint, it is possible for a constrained branch itself to be collapsed. If you care, be careful to check whether this has happened or turn off branch collapsing. Saving site likelihoods to file ch.n.const.sitelikes.log ... ####################################################### Completed 1 replicate search(es) (of 1). Results: Replicate 1 : -210.6358 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: 1.745 3.199 0.2101 2.841 5.925 1 0.241 0.344 0.215 0.200 1.250 0.170 Treelengths: TL rep 1: 2.434 Saving final tree from best search rep (#1) to ch.n.const.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.const.internalstates.log ####################################################### TREEFILES PASS Running checkpoint test ./check/p.3diff.conf Running checkpoint test ./check/p.3diff.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./check/p.3diff.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.byPos.11x2178.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful Reading SETS block...storing read block: SETS successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #1 ("1stpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 4 Summary of data: 11 sequences. 441 constant characters. 171 parsimony-informative characters. 113 uninformative variable characters. 725 total characters. 237 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #2 ("2ndpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 5 Summary of data: 11 sequences. 527 constant characters. 90 parsimony-informative characters. 108 uninformative variable characters. 725 total characters. 158 unique patterns in compressed data matrix. GARLI data subset 3 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #3 ("3rdpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 6 Summary of data: 11 sequences. 102 constant characters. 507 parsimony-informative characters. 116 uninformative variable characters. 725 total characters. 548 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 11 MB good approx 10 MB to 9 MB low approx 8 MB to 5 MB very low approx 4 MB to 4 MB the minimum required availablememory is 4 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 16.0 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/p.3diff.start Reading TREES block...storing read block: TREES successful Reading GARLI block...storing read block: GARLI successful STARTING RUN Bootstrap reweighting... Subset 1: Random seed for bootstrap reweighting: 42 Subset 2: Random seed for bootstrap reweighting: 655766889 Subset 3: Random seed for bootstrap reweighting: 486988955 >>>Bootstrap rep 1 (of 1) <<< Obtained starting tree 1 from Nexus Obtained starting or fixed model parameter values from Nexus: MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) AC = 1.000, AG = 10.000, AT = 2.000, CG = 2.000, CT = 0.010, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3150 0.1749 0.3006 0.2095 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.6000 Substitution rate categories under this model: rate proportion 0.0531 0.2500 0.3123 0.2500 0.8813 0.2500 2.7533 0.2500 Model 2 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) AC = 4.000, AG = 4.000, AT = 1.000, CG = 4.000, CT = 4.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1000 0.2000 0.3000 0.4000 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.4000 Substitution rate categories under this model: rate proportion 0.0167 0.2500 0.1818 0.2500 0.7313 0.2500 3.0702 0.2500 Model 3 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) AC = 1.000, AG = 2.000, AT = 3.000, CG = 5.000, CT = 2.000, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.4000 0.2000 0.3000 0.1000 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.5000 with an invariant (invariable) site category, proportion estimated 0.0100 Substitution rate categories under this model: rate proportion 0.0000 0.0100 0.0334 0.2475 0.2519 0.2475 0.8203 0.2475 2.8944 0.2475 Subset rate multipliers: 0.54 0.30 2.16 Starting with seed=1 Initial ln Likelihood: -17331.1409 optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates... pass 1:+ 3336.674 (branch=2061.91 scale= 45.13 alpha=125.85 freqs=435.78 rel rates=661.66 pinv= 0.00 subset rates= 6.34) pass 2:+ 338.355 (branch= 41.98 scale= 1.04 alpha= 22.50 freqs=192.29 rel rates= 77.24 pinv= 2.39 subset rates= 0.92) pass 3:+ 222.683 (branch= 0.46 scale= 0.67 alpha= 8.57 freqs= 98.23 rel rates=113.31 pinv= 0.80 subset rates= 0.64) pass 4:+ 44.580 (branch= 0.51 scale= 0.00 alpha= 1.57 freqs= 22.89 rel rates= 19.62 pinv= 0.00 subset rates= 0.00) pass 5:+ 8.682 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 4.12 rel rates= 4.53 pinv= 0.02 subset rates= 0.00) pass 6:+ 1.298 (branch= 0.59 scale= 0.00 alpha= 0.01 freqs= 0.65 rel rates= 0.01 pinv= 0.03 subset rates= 0.00) pass 7:+ 1.354 (branch= 0.00 scale= 0.49 alpha= 0.72 freqs= 0.12 rel rates= 0.02 pinv= 0.01 subset rates= 0.00) pass 8:+ 0.126 (branch= 0.00 scale= 0.00 alpha= 0.01 freqs= 0.09 rel rates= 0.02 pinv= 0.01 subset rates= 0.00) lnL after optimization: -13377.3893 gen current_lnL precision last_tree_imp 0 -13377.3893 0.500 0 100 -13375.8793 0.500 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./restart/p.3diff.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/z.byPos.11x2178.nex ... Reading DATA block...storing implied block: TAXA storing read block: DATA successful Reading SETS block...storing read block: SETS successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY TO EACH DATA SUBSET (no linkage) GARLI data subset 1 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #1 ("1stpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 4 Summary of data: 11 sequences. 441 constant characters. 171 parsimony-informative characters. 113 uninformative variable characters. 725 total characters. 237 unique patterns in compressed data matrix. GARLI data subset 2 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #2 ("2ndpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 5 Summary of data: 11 sequences. 527 constant characters. 90 parsimony-informative characters. 108 uninformative variable characters. 725 total characters. 158 unique patterns in compressed data matrix. GARLI data subset 3 CHARACTERS block #1 ("Untitled DATA Block 1") CHARPARTITION subset #3 ("3rdpos") Data read as Nucleotide data, modeled as Nucleotide data Excluded character numbers: 6 Summary of data: 11 sequences. 102 constant characters. 507 parsimony-informative characters. 116 uninformative variable characters. 725 total characters. 548 unique patterns in compressed data matrix. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 11 MB good approx 10 MB to 9 MB low approx 8 MB to 5 MB very low approx 4 MB to 4 MB the minimum required availablememory is 4 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 16.0 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/p.3diff.start Reading TREES block...storing read block: TREES successful Reading GARLI block...storing read block: GARLI successful STARTING RUN Subset 1: Random seed for bootstrap reweighting: 42 Subset 2: Random seed for bootstrap reweighting: 655766889 Subset 3: Random seed for bootstrap reweighting: 486988955 Restarting from checkpoint... Bootstrap rep 1 (of 1) generation 167, seed 1096729108, best lnL -13374.793 gen current_lnL precision last_tree_imp 167 -13374.7931 0.500 0 200 -13373.8436 0.500 0 NOTE: ****Specified time limit (1 seconds) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) AC = 1.179, AG = 1.959, AT = 0.891, CG = 0.891, CT = 2.980, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3109 0.1852 0.3040 0.1998 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.3450 Substitution rate categories under this model: rate proportion 0.0096 0.2500 0.1396 0.2500 0.6641 0.2500 3.1866 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 = 3.040, AG = 4.757, AT = 0.963, CG = 4.757, CT = 3.040, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2834 0.1726 0.1642 0.3797 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.2509 Substitution rate categories under this model: rate proportion 0.0022 0.2500 0.0673 0.2500 0.5033 0.2500 3.4272 0.2500 Model 3 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) AC = 1.000, AG = 5.493, AT = 4.468, CG = 0.654, CT = 5.493, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.1569 0.3440 0.2780 0.2211 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 3.7874 with an invariant (invariable) site category, proportion estimated 0.0453 Substitution rate categories under this model: rate proportion 0.0000 0.0453 0.4423 0.2387 0.7675 0.2387 1.0844 0.2387 1.7058 0.2387 Subset rate multipliers: 0.52 0.29 2.19 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 : -13373.3070 (TERMINATED PREMATURELY) Parameter estimates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha rep 1: 1.179 1.959 0.8911 0.8911 2.98 1 0.311 0.185 0.304 0.200 0.345 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: 3.04 4.757 0.9634 4.757 3.04 1 0.283 0.173 0.164 0.380 0.251 Partition model subset 3: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv rep 1: 1 5.493 4.468 0.6538 5.493 1 0.157 0.344 0.278 0.221 3.787 0.045 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 1.778 0.521 0.286 2.193 Saving best tree to bootstrap file ch.p.3diff.boot.tre WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mk.ssr.conf Running checkpoint test ./check/p.mk.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./check/p.mk.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, modeled as Standard k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN >>>Search rep 1 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -609.1934 optimizing: starting branch lengths, subset rates... pass 1:+ 130.207 (branch= 124.97 scale= 0.94 subset rates= 4.30) pass 2:+ 9.055 (branch= 8.14 scale= 0.00 subset rates= 0.91) pass 3:+ 1.801 (branch= 1.66 scale= 0.02 subset rates= 0.12) pass 4:+ 0.303 (branch= 0.30 scale= 0.00 subset rates= 0.00) pass 5:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -467.8152 gen current_lnL precision last_tree_imp 0 -467.8152 0.010 0 100 -467.7854 0.010 76 200 -467.7768 0.010 76 300 -467.7654 0.010 76 400 -467.7615 0.010 76 500 -467.7562 0.010 76 600 -467.7505 0.010 76 700 -467.7495 0.010 76 800 -467.7483 0.010 76 900 -467.7471 0.010 76 1000 -467.7427 0.010 76 1100 -467.7372 0.010 76 1200 -467.7330 0.010 76 1300 -467.7317 0.010 76 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./restart/p.mk.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, modeled as Standard k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Restarting from checkpoint... Search rep 1 (of 5) generation 1345, seed 1927362789, best lnL -467.731 gen current_lnL precision last_tree_imp 1345 -467.7313 0.010 76 1400 -467.7307 0.010 76 1500 -467.7301 0.010 76 1600 -467.7294 0.010 76 1700 -467.7252 0.010 76 1800 -467.7239 0.010 76 1900 -467.7239 0.010 76 2000 -467.7234 0.010 76 2100 -467.7228 0.010 76 2200 -467.7218 0.010 76 2300 -467.7216 0.010 76 2400 -467.7209 0.010 76 2500 -467.7205 0.010 76 2600 -467.7205 0.010 76 2700 -467.7197 0.010 76 2800 -467.7190 0.010 76 2900 -467.7186 0.010 76 NOTE: ****Specified time limit (5 seconds) reached... Current score = -467.7186 Performing final optimizations... pass 1 : -467.7158 (branch= 0.0000 subset rates= 0.0028) pass 2 : -467.6948 (branch= 0.0184 subset rates= 0.0026) pass 3 : -467.6911 (branch= 0.0014 subset rates= 0.0022) pass 4 : -467.6859 (branch= 0.0045 subset rates= 0.0007) pass 5 : -467.6831 (branch= 0.0028 subset rates= 0.0000) pass 6 : -467.6816 (branch= 0.0015 subset rates= 0.0000) pass 7 : -467.6801 (branch= 0.0011 subset rates= 0.0004) pass 8 : -467.6792 (branch= 0.0009 subset rates= 0.0000) pass 9 : -467.6788 (branch= 0.0004 subset rates= 0.0000) pass 10: -467.6786 (branch= 0.0001 subset rates= 0.0000) pass 11: -467.6786 (branch= 0.0001 subset rates= 0.0000) pass 12: -467.6785 (branch= 0.0000 subset rates= 0.0000) pass 13: -467.6785 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6785 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.79 1.48 2.18 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. >>>Terminated Search rep 1 (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 1 replicate search(es) (of 5). Results: Replicate 1 : -467.6785 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 3.844 0.786 1.484 2.175 Saving final tree from best search rep (#1) to ch.p.mk.ssr.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkO.ssr.conf Running checkpoint test ./check/p.mkO.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./check/p.mkO.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, modeled as Standard ordered k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN >>>Search rep 1 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mk model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -641.9257 optimizing: starting branch lengths, subset rates... pass 1:+ 147.096 (branch= 136.58 scale= 0.83 subset rates= 9.68) pass 2:+ 12.450 (branch= 8.46 scale= 0.00 subset rates= 3.99) pass 3:+ 3.552 (branch= 2.32 scale= 0.03 subset rates= 1.21) pass 4:+ 0.757 (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: -477.9409 gen current_lnL precision last_tree_imp 0 -477.9409 0.010 0 100 -477.8603 0.010 76 200 -477.8233 0.010 152 300 -477.7401 0.010 215 400 -477.7335 0.010 215 500 -477.3190 0.010 455 600 -477.3000 0.010 555 700 -477.2971 0.010 555 800 -477.2925 0.010 555 900 -477.2796 0.010 555 1000 -477.2780 0.010 555 1100 -477.2715 0.010 555 1200 -477.2661 0.010 555 1300 -477.2629 0.010 555 1400 -477.2604 0.010 555 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./restart/p.mkO.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, modeled as Standard ordered k-state data NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.5 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Restarting from checkpoint... Search rep 1 (of 5) generation 1443, seed 677769925, best lnL -477.260 gen current_lnL precision last_tree_imp 1443 -477.2604 0.010 555 1500 -477.2601 0.010 555 1600 -477.2577 0.010 555 1700 -477.2572 0.010 555 1800 -477.2565 0.010 555 1900 -477.2564 0.010 555 2000 -477.2546 0.010 555 2100 -477.2536 0.010 555 2200 -477.2522 0.010 555 2300 -477.2519 0.010 555 2400 -477.2514 0.010 555 NOTE: ****Specified time limit (5 seconds) reached... Current score = -477.2509 Performing final optimizations... pass 1 : -477.2475 (branch= 0.0000 subset rates= 0.0035) pass 2 : -477.2252 (branch= 0.0216 subset rates= 0.0007) pass 3 : -477.2181 (branch= 0.0041 subset rates= 0.0030) pass 4 : -477.2166 (branch= 0.0015 subset rates= 0.0000) pass 5 : -477.2153 (branch= 0.0013 subset rates= 0.0000) pass 6 : -477.2135 (branch= 0.0018 subset rates= 0.0000) pass 7 : -477.2127 (branch= 0.0008 subset rates= 0.0000) pass 8 : -477.2123 (branch= 0.0003 subset rates= 0.0001) pass 9 : -477.2121 (branch= 0.0002 subset rates= 0.0000) pass 10: -477.2120 (branch= 0.0002 subset rates= 0.0000) pass 11: -477.2119 (branch= 0.0000 subset rates= 0.0000) pass 12: -477.2119 (branch= 0.0000 subset rates= 0.0000) pass 13: -477.2119 (branch= 0.0000 subset rates= 0.0000) pass 14: -477.2119 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.2119 Time used so far = 0 hours, 0 minutes and 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: 0.64 1.91 2.62 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. >>>Terminated Search rep 1 (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 1 replicate search(es) (of 5). Results: Replicate 1 : -477.2119 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.671 0.643 1.908 2.618 Saving final tree from best search rep (#1) to ch.p.mkO.ssr.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkv.ssr.conf Running checkpoint test ./check/p.mkv.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./check/p.mkv.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, variable only, modeled as Standard k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Bootstrap reweighting... Subset 1: Random seed for bootstrap reweighting: 42 Subset 2: Random seed for bootstrap reweighting: 1339106791 Subset 3: Random seed for bootstrap reweighting: 974568031 >>>Bootstrap rep 1 (of 1) Search rep 1 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -602.2288 optimizing: starting branch lengths, subset rates... pass 1:+ 152.798 (branch= 152.15 scale= 0.58 subset rates= 0.07) pass 2:+ 9.798 (branch= 9.64 scale= 0.00 subset rates= 0.16) pass 3:+ 0.368 (branch= 0.35 scale= 0.00 subset rates= 0.02) pass 4:+ 0.040 (branch= 0.04 scale= 0.00 subset rates= 0.00) pass 5:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) lnL after optimization: -439.2245 gen current_lnL precision last_tree_imp 0 -439.2245 0.010 0 100 -430.2565 0.010 92 200 -427.7102 0.010 179 300 -426.9763 0.010 293 400 -425.6930 0.010 365 500 -425.6677 0.010 365 600 -425.6512 0.010 365 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./restart/p.mkv.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard k-state data, variable only, modeled as Standard k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Subset 1: Random seed for bootstrap reweighting: 42 Subset 2: Random seed for bootstrap reweighting: 1339106791 Subset 3: Random seed for bootstrap reweighting: 974568031 Restarting from checkpoint... Bootstrap rep 1 (of 1) Search rep 1 (of 5) generation 682, seed 2130530188, best lnL -425.636 gen current_lnL precision last_tree_imp 682 -425.6358 0.010 365 700 -425.6318 0.010 365 800 -425.6212 0.010 365 900 -425.6126 0.010 365 1000 -425.6095 0.010 365 1100 -425.6090 0.010 365 1200 -425.6083 0.010 365 1300 -425.6068 0.010 365 1400 -425.6058 0.010 365 1500 -425.6042 0.010 365 1600 -425.6022 0.010 365 1700 -425.5976 0.010 365 1800 -425.5972 0.010 365 NOTE: ****Specified time limit (5 seconds) reached... Current score = -425.5972 Performing final optimizations... pass 1 : -425.5861 (branch= 0.0000 subset rates= 0.0111) pass 2 : -425.5644 (branch= 0.0217 subset rates= 0.0000) pass 3 : -425.5554 (branch= 0.0090 subset rates= 0.0000) pass 4 : -425.5526 (branch= 0.0028 subset rates= 0.0000) pass 5 : -425.5515 (branch= 0.0011 subset rates= 0.0000) pass 6 : -425.5505 (branch= 0.0010 subset rates= 0.0000) pass 7 : -425.5492 (branch= 0.0012 subset rates= 0.0000) pass 8 : -425.5489 (branch= 0.0003 subset rates= 0.0000) pass 9 : -425.5488 (branch= 0.0001 subset rates= 0.0000) pass 10: -425.5487 (branch= 0.0000 subset rates= 0.0000) pass 11: -425.5487 (branch= 0.0000 subset rates= 0.0000) pass 12: -425.5487 (branch= 0.0000 subset rates= 0.0000) pass 13: -425.5487 (branch= 0.0000 subset rates= 0.0000) pass 14: -425.5487 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.5487 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 2 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (standard data) Character change matrix: One rate (symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.87 1.53 1.12 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 9 branches were collapsed. >>>Terminated Bootstrap rep 1 (of 1) Search rep 1 (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 1 replicate search(es) (of 5). Results: Replicate 1 : -425.5487 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 3.036 0.867 1.534 1.123 Saving tree from best search rep (#1) to bootstrap file ch.p.mkv.ssr.boot.tre WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkvO.ssr.conf Running checkpoint test ./check/p.mkvO.ssr.conf Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./check/p.mkvO.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, variable only, modeled as Standard ordered k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN >>>Search rep 1 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 1.00 1.00 1.00 Starting with seed=1 Initial ln Likelihood: -637.9212 optimizing: starting branch lengths, subset rates... pass 1:+ 144.867 (branch= 134.40 scale= 0.48 subset rates= 9.98) pass 2:+ 12.967 (branch= 8.30 scale= 0.00 subset rates= 4.67) pass 3:+ 3.846 (branch= 2.24 scale= 0.02 subset rates= 1.58) pass 4:+ 1.161 (branch= 0.58 scale= 0.01 subset rates= 0.57) pass 5:+ 0.157 (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: -474.8624 gen current_lnL precision last_tree_imp 0 -474.8624 0.010 0 100 -474.7511 0.010 68 200 -474.7182 0.010 68 300 -474.6978 0.010 68 400 -474.6394 0.010 329 500 -474.1553 0.010 455 600 -474.1358 0.010 560 700 -474.0415 0.010 653 800 -474.0256 0.010 653 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF (set restart = 1 in the config file). IF YOU WANT TO USE THE PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY ADD "end;" TO THE TREE FILES. Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## This is GARLI 2.1: maximum likelihood phylogenetic inference using nucleotide, amino acid, codon and morphology-like data, as well as partitioned models. General program usage is extensively documented here: http://www.nescent.org/wg/garli/ See this page for details on partitioned model usage: http://www.nescent.org/wg_garli/Using_partitioned_models and this page for details on Mkv mophology model usage: http://www.nescent.org/wg_garli/Mkv_morphology_model PLEASE LET ME KNOW OF ANY PROBLEMS AT: garli.support@gmail.com ############################################################## Compiled Nov 9 2024 22:34:46 using GNU gcc compiler version 14.2.0 Using NCL version 2.1.17 ####################################################### Reading config file ./restart/p.mkvO.ssr.conf ################################################### READING OF DATA Attempting to read data file in Nexus format (using NCL): data/L2001.30x52.nex ... Reading CHARACTERS block... Warning: Skipping command: OPTIONS at line 23, column (approximately) 9 (file position 611) storing implied block: TAXA storing read block: CHARACTERS found standard data... successful Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS successful ################################################### PARTITIONING OF DATA AND MODELS GARLI data subset 1 CHARACTERS block #1 ("Untitled CHARACTERS Block 1") Data read as Standard ordered k-state data, variable only, modeled as Standard ordered k-state data, variable only NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 2 states: chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115 Summary of data: 30 sequences. 0 constant characters. 39 parsimony-informative characters. 0 uninformative variable characters. 39 total characters. 39 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity: char 90 Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity: char 90 Subset of data with 3 states: chars 54 61 62 64 71 72 83 90-102 \ 6 Summary of data: 30 sequences. 0 constant characters. 10 parsimony-informative characters. 0 uninformative variable characters. 10 total characters. 10 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 Subset of data with 4 states: chars 52 59 73 Summary of data: 30 sequences. 0 constant characters. 0 parsimony-informative characters. 3 uninformative variable characters. 3 total characters. 3 unique patterns in compressed data matrix. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 5 observed states. NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored. Excluded characters: 1-45 74-82 85 86 105 108-112 114 116-118 NOTE: No characters found with 6 observed states. ################################################### NOTE: Unlike many programs, the amount of system memory that Garli will use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed) For this dataset: Mem level availablememory setting great >= 1 MB good approx 0 MB to 1 MB low approx 0 MB to 1 MB very low approx 0 MB to 1 MB the minimum required availablememory is 1 MB You specified that Garli should use at most 512.0 MB of memory. Garli will actually use approx. 0.6 MB of memory **Your memory level is: great (you don't need to change anything)** ####################################################### Loading starting model and/or tree from file data/L.start Reading TREES block...storing read block: TREES successful STARTING RUN Restarting from checkpoint... Search rep 1 (of 5) generation 857, seed 1964298825, best lnL -474.020 gen current_lnL precision last_tree_imp 857 -474.0205 0.010 653 900 -474.0163 0.010 653 1000 -474.0079 0.010 653 1100 -474.0062 0.010 653 1200 -474.0018 0.010 653 1300 -474.0004 0.010 653 1400 -473.9972 0.010 653 1500 -473.9932 0.010 653 1600 -473.9890 0.010 653 1700 -473.9880 0.010 653 1800 -473.9876 0.010 653 1900 -473.9835 0.010 653 2000 -473.9824 0.010 653 NOTE: ****Specified time limit (5 seconds) reached... Current score = -473.9824 Performing final optimizations... pass 1 : -473.9824 (branch= 0.0000 subset rates= 0.0000) pass 2 : -473.9623 (branch= 0.0192 subset rates= 0.0009) pass 3 : -473.9607 (branch= 0.0000 subset rates= 0.0016) pass 4 : -473.9588 (branch= 0.0018 subset rates= 0.0000) pass 5 : -473.9533 (branch= 0.0053 subset rates= 0.0003) pass 6 : -473.9520 (branch= 0.0013 subset rates= 0.0000) pass 7 : -473.9513 (branch= 0.0007 subset rates= 0.0000) pass 8 : -473.9512 (branch= 0.0001 subset rates= 0.0000) pass 9 : -473.9510 (branch= 0.0002 subset rates= 0.0000) pass 10: -473.9509 (branch= 0.0001 subset rates= 0.0000) pass 11: -473.9508 (branch= 0.0000 subset rates= 0.0000) pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) pass 13: -473.9508 (branch= 0.0000 subset rates= 0.0000) pass 14: -473.9508 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -473.9508 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 2 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.50, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 2 Number of states = 3 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.33, fixed) Rate Heterogeneity Model: no rate heterogeneity Model 3 Number of states = 4 (ordered standard data) Character change matrix: One rate (ordered symmetric one rate Mkv model) Equilibrium State Frequencies: equal (0.25, fixed) Rate Heterogeneity Model: no rate heterogeneity Subset rate multipliers: 0.59 2.06 2.80 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. >>>Terminated Search rep 1 (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 1 replicate search(es) (of 5). Results: Replicate 1 : -473.9508 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: Model contains no estimated parameters Partition model subset 2: Model contains no estimated parameters Partition model subset 3: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.349 0.589 2.064 2.802 Saving final tree from best search rep (#1) to ch.p.mkvO.ssr.best.tre ####################################################### TREEFILES PASS ALL TESTS COMPLETED SUCCESSFULLY make[4]: Leaving directory '/build/reproducible-path/garli-2.1/tests' make[3]: Leaving directory '/build/reproducible-path/garli-2.1/tests' make[3]: Entering directory '/build/reproducible-path/garli-2.1' make[3]: Leaving directory '/build/reproducible-path/garli-2.1' make[2]: Leaving directory '/build/reproducible-path/garli-2.1' # restore original test dir rm -rf tests mv tests.bak tests make[1]: Leaving directory '/build/reproducible-path/garli-2.1' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j20 install DESTDIR=/build/reproducible-path/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/garli-2.1' Making install in src make[2]: Entering directory '/build/reproducible-path/garli-2.1/src' make[3]: Entering directory '/build/reproducible-path/garli-2.1/src' /usr/bin/mkdir -p '/build/reproducible-path/garli-2.1/debian/tmp/usr/bin' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/install -c Garli '/build/reproducible-path/garli-2.1/debian/tmp/usr/bin' make install-exec-hook make[4]: Entering directory '/build/reproducible-path/garli-2.1/src' cd /build/reproducible-path/garli-2.1/debian/tmp/usr/bin && \ mv -f Garli Garli-2.1 && \ ln -s Garli-2.1 Garli make[4]: Leaving directory '/build/reproducible-path/garli-2.1/src' make[3]: Leaving directory '/build/reproducible-path/garli-2.1/src' make[2]: Leaving directory '/build/reproducible-path/garli-2.1/src' Making install in tests make[2]: Entering directory '/build/reproducible-path/garli-2.1/tests' make[3]: Entering directory '/build/reproducible-path/garli-2.1/tests' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/garli-2.1/tests' make[2]: Leaving directory '/build/reproducible-path/garli-2.1/tests' make[2]: Entering directory '/build/reproducible-path/garli-2.1' make[3]: Entering directory '/build/reproducible-path/garli-2.1' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/garli-2.1' make[2]: Leaving directory '/build/reproducible-path/garli-2.1' make[1]: Leaving directory '/build/reproducible-path/garli-2.1' dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-8_amd64.deb'. dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-8_all.deb'. dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-8_amd64.deb'. dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-8_amd64.deb'. dpkg-deb: building package 'garli' in '../garli_2.1-8_amd64.deb'. dpkg-genbuildinfo --build=binary -O../garli_2.1-8_amd64.buildinfo dpkg-genchanges --build=binary -O../garli_2.1-8_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/229569 and its subdirectories I: Current time: Sat Nov 9 17:33:09 -12 2024 I: pbuilder-time-stamp: 1731216789 Sun Nov 10 05:33:12 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Sun Nov 10 05:33:12 UTC 2024 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Sun Nov 10 05:37:40 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Sun Nov 10 05:37:41 UTC 2024 I: garli_2.1-8_amd64.changes: Format: 1.8 Date: Sat, 09 Nov 2024 23:34:46 +0100 Source: garli Binary: garli garli-dbgsym garli-examples garli-mpi garli-mpi-dbgsym Architecture: amd64 all Version: 2.1-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: garli - phylogenetic analysis of molecular sequence data using maximum-li garli-examples - phylogenetic analysis of molecular sequence data (examples) garli-mpi - phylogenetic analysis of molecular sequence data using maximum-li Closes: 1044308 1084928 Changes: garli (2.1-8) unstable; urgency=medium . * Team upload. * d/control: migrate to mpi-default-*. (Closes: #1084928) * d/clean: also clean debian/mpi/Garli-mpi. (Closes: #1044308) * d/control: declare compliance to standards version 4.7.0. Checksums-Sha1: 2cd50e81e907b7c831497ef5dde379dc2fbd758f 9397616 garli-dbgsym_2.1-8_amd64.deb 1d75b6608a0154508e024e9cd66a46061ba937bd 103504 garli-examples_2.1-8_all.deb 780ea6a5f114d0ab74971bee340d9445be0e1d33 9788416 garli-mpi-dbgsym_2.1-8_amd64.deb bcfbd7b9c435d5b1ec76b749dc84e06a0a5c10d7 636916 garli-mpi_2.1-8_amd64.deb 7920189d384a098fa8e0362680fc8706b6d76ea1 8342 garli_2.1-8_amd64.buildinfo 1c4799088bb06505b268a481a28145b9ac9c06df 656648 garli_2.1-8_amd64.deb Checksums-Sha256: bace02daf802e62b26779b364935cf8e4b04b7bca4a34febe63beb3f95ef3370 9397616 garli-dbgsym_2.1-8_amd64.deb ede0b382bb70332f1e4f44ab850053e14608732c2e4c551cb7fa5ba84646d7df 103504 garli-examples_2.1-8_all.deb 0cb07e283ff06ff22710c07a16bfd5d180ea6bfb1d60982b0bf4677e66013218 9788416 garli-mpi-dbgsym_2.1-8_amd64.deb ed15d2d0003b60ea4d6ec995dda5d12a7c7aae0c0663f6d00cf8bfc0027eb0dd 636916 garli-mpi_2.1-8_amd64.deb 8d6f2c99ef4a0d48f16a5c1545da669f6dd84a48e62b34b08d8f4f1037a0c712 8342 garli_2.1-8_amd64.buildinfo e2cab6c09ac3c709716b52052e36a3067477903ece7b6b0c1af7e6591e040572 656648 garli_2.1-8_amd64.deb Files: ffc421bfa23087865da7f56214cc05c9 9397616 debug optional garli-dbgsym_2.1-8_amd64.deb bc720e7dcf0455006e4f7d980abd4d25 103504 science optional garli-examples_2.1-8_all.deb d697baf8e33cf1f20a3bddd114db81ac 9788416 debug optional garli-mpi-dbgsym_2.1-8_amd64.deb 73054cc5d1a7e633d81d69758afa33f7 636916 science optional garli-mpi_2.1-8_amd64.deb de38ac7e7699fa30d06ef640e8a7cfd9 8342 science optional garli_2.1-8_amd64.buildinfo c8f22e585231f50d128f65213f232c6a 656648 science optional garli_2.1-8_amd64.deb Sun Nov 10 05:37:42 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_9-22654.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.N2DF4RH9/garli_2.1-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.N2DF4RH9/garli_2.1-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.N2DF4RH9/garli_2.1-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.N2DF4RH9/b1/garli_2.1-8_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.N2DF4RH9/b2/garli_2.1-8_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.584s) 0.583s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.228s) 0.228s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 926ms CPU time consumed: 927ms Sun Nov 10 05:37:44 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Sun Nov 10 05:37:44 UTC 2024 I: garli from unstable built successfully and reproducibly on amd64. Sun Nov 10 05:37:45 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Nov 10 05:37:45 UTC 2024 I: Submitting 12K b1/garli_2.1-8_amd64.buildinfo.asc Sun Nov 10 05:37:46 UTC 2024 I: Submitting 12K b2/garli_2.1-8_amd64.buildinfo.asc Sun Nov 10 05:37:47 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Nov 10 05:37:47 UTC 2024 I: Done submitting .buildinfo files. Sun Nov 10 05:37:47 UTC 2024 I: Removing signed garli_2.1-8_amd64.buildinfo.asc files: removed './b1/garli_2.1-8_amd64.buildinfo.asc' removed './b2/garli_2.1-8_amd64.buildinfo.asc'