Sun Jan 12 05:36:53 UTC 2025  I: starting to build garli/trixie/armhf on jenkins on '2025-01-12 05:36'
Sun Jan 12 05:36:53 UTC 2025  I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_32/23626/console.log
Sun Jan 12 05:36:53 UTC 2025  I: Downloading source for trixie/garli=2.1-9
--2025-01-12 05:36:54--  http://deb.debian.org/debian/pool/main/g/garli/garli_2.1-9.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2186 (2.1K) [text/prs.lines.tag]
Saving to: ‘garli_2.1-9.dsc’

     0K ..                                                    100%  435M=0s

2025-01-12 05:36:54 (435 MB/s) - ‘garli_2.1-9.dsc’ saved [2186/2186]

Sun Jan 12 05:36:54 UTC 2025  I: garli_2.1-9.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 3.0 (quilt)
Source: garli
Binary: garli, garli-mpi, garli-examples
Architecture: any all
Version: 2.1-9
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://github.com/Ashod/garli
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/garli
Vcs-Git: https://salsa.debian.org/med-team/garli.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), libncl-dev, mpi-default-dev, ncl-tools, bc
Package-List:
 garli deb science optional arch=any
 garli-examples deb science optional arch=all
 garli-mpi deb science optional arch=any
Checksums-Sha1:
 a7a5cb81f92ed19672324b5aacf8c7da1f6a2df3 1248730 garli_2.1.orig.tar.gz
 03357cb420644769d7123b89aeb933dca5f02fc6 5072 garli_2.1-9.debian.tar.xz
Checksums-Sha256:
 00aa31af5d8ecc2cb9bd276ce93b6580ae6cff93f4f5e1145d95d5fe6359e1b6 1248730 garli_2.1.orig.tar.gz
 11ae86ea4dcf9b875b85761819eb466c627e32912073a5dc08c28f19cea8e0af 5072 garli_2.1-9.debian.tar.xz
Files:
 83d6720df816365182291306383d056c 1248730 garli_2.1.orig.tar.gz
 c01e4bc42638d26bb8ef30388b77a867 5072 garli_2.1-9.debian.tar.xz
Dgit: 81831dac4c7f11278ba4d060cc3632f00bf4ccc2 debian archive/debian/2.1-9 https://git.dgit.debian.org/garli

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Sun Jan 12 05:36:54 UTC 2025  I: Checking whether the package is not for us
Sun Jan 12 05:36:54 UTC 2025  I: Starting 1st build on remote node virt64c-armhf-rb.debian.net.
Sun Jan 12 05:36:54 UTC 2025  I: Preparing to do remote build '1' on virt64c-armhf-rb.debian.net.
Sun Jan 12 05:54:35 UTC 2025  I: Deleting $TMPDIR on virt64c-armhf-rb.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sat Jan 11 17:37:00 -12 2025
I: pbuilder-time-stamp: 1736660220
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [garli_2.1-9.dsc]
I: copying [./garli_2.1.orig.tar.gz]
I: copying [./garli_2.1-9.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./garli_2.1-9.dsc: unsupported subcommand
dpkg-source: info: extracting garli in garli-2.1
dpkg-source: info: unpacking garli_2.1.orig.tar.gz
dpkg-source: info: unpacking garli_2.1-9.debian.tar.xz
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/32626/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='armhf'
  DEBIAN_FRONTEND='noninteractive'
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 '
  DISTRIBUTION='trixie'
  HOME='/root'
  HOST_ARCH='armhf'
  IFS=' 	
  '
  INVOCATION_ID='8e01230d5da1407fbf1c4d11168e56b8'
  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='32626'
  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.HHFUF2XE/pbuilderrc_c87e --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HHFUF2XE/b1 --logfile b1/build.log garli_2.1-9.dsc'
  SUDO_GID='113'
  SUDO_UID='107'
  SUDO_USER='jenkins'
  TERM='unknown'
  TZ='/usr/share/zoneinfo/Etc/GMT+12'
  USER='root'
  _='/usr/bin/systemd-run'
  http_proxy='http://10.0.0.15:3142/'
I: uname -a
  Linux virt64c 6.1.0-29-arm64 #1 SMP Debian 6.1.123-1 (2025-01-02) aarch64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/32626/tmp/hooks/D02_print_environment finished
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: armhf
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
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 ... 19567 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-arm-linux-gnueabihf{a} groff-base{a} hwloc-nox{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libhwloc-dev{a} libhwloc15{a} libicu72{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmpich-dev{a} libmpich12{a} libncl-dev{a} libncl2{a} libnuma-dev{a} libnuma1{a} libpipeline1{a} libreadline8t64{a} libslurm42t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} mpi-default-dev{a} mpich{a} ncl-tools{a} po-debconf{a} readline-common{a} sensible-utils{a} 
The following packages are RECOMMENDED but will NOT be installed:
  curl libarchive-cpio-perl libhwloc-plugins libmail-sendmail-perl lynx wget 
0 packages upgraded, 52 newly installed, 0 to remove and 0 not upgraded.
Need to get 36.0 MB of archives. After unpacking 122 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main armhf readline-common all 8.2-6 [69.4 kB]
Get: 2 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.24 [24.8 kB]
Get: 3 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB]
Get: 4 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB]
Get: 5 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3+b1 [42.3 kB]
Get: 6 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.22.5-4 [196 kB]
Get: 7 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB]
Get: 8 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-7 [1095 kB]
Get: 9 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.2-13 [84.7 kB]
Get: 10 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB]
Get: 11 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.13.0-1 [1382 kB]
Get: 12 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-5 [272 kB]
Get: 13 http://deb.debian.org/debian trixie/main armhf autoconf all 2.72-3 [493 kB]
Get: 14 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 15 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get: 16 http://deb.debian.org/debian trixie/main armhf autopoint all 0.22.5-4 [723 kB]
Get: 17 http://deb.debian.org/debian trixie/main armhf libreadline8t64 armhf 8.2-6 [146 kB]
Get: 18 http://deb.debian.org/debian trixie/main armhf bc armhf 1.07.1-4 [97.8 kB]
Get: 19 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.23 [90.6 kB]
Get: 20 http://deb.debian.org/debian trixie/main armhf libtool all 2.5.4-2 [539 kB]
Get: 21 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 22 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 23 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 24 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 25 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.192-4 [184 kB]
Get: 26 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB]
Get: 27 http://deb.debian.org/debian trixie/main armhf libunistring5 armhf 1.3-1 [444 kB]
Get: 28 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-5+b1 [9088 kB]
Get: 29 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB]
Get: 30 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.22.5-4 [1489 kB]
Get: 31 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 32 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 33 http://deb.debian.org/debian trixie/main armhf debhelper all 13.23 [919 kB]
Get: 34 http://deb.debian.org/debian trixie/main armhf libgfortran5 armhf 14.2.0-12 [263 kB]
Get: 35 http://deb.debian.org/debian trixie/main armhf libgfortran-14-dev armhf 14.2.0-12 [317 kB]
Get: 36 http://deb.debian.org/debian trixie/main armhf gfortran-14-arm-linux-gnueabihf armhf 14.2.0-12 [8720 kB]
Get: 37 http://deb.debian.org/debian trixie/main armhf gfortran-14 armhf 14.2.0-12 [13.4 kB]
Get: 38 http://deb.debian.org/debian trixie/main armhf libhwloc15 armhf 2.11.2-1 [134 kB]
Get: 39 http://deb.debian.org/debian trixie/main armhf hwloc-nox armhf 2.11.2-1 [201 kB]
Get: 40 http://deb.debian.org/debian trixie/main armhf libnuma1 armhf 2.0.18-1+b1 [18.9 kB]
Get: 41 http://deb.debian.org/debian trixie/main armhf libnuma-dev armhf 2.0.18-1+b1 [34.6 kB]
Get: 42 http://deb.debian.org/debian trixie/main armhf libltdl7 armhf 2.5.4-2 [412 kB]
Get: 43 http://deb.debian.org/debian trixie/main armhf libltdl-dev armhf 2.5.4-2 [163 kB]
Get: 44 http://deb.debian.org/debian trixie/main armhf libhwloc-dev armhf 2.11.2-1 [226 kB]
Get: 45 http://deb.debian.org/debian trixie/main armhf libmpich12 armhf 4.2.1-5 [1417 kB]
Get: 46 http://deb.debian.org/debian trixie/main armhf libslurm42t64 armhf 24.11.0-1.1 [694 kB]
Get: 47 http://deb.debian.org/debian trixie/main armhf mpich armhf 4.2.1-5 [203 kB]
Get: 48 http://deb.debian.org/debian trixie/main armhf libmpich-dev armhf 4.2.1-5 [2269 kB]
Get: 49 http://deb.debian.org/debian trixie/main armhf libncl2 armhf 2.1.21+git20210811.b1213a7-6 [318 kB]
Get: 50 http://deb.debian.org/debian trixie/main armhf libncl-dev armhf 2.1.21+git20210811.b1213a7-6 [537 kB]
Get: 51 http://deb.debian.org/debian trixie/main armhf mpi-default-dev armhf 1.18 [3372 B]
Get: 52 http://deb.debian.org/debian trixie/main armhf ncl-tools armhf 2.1.21+git20210811.b1213a7-6 [130 kB]
Fetched 36.0 MB in 1s (28.4 MB/s)
Preconfiguring packages ...
Selecting previously unselected package readline-common.
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(Reading database ... 19567 files and directories currently installed.)
Preparing to unpack .../00-readline-common_8.2-6_all.deb ...
Unpacking readline-common (8.2-6) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:armhf.
Preparing to unpack .../03-libmagic1t64_1%3a5.45-3+b1_armhf.deb ...
Unpacking libmagic1t64:armhf (1:5.45-3+b1) ...
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Preparing to unpack .../04-file_1%3a5.45-3+b1_armhf.deb ...
Unpacking file (1:5.45-3+b1) ...
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Preparing to unpack .../05-gettext-base_0.22.5-4_armhf.deb ...
Unpacking gettext-base (0.22.5-4) ...
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Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_armhf.deb ...
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Unpacking bsdextrautils (2.40.2-13) ...
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Unpacking libpipeline1:armhf (1.5.8-1) ...
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Unpacking m4 (1.4.19-5) ...
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Preparing to unpack .../16-libreadline8t64_8.2-6_armhf.deb ...
Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64'
Unpacking libreadline8t64:armhf (8.2-6) ...
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I: Building the package
I: Running cd /build/reproducible-path/garli-2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S  > ../garli_2.1-9_source.changes
dpkg-buildpackage: info: source package garli
dpkg-buildpackage: info: source version 2.1-9
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 debian/rules clean
dh clean
   dh_clean
 debian/rules binary
dh binary
   dh_update_autotools_config
   dh_autoreconf
aclocal: warning: couldn't open directory 'config/m4': No such file or directory
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configure.ac:8: You should run autoupdate.
./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from...
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./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
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config/acx_mpi.m4:74: ACX_MPI is expanded from...
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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=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-ncl=/usr --enable-mpi
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking target system type... arm-unknown-linux-gnueabihf
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /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 -j3
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..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o condlike.o condlike.cpp
In file included from bipartition.cpp:20:
reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
      |                                         ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
      |                                         ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
/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<num;i++)
      |                          ^
mpic++ -DHAVE_CONFIG_H -I. -I..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configoptions.o configoptions.cpp
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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)':
adaptation.cpp:271:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  271 |         fread((char *) this, 1, scalarSize, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:278:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  278 |         fread((char *) improvetotal, sizeof(FLOAT_TYPE), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:280:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  280 |         fread((char *) randNNI, sizeof(FLOAT_TYPE), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:281:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  281 |         fread((char *) randNNInum, sizeof(int), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:283:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  283 |         fread((char *) exNNI, sizeof(FLOAT_TYPE), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:284:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  284 |         fread((char *) exNNInum, sizeof(int), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:286:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  286 |         fread((char *) randSPR, sizeof(FLOAT_TYPE), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:287:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  287 |         fread((char *) randSPRnum, sizeof(int), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:289:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  289 |         fread((char *) limSPR, sizeof(FLOAT_TYPE), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:290:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  290 |         fread((char *) limSPRnum, sizeof(int), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:292:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  292 |         fread((char *) exlimSPR, sizeof(FLOAT_TYPE), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:293:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  293 |         fread((char *) exlimSPRnum, sizeof(int), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:295:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  295 |         fread((char *) randRecom, sizeof(FLOAT_TYPE), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:296:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  296 |         fread((char *) randRecomnum, sizeof(int), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:298:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  298 |         fread((char *) bipartRecom, sizeof(FLOAT_TYPE), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:299:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  299 |         fread((char *) bipartRecomnum, sizeof(int), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:301:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  301 |         fread((char *) onlyBrlen, sizeof(FLOAT_TYPE), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:302:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  302 |         fread((char *) onlyBrlennum, sizeof(int), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:304:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  304 |         fread((char *) anyModel, sizeof(FLOAT_TYPE), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:305:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  305 |         fread((char *) anyModelnum, sizeof(int), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mpic++ -DHAVE_CONFIG_H -I. -I..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configreader.o configreader.cpp
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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
In file included from /usr/include/stdio.h: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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
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/arm-linux-gnueabihf/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 ());
      |                                   ~~~~~~~~~~~~~~~~~
mpic++ -DHAVE_CONFIG_H -I. -I..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o funcs.o funcs.cpp
In file included from tree.h:35,
                 from individual.h:21,
                 from population.h:31,
                 from funcs.h:25,
                 from configreader.cpp:30:
reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
      |                                         ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
/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<num;i++)
      |                          ^
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
      |                                         ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
/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<num;i++)
      |                          ^
configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)':
configreader.cpp:602:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  602 |         fread(&ch, sizeof(char), 1, file);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
configreader.cpp:605:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  605 |                 fread(&ch, sizeof(char), 1, file);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)':
datamatr.cpp:1390:15: 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);
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
In file included from /usr/include/stdio.h: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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
mpic++ -DHAVE_CONFIG_H -I. -I..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlimain.o garlimain.cpp
garlimain.cpp:434:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
  434 |                         outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__);
      |                                                                  ^~~~~~~~
garlimain.cpp:434:76: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
  434 |                         outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__);
      |                                                                            ^~~~~~~~
In file included from /usr/include/stdio.h:970,
                 from /usr/include/c++/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
mpic++ -DHAVE_CONFIG_H -I. -I..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlireader.o garlireader.cpp
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
      |                                         ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
/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<num;i++)
      |                          ^
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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
mpic++ -DHAVE_CONFIG_H -I. -I..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o individual.o individual.cpp
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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 17 bytes into a destination of size 10
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
In file included from tree.h:35,
                 from individual.h:21,
                 from population.h:31,
                 from funcs.h:25,
                 from individual.cpp:28:
reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
      |                                         ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
/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<num;i++)
      |                          ^
In file included from /usr/include/c++/14/vector:65,
                 from /usr/include/ncl/ncl.h:60:
/usr/include/c++/14/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const ProcessedNxsToken*, vector<ProcessedNxsToken> >; _ForwardIterator = ProcessedNxsToken*]':
/usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const ProcessedNxsToken*, std::vector<ProcessedNxsToken> >' changed in GCC 7.1
  113 |     __do_uninit_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const ProcessedNxsToken*, std::vector<ProcessedNxsToken> >' changed in GCC 7.1
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const ProcessedNxsToken*, std::vector<ProcessedNxsToken> >; _ForwardIterator = ProcessedNxsToken*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const ProcessedNxsToken*, vector<ProcessedNxsToken> >; _ForwardIterator = ProcessedNxsToken*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const ProcessedNxsToken*, vector<ProcessedNxsToken> >; _ForwardIterator = ProcessedNxsToken*; _Tp = ProcessedNxsToken]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37,
    inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const ProcessedNxsToken*, std::vector<ProcessedNxsToken> >; _Tp = ProcessedNxsToken; _Alloc = std::allocator<ProcessedNxsToken>]' at /usr/include/c++/14/bits/stl_vector.h:1624:35,
    inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = ProcessedNxsToken; _Alloc = std::allocator<ProcessedNxsToken>]' at /usr/include/c++/14/bits/vector.tcc:238:44,
    inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator<std::vector<ProcessedNxsToken> >; _Tp = std::vector<ProcessedNxsToken>; _Alloc = std::allocator<std::vector<ProcessedNxsToken> >]' at /usr/include/c++/14/bits/list.tcc:316:21:
/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const ProcessedNxsToken*, std::vector<ProcessedNxsToken> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const ProcessedNxsToken*, std::vector<ProcessedNxsToken> >; _ForwardIterator = ProcessedNxsToken*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const ProcessedNxsToken*, vector<ProcessedNxsToken> >; _ForwardIterator = ProcessedNxsToken*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const ProcessedNxsToken*, vector<ProcessedNxsToken> >; _ForwardIterator = ProcessedNxsToken*; _Tp = ProcessedNxsToken]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = ProcessedNxsToken; _Alloc = std::allocator<ProcessedNxsToken>]' at /usr/include/c++/14/bits/stl_vector.h:606:31,
    inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector<ProcessedNxsToken>; _Args = {const std::vector<ProcessedNxsToken, std::allocator<ProcessedNxsToken> >&}; _Tp = std::_List_node<std::vector<ProcessedNxsToken> >]' at /usr/include/c++/14/bits/new_allocator.h:191:4,
    inlined from 'static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector<ProcessedNxsToken>; _Args = {const std::vector<ProcessedNxsToken, std::allocator<ProcessedNxsToken> >&}; _Tp = std::_List_node<std::vector<ProcessedNxsToken> >]' at /usr/include/c++/14/bits/alloc_traits.h:569:17,
    inlined from 'std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const std::vector<ProcessedNxsToken, std::allocator<ProcessedNxsToken> >&}; _Tp = std::vector<ProcessedNxsToken>; _Alloc = std::allocator<std::vector<ProcessedNxsToken> >]' at /usr/include/c++/14/bits/stl_list.h:713:33,
    inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const std::vector<ProcessedNxsToken, std::allocator<ProcessedNxsToken> >&}; _Tp = std::vector<ProcessedNxsToken>; _Alloc = std::allocator<std::vector<ProcessedNxsToken> >]' at /usr/include/c++/14/bits/stl_list.h:2004:32,
    inlined from 'std::__cxx11::list<_Tp, _Alloc>::reference std::__cxx11::list<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {const std::vector<ProcessedNxsToken, std::allocator<ProcessedNxsToken> >&}; _Tp = std::vector<ProcessedNxsToken>; _Alloc = std::allocator<std::vector<ProcessedNxsToken> >]' at /usr/include/c++/14/bits/stl_list.h:1321:19,
    inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_initialize_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator<std::vector<ProcessedNxsToken> >; _Tp = std::vector<ProcessedNxsToken>; _Alloc = std::allocator<std::vector<ProcessedNxsToken> >]' at /usr/include/c++/14/bits/stl_list.h:1933:18,
    inlined from 'std::__cxx11::list<_Tp, _Alloc>::list(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = std::_List_const_iterator<std::vector<ProcessedNxsToken> >; <template-parameter-2-2> = void; _Tp = std::vector<ProcessedNxsToken>; _Alloc = std::allocator<std::vector<ProcessedNxsToken> >]' at /usr/include/c++/14/bits/stl_list.h:882:26,
    inlined from 'std::__cxx11::list<_Tp, _Alloc>::iterator std::__cxx11::list<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = std::_List_const_iterator<std::vector<ProcessedNxsToken> >; <template-parameter-2-2> = void; _Tp = std::vector<ProcessedNxsToken>; _Alloc = std::allocator<std::vector<ProcessedNxsToken> >]' at /usr/include/c++/14/bits/list.tcc:137:7,
    inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator<std::vector<ProcessedNxsToken> >; _Tp = std::vector<ProcessedNxsToken>; _Alloc = std::allocator<std::vector<ProcessedNxsToken> >]' at /usr/include/c++/14/bits/list.tcc:320:17:
/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const ProcessedNxsToken*, std::vector<ProcessedNxsToken> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
mpic++ -DHAVE_CONFIG_H -I. -I..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp
linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)':
linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
 1322 |         register int            nsq = n * n;
      |                                 ^~~
mpic++ -DHAVE_CONFIG_H -I. -I..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp
In file included from tree.h:35,
                 from individual.h:21,
                 from model.cpp:26:
reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
      |                                         ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
/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)
      |     ^~~~~~~
mpic++ -DHAVE_CONFIG_H -I. -I..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp
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)
      |     ^~~~~~~
model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)':
model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 3666 |                         fread(r+i, sizeof(FLOAT_TYPE), 1, in);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp:3675:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 3675 |                         fread(&o, sizeof(FLOAT_TYPE), 1, in);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp:3677:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 3677 |                         fread(&o, sizeof(FLOAT_TYPE), 1, in);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp:3684:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 3684 |                 fread((char*) &(b[i]), sizeof(FLOAT_TYPE), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp:3691:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 3691 |                         fread((char*) &(rateMults[i]), sizeof(FLOAT_TYPE), 1, in);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp:3692:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 3692 |                         fread((char*) &(rateProbs[i]), sizeof(FLOAT_TYPE), 1, in);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp:3699:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 3699 |                         fread((char*) &a, sizeof(FLOAT_TYPE), 1, in);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp:3705:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 3705 |                 fread((char*) &p, sizeof(FLOAT_TYPE), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp:3710:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 3710 |                 fread((char*) &x, sizeof(FLOAT_TYPE), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp:3713:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 3713 |                 fread((char*) &x, sizeof(FLOAT_TYPE), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)':
model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 4956 |                         fread(dummy, sizeof(FLOAT_TYPE), 1, in);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from tree.h:35,
                 from optimization.cpp:19:
reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
      |                                         ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
/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<num;i++)
      |                          ^
optimization.cpp: In member function 'std::pair<double, double> Tree::CalcDerivativesRateHet(TreeNode*, TreeNode*)':
optimization.cpp:1099:87: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
 1099 | pair<FLOAT_TYPE, FLOAT_TYPE> Tree::CalcDerivativesRateHet(TreeNode *nd1, TreeNode *nd2){
      |                                                                                       ^
In file included from tree.h:35,
                 from individual.h:21,
                 from population.h:31,
                 from population.cpp:45:
reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
      |                                         ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
/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<num;i++)
      |                          ^
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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
population.cpp: In member function 'void Population::RunTests()':
population.cpp:875:46: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
  875 |                 tree0->CalcDerivativesRateHet(nd->anc, nd);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
reconnode.h: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)':
reconnode.h:388:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  388 |                 fread(&unique, scalarSize, 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
reconnode.h: In constructor 'Swap::Swap(FILE*&)':
reconnode.h:264:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  264 |                 fread(&count, scalarSize, 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from treenode.h:30,
                 from tree.h:31:
bipartition.h: In member function 'void Bipartition::BinaryInput(FILE*&)':
bipartition.h:518:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  518 |                 fread((char*) rep, sizeof(unsigned int), nBlocks, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
population.cpp: In member function 'void Population::ReadPopulationCheckpoint()':
population.cpp:1880:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1880 |         fread((char *) &seed, sizeof(seed), 1, pin);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
population.cpp:1887:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1887 |         fread((char *) &t, sizeof(t), 1, pin);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
population.cpp:1896:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1896 |         fread(this, scalarSize, 1, pin);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h: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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
In file included from /usr/include/stdio.h: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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)':
population.cpp:3066:50: warning: '%d' directive writing between 1 and 9 bytes into a region of size 8 [-Wformat-overflow=]
 3066 |                                 sprintf(oStr, "R(%d)", d + 1);
      |                                                  ^~
population.cpp:3066:47: note: directive argument in the range [1, 536870911]
 3066 |                                 sprintf(oStr, "R(%d)", d + 1);
      |                                               ^~~~~~~
In function 'int sprintf(char*, const char*, ...)',
    inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 13 bytes into a destination of size 10
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
mpic++ -DHAVE_CONFIG_H -I. -I..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp
In file included from /usr/include/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
mpic++ -DHAVE_CONFIG_H -I. -I..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp
In file included from tree.h:35,
                 from individual.h:21,
                 from population.h:31,
                 from funcs.h:25,
                 from tree.cpp:33:
reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
      |                                         ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
/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<num;i++)
      |                          ^
tree.cpp: In member function 'std::pair<double, double> Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE)':
tree.cpp:8463:87: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
 8463 | pair<FLOAT_TYPE, FLOAT_TYPE> Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE optPrecision){
      |                                                                                       ^
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
      |                                         ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
/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<num;i++)
      |                          ^
tree.cpp: In member function 'void Tree::ReadBinaryFormattedTree(FILE*)':
tree.cpp:6808:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6808 |         fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6815:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6815 |         fread((char*) &lnL, sizeof(FLOAT_TYPE), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6816:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6816 |         fread((char*) &numTipsAdded, sizeof(numTipsAdded), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6817:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6817 |         fread((char*) &numNodesAdded, sizeof(numNodesAdded), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6818:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6818 |         fread((char*) &numBranchesAdded, sizeof(numBranchesAdded), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6819:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6819 |         fread((char*) &numNodesTotal, sizeof(numNodesTotal), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6823:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6823 |         fread((char*) &dum, sizeof(dum), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6826:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6826 |         fread((char*) &dum, sizeof(dum), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6829:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6829 |         fread((char*) &dum, sizeof(dum), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6833:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6833 |         fread((char*) &dum, sizeof(dum), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6837:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6837 |         fread((char*) &dum, sizeof(dum), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6841:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6841 |         fread((char*) &allNodes[0]->dlen, sizeof(FLOAT_TYPE), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6845:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6845 |                 fread(&dum, sizeof(dum), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6849:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6849 |                 fread(&dum, sizeof(dum), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6855:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6855 |                 fread(&dum, sizeof(dum), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6858:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6858 |                 fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6862:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6862 |                 fread((char*) &dum, sizeof(dum), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6865:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6865 |                 fread((char*) &dum, sizeof(dum), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6868:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6868 |                 fread((char*) &dum, sizeof(dum), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6872:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6872 |                 fread((char*) &dum, sizeof(dum), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6878:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6878 |                 fread((char*) &dum, sizeof(dum), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6881 |                 fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h: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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
In file included from /usr/include/stdio.h: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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
mpic++  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-z,relro -Wl,-z,now -L/usr/lib -o Garli adaptation.o bipartition.o condlike.o configoptions.o configreader.o datamatr.o funcs.o garlimain.o garlireader.o individual.o linalg.o model.o optimization.o population.o rng.o sequencedata.o set.o translatetable.o tree.o treenode.o mpitrick.o  -lncl -lncl
make[4]: Leaving directory '/build/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=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-ncl=/usr
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking target system type... arm-unknown-linux-gnueabihf
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /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 -j3
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..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o condlike.o condlike.cpp
In file included from bipartition.cpp:20:
reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
      |                                         ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
      |                                         ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
/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<num;i++)
      |                          ^
g++ -DHAVE_CONFIG_H -I. -I..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configoptions.o configoptions.cpp
adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)':
adaptation.cpp:271:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  271 |         fread((char *) this, 1, scalarSize, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:278:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  278 |         fread((char *) improvetotal, sizeof(FLOAT_TYPE), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:280:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  280 |         fread((char *) randNNI, sizeof(FLOAT_TYPE), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:281:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  281 |         fread((char *) randNNInum, sizeof(int), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:283:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  283 |         fread((char *) exNNI, sizeof(FLOAT_TYPE), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:284:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  284 |         fread((char *) exNNInum, sizeof(int), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:286:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  286 |         fread((char *) randSPR, sizeof(FLOAT_TYPE), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:287:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  287 |         fread((char *) randSPRnum, sizeof(int), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:289:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  289 |         fread((char *) limSPR, sizeof(FLOAT_TYPE), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:290:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  290 |         fread((char *) limSPRnum, sizeof(int), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:292:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  292 |         fread((char *) exlimSPR, sizeof(FLOAT_TYPE), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:293:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  293 |         fread((char *) exlimSPRnum, sizeof(int), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:295:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  295 |         fread((char *) randRecom, sizeof(FLOAT_TYPE), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:296:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  296 |         fread((char *) randRecomnum, sizeof(int), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:298:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  298 |         fread((char *) bipartRecom, sizeof(FLOAT_TYPE), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:299:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  299 |         fread((char *) bipartRecomnum, sizeof(int), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:301:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  301 |         fread((char *) onlyBrlen, sizeof(FLOAT_TYPE), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:302:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  302 |         fread((char *) onlyBrlennum, sizeof(int), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:304:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  304 |         fread((char *) anyModel, sizeof(FLOAT_TYPE), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
adaptation.cpp:305:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  305 |         fread((char *) anyModelnum, sizeof(int), intervalsToStore, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
In file included from /usr/include/stdio.h: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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
In file included from /usr/include/stdio.h: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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
g++ -DHAVE_CONFIG_H -I. -I..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configreader.o configreader.cpp
configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)':
configoptions.cpp:337:40: 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/arm-linux-gnueabihf/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 ());
      |                                   ~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o funcs.o funcs.cpp
In file included from tree.h:35,
                 from individual.h:21,
                 from population.h:31,
                 from funcs.h:25,
                 from configreader.cpp:30:
reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
      |                                         ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
/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<num;i++)
      |                          ^
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
      |                                         ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
/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<num;i++)
      |                          ^
configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)':
configreader.cpp:602:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  602 |         fread(&ch, sizeof(char), 1, file);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
configreader.cpp:605:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  605 |                 fread(&ch, sizeof(char), 1, file);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)':
datamatr.cpp:1390:15: 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);
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
In file included from /usr/include/stdio.h: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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
g++ -DHAVE_CONFIG_H -I. -I..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlimain.o garlimain.cpp
garlimain.cpp:434:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
  434 |                         outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__);
      |                                                                  ^~~~~~~~
garlimain.cpp:434:76: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
  434 |                         outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__);
      |                                                                            ^~~~~~~~
In file included from /usr/include/stdio.h:970,
                 from /usr/include/c++/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
g++ -DHAVE_CONFIG_H -I. -I..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlireader.o garlireader.cpp
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
      |                                         ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
/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<num;i++)
      |                          ^
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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
g++ -DHAVE_CONFIG_H -I. -I..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o individual.o individual.cpp
In file included from /usr/include/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
In file included from tree.h:35,
                 from individual.h:21,
                 from population.h:31,
                 from funcs.h:25,
                 from individual.cpp:28:
reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
      |                                         ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
/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<num;i++)
      |                          ^
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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
In file included from /usr/include/c++/14/vector:65,
                 from /usr/include/ncl/ncl.h:60:
/usr/include/c++/14/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const ProcessedNxsToken*, vector<ProcessedNxsToken> >; _ForwardIterator = ProcessedNxsToken*]':
/usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const ProcessedNxsToken*, std::vector<ProcessedNxsToken> >' changed in GCC 7.1
  113 |     __do_uninit_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const ProcessedNxsToken*, std::vector<ProcessedNxsToken> >' changed in GCC 7.1
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const ProcessedNxsToken*, std::vector<ProcessedNxsToken> >; _ForwardIterator = ProcessedNxsToken*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const ProcessedNxsToken*, vector<ProcessedNxsToken> >; _ForwardIterator = ProcessedNxsToken*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const ProcessedNxsToken*, vector<ProcessedNxsToken> >; _ForwardIterator = ProcessedNxsToken*; _Tp = ProcessedNxsToken]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37,
    inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const ProcessedNxsToken*, std::vector<ProcessedNxsToken> >; _Tp = ProcessedNxsToken; _Alloc = std::allocator<ProcessedNxsToken>]' at /usr/include/c++/14/bits/stl_vector.h:1624:35,
    inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = ProcessedNxsToken; _Alloc = std::allocator<ProcessedNxsToken>]' at /usr/include/c++/14/bits/vector.tcc:238:44,
    inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator<std::vector<ProcessedNxsToken> >; _Tp = std::vector<ProcessedNxsToken>; _Alloc = std::allocator<std::vector<ProcessedNxsToken> >]' at /usr/include/c++/14/bits/list.tcc:316:21:
/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const ProcessedNxsToken*, std::vector<ProcessedNxsToken> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const ProcessedNxsToken*, std::vector<ProcessedNxsToken> >; _ForwardIterator = ProcessedNxsToken*; bool _TrivialValueTypes = false]',
    inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const ProcessedNxsToken*, vector<ProcessedNxsToken> >; _ForwardIterator = ProcessedNxsToken*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15,
    inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const ProcessedNxsToken*, vector<ProcessedNxsToken> >; _ForwardIterator = ProcessedNxsToken*; _Tp = ProcessedNxsToken]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37,
    inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = ProcessedNxsToken; _Alloc = std::allocator<ProcessedNxsToken>]' at /usr/include/c++/14/bits/stl_vector.h:606:31,
    inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector<ProcessedNxsToken>; _Args = {const std::vector<ProcessedNxsToken, std::allocator<ProcessedNxsToken> >&}; _Tp = std::_List_node<std::vector<ProcessedNxsToken> >]' at /usr/include/c++/14/bits/new_allocator.h:191:4,
    inlined from 'static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector<ProcessedNxsToken>; _Args = {const std::vector<ProcessedNxsToken, std::allocator<ProcessedNxsToken> >&}; _Tp = std::_List_node<std::vector<ProcessedNxsToken> >]' at /usr/include/c++/14/bits/alloc_traits.h:569:17,
    inlined from 'std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const std::vector<ProcessedNxsToken, std::allocator<ProcessedNxsToken> >&}; _Tp = std::vector<ProcessedNxsToken>; _Alloc = std::allocator<std::vector<ProcessedNxsToken> >]' at /usr/include/c++/14/bits/stl_list.h:713:33,
    inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const std::vector<ProcessedNxsToken, std::allocator<ProcessedNxsToken> >&}; _Tp = std::vector<ProcessedNxsToken>; _Alloc = std::allocator<std::vector<ProcessedNxsToken> >]' at /usr/include/c++/14/bits/stl_list.h:2004:32,
    inlined from 'std::__cxx11::list<_Tp, _Alloc>::reference std::__cxx11::list<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {const std::vector<ProcessedNxsToken, std::allocator<ProcessedNxsToken> >&}; _Tp = std::vector<ProcessedNxsToken>; _Alloc = std::allocator<std::vector<ProcessedNxsToken> >]' at /usr/include/c++/14/bits/stl_list.h:1321:19,
    inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_initialize_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator<std::vector<ProcessedNxsToken> >; _Tp = std::vector<ProcessedNxsToken>; _Alloc = std::allocator<std::vector<ProcessedNxsToken> >]' at /usr/include/c++/14/bits/stl_list.h:1933:18,
    inlined from 'std::__cxx11::list<_Tp, _Alloc>::list(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = std::_List_const_iterator<std::vector<ProcessedNxsToken> >; <template-parameter-2-2> = void; _Tp = std::vector<ProcessedNxsToken>; _Alloc = std::allocator<std::vector<ProcessedNxsToken> >]' at /usr/include/c++/14/bits/stl_list.h:882:26,
    inlined from 'std::__cxx11::list<_Tp, _Alloc>::iterator std::__cxx11::list<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = std::_List_const_iterator<std::vector<ProcessedNxsToken> >; <template-parameter-2-2> = void; _Tp = std::vector<ProcessedNxsToken>; _Alloc = std::allocator<std::vector<ProcessedNxsToken> >]' at /usr/include/c++/14/bits/list.tcc:137:7,
    inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator<std::vector<ProcessedNxsToken> >; _Tp = std::vector<ProcessedNxsToken>; _Alloc = std::allocator<std::vector<ProcessedNxsToken> >]' at /usr/include/c++/14/bits/list.tcc:320:17:
/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const ProcessedNxsToken*, std::vector<ProcessedNxsToken> >' changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp
linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)':
linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
 1322 |         register int            nsq = n * n;
      |                                 ^~~
g++ -DHAVE_CONFIG_H -I. -I..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp
In file included from tree.h:35,
                 from individual.h:21,
                 from model.cpp:26:
reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
      |                                         ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
      |                                         ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
/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<num;i++)
      |                          ^
optimization.cpp: In member function 'std::pair<double, double> Tree::CalcDerivativesRateHet(TreeNode*, TreeNode*)':
optimization.cpp:1099:87: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
 1099 | pair<FLOAT_TYPE, FLOAT_TYPE> Tree::CalcDerivativesRateHet(TreeNode *nd1, TreeNode *nd2){
      |                                                                                       ^
model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)':
model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 3666 |                         fread(r+i, sizeof(FLOAT_TYPE), 1, in);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp:3675:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 3675 |                         fread(&o, sizeof(FLOAT_TYPE), 1, in);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp:3677:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 3677 |                         fread(&o, sizeof(FLOAT_TYPE), 1, in);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp:3684:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 3684 |                 fread((char*) &(b[i]), sizeof(FLOAT_TYPE), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp:3691:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 3691 |                         fread((char*) &(rateMults[i]), sizeof(FLOAT_TYPE), 1, in);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp:3692:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 3692 |                         fread((char*) &(rateProbs[i]), sizeof(FLOAT_TYPE), 1, in);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp:3699:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 3699 |                         fread((char*) &a, sizeof(FLOAT_TYPE), 1, in);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp:3705:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 3705 |                 fread((char*) &p, sizeof(FLOAT_TYPE), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp:3710:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 3710 |                 fread((char*) &x, sizeof(FLOAT_TYPE), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp:3713:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 3713 |                 fread((char*) &x, sizeof(FLOAT_TYPE), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)':
model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 4956 |                         fread(dummy, sizeof(FLOAT_TYPE), 1, in);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from tree.h:35,
                 from individual.h:21,
                 from population.h:31,
                 from population.cpp:45:
reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
      |                                         ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
/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<num;i++)
      |                          ^
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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
In file included from /usr/include/stdio.h: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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
population.cpp: In member function 'void Population::RunTests()':
population.cpp:875:46: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
  875 |                 tree0->CalcDerivativesRateHet(nd->anc, nd);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
reconnode.h: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)':
reconnode.h:388:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  388 |                 fread(&unique, scalarSize, 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
reconnode.h: In constructor 'Swap::Swap(FILE*&)':
reconnode.h:264:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  264 |                 fread(&count, scalarSize, 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from treenode.h:30,
                 from tree.h:31:
bipartition.h: In member function 'void Bipartition::BinaryInput(FILE*&)':
bipartition.h:518:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  518 |                 fread((char*) rep, sizeof(unsigned int), nBlocks, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
population.cpp: In member function 'void Population::ReadPopulationCheckpoint()':
population.cpp:1880:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1880 |         fread((char *) &seed, sizeof(seed), 1, pin);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
population.cpp:1887:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1887 |         fread((char *) &t, sizeof(t), 1, pin);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
population.cpp:1896:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1896 |         fread(this, scalarSize, 1, pin);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h: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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
g++ -DHAVE_CONFIG_H -I. -I..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp
population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)':
population.cpp:3066:50: warning: '%d' directive writing between 1 and 9 bytes into a region of size 8 [-Wformat-overflow=]
 3066 |                                 sprintf(oStr, "R(%d)", d + 1);
      |                                                  ^~
population.cpp:3066:47: note: directive argument in the range [1, 536870911]
 3066 |                                 sprintf(oStr, "R(%d)", d + 1);
      |                                               ^~~~~~~
In function 'int sprintf(char*, const char*, ...)',
    inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 13 bytes into a destination of size 10
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp
In file included from /usr/include/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
g++ -DHAVE_CONFIG_H -I. -I..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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..  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp
In file included from tree.h:35,
                 from individual.h:21,
                 from population.h:31,
                 from funcs.h:25,
                 from tree.cpp:33:
reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
      |                                         ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
      |                         ^~~~~~~~~~~~~~~
/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<num;i++)
      |                          ^
tree.cpp: In member function 'std::pair<double, double> Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE)':
tree.cpp:8463:87: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
 8463 | pair<FLOAT_TYPE, FLOAT_TYPE> Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE optPrecision){
      |                                                                                       ^
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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
tree.cpp: In member function 'void Tree::ReadBinaryFormattedTree(FILE*)':
tree.cpp:6808:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6808 |         fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6815:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6815 |         fread((char*) &lnL, sizeof(FLOAT_TYPE), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6816:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6816 |         fread((char*) &numTipsAdded, sizeof(numTipsAdded), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6817:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6817 |         fread((char*) &numNodesAdded, sizeof(numNodesAdded), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6818:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6818 |         fread((char*) &numBranchesAdded, sizeof(numBranchesAdded), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6819:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6819 |         fread((char*) &numNodesTotal, sizeof(numNodesTotal), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6823:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6823 |         fread((char*) &dum, sizeof(dum), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6826:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6826 |         fread((char*) &dum, sizeof(dum), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6829:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6829 |         fread((char*) &dum, sizeof(dum), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6833:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6833 |         fread((char*) &dum, sizeof(dum), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6837:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6837 |         fread((char*) &dum, sizeof(dum), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6841:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6841 |         fread((char*) &allNodes[0]->dlen, sizeof(FLOAT_TYPE), 1, in);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6845:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6845 |                 fread(&dum, sizeof(dum), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6849:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6849 |                 fread(&dum, sizeof(dum), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6855:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6855 |                 fread(&dum, sizeof(dum), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6858:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6858 |                 fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6862:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6862 |                 fread((char*) &dum, sizeof(dum), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6865:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6865 |                 fread((char*) &dum, sizeof(dum), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6868:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6868 |                 fread((char*) &dum, sizeof(dum), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6872:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6872 |                 fread((char*) &dum, sizeof(dum), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6878:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6878 |                 fread((char*) &dum, sizeof(dum), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 6881 |                 fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in);
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h: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/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
g++  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-z,relro -Wl,-z,now -L/usr/lib -o Garli adaptation.o bipartition.o condlike.o configoptions.o configreader.o datamatr.o funcs.o garlimain.o garlireader.o individual.o linalg.o model.o optimization.o population.o rng.o sequencedata.o set.o translatetable.o tree.o treenode.o mpitrick.o  -lncl -lncl
make[3]: Leaving directory '/build/reproducible-path/garli-2.1/src'
Making all in tests
make[3]: Entering directory '/build/reproducible-path/garli-2.1/tests'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/build/reproducible-path/garli-2.1/tests'
make[3]: Entering directory '/build/reproducible-path/garli-2.1'
make[3]: Leaving directory '/build/reproducible-path/garli-2.1'
make[2]: Leaving directory '/build/reproducible-path/garli-2.1'
make[1]: Leaving directory '/build/reproducible-path/garli-2.1'
   debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/garli-2.1'
cp -a tests tests.bak
# get (mostly!) reproducible test results and avoid failures as described in bug #907905
find tests -name "*.conf" -exec sed -i~ 's/randseed *= *-1/randseed = 1\nbootstrapseed = 42/' \{\} \;
dh_auto_test
	make -j3 check "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1
make[2]: Entering directory '/build/reproducible-path/garli-2.1'
Making check in src
make[3]: Entering directory '/build/reproducible-path/garli-2.1/src'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/reproducible-path/garli-2.1/src'
Making check in tests
make[3]: Entering directory '/build/reproducible-path/garli-2.1/tests'
make  check-local
make[4]: Entering directory '/build/reproducible-path/garli-2.1/tests'
./runtests.sh . ../src/Garli /usr/bin/NEXUSvalidator
Linking to data ....
data folder already exists
**************************
Running internal tests ...
**************************
Running internal test ./internal/a.G3.conf
Running internal test ./internal/a.G3.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./internal/a.G3.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/moore.matK90-120.nex ...
Reading DATA block...storing implied block: TAXA
storing read block: DATA
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Amino acid data
WARNING: Not all amino acids were observed in this dataset.
	One pseudo-count will be added to each amino acid
	for calculation of the empirical frequencies. You
	should probably use a statefrequencies setting other 
	than emprical.

	Summary of data:
	  86 sequences.
	  2 constant characters.
	  6 parsimony-informative characters.
	  2 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 5 MB
  good			approx 4 MB to 2 MB
  low			approx 2 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 5.8 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Loading starting model and/or tree from file data/moore.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN
starting internal tests...
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 20 (amino acid data)
  Amino Acid Rate Matrix: Jones
  Equilibrium State Frequencies: empirical (observed) values (+F)
    (ACDEFGHIKLMNPQRSTVWY)
    0.0088 0.0022 0.0131 0.3020 0.0985 
    0.0088 0.0109 0.0284 0.0810 0.0503 
    0.1794 0.0022 0.0044 0.1575 0.0109 
    0.0109 0.0044 0.0044 0.0022 0.0197 
  Rate Heterogeneity Model:
    3 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.0500
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0500
      0.0603	0.3167
      0.4894	0.3167
      2.4503	0.3167

Starting with seed=1

WARNING: Polytomies found in start tree.  These were arbitrarily resolved.
Initial ln Likelihood: -534.6163
optimizing: starting branch lengths, alpha shape, prop. invar...
pass 1:+   97.093 (branch=  90.61 scale=  6.48 alpha=  0.00 pinv=  0.00)
pass 2:+   26.504 (branch=  20.56 scale=  5.94 alpha=  0.00 pinv=  0.00)
pass 3:+    7.183 (branch=   6.27 scale=  0.91 alpha=  0.00 pinv=  0.00)
pass 4:+    2.513 (branch=   1.73 scale=  0.78 alpha=  0.00 pinv=  0.00)
pass 5:+    1.030 (branch=   0.48 scale=  0.55 alpha=  0.00 pinv=  0.00)
pass 6:+    0.375 (branch=   0.37 scale=  0.00 alpha=  0.00 pinv=  0.00)
lnL after optimization: -399.9190
WARNING: You are running internal tests with NDEBUG defined!
It should not be defined for full error checking.
******Successfully completed tests.******
Running internal test ./internal/a.G4.conf
Running internal test ./internal/a.G4.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./internal/a.G4.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/moore.matK90-120.nex ...
Reading DATA block...storing implied block: TAXA
storing read block: DATA
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Amino acid data
WARNING: Not all amino acids were observed in this dataset.
	One pseudo-count will be added to each amino acid
	for calculation of the empirical frequencies. You
	should probably use a statefrequencies setting other 
	than emprical.

	Summary of data:
	  86 sequences.
	  2 constant characters.
	  6 parsimony-informative characters.
	  2 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 6 MB
  good			approx 5 MB to 4 MB
  low			approx 3 MB to 2 MB
  very low		approx 2 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 7.7 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Loading starting model and/or tree from file data/moore.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN
starting internal tests...
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 20 (amino acid data)
  Amino Acid Rate Matrix: Jones
  Equilibrium State Frequencies: empirical (observed) values (+F)
    (ACDEFGHIKLMNPQRSTVWY)
    0.0088 0.0022 0.0131 0.3020 0.0985 
    0.0088 0.0109 0.0284 0.0810 0.0503 
    0.1794 0.0022 0.0044 0.1575 0.0109 
    0.0109 0.0044 0.0044 0.0022 0.0197 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.0500
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0500
      0.0334	0.2375
      0.2519	0.2375
      0.8203	0.2375
      2.8944	0.2375

Starting with seed=1

WARNING: Polytomies found in start tree.  These were arbitrarily resolved.
Initial ln Likelihood: -532.4673
optimizing: starting branch lengths, alpha shape, prop. invar...
pass 1:+   92.949 (branch=  88.74 scale=  4.20 alpha=  0.00 pinv=  0.00)
pass 2:+   25.801 (branch=  20.07 scale=  5.73 alpha=  0.00 pinv=  0.00)
pass 3:+    9.142 (branch=   7.26 scale=  1.88 alpha=  0.00 pinv=  0.00)
pass 4:+    3.445 (branch=   2.67 scale=  0.78 alpha=  0.00 pinv=  0.00)
pass 5:+    0.802 (branch=   0.25 scale=  0.55 alpha=  0.00 pinv=  0.00)
pass 6:+    0.294 (branch=   0.29 scale=  0.00 alpha=  0.00 pinv=  0.00)
lnL after optimization: -400.0333
WARNING: You are running internal tests with NDEBUG defined!
It should not be defined for full error checking.
******Successfully completed tests.******
Running internal test ./internal/a.conf
Running internal test ./internal/a.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./internal/a.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/moore.matK90-120.nex ...
Reading DATA block...storing implied block: TAXA
storing read block: DATA
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Amino acid data
WARNING: Not all amino acids were observed in this dataset.
	One pseudo-count will be added to each amino acid
	for calculation of the empirical frequencies. You
	should probably use a statefrequencies setting other 
	than emprical.

	Summary of data:
	  86 sequences.
	  2 constant characters.
	  6 parsimony-informative characters.
	  2 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 2 MB
  good			approx 2 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 2.0 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Loading starting model and/or tree from file data/moore.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN
starting internal tests...
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 20 (amino acid data)
  Amino Acid Rate Matrix: Jones
  Equilibrium State Frequencies: empirical (observed) values (+F)
    (ACDEFGHIKLMNPQRSTVWY)
    0.0088 0.0022 0.0131 0.3020 0.0985 
    0.0088 0.0109 0.0284 0.0810 0.0503 
    0.1794 0.0022 0.0044 0.1575 0.0109 
    0.0109 0.0044 0.0044 0.0022 0.0197 
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

WARNING: Polytomies found in start tree.  These were arbitrarily resolved.
NOTE: Model contains no mutable parameters!
Setting model mutation weight to zero.

Initial ln Likelihood: -567.2416
optimizing: starting branch lengths...
pass 1:+  135.572 (branch= 118.31 scale= 17.26)
pass 2:+   21.497 (branch=  16.34 scale=  5.15)
pass 3:+    6.821 (branch=   6.09 scale=  0.73)
pass 4:+    2.066 (branch=   1.47 scale=  0.59)
pass 5:+    1.595 (branch=   1.59 scale=  0.00)
pass 6:+    1.322 (branch=   0.81 scale=  0.51)
pass 7:+    0.354 (branch=   0.35 scale=  0.00)
lnL after optimization: -398.0145
WARNING: You are running internal tests with NDEBUG defined!
It should not be defined for full error checking.
******Successfully completed tests.******
Running internal test ./internal/c.M3x2.conf
Running internal test ./internal/c.M3x2.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./internal/c.M3x2.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/z.11x30.stop.nex ...
Reading DATA block...storing implied block: TAXA
storing read block: DATA
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Codon data
Warning: stop codon TAA found at codon site 11 (nuc site 31) in taxon MorNa6.
	Treating as missing data because ignorestopcodons = 1 is set in configuration file.
Warning: stop codon TAA found at codon site 11 (nuc site 31) in taxon ClownNa6.
	Treating as missing data because ignorestopcodons = 1 is set in configuration file.
Base usage at codon positions:
                A         C         G         T
 pos 1      0.27184   0.35922   0.21359   0.15534
 pos 2      0.32039   0.20388   0.07767   0.39806
 pos 3      0.12621   0.37864   0.26214   0.23301
 all pos    0.23948   0.31392   0.18447   0.26214

	Summary of data:
	  11 sequences.
	  0 constant characters.
	  9 parsimony-informative characters.
	  1 uninformative variable characters.
	  1 characters were completely missing or ambiguous (removed).
	  10 total characters (11 before removing empty columns).
	  10 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 1.3 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
STARTING RUN
starting internal tests...
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 61 (codon data, standard code)
  Nucleotide Relative Rate Matrix Assumed by Codon Model:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: 
    empirical values calculated by F3x4 method (fixed)
    (AAA, AAC, AAG, AAT, ACA, ... etc)
    0.0112 0.0337 0.0233 0.0207 0.0071 
    0.0214 0.0148 0.0132 0.0027 0.0082 
    0.0057 0.0050 0.0139 0.0418 0.0290 
    0.0258 0.0148 0.0445 0.0308 0.0274 
    0.0094 0.0283 0.0196 0.0174 0.0036 
    0.0108 0.0075 0.0066 0.0184 0.0553 
    0.0383 0.0340 0.0088 0.0265 0.0183 
    0.0163 0.0056 0.0168 0.0117 0.0104 
    0.0021 0.0064 0.0044 0.0039 0.0110 
    0.0329 0.0228 0.0202 0.0192 0.0118 
    0.0041 0.0122 0.0085 0.0075 0.0047 
    0.0032 0.0029 0.0080 0.0239 0.0166 
    0.0147 
  Rate Heterogeneity Model:
    2 nonsynonymous rate categories, rate and proportion of each estimated
     (this is effectively the M3 model of PAML)
      dN/dS	Proportion
      0.2500	0.5000
      0.5000	0.5000

Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 4.421 lnL
Optimizing branchlengths... improved 0.690 lnL
 7  8  9  10  11 
Initial ln Likelihood: -215.5693
optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters...
pass 1:+    6.143 (branch=   0.00 scale=  0.00 omega=  0.01 rel rates=  6.13)
pass 2:+    0.420 (branch=   0.00 scale=  0.00 omega=  0.01 rel rates=  0.41)
lnL after optimization: -209.0069
WARNING: You are running internal tests with NDEBUG defined!
It should not be defined for full error checking.
******Successfully completed tests.******
Running internal test ./internal/c.conf
Running internal test ./internal/c.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./internal/c.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Codon data
Base usage at codon positions:
                A         C         G         T
 pos 1      0.27723   0.36634   0.21782   0.13861
 pos 2      0.30693   0.20792   0.07921   0.40594
 pos 3      0.10891   0.38614   0.26733   0.23762
 all pos    0.23102   0.32013   0.18812   0.26073

	Summary of data:
	  11 sequences.
	  0 constant characters.
	  9 parsimony-informative characters.
	  1 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.6 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
STARTING RUN
starting internal tests...
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 61 (codon data, standard code)
  One estimated dN/dS ratio (aka omega) = 0.250000
  Nucleotide Relative Rate Matrix Assumed by Codon Model:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: 
    empirical values calculated by F3x4 method (fixed)
    (AAA, AAC, AAG, AAT, ACA, ... etc)
    0.0094 0.0334 0.0231 0.0206 0.0064 
    0.0226 0.0157 0.0139 0.0024 0.0086 
    0.0060 0.0053 0.0125 0.0442 0.0306 
    0.0272 0.0125 0.0442 0.0306 0.0272 
    0.0084 0.0299 0.0207 0.0184 0.0032 
    0.0114 0.0079 0.0070 0.0165 0.0584 
    0.0405 0.0360 0.0074 0.0263 0.0182 
    0.0162 0.0050 0.0178 0.0123 0.0110 
    0.0019 0.0068 0.0047 0.0042 0.0098 
    0.0347 0.0241 0.0214 0.0167 0.0103 
    0.0032 0.0113 0.0078 0.0070 0.0043 
    0.0030 0.0027 0.0062 0.0221 0.0153 
    0.0136 
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 0.001 lnL
Optimizing branchlengths... improved 0.000 lnL
 7  8  9  10  11 
Initial ln Likelihood: -225.6424
optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters...
pass 1:+   10.932 (branch=   2.26 scale=  0.50 omega=  0.00 rel rates=  8.17)
pass 2:+    0.925 (branch=   0.64 scale=  0.00 omega=  0.28 rel rates=  0.00)
pass 3:+    0.733 (branch=   0.04 scale=  0.68 omega=  0.01 rel rates=  0.00)
pass 4:+    0.015 (branch=   0.00 scale=  0.00 omega=  0.01 rel rates=  0.00)
lnL after optimization: -213.0377
WARNING: You are running internal tests with NDEBUG defined!
It should not be defined for full error checking.
******Successfully completed tests.******
Running internal test ./internal/n.G3.conf
Running internal test ./internal/n.G3.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./internal/n.G3.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/moore.matK90-120.nex ...
Reading DATA block...storing implied block: TAXA
storing read block: DATA
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  86 sequences.
	  10 constant characters.
	  13 parsimony-informative characters.
	  7 uninformative variable characters.
	  30 total characters.
	  24 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 2 MB
  good			approx 2 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 2.9 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1

#######################################################
STARTING RUN
starting internal tests...
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.4638 0.0976 0.2304 0.2082 
  Rate Heterogeneity Model:
    3 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.0833
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0833
      0.0603	0.3056
      0.4894	0.3056
      2.4503	0.3056

Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6  7  8  9  10  11  12  13  14  15  16  17  18  19  20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39  40  41  42  43  44 
Optimizing parameters... improved 2.070 lnL
Optimizing branchlengths... improved 1.544 lnL
 45  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79  80  81  82  83  84  85  86 
Initial ln Likelihood: -351.3160
optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs...
pass 1:+   11.635 (branch=   3.88 scale=  0.50 alpha=  0.97 freqs=  0.05 rel rates=  6.23 pinv=  0.01)
pass 2:+    1.385 (branch=   0.93 scale=  0.41 alpha=  0.00 freqs=  0.03 rel rates=  0.00 pinv=  0.01)
pass 3:+    0.338 (branch=   0.30 scale=  0.00 alpha=  0.00 freqs=  0.03 rel rates=  0.00 pinv=  0.01)
lnL after optimization: -337.9573
WARNING: You are running internal tests with NDEBUG defined!
It should not be defined for full error checking.
******Successfully completed tests.******
Running internal test ./internal/n.G4.conf
Running internal test ./internal/n.G4.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./internal/n.G4.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/moore.matK90-120.nex ...
Reading DATA block...storing implied block: TAXA
storing read block: DATA
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  86 sequences.
	  10 constant characters.
	  13 parsimony-informative characters.
	  7 uninformative variable characters.
	  30 total characters.
	  24 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 4 MB
  good			approx 3 MB to 2 MB
  low			approx 2 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 3.8 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1

#######################################################
STARTING RUN
starting internal tests...
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.4638 0.0976 0.2304 0.2082 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.0833
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0833
      0.0334	0.2292
      0.2519	0.2292
      0.8203	0.2292
      2.8944	0.2292

Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6  7  8  9  10  11  12  13  14  15  16  17  18  19  20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39  40  41  42  43  44 
Optimizing parameters... improved 2.099 lnL
Optimizing branchlengths... improved 1.492 lnL
 45  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79  80  81  82  83  84  85  86 
Initial ln Likelihood: -363.1701
optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs...
pass 1:+   13.147 (branch=   2.38 scale=  2.97 alpha=  0.67 freqs=  1.24 rel rates=  5.88 pinv=  0.01)
pass 2:+    2.663 (branch=   2.63 scale=  0.00 alpha=  0.00 freqs=  0.03 rel rates=  0.00 pinv=  0.00)
pass 3:+    0.035 (branch=   0.00 scale=  0.00 alpha=  0.00 freqs=  0.03 rel rates=  0.00 pinv=  0.00)
lnL after optimization: -347.3249
WARNING: You are running internal tests with NDEBUG defined!
It should not be defined for full error checking.
******Successfully completed tests.******
Running internal test ./internal/n.conf
Running internal test ./internal/n.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./internal/n.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/moore.matK90-120.nex ...
Reading DATA block...storing implied block: TAXA
storing read block: DATA
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  86 sequences.
	  10 constant characters.
	  13 parsimony-informative characters.
	  7 uninformative variable characters.
	  30 total characters.
	  24 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 1.0 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1

#######################################################
STARTING RUN
starting internal tests...
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     1 rate
  Equilibrium State Frequencies: estimated
    (ACGT) 0.4638 0.0976 0.2304 0.2082 
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6  7  8  9  10  11  12  13  14  15  16  17  18  19  20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39  40  41  42  43  44 
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 2.038 lnL
 45  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79  80  81  82  83  84  85  86 
Initial ln Likelihood: -371.0442
optimizing: starting branch lengths, eq freqs...
pass 1:+    3.897 (branch=   2.20 scale=  0.00 freqs=  1.70)
pass 2:+    0.641 (branch=   0.60 scale=  0.00 freqs=  0.04)
pass 3:+    0.073 (branch=   0.03 scale=  0.00 freqs=  0.04)
lnL after optimization: -366.4339
WARNING: You are running internal tests with NDEBUG defined!
It should not be defined for full error checking.
******Successfully completed tests.******
Running internal test ./internal/p.3diff.conf
Running internal test ./internal/p.3diff.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./internal/p.3diff.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/z.byPos.11x2178.nex ...
Reading DATA block...storing implied block: TAXA
storing read block: DATA
 successful
Reading SETS block...storing read block: SETS
 successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS

CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY
	TO EACH DATA SUBSET (no linkage)

GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	CHARPARTITION subset #1 ("1stpos")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Excluded character numbers: 4
	
	Summary of data:
	  11 sequences.
	  441 constant characters.
	  171 parsimony-informative characters.
	  113 uninformative variable characters.
	  725 total characters.
	  237 unique patterns in compressed data matrix.
GARLI data subset 2
	CHARACTERS block #1 ("Untitled DATA Block 1")
	CHARPARTITION subset #2 ("2ndpos")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Excluded character numbers: 5
	
	Summary of data:
	  11 sequences.
	  527 constant characters.
	  90 parsimony-informative characters.
	  108 uninformative variable characters.
	  725 total characters.
	  158 unique patterns in compressed data matrix.
GARLI data subset 3
	CHARACTERS block #1 ("Untitled DATA Block 1")
	CHARPARTITION subset #3 ("3rdpos")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Excluded character numbers: 6
	
	Summary of data:
	  11 sequences.
	  102 constant characters.
	  507 parsimony-informative characters.
	  116 uninformative variable characters.
	  725 total characters.
	  548 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 11 MB
  good			approx 10 MB to 9 MB
  low			approx 8 MB to 5 MB
  very low		approx 4 MB to 4 MB
the minimum required availablememory is 4 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 16.0 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
STARTING RUN
starting internal tests...
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix: 
    User specified matrix type: ( 0 1 2 2 3 4 ) 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.3150 0.1749 0.3006 0.2095 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    Substitution rate categories under this model:
      rate	proportion
      0.0334	0.2500
      0.2519	0.2500
      0.8203	0.2500
      2.8944	0.2500

Model 2
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix: 
    User specified matrix type: ( 0 1 2 1 0 3 ) 
    AC = 4.000, AG = 4.000, AT = 1.000, CG = 4.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2706 0.1568 0.1630 0.4096 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    Substitution rate categories under this model:
      rate	proportion
      0.0334	0.2500
      0.2519	0.2500
      0.8203	0.2500
      2.8944	0.2500

Model 3
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix: 
    User specified matrix type: ( 0 1 2 3 1 0 ) 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.1462 0.3614 0.2906 0.2018 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.0352
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0352
      0.0334	0.2412
      0.2519	0.2412
      0.8203	0.2412
      2.8944	0.2412

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 168.526 lnL
Optimizing branchlengths... improved 66.084 lnL
 7  8  9  10  11 
Initial ln Likelihood: -13699.7841
optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates...
pass 1:+  209.568 (branch=   7.95 scale=  0.00 alpha= 35.56 freqs= 28.70 rel rates= 62.31 pinv=  0.00 subset rates= 75.04)
pass 2:+   77.990 (branch=   2.27 scale=  0.00 alpha=  4.14 freqs= 11.22 rel rates=  3.32 pinv=  0.86 subset rates= 56.18)
pass 3:+   48.437 (branch=   6.88 scale=  0.73 alpha=  4.15 freqs=  1.22 rel rates=  1.34 pinv=  0.01 subset rates= 34.10)
pass 4:+   15.263 (branch=   0.00 scale=  0.79 alpha=  0.64 freqs=  1.21 rel rates=  0.57 pinv=  0.01 subset rates= 12.04)
pass 5:+    5.799 (branch=   0.00 scale=  0.00 alpha=  0.01 freqs=  0.10 rel rates=  0.77 pinv=  0.02 subset rates=  4.91)
pass 6:+    0.133 (branch=   0.00 scale=  0.00 alpha=  0.01 freqs=  0.10 rel rates=  0.01 pinv=  0.01 subset rates=  0.00)
lnL after optimization: -13342.5949
WARNING: You are running internal tests with NDEBUG defined!
It should not be defined for full error checking.
******Successfully completed tests.******
Running internal test ./internal/p.mk.conf
Running internal test ./internal/p.mk.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./internal/p.mk.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard k-state data,
	modeled as Standard k-state data
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 1 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.4 MB of memory

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN
starting internal tests...
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

NOTE: Model contains no mutable parameters!
Setting model mutation weight to zero.

Initial ln Likelihood: -609.1934
optimizing: starting branch lengths...
pass 1:+  125.912 (branch= 124.97 scale=  0.94)
pass 2:+    7.205 (branch=   7.20 scale=  0.00)
pass 3:+    1.518 (branch=   1.48 scale=  0.03)
pass 4:+    0.225 (branch=   0.22 scale=  0.00)
pass 5:+    0.014 (branch=   0.01 scale=  0.00)
pass 6:+    0.000 (branch=   0.00 scale=  0.00)
lnL after optimization: -474.3188
WARNING: You are running internal tests with NDEBUG defined!
It should not be defined for full error checking.
******Successfully completed tests.******
Running internal test ./internal/p.mk.ssr.conf
Running internal test ./internal/p.mk.ssr.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./internal/p.mk.ssr.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard k-state data,
	modeled as Standard k-state data
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 1 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.4 MB of memory

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN
starting internal tests...
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=1

Initial ln Likelihood: -609.1934
optimizing: starting branch lengths, subset rates...
pass 1:+  130.207 (branch= 124.97 scale=  0.94 subset rates=  4.29)
pass 2:+    9.055 (branch=   8.14 scale=  0.00 subset rates=  0.91)
pass 3:+    1.801 (branch=   1.66 scale=  0.02 subset rates=  0.12)
pass 4:+    0.304 (branch=   0.30 scale=  0.00 subset rates=  0.00)
pass 5:+    0.012 (branch=   0.01 scale=  0.00 subset rates=  0.00)
pass 6:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
lnL after optimization: -467.8138
WARNING: You are running internal tests with NDEBUG defined!
It should not be defined for full error checking.
******Successfully completed tests.******
Running internal test ./internal/p.mkO.conf
Running internal test ./internal/p.mkO.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./internal/p.mkO.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard ordered k-state data,
	modeled as Standard ordered k-state data
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 1 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.4 MB of memory

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN
starting internal tests...
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

NOTE: Model contains no mutable parameters!
Setting model mutation weight to zero.

Initial ln Likelihood: -641.9257
optimizing: starting branch lengths...
pass 1:+  137.411 (branch= 136.58 scale=  0.83)
pass 2:+    7.774 (branch=   7.77 scale=  0.00)
pass 3:+    1.542 (branch=   1.52 scale=  0.02)
pass 4:+    0.091 (branch=   0.09 scale=  0.00)
pass 5:+    0.000 (branch=   0.00 scale=  0.00)
lnL after optimization: -495.1076
WARNING: You are running internal tests with NDEBUG defined!
It should not be defined for full error checking.
******Successfully completed tests.******
Running internal test ./internal/p.mkO.ssr.conf
Running internal test ./internal/p.mkO.ssr.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./internal/p.mkO.ssr.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard ordered k-state data,
	modeled as Standard ordered k-state data
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 1 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.4 MB of memory

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN
starting internal tests...
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=1

Initial ln Likelihood: -641.9257
optimizing: starting branch lengths, subset rates...
pass 1:+  147.096 (branch= 136.58 scale=  0.83 subset rates=  9.68)
pass 2:+   12.451 (branch=   8.46 scale=  0.00 subset rates=  3.99)
pass 3:+    3.549 (branch=   2.32 scale=  0.03 subset rates=  1.20)
pass 4:+    0.759 (branch=   0.51 scale=  0.00 subset rates=  0.25)
pass 5:+    0.120 (branch=   0.11 scale=  0.00 subset rates=  0.01)
pass 6:+    0.011 (branch=   0.01 scale=  0.00 subset rates=  0.00)
pass 7:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
lnL after optimization: -477.9402
WARNING: You are running internal tests with NDEBUG defined!
It should not be defined for full error checking.
******Successfully completed tests.******
Running internal test ./internal/p.mkv.conf
Running internal test ./internal/p.mkv.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./internal/p.mkv.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard k-state data, variable only,
	modeled as Standard k-state data, variable only
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 1 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.5 MB of memory

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN
starting internal tests...
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

NOTE: Model contains no mutable parameters!
Setting model mutation weight to zero.

Initial ln Likelihood: -605.5989
optimizing: starting branch lengths...
pass 1:+  124.584 (branch= 123.99 scale=  0.59)
pass 2:+    6.980 (branch=   6.98 scale=  0.00)
pass 3:+    1.324 (branch=   1.31 scale=  0.02)
pass 4:+    0.161 (branch=   0.16 scale=  0.00)
pass 5:+    0.013 (branch=   0.01 scale=  0.00)
pass 6:+    0.000 (branch=   0.00 scale=  0.00)
lnL after optimization: -472.5370
WARNING: You are running internal tests with NDEBUG defined!
It should not be defined for full error checking.
******Successfully completed tests.******
Running internal test ./internal/p.mkv.ssr.conf
Running internal test ./internal/p.mkv.ssr.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./internal/p.mkv.ssr.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard k-state data, variable only,
	modeled as Standard k-state data, variable only
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 1 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.5 MB of memory

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN
starting internal tests...
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=1

Initial ln Likelihood: -605.5989
optimizing: starting branch lengths, subset rates...
pass 1:+  129.564 (branch= 123.99 scale=  0.59 subset rates=  4.98)
pass 2:+    9.272 (branch=   7.97 scale=  0.00 subset rates=  1.30)
pass 3:+    1.741 (branch=   1.57 scale=  0.00 subset rates=  0.17)
pass 4:+    0.311 (branch=   0.31 scale=  0.00 subset rates=  0.00)
pass 5:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
lnL after optimization: -464.7113
WARNING: You are running internal tests with NDEBUG defined!
It should not be defined for full error checking.
******Successfully completed tests.******
Running internal test ./internal/p.mkvO.conf
Running internal test ./internal/p.mkvO.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./internal/p.mkvO.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard ordered k-state data, variable only,
	modeled as Standard ordered k-state data, variable only
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 1 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.5 MB of memory

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN
starting internal tests...
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

NOTE: Model contains no mutable parameters!
Setting model mutation weight to zero.

Initial ln Likelihood: -637.9212
optimizing: starting branch lengths...
pass 1:+  134.883 (branch= 134.40 scale=  0.48)
pass 2:+    7.290 (branch=   7.29 scale=  0.00)
pass 3:+    1.758 (branch=   1.73 scale=  0.03)
pass 4:+    0.187 (branch=   0.19 scale=  0.00)
pass 5:+    0.011 (branch=   0.01 scale=  0.00)
pass 6:+    0.000 (branch=   0.00 scale=  0.00)
lnL after optimization: -493.7915
WARNING: You are running internal tests with NDEBUG defined!
It should not be defined for full error checking.
******Successfully completed tests.******
Running internal test ./internal/p.mkvO.ssr.conf
Running internal test ./internal/p.mkvO.ssr.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./internal/p.mkvO.ssr.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard ordered k-state data, variable only,
	modeled as Standard ordered k-state data, variable only
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 1 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.5 MB of memory

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN
starting internal tests...
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=1

Initial ln Likelihood: -637.9212
optimizing: starting branch lengths, subset rates...
pass 1:+  144.867 (branch= 134.40 scale=  0.48 subset rates=  9.98)
pass 2:+   12.967 (branch=   8.30 scale=  0.00 subset rates=  4.67)
pass 3:+    3.846 (branch=   2.24 scale=  0.02 subset rates=  1.58)
pass 4:+    1.162 (branch=   0.58 scale=  0.01 subset rates=  0.57)
pass 5:+    0.156 (branch=   0.12 scale=  0.00 subset rates=  0.03)
pass 6:+    0.044 (branch=   0.04 scale=  0.00 subset rates=  0.00)
pass 7:+    0.015 (branch=   0.02 scale=  0.00 subset rates=  0.00)
pass 8:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
lnL after optimization: -474.8632
WARNING: You are running internal tests with NDEBUG defined!
It should not be defined for full error checking.
******Successfully completed tests.******
**************************
Running scoring tests ...
**************************
Running scoring test ./scoring/a.G3.conf
Running scoring test ./scoring/a.G3.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./scoring/a.G3.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/z.11x2178.AA.nex ...
Reading TAXA block...storing read block: TAXA
 successful
Reading CHARACTERS block...storing read block: CHARACTERS
 found protein data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful
Reading CODONS block...storing read block: CODONS
 successful
Reading MESQUITECHARMODELS block...storing read block: MESQUITECHARMODELS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Protein translation of Character Matrix")
	Data read as Amino acid data,
	modeled as Amino acid data
	Found wtset "equal" with data, applying...
	Summary of data:
	  11 sequences.
	  389 constant characters.
	  190 parsimony-informative characters.
	  147 uninformative variable characters.
	  1 characters were completely missing or ambiguous (removed).
	  726 total characters (727 before removing empty columns).
	  343 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 13 MB
  good			approx 12 MB to 9 MB
  low			approx 8 MB to 5 MB
  very low		approx 4 MB to 2 MB
the minimum required availablememory is 2 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 5 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 18.0 MB of memory

#######################################################
Found outgroup specification:  1 2

#######################################################
Loading starting model and/or tree from file data/a.G3.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN
Optimizing tree 1 ...
Obtained starting tree 1 from Nexus
Obtained starting or fixed model parameter values from configuration file:
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 20 (amino acid data)
  Amino Acid Rate Matrix: WAG
  Equilibrium State Frequencies: empirical (observed) values (+F)
    (ACDEFGHIKLMNPQRSTVWY)
    0.0500 0.0252 0.0458 0.0579 0.0750 
    0.0561 0.0078 0.0882 0.0489 0.1128 
    0.0438 0.0500 0.0296 0.0252 0.0373 
    0.0552 0.0444 0.0906 0.0217 0.0346 
  Rate Heterogeneity Model:
    3 discrete gamma distributed rate categories, alpha param estimated
      0.4368
    Substitution rate categories under this model:
      rate	proportion
      0.0437	0.3333
      0.4372	0.3333
      2.5190	0.3333

Starting with seed=1

Initial ln Likelihood: -6242.8631
optimizing: starting branch lengths, alpha shape...
pass 1:+    0.000 (branch=   0.00 scale=  0.00 alpha=  0.00)
lnL after optimization: -6242.8629
Current score = -6242.8629
Performing final optimizations...
pass 1 : -6242.8629   (branch= 0.0000  alpha= 0.0000)
pass 2 : -6242.8595   (branch= 0.0034  alpha= 0.0000)
pass 3 : -6242.8595   (branch= 0.0000  alpha= 0.0000)
pass 4 : -6242.8595   (branch= 0.0000  alpha= 0.0000)
pass 5 : -6242.8591   (branch= 0.0004  alpha= 0.0000)
pass 6 : -6242.8586   (branch= 0.0005  alpha= 0.0000)
pass 7 : -6242.8585   (branch= 0.0001  alpha= 0.0000)
pass 8 : -6242.8583   (branch= 0.0002  alpha= 0.0000)
pass 9 : -6242.8582   (branch= 0.0001  alpha= 0.0000)
pass 10: -6242.8581   (branch= 0.0001  alpha= 0.0000)
pass 11: -6242.8580   (branch= 0.0000  alpha= 0.0000)
pass 12: -6242.8580   (branch= 0.0000  alpha= 0.0000)
pass 13: -6242.8580   (branch= 0.0000  alpha= 0.0000)
Looking for minimum length branches...
Final score = -6242.8580
Time used = 0 hours, 0 minutes and 2 seconds
Writing site likelihoods for tree 1 ...

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -6242.8580       

Parameter estimates:
        alpha
rep 1:  0.436

Treelengths:
          TL 
rep 1:  1.345

NOTE: collapsebranches setting ignored when writing and comparing optimized trees...

Writing optimized trees and models to scr.a.G3.best.all.tre
***********TEST**************
***Score is 6242.85802
***Expected is 6242.85802
***SCORE DIFFERENCE IS 0
***ALLOWED ERROR IS 0.01
***Scoring OK for ./scoring/a.G3.conf ***
Running scoring test ./scoring/a.G4.conf
Running scoring test ./scoring/a.G4.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./scoring/a.G4.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/z.11x2178.nex ...
Reading DATA block...storing implied block: TAXA
storing read block: DATA
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Amino acid data
Some sites treated as missing data for taxon SterNa6 due to ambiguity in translation.
	Aminoacids coded as missing for that taxon: 708 

	Summary of data:
	  11 sequences.
	  389 constant characters.
	  190 parsimony-informative characters.
	  147 uninformative variable characters.
	  726 total characters.
	  343 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 17 MB
  good			approx 16 MB to 13 MB
  low			approx 12 MB to 6 MB
  very low		approx 5 MB to 3 MB
the minimum required availablememory is 3 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 6 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 23.9 MB of memory

#######################################################
Found outgroup specification:  1-5

#######################################################
Loading starting model and/or tree from file data/a.G4.start
Reading TREES block...storing read block: TREES
 successful
Reading GARLI block...storing read block: GARLI
 successful
STARTING RUN
Optimizing tree 1 ...
Obtained starting tree 1 from Nexus
Obtained starting or fixed model parameter values from Nexus:
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 20 (amino acid data)
  Amino Acid Rate Matrix:  values specified by user (fixed)
  Equilibrium State Frequencies: empirical (observed) values (+F)
    (ACDEFGHIKLMNPQRSTVWY)
    0.0500 0.0252 0.0458 0.0579 0.0750 
    0.0561 0.0078 0.0882 0.0489 0.1128 
    0.0438 0.0500 0.0296 0.0252 0.0373 
    0.0552 0.0444 0.0906 0.0217 0.0346 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.4616
    Substitution rate categories under this model:
      rate	proportion
      0.0265	0.2500
      0.2261	0.2500
      0.7902	0.2500
      2.9572	0.2500

Starting with seed=1

Initial ln Likelihood: -6249.1664
optimizing: starting branch lengths, alpha shape...
pass 1:+    1.482 (branch=   0.00 scale=  1.47 alpha=  0.01)
pass 2:+    0.010 (branch=   0.00 scale=  0.00 alpha=  0.01)
lnL after optimization: -6247.6743
Current score = -6247.6743
Performing final optimizations...
pass 1 : -6247.0539   (branch= 0.2066  alpha= 0.4138)
pass 2 : -6247.0347   (branch= 0.0192  alpha= 0.0000)
pass 3 : -6247.0279   (branch= 0.0068  alpha= 0.0000)
pass 4 : -6247.0255   (branch= 0.0023  alpha= 0.0000)
pass 5 : -6247.0234   (branch= 0.0022  alpha= 0.0000)
pass 6 : -6247.0228   (branch= 0.0005  alpha= 0.0000)
pass 7 : -6247.0226   (branch= 0.0002  alpha= 0.0000)
pass 8 : -6247.0223   (branch= 0.0002  alpha= 0.0000)
pass 9 : -6247.0222   (branch= 0.0001  alpha= 0.0000)
pass 10: -6247.0222   (branch= 0.0000  alpha= 0.0000)
Looking for minimum length branches...
Final score = -6247.0222
Time used = 0 hours, 0 minutes and 2 seconds
Writing site likelihoods for tree 1 ...

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -6247.0222       

Parameter estimates:
        alpha
rep 1:  0.423

Treelengths:
          TL 
rep 1:  1.467

NOTE: collapsebranches setting ignored when writing and comparing optimized trees...

Writing optimized trees and models to scr.a.G4.best.all.tre
***********TEST**************
***Score is 6247.02222
***Expected is 6247.02222
***SCORE DIFFERENCE IS 0
***ALLOWED ERROR IS 0.01
***Scoring OK for ./scoring/a.G4.conf ***
Running scoring test ./scoring/a.conf
Running scoring test ./scoring/a.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./scoring/a.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/z.11x2178.nex ...
Reading DATA block...storing implied block: TAXA
storing read block: DATA
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Amino acid data
Some sites treated as missing data for taxon SterNa6 due to ambiguity in translation.
	Aminoacids coded as missing for that taxon: 708 

	Summary of data:
	  11 sequences.
	  389 constant characters.
	  190 parsimony-informative characters.
	  147 uninformative variable characters.
	  726 total characters.
	  343 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 4 MB
  good			approx 3 MB to 3 MB
  low			approx 2 MB to 2 MB
  very low		approx 1 MB to 1 MB
the minimum required availablememory is 1 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 2 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 6.1 MB of memory

#######################################################
Found outgroup specification:  1

#######################################################
Loading starting model and/or tree from file data/a.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN
Optimizing tree 1 ...
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 20 (amino acid data)
  Amino Acid Rate Matrix: WAG
  Equilibrium State Frequencies: empirical (observed) values (+F)
    (ACDEFGHIKLMNPQRSTVWY)
    0.0500 0.0252 0.0458 0.0579 0.0750 
    0.0561 0.0078 0.0882 0.0489 0.1128 
    0.0438 0.0500 0.0296 0.0252 0.0373 
    0.0552 0.0444 0.0906 0.0217 0.0346 
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

NOTE: Model contains no mutable parameters!
Setting model mutation weight to zero.

Initial ln Likelihood: -6434.5146
optimizing: starting branch lengths...
pass 1:+    0.000 (branch=   0.00 scale=  0.00)
lnL after optimization: -6434.5146
Current score = -6434.5146
Performing final optimizations...
pass 1 : -6434.5146   (branch= 0.0000)
pass 2 : -6434.5101   (branch= 0.0045)
pass 3 : -6434.5101   (branch= 0.0000)
pass 4 : -6434.5101   (branch= 0.0000)
pass 5 : -6434.5101   (branch= 0.0000)
pass 6 : -6434.5092   (branch= 0.0009)
pass 7 : -6434.5092   (branch= 0.0000)
pass 8 : -6434.5092   (branch= 0.0000)
pass 9 : -6434.5092   (branch= 0.0000)
pass 10: -6434.5092   (branch= 0.0000)
pass 11: -6434.5092   (branch= 0.0000)
Looking for minimum length branches...
Final score = -6434.5092
Time used = 0 hours, 0 minutes and 1 seconds
Writing site likelihoods for tree 1 ...

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -6434.5092       

Parameter estimates:
	 Model contains no estimated parameters

Treelengths:
          TL 
rep 1:  1.143

NOTE: collapsebranches setting ignored when writing and comparing optimized trees...

Writing optimized trees and models to scr.a.best.all.tre
***********TEST**************
***Score is 6434.50916
***Expected is 6434.50916
***SCORE DIFFERENCE IS 0
***ALLOWED ERROR IS 0.01
***Scoring OK for ./scoring/a.conf ***
Running scoring test ./scoring/c.M3x2.conf
Running scoring test ./scoring/c.M3x2.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./scoring/c.M3x2.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/z.11x2178.nex ...
Reading DATA block...storing implied block: TAXA
storing read block: DATA
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Codon data
Gaps or ambiguity codes found within codon for taxon SterNa6.
	Codons coded as missing for that taxon: 708 
Gaps or ambiguity codes found within codon for taxon PinniNa6.
	Codons coded as missing for that taxon: 513 646 
	Summary of data:
	  11 sequences.
	  72 constant characters.
	  527 parsimony-informative characters.
	  127 uninformative variable characters.
	  726 total characters.
	  668 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 47 MB
  good			approx 46 MB to 36 MB
  low			approx 35 MB to 18 MB
  very low		approx 17 MB to 7 MB
the minimum required availablememory is 7 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 15 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 70.8 MB of memory

#######################################################
Found outgroup specification:  1 2

#######################################################
Loading starting model and/or tree from file data/c.M3x2.start
Reading TREES block...storing read block: TREES
 successful
Reading GARLI block...storing read block: GARLI
 successful
STARTING RUN
Optimizing tree 1 ...
Obtained starting tree 1 from Nexus
Obtained starting or fixed model parameter values from Nexus:
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 61 (codon data, standard code)
  Nucleotide Relative Rate Matrix Assumed by Codon Model:     6 rates 
    Values specified by user (fixed)
    AC = 1.260, AG = 2.449, AT = 1.259, CG = 0.687, CT = 1.396, GT = 1.000
  Equilibrium State Frequencies: empirical (observed) values, fixed:
    (AAA, AAC, AAG, AAT, ACA, ... etc)
    0.0179 0.0349 0.0309 0.0152 0.0114 
    0.0181 0.0065 0.0084 0.0095 0.0122 
    0.0083 0.0104 0.0094 0.0507 0.0438 
    0.0281 0.0078 0.0049 0.0174 0.0029 
    0.0087 0.0102 0.0023 0.0085 0.0034 
    0.0080 0.0029 0.0051 0.0072 0.0286 
    0.0417 0.0152 0.0204 0.0307 0.0375 
    0.0151 0.0119 0.0221 0.0043 0.0118 
    0.0166 0.0168 0.0134 0.0093 0.0080 
    0.0260 0.0435 0.0130 0.0220 0.0127 
    0.0077 0.0130 0.0034 0.0085 0.0159 
    0.0217 0.0093 0.0061 0.0469 0.0139 
    0.0281 
  Rate Heterogeneity Model:
    2 nonsynonymous rate categories, rate and proportion of each estimated
     (this is effectively the M3 model of PAML)
      dN/dS	Proportion
      0.0200	0.6965
      0.2936	0.3035

Starting with seed=1

Initial ln Likelihood: -12956.1235
Current score = -12956.1235
Performing final optimizations...
pass 1 : -12956.1235   (branch= 0.0000  omega= 0.0000)
pass 2 : -12956.1235   (branch= 0.0000  omega= 0.0000)
pass 3 : -12956.1235   (branch= 0.0000  omega= 0.0000)
pass 4 : -12956.1235   (branch= 0.0000  omega= 0.0000)
pass 5 : -12956.1235   (branch= 0.0000  omega= 0.0000)
pass 6 : -12956.1235   (branch= 0.0000  omega= 0.0000)
pass 7 : -12956.1235   (branch= 0.0000  omega= 0.0000)
pass 8 : -12956.1235   (branch= 0.0000  omega= 0.0000)
pass 9 : -12956.1235   (branch= 0.0000  omega= 0.0000)
pass 10: -12956.1235   (branch= 0.0000  omega= 0.0000)
Looking for minimum length branches...
Final score = -12956.1235
Time used = 0 hours, 0 minutes and 48 seconds
Writing site likelihoods for tree 1 ...

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -12956.1235       

Parameter estimates:
         w(0)  p(0)  w(1)  p(1)  r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT)
rep 1:  0.020 0.696 0.294 0.304   1.26  2.449  1.259 0.6866  1.396      1

Treelengths:
          TL 
rep 1:  5.371

NOTE: collapsebranches setting ignored when writing and comparing optimized trees...

Writing optimized trees and models to scr.c.M3x2.best.all.tre
***********TEST**************
***Score is 12956.12351
***Expected is 12956.1235
***SCORE DIFFERENCE IS .00001
***ALLOWED ERROR IS 0.01
***Scoring OK for ./scoring/c.M3x2.conf ***
Running scoring test ./scoring/c.conf
Running scoring test ./scoring/c.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./scoring/c.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/z.11x2178.nex ...
Reading DATA block...storing implied block: TAXA
storing read block: DATA
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Codon data
Gaps or ambiguity codes found within codon for taxon SterNa6.
	Codons coded as missing for that taxon: 708 
Gaps or ambiguity codes found within codon for taxon PinniNa6.
	Codons coded as missing for that taxon: 513 646 
	Summary of data:
	  11 sequences.
	  72 constant characters.
	  527 parsimony-informative characters.
	  127 uninformative variable characters.
	  726 total characters.
	  668 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 24 MB
  good			approx 23 MB to 18 MB
  low			approx 17 MB to 9 MB
  very low		approx 8 MB to 4 MB
the minimum required availablememory is 4 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 8 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 35.5 MB of memory

#######################################################
Found outgroup specification:  1 2

#######################################################
Loading starting model and/or tree from file data/c.start
Reading TREES block...storing read block: TREES
 successful
Reading GARLI block...storing read block: GARLI
 successful
STARTING RUN
Optimizing tree 1 ...
Obtained starting tree 1 from Nexus
Obtained starting or fixed model parameter values from Nexus:
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 61 (codon data, standard code)
  One dN/dS ratio (aka omega).
    Value provided by user (fixed) = 0.087400
  Nucleotide Relative Rate Matrix Assumed by Codon Model:     6 rates 
    AC = 1.265, AG = 2.362, AT = 1.151, CG = 0.706, CT = 1.402, GT = 1.000
  Equilibrium State Frequencies: empirical (observed) values, fixed:
    (AAA, AAC, AAG, AAT, ACA, ... etc)
    0.0179 0.0349 0.0309 0.0152 0.0114 
    0.0181 0.0065 0.0084 0.0095 0.0122 
    0.0083 0.0104 0.0094 0.0507 0.0438 
    0.0281 0.0078 0.0049 0.0174 0.0029 
    0.0087 0.0102 0.0023 0.0085 0.0034 
    0.0080 0.0029 0.0051 0.0072 0.0286 
    0.0417 0.0152 0.0204 0.0307 0.0375 
    0.0151 0.0119 0.0221 0.0043 0.0118 
    0.0166 0.0168 0.0134 0.0093 0.0080 
    0.0260 0.0435 0.0130 0.0220 0.0127 
    0.0077 0.0130 0.0034 0.0085 0.0159 
    0.0217 0.0093 0.0061 0.0469 0.0139 
    0.0281 
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

Initial ln Likelihood: -13269.2298
Current score = -13269.2298
Performing final optimizations...
pass 1 : -13269.2298   (branch= 0.0000  rel rates= 0.0000)
pass 2 : -13269.2298   (branch= 0.0000  rel rates= 0.0000)
pass 3 : -13269.2298   (branch= 0.0000  rel rates= 0.0000)
pass 4 : -13269.2298   (branch= 0.0000  rel rates= 0.0000)
pass 5 : -13269.2298   (branch= 0.0000  rel rates= 0.0000)
pass 6 : -13269.2298   (branch= 0.0000  rel rates= 0.0000)
pass 7 : -13269.2298   (branch= 0.0000  rel rates= 0.0000)
pass 8 : -13269.2298   (branch= 0.0000  rel rates= 0.0000)
pass 9 : -13269.2298   (branch= 0.0000  rel rates= 0.0000)
pass 10: -13269.2298   (branch= 0.0000  rel rates= 0.0000)
Looking for minimum length branches...
Final score = -13269.2298
Time used = 0 hours, 0 minutes and 35 seconds
Writing site likelihoods for tree 1 ...

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -13269.2298       

Parameter estimates:
         w(0)  p(0)  r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT)
rep 1:  0.087 1.000  1.265  2.362  1.151 0.7058  1.402      1

Treelengths:
          TL 
rep 1:  5.169

NOTE: collapsebranches setting ignored when writing and comparing optimized trees...

Writing optimized trees and models to scr.c.best.all.tre
***********TEST**************
***Score is 13269.22979
***Expected is 13269.229793
***SCORE DIFFERENCE IS -.000003
***ALLOWED ERROR IS 0.01
***Scoring OK for ./scoring/c.conf ***
Running scoring test ./scoring/g.dnaBnoZ.conf
Running scoring test ./scoring/g.dnaBnoZ.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./scoring/g.dnaBnoZ.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/dnaGap.8x1K.nex ...
Reading TAXA block...storing read block: TAXA
 successful
Reading CHARACTERS block...storing read block: CHARACTERS
 found dna data... successful
Reading CHARACTERS block...storing read block: CHARACTERS
 found standard data... successful
Reading TREES block...storing read block: TREES
 successful

###################################################
PARTITIONING OF DATA AND MODELS

CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY
	TO EACH DATA SUBSET (no linkage)

GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1GapsAsMissing")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  8 sequences.
	  428 constant characters.
	  129 parsimony-informative characters.
	  100 uninformative variable characters.
	  343 characters were completely missing or ambiguous (removed).
	  657 total characters (1000 before removing empty columns).
	  239 unique patterns in compressed data matrix.
GARLI data subset 2
	CHARACTERS block #2 ("Untitled DATA Block 1GapsAsBinary")
	Data read as Binary data, no constant state 0 chars,
	modeled as Binary data, no constant state 0 chars
	NOTE: entirely missing characters removed from matrix:  1 25 29-34 36 37 52-54 61 67-69 84 85 87 95 96 99 106 110-116 125 138-145 163-165 167 169-177 188 197-199 202-210 213 216-218 228-231 233-236 238-240 247 249 256 257 260 266-270 \ 2 271-277 281-285 290-294 298-300 311 312 322 325 331 332 336-338 344 359 369 373-378 397 404-406 413 416 417 420-426 439-442 450-454 \ 2 455-460 462 471 474-479 487-490 492 494 495 497 502-506 510 521-526 532 533 538-541 544 547 551-553 562 570-572 577 579 609 610 614 615 622 624-626 639 640 647-650 653 655-660 667 668 673-676 679 680 685 695 696 701-705 708-713 716 717 731 742-749 751-755 762 763 770 771 783 788 791-793 804 806-808 813 821-825 827 830-832 840 842 843 845 850 851 856-865 886-894 896 897 903-905 913 914 924 927 948-956 963-971 976-981 991-993 996
	Subset of data with 2 states:
	  chars 1-1000
	Summary of data:
	  8 sequences.
	  502 constant characters.
	  39 parsimony-informative characters.
	  116 uninformative variable characters.
	  343 characters were completely missing or ambiguous (removed).
	  657 total characters (1000 before removing empty columns).
	  24 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 2 MB
  good			approx 1 MB to 2 MB
  low			approx 1 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 1 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 2.3 MB of memory

#######################################################
Found outgroup specification:  1

#######################################################
STARTING RUN
Optimizing tree 1 ...
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.3220 0.2180 0.1602 0.2999 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.1629
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.1629
      0.0334	0.2093
      0.2519	0.2093
      0.8203	0.2093
      2.8944	0.2093

Model 2
  Number of states = 2 (binary data)
  Character change matrix:
    Binary, no all-zero columns (2-state symmetric one rate model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00
Starting with seed=1

Initial ln Likelihood: -4043.7391
optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates...
pass 1:+  532.047 (branch= 438.84 scale=  6.77 alpha= 15.79 freqs=  3.30 rel rates=  8.48 pinv=  0.00 subset rates= 58.86)
pass 2:+   88.209 (branch=  42.39 scale=  0.83 alpha=  0.82 freqs=  0.72 rel rates=  0.01 pinv=  0.00 subset rates= 43.45)
pass 3:+   34.899 (branch=   0.70 scale=  2.02 alpha=  1.89 freqs=  0.04 rel rates=  0.72 pinv=  0.00 subset rates= 29.52)
pass 4:+   17.437 (branch=   4.66 scale=  2.38 alpha=  1.70 freqs=  0.05 rel rates=  0.01 pinv=  0.00 subset rates=  8.64)
pass 5:+   10.201 (branch=   4.19 scale=  1.64 alpha=  0.69 freqs=  0.05 rel rates=  2.14 pinv=  0.00 subset rates=  1.49)
pass 6:+    1.986 (branch=   0.00 scale=  1.92 alpha=  0.00 freqs=  0.06 rel rates=  0.01 pinv=  0.00 subset rates=  0.00)
pass 7:+    0.532 (branch=   0.47 scale=  0.00 alpha=  0.00 freqs=  0.06 rel rates=  0.01 pinv=  0.00 subset rates=  0.00)
pass 8:+    0.057 (branch=   0.00 scale=  0.00 alpha=  0.00 freqs=  0.05 rel rates=  0.01 pinv=  0.00 subset rates=  0.00)
lnL after optimization: -3358.3708
Current score = -3358.3708
Performing final optimizations...
pass 1 : -3355.4801   (branch= 0.9931  alpha= 0.0078  pinv= 0.0071  eq freqs= 0.1960  rel rates= 1.3008  subset rates= 0.3859)
pass 2 : -3354.0738   (branch= 0.5295  alpha= 0.0090  pinv= 0.0117  eq freqs= 0.0202  rel rates= 0.6733  subset rates= 0.1627)
pass 3 : -3353.2074   (branch= 0.3029  alpha= 0.0000  pinv= 0.0088  eq freqs= 0.0143  rel rates= 0.4607  subset rates= 0.0797)
pass 4 : -3352.5841   (branch= 0.1779  alpha= 0.0022  pinv= 0.0160  eq freqs= 0.0064  rel rates= 0.3739  subset rates= 0.0469)
pass 5 : -3352.1392   (branch= 0.0811  alpha= 0.0062  pinv= 0.0163  eq freqs= 0.0025  rel rates= 0.3066  subset rates= 0.0323)
pass 6 : -3351.7984   (branch= 0.0566  alpha= 0.0067  pinv= 0.0165  eq freqs= 0.0008  rel rates= 0.2471  subset rates= 0.0132)
pass 7 : -3351.5324   (branch= 0.0327  alpha= 0.0085  pinv= 0.0159  eq freqs= 0.0006  rel rates= 0.1993  subset rates= 0.0089)
pass 8 : -3351.3163   (branch= 0.0193  alpha= 0.0099  pinv= 0.0150  eq freqs= 0.0005  rel rates= 0.1659  subset rates= 0.0054)
pass 9 : -3351.1433   (branch= 0.0107  alpha= 0.0106  pinv= 0.0140  eq freqs= 0.0005  rel rates= 0.1334  subset rates= 0.0039)
pass 10: -3351.0014   (branch= 0.0064  alpha= 0.0106  pinv= 0.0138  eq freqs= 0.0004  rel rates= 0.1081  subset rates= 0.0025)
pass 11: -3350.8849   (branch= 0.0049  alpha= 0.0103  pinv= 0.0127  eq freqs= 0.0003  rel rates= 0.0871  subset rates= 0.0012)
pass 12: -3350.7888   (branch= 0.0029  alpha= 0.0098  pinv= 0.0116  eq freqs= 0.0002  rel rates= 0.0715  subset rates= 0.0000)
pass 13: -3350.7057   (branch= 0.0007  alpha= 0.0097  pinv= 0.0105  eq freqs= 0.0002  rel rates= 0.0604  subset rates= 0.0017)
pass 14: -3350.6391   (branch= 0.0014  alpha= 0.0090  pinv= 0.0090  eq freqs= 0.0002  rel rates= 0.0470  subset rates= 0.0000)
pass 15: -3350.5823   (branch= 0.0004  alpha= 0.0081  pinv= 0.0081  eq freqs= 0.0001  rel rates= 0.0401  subset rates= 0.0000)
pass 16: -3350.5332   (branch= 0.0001  alpha= 0.0079  pinv= 0.0073  eq freqs= 0.0001  rel rates= 0.0338  subset rates= 0.0000)
pass 17: -3350.4917   (branch= 0.0000  alpha= 0.0074  pinv= 0.0065  eq freqs= 0.0001  rel rates= 0.0274  subset rates= 0.0000)
pass 18: -3350.4553   (branch= 0.0000  alpha= 0.0066  pinv= 0.0059  eq freqs= 0.0001  rel rates= 0.0228  subset rates= 0.0010)
pass 19: -3350.4257   (branch= 0.0005  alpha= 0.0055  pinv= 0.0053  eq freqs= 0.0001  rel rates= 0.0183  subset rates= 0.0000)
pass 20: -3350.3999   (branch= 0.0001  alpha= 0.0048  pinv= 0.0047  eq freqs= 0.0000  rel rates= 0.0161  subset rates= 0.0000)
 optimization up to ...
pass 30: -3350.2715   (branch= 0.0001  alpha= 0.0273  pinv= 0.0248  eq freqs= 0.0002  rel rates= 0.0761  subset rates= 0.0000)
 optimization up to ...
pass 40: -3350.2418   (branch= 0.0000  alpha= 0.0065  pinv= 0.0060  eq freqs= 0.0000  rel rates= 0.0171  subset rates= 0.0000)
 optimization up to ...
pass 50: -3350.2352   (branch= 0.0000  alpha= 0.0013  pinv= 0.0012  eq freqs= 0.0000  rel rates= 0.0042  subset rates= 0.0000)
 optimization up to ...
pass 60: -3350.2336   (branch= 0.0000  alpha= 0.0002  pinv= 0.0002  eq freqs= 0.0000  rel rates= 0.0011  subset rates= 0.0000)
 optimization up to ...
pass 70: -3350.2333   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0002  subset rates= 0.0000)
 optimization up to ...
pass 75: -3350.2332   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0001  subset rates= 0.0000)
Looking for minimum length branches...
Final score = -3350.2333
Time used = 0 hours, 0 minutes and 2 seconds
Writing site likelihoods for tree 1 ...

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -3350.2333       

Parameter estimates:

Partition model subset 1:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
rep 1:   3.112  10.41  2.688  0.001  21.89      1 0.333 0.222 0.157 0.288 0.578 0.366

Partition model subset 2:
	 Model contains no estimated parameters

Treelengths and subset rate multipliers:
          TL   R(1)  R(2)
rep 1:  0.789 1.820 0.180

NOTE: collapsebranches setting ignored when writing and comparing optimized trees...

Writing optimized trees and models to scr.g.dnaBnoZ.best.all.tre
***********TEST**************
***Score is 3350.23325
***Expected is 3350.2345
***SCORE DIFFERENCE IS -.00125
***ALLOWED ERROR IS 0.01
***Scoring OK for ./scoring/g.dnaBnoZ.conf ***
Running scoring test ./scoring/g.dnaMix.conf
Running scoring test ./scoring/g.dnaMix.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./scoring/g.dnaMix.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/dnaGap.8x1K.nex ...
Reading TAXA block...storing read block: TAXA
 successful
Reading CHARACTERS block...storing read block: CHARACTERS
 found dna data... successful
Reading CHARACTERS block...storing read block: CHARACTERS
 found standard data... successful
Reading TREES block...storing read block: TREES
 successful

###################################################
PARTITIONING OF DATA AND MODELS

CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY
	TO EACH DATA SUBSET (no linkage)

GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1GapsAsMissing")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  8 sequences.
	  428 constant characters.
	  129 parsimony-informative characters.
	  100 uninformative variable characters.
	  343 characters were completely missing or ambiguous (removed).
	  657 total characters (1000 before removing empty columns).
	  239 unique patterns in compressed data matrix.
GARLI data subset 2
	CHARACTERS block #2 ("Untitled DATA Block 1GapsAsBinary")
	Data read as Gap-coded data, oriented with respect to time,
	modeled as Gap-coded data, oriented with respect to time
	Summary of data:
	  8 sequences.
	  502 constant characters.
	  39 parsimony-informative characters.
	  116 uninformative variable characters.
	  343 characters were completely missing or ambiguous (removed).
	  657 total characters (1000 before removing empty columns).
	  24 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 2 MB
  good			approx 1 MB to 2 MB
  low			approx 1 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 1 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 2.7 MB of memory

#######################################################
WARNING - specified outgroup (1) being ignored due to inference of a rooted true

#######################################################
STARTING RUN
Optimizing tree 1 ...
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.3220 0.2180 0.1602 0.2999 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.1629
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.1629
      0.0334	0.2093
      0.2519	0.2093
      0.8203	0.2093
      2.8944	0.2093

Model 2
  Number of states = 2 (0/1 coding of gaps)
  Character change matrix: irreversible matrix
    deletion rate parameter only estimated if using a partitioned
    model without subset rates
    deletion rate = 1.000
  Equilibrium State Frequencies: proportion of inserted sites parameter
    insert proportion = 0.500
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

Initial ln Likelihood: -4257.0961
optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, ins rate, del rate...
pass 1:+  640.405 (branch= 431.06 scale=  2.03 alpha=  9.92 freqs=  3.07 rel rates=  7.29 pinv=  0.00 ins/del=187.03)
pass 2:+  169.102 (branch=  75.12 scale=  1.32 alpha=  0.88 freqs=  0.65 rel rates=  0.01 pinv=  0.00 ins/del= 91.12)
pass 3:+   55.144 (branch=   7.14 scale=  1.85 alpha=  1.09 freqs=  0.05 rel rates=  0.90 pinv=  0.00 ins/del= 44.12)
pass 4:+   25.231 (branch=   7.02 scale=  1.52 alpha=  0.69 freqs=  0.06 rel rates=  0.01 pinv=  0.00 ins/del= 15.94)
pass 5:+   14.361 (branch=   7.97 scale=  1.87 alpha=  0.01 freqs=  0.05 rel rates=  2.45 pinv=  0.00 ins/del=  2.01)
pass 6:+   10.438 (branch=   7.36 scale=  2.34 alpha=  0.01 freqs=  0.07 rel rates=  0.00 pinv=  0.00 ins/del=  0.66)
pass 7:+    6.158 (branch=   5.23 scale=  0.83 alpha=  0.01 freqs=  0.06 rel rates=  0.00 pinv=  0.00 ins/del=  0.03)
pass 8:+    3.640 (branch=   2.31 scale=  0.00 alpha=  0.00 freqs=  0.05 rel rates=  0.60 pinv=  0.00 ins/del=  0.67)
pass 9:+    0.148 (branch=   0.08 scale=  0.00 alpha=  0.00 freqs=  0.06 rel rates=  0.00 pinv=  0.00 ins/del=  0.00)
lnL after optimization: -3332.4700
Current score = -3332.4700
Performing final optimizations...
pass 1 : -3329.9872   (branch= 1.3745  alpha= 0.0217  pinv= 0.0099  eq freqs= 0.2403  rel rates= 0.7610  ins/del rates= 0.0754)
pass 2 : -3328.9659   (branch= 0.3685  alpha= 0.0000  pinv= 0.0130  eq freqs= 0.0040  rel rates= 0.5672  ins/del rates= 0.0686)
pass 3 : -3328.3611   (branch= 0.1485  alpha= 0.0057  pinv= 0.0143  eq freqs= 0.0130  rel rates= 0.3796  ins/del rates= 0.0437)
pass 4 : -3327.9018   (branch= 0.0826  alpha= 0.0070  pinv= 0.0147  eq freqs= 0.0031  rel rates= 0.3239  ins/del rates= 0.0279)
pass 5 : -3327.5623   (branch= 0.0510  alpha= 0.0076  pinv= 0.0148  eq freqs= 0.0008  rel rates= 0.2476  ins/del rates= 0.0177)
pass 6 : -3327.2964   (branch= 0.0330  alpha= 0.0080  pinv= 0.0145  eq freqs= 0.0011  rel rates= 0.1981  ins/del rates= 0.0111)
pass 7 : -3327.0823   (branch= 0.0212  alpha= 0.0094  pinv= 0.0139  eq freqs= 0.0007  rel rates= 0.1614  ins/del rates= 0.0075)
pass 8 : -3326.9071   (branch= 0.0138  alpha= 0.0097  pinv= 0.0132  eq freqs= 0.0005  rel rates= 0.1331  ins/del rates= 0.0050)
pass 9 : -3326.7651   (branch= 0.0091  alpha= 0.0099  pinv= 0.0124  eq freqs= 0.0004  rel rates= 0.1070  ins/del rates= 0.0033)
pass 10: -3326.6477   (branch= 0.0061  alpha= 0.0096  pinv= 0.0122  eq freqs= 0.0003  rel rates= 0.0869  ins/del rates= 0.0022)
pass 11: -3326.5503   (branch= 0.0041  alpha= 0.0093  pinv= 0.0113  eq freqs= 0.0002  rel rates= 0.0710  ins/del rates= 0.0015)
pass 12: -3326.4699   (branch= 0.0028  alpha= 0.0089  pinv= 0.0098  eq freqs= 0.0002  rel rates= 0.0578  ins/del rates= 0.0010)
pass 13: -3326.4023   (branch= 0.0019  alpha= 0.0084  pinv= 0.0090  eq freqs= 0.0001  rel rates= 0.0475  ins/del rates= 0.0007)
pass 14: -3326.3449   (branch= 0.0013  alpha= 0.0079  pinv= 0.0082  eq freqs= 0.0001  rel rates= 0.0396  ins/del rates= 0.0005)
pass 15: -3326.2956   (branch= 0.0009  alpha= 0.0073  pinv= 0.0075  eq freqs= 0.0001  rel rates= 0.0332  ins/del rates= 0.0003)
pass 16: -3326.2539   (branch= 0.0005  alpha= 0.0069  pinv= 0.0068  eq freqs= 0.0001  rel rates= 0.0272  ins/del rates= 0.0002)
pass 17: -3326.2181   (branch= 0.0003  alpha= 0.0063  pinv= 0.0061  eq freqs= 0.0001  rel rates= 0.0229  ins/del rates= 0.0001)
pass 18: -3326.1870   (branch= 0.0002  alpha= 0.0056  pinv= 0.0055  eq freqs= 0.0000  rel rates= 0.0196  ins/del rates= 0.0001)
pass 19: -3326.1600   (branch= 0.0001  alpha= 0.0051  pinv= 0.0049  eq freqs= 0.0000  rel rates= 0.0167  ins/del rates= 0.0000)
pass 20: -3326.1365   (branch= 0.0001  alpha= 0.0046  pinv= 0.0044  eq freqs= 0.0000  rel rates= 0.0143  ins/del rates= 0.0000)
 optimization up to ...
pass 30: -3326.0190   (branch= 0.0002  alpha= 0.0258  pinv= 0.0240  eq freqs= 0.0002  rel rates= 0.0674  ins/del rates= 0.0001)
 optimization up to ...
pass 40: -3325.9906   (branch= 0.0001  alpha= 0.0067  pinv= 0.0062  eq freqs= 0.0000  rel rates= 0.0154  ins/del rates= 0.0000)
 optimization up to ...
pass 50: -3325.9841   (branch= 0.0000  alpha= 0.0015  pinv= 0.0013  eq freqs= 0.0000  rel rates= 0.0037  ins/del rates= 0.0000)
 optimization up to ...
pass 60: -3325.9825   (branch= 0.0000  alpha= 0.0003  pinv= 0.0003  eq freqs= 0.0000  rel rates= 0.0009  ins/del rates= 0.0000)
 optimization up to ...
pass 70: -3325.9822   (branch= 0.0000  alpha= 0.0001  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0002  ins/del rates= 0.0000)
 optimization up to ...
pass 75: -3325.9822   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000  ins/del rates= 0.0000)
Looking for minimum length branches...
Final score = -3325.9822
Time used = 0 hours, 0 minutes and 4 seconds
Writing site likelihoods for tree 1 ...

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -3325.9822       

Parameter estimates:

Partition model subset 1:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
rep 1:   3.062  10.26  2.659  0.001  21.53      1 0.333 0.222 0.157 0.288 0.574 0.361

Partition model subset 2:
          ins   del
rep 1:  0.053 0.145
	 **ins = proportion of columns that experienced an insertion
	 **del = deletion rate relative to nucleotide substitution rate

Treelengths:
          TL 
rep 1:  1.417

NOTE: collapsebranches setting ignored when writing and comparing optimized trees...

Writing optimized trees and models to scr.g.dnaMix.best.all.tre
***********TEST**************
***Score is 3325.98218
***Expected is 3325.98222
***SCORE DIFFERENCE IS -.00004
***ALLOWED ERROR IS 0.01
***Scoring OK for ./scoring/g.dnaMix.conf ***
Running scoring test ./scoring/n.G4.conf
Running scoring test ./scoring/n.G4.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./scoring/n.G4.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/z.11x2178.wtset.nex ...
Reading DATA block...storing implied block: TAXA
storing read block: DATA
 successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Excluded character numbers: 816 1012 1019 1022 1995 2180
	
	Found wtset "compensate" with data, applying...
	Summary of data:
	  11 sequences.
	  1072 constant characters.
	  768 parsimony-informative characters.
	  338 uninformative variable characters.
	  1 characters were completely missing or ambiguous (removed).
	  2178 total characters (2179 before removing empty columns).
	  845 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 8 MB
  good			approx 7 MB to 6 MB
  low			approx 5 MB to 3 MB
  very low		approx 2 MB to 2 MB
the minimum required availablememory is 2 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 4 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 12.1 MB of memory

#######################################################
Found outgroup specification:  2

#######################################################
Loading starting model and/or tree from file data/n.G4.start
Reading TREES block...storing read block: TREES
 successful
Reading PAUP block...storing read block: PAUP
 successful
Reading GARLI block...storing read block: GARLI
 successful
STARTING RUN
Optimizing tree 1 ...
Obtained starting tree 1 from Nexus
Obtained starting or fixed model parameter values from Nexus:
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.532, AG = 3.880, AT = 1.559, CG = 1.283, CT = 4.738, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2442 0.2425 0.2497 0.2635 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      1.2505
    with an invariant (invariable) site category, proportion estimated
      0.3018
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.3018
      0.1841	0.1746
      0.5410	0.1746
      1.0317	0.1746
      2.2433	0.1746

Starting with seed=1

Initial ln Likelihood: -13930.5181
optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs...
pass 1:+    0.000 (branch=   0.00 scale=  0.00 alpha=  0.00 freqs=  0.00 rel rates=  0.00 pinv=  0.00)
lnL after optimization: -13930.5181
Current score = -13930.5181
Performing final optimizations...
pass 1 : -13930.5181   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
pass 2 : -13930.5181   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
pass 3 : -13930.5181   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
pass 4 : -13930.5181   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
pass 5 : -13930.5180   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
pass 6 : -13930.5180   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
pass 7 : -13930.5180   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
pass 8 : -13930.5180   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
pass 9 : -13930.5180   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
pass 10: -13930.5180   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
Looking for minimum length branches...
Final score = -13930.5180
Time used = 0 hours, 0 minutes and 1 seconds
Writing site likelihoods for tree 1 ...

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -13930.5180       

Parameter estimates:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
rep 1:   1.531  3.879  1.558  1.283  4.736      1 0.244 0.243 0.250 0.263 1.252 0.302

Treelengths:
          TL 
rep 1:  1.577

NOTE: collapsebranches setting ignored when writing and comparing optimized trees...

Writing optimized trees and models to scr.n.G4.best.all.tre
***********TEST**************
***Score is 13917.56622
***Expected is 13917.56622
***SCORE DIFFERENCE IS 0
***ALLOWED ERROR IS 0.01
***Scoring OK for ./scoring/n.G4.conf ***
Running scoring test ./scoring/n.G5.conf
Running scoring test ./scoring/n.G5.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./scoring/n.G5.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/z.11x2178.wtset.nex ...
Reading DATA block...storing implied block: TAXA
storing read block: DATA
 successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Excluded character numbers: 816 1012 1019 1022 1995 2180
	
	Found wtset "compensate" with data, applying...
	Summary of data:
	  11 sequences.
	  1072 constant characters.
	  768 parsimony-informative characters.
	  338 uninformative variable characters.
	  1 characters were completely missing or ambiguous (removed).
	  2178 total characters (2179 before removing empty columns).
	  845 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 10 MB
  good			approx 10 MB to 8 MB
  low			approx 7 MB to 4 MB
  very low		approx 3 MB to 2 MB
the minimum required availablememory is 2 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 4 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 15.0 MB of memory

#######################################################
Found outgroup specification:  1

#######################################################
Loading starting model and/or tree from file data/n.G5.start
Reading TREES block...storing read block: TREES
 successful
Reading GARLI block...storing read block: GARLI
 successful
Reading PAUP block...storing read block: PAUP
 successful
STARTING RUN
Optimizing tree 1 ...
Obtained starting tree 1 from Nexus
Obtained starting or fixed model parameter values from Nexus:
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.530, AG = 3.881, AT = 1.553, CG = 1.285, CT = 4.742, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2445 0.2424 0.2496 0.2636 
  Rate Heterogeneity Model:
    5 discrete gamma distributed rate categories, alpha param estimated
      1.3438
    with an invariant (invariable) site category, proportion estimated
      0.3098
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.3098
      0.1655	0.1380
      0.4459	0.1380
      0.7709	0.1380
      1.2349	0.1380
      2.3828	0.1380

Starting with seed=1

Initial ln Likelihood: -13931.0233
optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs...
pass 1:+    0.000 (branch=   0.00 scale=  0.00 alpha=  0.00 freqs=  0.00 rel rates=  0.00 pinv=  0.00)
lnL after optimization: -13931.0233
Current score = -13931.0233
Performing final optimizations...
pass 1 : -13931.0233   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
pass 2 : -13931.0233   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
pass 3 : -13931.0233   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
pass 4 : -13931.0232   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
pass 5 : -13931.0232   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
pass 6 : -13931.0232   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
pass 7 : -13931.0232   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
pass 8 : -13931.0232   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
pass 9 : -13931.0232   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
pass 10: -13931.0232   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
Looking for minimum length branches...
Final score = -13931.0232
Time used = 0 hours, 0 minutes and 1 seconds
Writing site likelihoods for tree 1 ...

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -13931.0232       

Parameter estimates:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
rep 1:    1.53   3.88  1.552  1.284  4.739      1 0.244 0.242 0.250 0.264 1.346 0.310

Treelengths:
          TL 
rep 1:  1.581

NOTE: collapsebranches setting ignored when writing and comparing optimized trees...

Writing optimized trees and models to scr.n.G5.best.all.tre
***********TEST**************
***Score is 13918.08407
***Expected is 13918.08407
***SCORE DIFFERENCE IS 0
***ALLOWED ERROR IS 0.01
***Scoring OK for ./scoring/n.G5.conf ***
Running scoring test ./scoring/n.conf
Running scoring test ./scoring/n.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./scoring/n.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/z.11x2178.wtset.nex ...
Reading DATA block...storing implied block: TAXA
storing read block: DATA
 successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Excluded character numbers: 816 1012 1019 1022 1995 2180
	
	Found wtset "compensate" with data, applying...
	Summary of data:
	  11 sequences.
	  1072 constant characters.
	  768 parsimony-informative characters.
	  338 uninformative variable characters.
	  1 characters were completely missing or ambiguous (removed).
	  2178 total characters (2179 before removing empty columns).
	  845 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 4 MB
  good			approx 3 MB to 2 MB
  low			approx 2 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 3.9 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1-3

#######################################################
Loading starting model and/or tree from file data/n.start
Reading GARLI block...storing read block: GARLI
 successful
STARTING RUN
Obtained starting or fixed model parameter values from Nexus:
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.869, AG = 3.671, AT = 1.221, CG = 1.853, CT = 4.414, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2554 0.2086 0.2382 0.2978 
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

creating random starting tree...
Initial ln Likelihood: -18359.9501
optimizing: starting branch lengths, rel rates, eq freqs...
pass 1:+ 2061.637 (branch=1982.89 scale= 74.28 freqs=  0.89 rel rates=  3.59)
pass 2:+  221.908 (branch= 220.60 scale=  0.00 freqs=  0.86 rel rates=  0.44)
pass 3:+    4.934 (branch=   4.75 scale=  0.00 freqs=  0.06 rel rates=  0.12)
pass 4:+    0.339 (branch=   0.30 scale=  0.00 freqs=  0.00 rel rates=  0.04)
pass 5:+    0.068 (branch=   0.07 scale=  0.00 freqs=  0.00 rel rates=  0.00)
pass 6:+    0.000 (branch=   0.00 scale=  0.00 freqs=  0.00 rel rates=  0.00)
lnL after optimization: -16071.0626
gen      current_lnL    precision  last_tree_imp  
0        -16071.0626      0.010           0 
100      -14502.0375      0.010          73 
200      -14502.0088      0.010          73 
300      -14501.0114      0.010          73 
400      -14500.3784      0.010          73 
500      -14499.9764      0.010          73 
600      -14499.5066      0.010          73 
700      -14499.2227      0.010          73 
800      -14499.0584      0.010          73 
900      -14499.0522      0.010          73 
1000     -14499.0522      0.010          73 
1100     -14498.9752      0.010          73 
1200     -14498.9747      0.010          73 
1300     -14498.9744      0.010          73 
1400     -14498.9744      0.010          73 
1500     -14498.9744      0.010          73 
1600     -14498.9598      0.010          73 
Reached termination condition!
last topological improvement at gen 73
Improvement over last 500 gen = 0.01547
Current score = -14498.9598
Performing final optimizations...
pass 1 : -14498.9266   (branch= 0.0118  eq freqs= 0.0156  rel rates= 0.0058)
pass 2 : -14498.8998   (branch= 0.0172  eq freqs= 0.0059  rel rates= 0.0037)
pass 3 : -14498.8921   (branch= 0.0061  eq freqs= 0.0014  rel rates= 0.0002)
pass 4 : -14498.8895   (branch= 0.0010  eq freqs= 0.0008  rel rates= 0.0008)
pass 5 : -14498.8878   (branch= 0.0006  eq freqs= 0.0001  rel rates= 0.0010)
pass 6 : -14498.8866   (branch= 0.0005  eq freqs= 0.0003  rel rates= 0.0005)
pass 7 : -14498.8860   (branch= 0.0004  eq freqs= 0.0001  rel rates= 0.0001)
pass 8 : -14498.8858   (branch= 0.0000  eq freqs= 0.0000  rel rates= 0.0001)
pass 9 : -14498.8856   (branch= 0.0001  eq freqs= 0.0000  rel rates= 0.0001)
pass 10: -14498.8855   (branch= 0.0000  eq freqs= 0.0000  rel rates= 0.0001)
pass 11: -14498.8855   (branch= 0.0000  eq freqs= 0.0000  rel rates= 0.0001)
pass 12: -14498.8854   (branch= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
pass 13: -14498.8854   (branch= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
pass 14: -14498.8854   (branch= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
pass 15: -14498.8853   (branch= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
Looking for minimum length branches...
Final score = -14498.8853
Time used = 0 hours, 0 minutes and 11 seconds

MODEL REPORT - Parameter values are FINAL
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.871, AG = 3.673, AT = 1.222, CG = 1.854, CT = 4.417, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2554 0.2085 0.2382 0.2978 
  Rate Heterogeneity Model:
    no rate heterogeneity

NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    No branches were short enough to be collapsed.

Saving site likelihoods to file scr.n.sitelikes.log ...
WARNING: Site likelihoods are being output when wtset compensate is in effect.
 Sites with weight > 1 will only be output once!

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -14498.8853       

Parameter estimates:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T)
rep 1:   1.871  3.673  1.222  1.854  4.417      1 0.255 0.209 0.238 0.298

Treelengths:
          TL 
rep 1:  1.298

Saving final tree from best search rep (#1) to scr.n.best.tre
#######################################################
***********TEST**************
***Score is 14486.03877
***Expected is 14486.03829
***SCORE DIFFERENCE IS .00048
***ALLOWED ERROR IS 0.01
***Scoring OK for ./scoring/n.conf ***
Running scoring test ./scoring/p.3diff.conf
Running scoring test ./scoring/p.3diff.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./scoring/p.3diff.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/z.byPos.11x2178.nex ...
Reading DATA block...storing implied block: TAXA
storing read block: DATA
 successful
Reading SETS block...storing read block: SETS
 successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS

CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY
	TO EACH DATA SUBSET (no linkage)

GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	CHARPARTITION subset #1 ("1stpos")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Excluded character numbers: 4
	
	Summary of data:
	  11 sequences.
	  441 constant characters.
	  171 parsimony-informative characters.
	  113 uninformative variable characters.
	  725 total characters.
	  237 unique patterns in compressed data matrix.
GARLI data subset 2
	CHARACTERS block #1 ("Untitled DATA Block 1")
	CHARPARTITION subset #2 ("2ndpos")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Excluded character numbers: 5
	
	Summary of data:
	  11 sequences.
	  527 constant characters.
	  90 parsimony-informative characters.
	  108 uninformative variable characters.
	  725 total characters.
	  158 unique patterns in compressed data matrix.
GARLI data subset 3
	CHARACTERS block #1 ("Untitled DATA Block 1")
	CHARPARTITION subset #3 ("3rdpos")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Excluded character numbers: 6
	
	Summary of data:
	  11 sequences.
	  102 constant characters.
	  507 parsimony-informative characters.
	  116 uninformative variable characters.
	  725 total characters.
	  548 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 9 MB
  good			approx 8 MB to 7 MB
  low			approx 6 MB to 4 MB
  very low		approx 3 MB to 2 MB
the minimum required availablememory is 2 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 4 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 13.5 MB of memory

#######################################################
Loading starting model and/or tree from file data/p.3diff.start
Reading TREES block...storing read block: TREES
 successful
Reading GARLI block...storing read block: GARLI
 successful
STARTING RUN
Optimizing tree 1 ...
Obtained starting tree 1 from Nexus
Obtained starting or fixed model parameter values from Nexus:
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix: 
    User specified matrix type: ( 0 1 2 2 3 4 ) 
    AC = 1.000, AG = 10.000, AT = 2.000, CG = 2.000, CT = 0.010, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.3150 0.1749 0.3006 0.2095 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.6000
    Substitution rate categories under this model:
      rate	proportion
      0.0531	0.2500
      0.3123	0.2500
      0.8813	0.2500
      2.7533	0.2500

Model 2
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix: 
    User specified matrix type: ( 0 1 2 1 0 3 ) 
    AC = 4.000, AG = 4.000, AT = 1.000, CG = 4.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.1000 0.2000 0.3000 0.4000 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.4000
    Substitution rate categories under this model:
      rate	proportion
      0.0167	0.2500
      0.1818	0.2500
      0.7313	0.2500
      3.0702	0.2500

Model 3
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix: 
    User specified matrix type: ( 0 1 2 3 1 0 ) 
    AC = 1.000, AG = 2.000, AT = 3.000, CG = 5.000, CT = 2.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.4000 0.2000 0.3000 0.1000 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.0100
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0100
      0.0334	0.2475
      0.2519	0.2475
      0.8203	0.2475
      2.8944	0.2475

Subset rate multipliers:
    0.54  0.30  2.16
Starting with seed=1

Initial ln Likelihood: -17270.1042
optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates...
pass 1:+ 3387.561 (branch=2073.05 scale= 39.85 alpha=118.40 freqs=413.09 rel rates=737.83 pinv=  0.00 subset rates=  5.33)
pass 2:+  327.990 (branch=  41.53 scale=  0.00 alpha= 19.91 freqs=187.33 rel rates= 77.79 pinv=  0.74 subset rates=  0.69)
pass 3:+  196.573 (branch=   1.56 scale=  1.04 alpha=  7.14 freqs= 83.86 rel rates=102.19 pinv=  0.01 subset rates=  0.77)
pass 4:+   36.660 (branch=   1.45 scale=  0.00 alpha=  0.68 freqs= 18.87 rel rates= 15.00 pinv=  0.00 subset rates=  0.65)
pass 5:+    4.518 (branch=   0.00 scale=  0.00 alpha=  0.02 freqs=  3.51 rel rates=  0.99 pinv=  0.01 subset rates=  0.00)
pass 6:+    0.901 (branch=   0.00 scale=  0.00 alpha=  0.01 freqs=  0.10 rel rates=  0.78 pinv=  0.01 subset rates=  0.00)
pass 7:+    0.107 (branch=   0.00 scale=  0.00 alpha=  0.02 freqs=  0.08 rel rates=  0.01 pinv=  0.01 subset rates=  0.00)
lnL after optimization: -13315.7937
Current score = -13315.7937
Performing final optimizations...
pass 1 : -13309.3589   (branch= 2.8300  alpha= 0.8831  pinv= 0.0157  eq freqs= 0.2322  rel rates= 1.8494  subset rates= 0.6243)
pass 2 : -13307.8685   (branch= 0.4258  alpha= 0.1992  pinv= 0.0130  eq freqs= 0.1299  rel rates= 0.6663  subset rates= 0.0562)
pass 3 : -13307.2724   (branch= 0.1089  alpha= 0.0561  pinv= 0.0031  eq freqs= 0.0074  rel rates= 0.4206  subset rates= 0.0000)
pass 4 : -13306.9015   (branch= 0.0214  alpha= 0.0163  pinv= 0.0021  eq freqs= 0.0108  rel rates= 0.2990  subset rates= 0.0213)
pass 5 : -13306.6670   (branch= 0.0102  alpha= 0.0063  pinv= 0.0015  eq freqs= 0.0062  rel rates= 0.2082  subset rates= 0.0021)
pass 6 : -13306.5170   (branch= 0.0033  alpha= 0.0030  pinv= 0.0005  eq freqs= 0.0036  rel rates= 0.1397  subset rates= 0.0000)
pass 7 : -13306.4171   (branch= 0.0023  alpha= 0.0006  pinv= 0.0001  eq freqs= 0.0031  rel rates= 0.0938  subset rates= 0.0000)
pass 8 : -13306.3499   (branch= 0.0007  alpha= 0.0003  pinv= 0.0000  eq freqs= 0.0020  rel rates= 0.0641  subset rates= 0.0000)
pass 9 : -13306.3046   (branch= 0.0003  alpha= 0.0001  pinv= 0.0000  eq freqs= 0.0015  rel rates= 0.0434  subset rates= 0.0000)
pass 10: -13306.2733   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0011  rel rates= 0.0300  subset rates= 0.0000)
pass 11: -13306.2525   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0006  rel rates= 0.0201  subset rates= 0.0000)
pass 12: -13306.2382   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0005  rel rates= 0.0138  subset rates= 0.0000)
pass 13: -13306.2276   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0003  rel rates= 0.0095  subset rates= 0.0008)
pass 14: -13306.2207   (branch= 0.0001  alpha= 0.0001  pinv= 0.0000  eq freqs= 0.0002  rel rates= 0.0066  subset rates= 0.0000)
pass 15: -13306.2160   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0045  subset rates= 0.0000)
pass 16: -13306.2130   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0029  subset rates= 0.0000)
pass 17: -13306.2108   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0021  subset rates= 0.0000)
pass 18: -13306.2094   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0014  subset rates= 0.0000)
pass 19: -13306.2084   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0010  subset rates= 0.0000)
pass 20: -13306.2077   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0007  subset rates= 0.0000)
 optimization up to ...
pass 30: -13306.2062   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0014  subset rates= 0.0000)
 optimization up to ...
pass 34: -13306.2061   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0001  subset rates= 0.0000)
Looking for minimum length branches...
Final score = -13306.2061
Time used = 0 hours, 0 minutes and 13 seconds
Writing site likelihoods for tree 1 ...

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -13306.2061       

Parameter estimates:

Partition model subset 1:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha
rep 1:   1.974  2.576  1.413  1.413  3.719      1 0.310 0.177 0.297 0.216 0.407

Partition model subset 2:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha
rep 1:   4.371  7.055  1.608  7.055  4.371      1 0.270 0.164 0.161 0.406 0.361

Partition model subset 3:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
rep 1:       1  4.939  3.388 0.4593  4.939      1 0.157 0.354 0.287 0.202 4.036 0.033

Treelengths and subset rate multipliers:
          TL   R(1)  R(2)  R(3)
rep 1:  1.694 0.541 0.301 2.159

NOTE: collapsebranches setting ignored when writing and comparing optimized trees...

Writing optimized trees and models to scr.p.3diff.best.all.tre
***********TEST**************
***Score is 13306.20613
***Expected is 13306.20608
***SCORE DIFFERENCE IS .00005
***ALLOWED ERROR IS 0.05
***Scoring OK for ./scoring/p.3diff.conf ***
Running scoring test ./scoring/p.mk.conf
Running scoring test ./scoring/p.mk.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./scoring/p.mk.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard k-state data,
	modeled as Standard k-state data
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 1 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.4 MB of memory

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN
Optimizing tree 1 ...
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

NOTE: Model contains no mutable parameters!
Setting model mutation weight to zero.

Initial ln Likelihood: -609.1934
optimizing: starting branch lengths...
pass 1:+  125.912 (branch= 124.97 scale=  0.94)
pass 2:+    7.205 (branch=   7.20 scale=  0.00)
pass 3:+    1.518 (branch=   1.48 scale=  0.03)
pass 4:+    0.225 (branch=   0.22 scale=  0.00)
pass 5:+    0.014 (branch=   0.01 scale=  0.00)
pass 6:+    0.000 (branch=   0.00 scale=  0.00)
lnL after optimization: -474.3188
Current score = -474.3188
Performing final optimizations...
pass 1 : -474.2925   (branch= 0.0264)
pass 2 : -474.2170   (branch= 0.0755)
pass 3 : -474.1996   (branch= 0.0173)
pass 4 : -474.1939   (branch= 0.0057)
pass 5 : -474.1908   (branch= 0.0031)
pass 6 : -474.1886   (branch= 0.0022)
pass 7 : -474.1872   (branch= 0.0014)
pass 8 : -474.1869   (branch= 0.0003)
pass 9 : -474.1867   (branch= 0.0002)
pass 10: -474.1865   (branch= 0.0002)
pass 11: -474.1864   (branch= 0.0001)
pass 12: -474.1864   (branch= 0.0000)
pass 13: -474.1864   (branch= 0.0000)
pass 14: -474.1864   (branch= 0.0000)
Looking for minimum length branches...
Final score = -474.1864
Time used = 0 hours, 0 minutes and 0 seconds
Writing site likelihoods for tree 1 ...

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -474.1864       

Parameter estimates:

Partition model subset 1:
	 Model contains no estimated parameters

Partition model subset 2:
	 Model contains no estimated parameters

Partition model subset 3:
	 Model contains no estimated parameters

Treelengths:
          TL 
rep 1:  3.854

NOTE: collapsebranches setting ignored when writing and comparing optimized trees...

Writing optimized trees and models to scr.p.mk.best.all.tre
***********TEST**************
***Score is 474.18638
***Expected is 474.1864
***SCORE DIFFERENCE IS -.00002
***ALLOWED ERROR IS 0.05
***Scoring OK for ./scoring/p.mk.conf ***
Running scoring test ./scoring/p.mk.ssr.conf
Running scoring test ./scoring/p.mk.ssr.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./scoring/p.mk.ssr.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard k-state data,
	modeled as Standard k-state data
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 1 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.4 MB of memory

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN
Optimizing tree 1 ...
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=1

Initial ln Likelihood: -609.1934
optimizing: starting branch lengths, subset rates...
pass 1:+  130.207 (branch= 124.97 scale=  0.94 subset rates=  4.29)
pass 2:+    9.055 (branch=   8.14 scale=  0.00 subset rates=  0.91)
pass 3:+    1.801 (branch=   1.66 scale=  0.02 subset rates=  0.12)
pass 4:+    0.304 (branch=   0.30 scale=  0.00 subset rates=  0.00)
pass 5:+    0.012 (branch=   0.01 scale=  0.00 subset rates=  0.00)
pass 6:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
lnL after optimization: -467.8138
Current score = -467.8138
Performing final optimizations...
pass 1 : -467.7837   (branch= 0.0218  subset rates= 0.0084)
pass 2 : -467.7131   (branch= 0.0705  subset rates= 0.0000)
pass 3 : -467.7054   (branch= 0.0077  subset rates= 0.0000)
pass 4 : -467.6967   (branch= 0.0087  subset rates= 0.0000)
pass 5 : -467.6866   (branch= 0.0073  subset rates= 0.0028)
pass 6 : -467.6817   (branch= 0.0044  subset rates= 0.0004)
pass 7 : -467.6801   (branch= 0.0016  subset rates= 0.0000)
pass 8 : -467.6799   (branch= 0.0002  subset rates= 0.0000)
pass 9 : -467.6796   (branch= 0.0003  subset rates= 0.0000)
pass 10: -467.6789   (branch= 0.0001  subset rates= 0.0007)
pass 11: -467.6785   (branch= 0.0004  subset rates= 0.0000)
pass 12: -467.6784   (branch= 0.0001  subset rates= 0.0000)
pass 13: -467.6784   (branch= 0.0000  subset rates= 0.0000)
pass 14: -467.6784   (branch= 0.0000  subset rates= 0.0000)
pass 15: -467.6783   (branch= 0.0000  subset rates= 0.0000)
Looking for minimum length branches...
Final score = -467.6783
Time used = 0 hours, 0 minutes and 0 seconds
Writing site likelihoods for tree 1 ...

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -467.6783       

Parameter estimates:

Partition model subset 1:
	 Model contains no estimated parameters

Partition model subset 2:
	 Model contains no estimated parameters

Partition model subset 3:
	 Model contains no estimated parameters

Treelengths and subset rate multipliers:
          TL   R(1)  R(2)  R(3)
rep 1:  3.841 0.787 1.478 2.174

NOTE: collapsebranches setting ignored when writing and comparing optimized trees...

Writing optimized trees and models to scr.p.mk.ssr.best.all.tre
***********TEST**************
***Score is 467.67834
***Expected is 467.6783
***SCORE DIFFERENCE IS .00004
***ALLOWED ERROR IS 0.05
***Scoring OK for ./scoring/p.mk.ssr.conf ***
Running scoring test ./scoring/p.mkO.conf
Running scoring test ./scoring/p.mkO.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./scoring/p.mkO.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard ordered k-state data,
	modeled as Standard ordered k-state data
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 1 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.4 MB of memory

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN
Optimizing tree 1 ...
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

NOTE: Model contains no mutable parameters!
Setting model mutation weight to zero.

Initial ln Likelihood: -641.9257
optimizing: starting branch lengths...
pass 1:+  137.411 (branch= 136.58 scale=  0.83)
pass 2:+    7.774 (branch=   7.77 scale=  0.00)
pass 3:+    1.542 (branch=   1.52 scale=  0.02)
pass 4:+    0.091 (branch=   0.09 scale=  0.00)
pass 5:+    0.000 (branch=   0.00 scale=  0.00)
lnL after optimization: -495.1076
Current score = -495.1076
Performing final optimizations...
pass 1 : -495.0677   (branch= 0.0399)
pass 2 : -494.9999   (branch= 0.0678)
pass 3 : -494.9820   (branch= 0.0179)
pass 4 : -494.9768   (branch= 0.0051)
pass 5 : -494.9724   (branch= 0.0044)
pass 6 : -494.9711   (branch= 0.0013)
pass 7 : -494.9709   (branch= 0.0002)
pass 8 : -494.9703   (branch= 0.0006)
pass 9 : -494.9702   (branch= 0.0001)
pass 10: -494.9701   (branch= 0.0001)
pass 11: -494.9701   (branch= 0.0000)
pass 12: -494.9700   (branch= 0.0000)
pass 13: -494.9700   (branch= 0.0000)
Looking for minimum length branches...
Final score = -494.9700
Time used = 0 hours, 0 minutes and 0 seconds
Writing site likelihoods for tree 1 ...

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -494.9700       

Parameter estimates:

Partition model subset 1:
	 Model contains no estimated parameters

Partition model subset 2:
	 Model contains no estimated parameters

Partition model subset 3:
	 Model contains no estimated parameters

Treelengths:
          TL 
rep 1:  4.503

NOTE: collapsebranches setting ignored when writing and comparing optimized trees...

Writing optimized trees and models to scr.p.mkO.best.all.tre
***********TEST**************
***Score is 494.97003
***Expected is 494.9700
***SCORE DIFFERENCE IS .00003
***ALLOWED ERROR IS 0.05
***Scoring OK for ./scoring/p.mkO.conf ***
Running scoring test ./scoring/p.mkO.ssr.conf
Running scoring test ./scoring/p.mkO.ssr.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./scoring/p.mkO.ssr.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard ordered k-state data,
	modeled as Standard ordered k-state data
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 1 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.4 MB of memory

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN
Optimizing tree 1 ...
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=1

Initial ln Likelihood: -641.9257
optimizing: starting branch lengths, subset rates...
pass 1:+  147.096 (branch= 136.58 scale=  0.83 subset rates=  9.68)
pass 2:+   12.451 (branch=   8.46 scale=  0.00 subset rates=  3.99)
pass 3:+    3.549 (branch=   2.32 scale=  0.03 subset rates=  1.20)
pass 4:+    0.759 (branch=   0.51 scale=  0.00 subset rates=  0.25)
pass 5:+    0.120 (branch=   0.11 scale=  0.00 subset rates=  0.01)
pass 6:+    0.011 (branch=   0.01 scale=  0.00 subset rates=  0.00)
pass 7:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
lnL after optimization: -477.9402
Current score = -477.9402
Performing final optimizations...
pass 1 : -477.8555   (branch= 0.0847  subset rates= 0.0000)
pass 2 : -477.7620   (branch= 0.0916  subset rates= 0.0020)
pass 3 : -477.7274   (branch= 0.0329  subset rates= 0.0017)
pass 4 : -477.7065   (branch= 0.0201  subset rates= 0.0008)
pass 5 : -477.6965   (branch= 0.0100  subset rates= 0.0000)
pass 6 : -477.6924   (branch= 0.0041  subset rates= 0.0000)
pass 7 : -477.6895   (branch= 0.0029  subset rates= 0.0000)
pass 8 : -477.6881   (branch= 0.0014  subset rates= 0.0000)
pass 9 : -477.6869   (branch= 0.0009  subset rates= 0.0003)
pass 10: -477.6859   (branch= 0.0009  subset rates= 0.0001)
pass 11: -477.6853   (branch= 0.0006  subset rates= 0.0000)
pass 12: -477.6850   (branch= 0.0003  subset rates= 0.0000)
pass 13: -477.6849   (branch= 0.0001  subset rates= 0.0000)
pass 14: -477.6848   (branch= 0.0001  subset rates= 0.0000)
pass 15: -477.6847   (branch= 0.0000  subset rates= 0.0000)
pass 16: -477.6847   (branch= 0.0000  subset rates= 0.0000)
pass 17: -477.6847   (branch= 0.0000  subset rates= 0.0000)
pass 18: -477.6847   (branch= 0.0000  subset rates= 0.0000)
Looking for minimum length branches...
Final score = -477.6847
Time used = 0 hours, 0 minutes and 0 seconds
Writing site likelihoods for tree 1 ...

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -477.6847       

Parameter estimates:

Partition model subset 1:
	 Model contains no estimated parameters

Partition model subset 2:
	 Model contains no estimated parameters

Partition model subset 3:
	 Model contains no estimated parameters

Treelengths and subset rate multipliers:
          TL   R(1)  R(2)  R(3)
rep 1:  4.918 0.629 1.903 2.812

NOTE: collapsebranches setting ignored when writing and comparing optimized trees...

Writing optimized trees and models to scr.p.mkO.ssr.best.all.tre
***********TEST**************
***Score is 477.68468
***Expected is 477.6848
***SCORE DIFFERENCE IS -.00012
***ALLOWED ERROR IS 0.05
***Scoring OK for ./scoring/p.mkO.ssr.conf ***
Running scoring test ./scoring/p.mkv.conf
Running scoring test ./scoring/p.mkv.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./scoring/p.mkv.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard k-state data, variable only,
	modeled as Standard k-state data, variable only
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 1 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.5 MB of memory

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN
Optimizing tree 1 ...
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

NOTE: Model contains no mutable parameters!
Setting model mutation weight to zero.

Initial ln Likelihood: -605.5989
optimizing: starting branch lengths...
pass 1:+  124.584 (branch= 123.99 scale=  0.59)
pass 2:+    6.980 (branch=   6.98 scale=  0.00)
pass 3:+    1.324 (branch=   1.31 scale=  0.02)
pass 4:+    0.161 (branch=   0.16 scale=  0.00)
pass 5:+    0.013 (branch=   0.01 scale=  0.00)
pass 6:+    0.000 (branch=   0.00 scale=  0.00)
lnL after optimization: -472.5370
Current score = -472.5370
Performing final optimizations...
pass 1 : -472.4890   (branch= 0.0480)
pass 2 : -472.4195   (branch= 0.0694)
pass 3 : -472.4053   (branch= 0.0142)
pass 4 : -472.3958   (branch= 0.0095)
pass 5 : -472.3935   (branch= 0.0024)
pass 6 : -472.3921   (branch= 0.0013)
pass 7 : -472.3917   (branch= 0.0005)
pass 8 : -472.3912   (branch= 0.0004)
pass 9 : -472.3908   (branch= 0.0004)
pass 10: -472.3907   (branch= 0.0001)
pass 11: -472.3906   (branch= 0.0001)
pass 12: -472.3906   (branch= 0.0000)
pass 13: -472.3906   (branch= 0.0000)
pass 14: -472.3906   (branch= 0.0000)
Looking for minimum length branches...
Final score = -472.3906
Time used = 0 hours, 0 minutes and 0 seconds
Writing site likelihoods for tree 1 ...

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -472.3906       

Parameter estimates:

Partition model subset 1:
	 Model contains no estimated parameters

Partition model subset 2:
	 Model contains no estimated parameters

Partition model subset 3:
	 Model contains no estimated parameters

Treelengths:
          TL 
rep 1:  3.621

NOTE: collapsebranches setting ignored when writing and comparing optimized trees...

Writing optimized trees and models to scr.p.mkv.best.all.tre
***********TEST**************
***Score is 472.39058
***Expected is 472.3906
***SCORE DIFFERENCE IS -.00002
***ALLOWED ERROR IS 0.05
***Scoring OK for ./scoring/p.mkv.conf ***
Running scoring test ./scoring/p.mkv.ssr.conf
Running scoring test ./scoring/p.mkv.ssr.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./scoring/p.mkv.ssr.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard k-state data, variable only,
	modeled as Standard k-state data, variable only
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 1 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.5 MB of memory

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN
Optimizing tree 1 ...
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=1

Initial ln Likelihood: -605.5989
optimizing: starting branch lengths, subset rates...
pass 1:+  129.564 (branch= 123.99 scale=  0.59 subset rates=  4.98)
pass 2:+    9.272 (branch=   7.97 scale=  0.00 subset rates=  1.30)
pass 3:+    1.741 (branch=   1.57 scale=  0.00 subset rates=  0.17)
pass 4:+    0.311 (branch=   0.31 scale=  0.00 subset rates=  0.00)
pass 5:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
lnL after optimization: -464.7113
Current score = -464.7113
Performing final optimizations...
pass 1 : -464.6741   (branch= 0.0277  subset rates= 0.0094)
pass 2 : -464.5915   (branch= 0.0810  subset rates= 0.0016)
pass 3 : -464.5742   (branch= 0.0137  subset rates= 0.0036)
pass 4 : -464.5605   (branch= 0.0126  subset rates= 0.0012)
pass 5 : -464.5544   (branch= 0.0061  subset rates= 0.0000)
pass 6 : -464.5510   (branch= 0.0018  subset rates= 0.0016)
pass 7 : -464.5497   (branch= 0.0008  subset rates= 0.0005)
pass 8 : -464.5487   (branch= 0.0010  subset rates= 0.0000)
pass 9 : -464.5480   (branch= 0.0007  subset rates= 0.0001)
pass 10: -464.5476   (branch= 0.0004  subset rates= 0.0001)
pass 11: -464.5474   (branch= 0.0002  subset rates= 0.0000)
pass 12: -464.5473   (branch= 0.0001  subset rates= 0.0000)
pass 13: -464.5473   (branch= 0.0000  subset rates= 0.0000)
pass 14: -464.5473   (branch= 0.0000  subset rates= 0.0000)
pass 15: -464.5473   (branch= 0.0000  subset rates= 0.0000)
Looking for minimum length branches...
Final score = -464.5473
Time used = 0 hours, 0 minutes and 0 seconds
Writing site likelihoods for tree 1 ...

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -464.5473       

Parameter estimates:

Partition model subset 1:
	 Model contains no estimated parameters

Partition model subset 2:
	 Model contains no estimated parameters

Partition model subset 3:
	 Model contains no estimated parameters

Treelengths and subset rate multipliers:
          TL   R(1)  R(2)  R(3)
rep 1:  3.400 0.771 1.640 2.469

NOTE: collapsebranches setting ignored when writing and comparing optimized trees...

Writing optimized trees and models to scr.p.mkv.ssr.best.all.tre
***********TEST**************
***Score is 464.54728
***Expected is 464.5473
***SCORE DIFFERENCE IS -.00002
***ALLOWED ERROR IS 0.05
***Scoring OK for ./scoring/p.mkv.ssr.conf ***
Running scoring test ./scoring/p.mkvO.conf
Running scoring test ./scoring/p.mkvO.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./scoring/p.mkvO.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard ordered k-state data, variable only,
	modeled as Standard ordered k-state data, variable only
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 1 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.5 MB of memory

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN
Optimizing tree 1 ...
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

NOTE: Model contains no mutable parameters!
Setting model mutation weight to zero.

Initial ln Likelihood: -637.9212
optimizing: starting branch lengths...
pass 1:+  134.883 (branch= 134.40 scale=  0.48)
pass 2:+    7.290 (branch=   7.29 scale=  0.00)
pass 3:+    1.758 (branch=   1.73 scale=  0.03)
pass 4:+    0.187 (branch=   0.19 scale=  0.00)
pass 5:+    0.011 (branch=   0.01 scale=  0.00)
pass 6:+    0.000 (branch=   0.00 scale=  0.00)
lnL after optimization: -493.7915
Current score = -493.7915
Performing final optimizations...
pass 1 : -493.7599   (branch= 0.0316)
pass 2 : -493.6921   (branch= 0.0678)
pass 3 : -493.6791   (branch= 0.0130)
pass 4 : -493.6729   (branch= 0.0062)
pass 5 : -493.6703   (branch= 0.0026)
pass 6 : -493.6691   (branch= 0.0012)
pass 7 : -493.6680   (branch= 0.0011)
pass 8 : -493.6679   (branch= 0.0001)
pass 9 : -493.6678   (branch= 0.0001)
pass 10: -493.6677   (branch= 0.0000)
pass 11: -493.6677   (branch= 0.0001)
pass 12: -493.6676   (branch= 0.0000)
pass 13: -493.6676   (branch= 0.0000)
Looking for minimum length branches...
Final score = -493.6676
Time used = 0 hours, 0 minutes and 0 seconds
Writing site likelihoods for tree 1 ...

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -493.6676       

Parameter estimates:

Partition model subset 1:
	 Model contains no estimated parameters

Partition model subset 2:
	 Model contains no estimated parameters

Partition model subset 3:
	 Model contains no estimated parameters

Treelengths:
          TL 
rep 1:  4.301

NOTE: collapsebranches setting ignored when writing and comparing optimized trees...

Writing optimized trees and models to scr.p.mkvO.best.all.tre
***********TEST**************
***Score is 493.66764
***Expected is 493.667
***SCORE DIFFERENCE IS .00064
***ALLOWED ERROR IS 0.05
***Scoring OK for ./scoring/p.mkvO.conf ***
Running scoring test ./scoring/p.mkvO.ssr.conf
Running scoring test ./scoring/p.mkvO.ssr.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./scoring/p.mkvO.ssr.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard ordered k-state data, variable only,
	modeled as Standard ordered k-state data, variable only
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

NOTE: Less memory is required when scoring or optimizing fixed trees.
	minimum of 1 availablememory would be required to search


You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.5 MB of memory

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN
Optimizing tree 1 ...
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=1

Initial ln Likelihood: -637.9212
optimizing: starting branch lengths, subset rates...
pass 1:+  144.867 (branch= 134.40 scale=  0.48 subset rates=  9.98)
pass 2:+   12.967 (branch=   8.30 scale=  0.00 subset rates=  4.67)
pass 3:+    3.846 (branch=   2.24 scale=  0.02 subset rates=  1.58)
pass 4:+    1.162 (branch=   0.58 scale=  0.01 subset rates=  0.57)
pass 5:+    0.156 (branch=   0.12 scale=  0.00 subset rates=  0.03)
pass 6:+    0.044 (branch=   0.04 scale=  0.00 subset rates=  0.00)
pass 7:+    0.015 (branch=   0.02 scale=  0.00 subset rates=  0.00)
pass 8:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
lnL after optimization: -474.8632
Current score = -474.8632
Performing final optimizations...
pass 1 : -474.7998   (branch= 0.0575  subset rates= 0.0059)
pass 2 : -474.6995   (branch= 0.0905  subset rates= 0.0099)
pass 3 : -474.6708   (branch= 0.0286  subset rates= 0.0000)
pass 4 : -474.6601   (branch= 0.0107  subset rates= 0.0000)
pass 5 : -474.6536   (branch= 0.0055  subset rates= 0.0011)
pass 6 : -474.6498   (branch= 0.0029  subset rates= 0.0010)
pass 7 : -474.6476   (branch= 0.0021  subset rates= 0.0000)
pass 8 : -474.6469   (branch= 0.0007  subset rates= 0.0000)
pass 9 : -474.6465   (branch= 0.0003  subset rates= 0.0001)
pass 10: -474.6460   (branch= 0.0004  subset rates= 0.0000)
pass 11: -474.6458   (branch= 0.0002  subset rates= 0.0000)
pass 12: -474.6457   (branch= 0.0001  subset rates= 0.0000)
pass 13: -474.6456   (branch= 0.0001  subset rates= 0.0000)
pass 14: -474.6456   (branch= 0.0000  subset rates= 0.0000)
pass 15: -474.6456   (branch= 0.0000  subset rates= 0.0000)
pass 16: -474.6456   (branch= 0.0000  subset rates= 0.0000)
Looking for minimum length branches...
Final score = -474.6456
Time used = 0 hours, 0 minutes and 0 seconds
Writing site likelihoods for tree 1 ...

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -474.6456       

Parameter estimates:

Partition model subset 1:
	 Model contains no estimated parameters

Partition model subset 2:
	 Model contains no estimated parameters

Partition model subset 3:
	 Model contains no estimated parameters

Treelengths and subset rate multipliers:
          TL   R(1)  R(2)  R(3)
rep 1:  4.583 0.587 2.014 2.996

NOTE: collapsebranches setting ignored when writing and comparing optimized trees...

Writing optimized trees and models to scr.p.mkvO.ssr.best.all.tre
***********TEST**************
***Score is 474.64557
***Expected is 474.6455633
***SCORE DIFFERENCE IS .0000067
***ALLOWED ERROR IS 0.05
***Scoring OK for ./scoring/p.mkvO.ssr.conf ***
**************************
Running constraint tests ...
**************************
Running constraint test n.neg.const
Running constraint test n.neg.const
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./const/n.neg.const.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  11 sequences.
	  11 constant characters.
	  17 parsimony-informative characters.
	  2 uninformative variable characters.
	  30 total characters.
	  25 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.4 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1

#######################################################
Loading constraints from file data/z.neg.const.tre
Found 1 negatively (conversely) constrained bipartition
     Bipartition 1: (1,2,3,4,5,11) | (6,7,8,9,10)
STARTING RUN
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2310 0.3201 0.1881 0.2607 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.0917
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0917
      0.0334	0.2271
      0.2519	0.2271
      0.8203	0.2271
      2.8944	0.2271

Starting with seed=1

creating likelihood stepwise addition starting tree (compatible with constraints)...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 0.004 lnL
Optimizing branchlengths... improved 0.000 lnL
 7  8  9  10  11 
Initial ln Likelihood: -227.5619
optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs...
pass 1:+    4.671 (branch=   0.06 scale=  0.00 alpha=  0.00 freqs=  2.00 rel rates=  2.60 pinv=  0.00)
pass 2:+    0.025 (branch=   0.00 scale=  0.00 alpha=  0.00 freqs=  0.02 rel rates=  0.00 pinv=  0.00)
lnL after optimization: -222.8653
gen      current_lnL    precision  last_tree_imp  
0        -222.8653        0.500           0 
500      -213.0501        0.500         495 
1000     -212.5074        0.500         628 
Optimization precision reduced 
   Optimizing parameters...    improved    1.331 lnL
   Optimizing branchlengths... improved    0.015 lnL
1500     -210.8784        0.010        1215 
2000     -210.6585        0.010        1215 
2500     -210.6111        0.010        1215 
3000     -210.5162        0.010        1215 
Reached termination condition!
last topological improvement at gen 1215
Improvement over last 500 gen = 0.03349
Current score = -210.5118
Performing final optimizations...
pass 1 : -210.1433   (branch= 0.0000  alpha= 0.0977  pinv= 0.2249  eq freqs= 0.0000  rel rates= 0.0460)
pass 2 : -209.5323   (branch= 0.0000  alpha= 0.3293  pinv= 0.2553  eq freqs= 0.0029  rel rates= 0.0235)
pass 3 : -209.3312   (branch= 0.0357  alpha= 0.1375  pinv= 0.0146  eq freqs= 0.0067  rel rates= 0.0067)
pass 4 : -209.2605   (branch= 0.0422  alpha= 0.0192  pinv= 0.0022  eq freqs= 0.0011  rel rates= 0.0060)
pass 5 : -209.2228   (branch= 0.0234  alpha= 0.0075  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0069)
pass 6 : -209.1997   (branch= 0.0108  alpha= 0.0028  pinv= 0.0010  eq freqs= 0.0002  rel rates= 0.0084)
pass 7 : -209.1781   (branch= 0.0076  alpha= 0.0023  pinv= 0.0003  eq freqs= 0.0003  rel rates= 0.0110)
pass 8 : -209.1598   (branch= 0.0049  alpha= 0.0013  pinv= 0.0001  eq freqs= 0.0005  rel rates= 0.0115)
pass 9 : -209.1462   (branch= 0.0024  alpha= 0.0001  pinv= 0.0000  eq freqs= 0.0005  rel rates= 0.0108)
pass 10: -209.1345   (branch= 0.0010  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0004  rel rates= 0.0102)
pass 11: -209.1247   (branch= 0.0005  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0003  rel rates= 0.0090)
pass 12: -209.1160   (branch= 0.0003  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0002  rel rates= 0.0082)
pass 13: -209.1081   (branch= 0.0002  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0075)
pass 14: -209.1010   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0069)
pass 15: -209.0943   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0065)
pass 16: -209.0881   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0060)
pass 17: -209.0822   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0058)
pass 18: -209.0768   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0054)
pass 19: -209.0715   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0052)
pass 20: -209.0667   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0047)
 optimization up to ...
pass 30: -208.9988   (branch= 0.0077  alpha= 0.0000  pinv= 0.0003  eq freqs= 0.0013  rel rates= 0.0587)
 optimization up to ...
pass 40: -208.8376   (branch= 0.0298  alpha= 0.0000  pinv= 0.0016  eq freqs= 0.0076  rel rates= 0.1223)
 optimization up to ...
pass 50: -208.6967   (branch= 0.0131  alpha= 0.0000  pinv= 0.0014  eq freqs= 0.0057  rel rates= 0.1208)
 optimization up to ...
pass 60: -208.6228   (branch= 0.0012  alpha= 0.0000  pinv= 0.0002  eq freqs= 0.0007  rel rates= 0.0719)
 optimization up to ...
pass 70: -208.5734   (branch= 0.0003  alpha= 0.0000  pinv= 0.0001  eq freqs= 0.0002  rel rates= 0.0488)
 optimization up to ...
pass 80: -208.5377   (branch= 0.0002  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0354)
 optimization up to ...
pass 90: -208.5105   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0269)
 optimization up to ...
pass 100: -208.4894   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0209)
 optimization up to ...
pass 110: -208.4724   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0169)
 optimization up to ...
pass 120: -208.4587   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0136)
 optimization up to ...
pass 130: -208.4472   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0114)
 optimization up to ...
pass 140: -208.4374   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0097)
 optimization up to ...
pass 150: -208.4292   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0082)
 optimization up to ...
pass 160: -208.4221   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0070)
 optimization up to ...
pass 170: -208.4160   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0061)
 optimization up to ...
pass 180: -208.4106   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0054)
 optimization up to ...
pass 190: -208.4059   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0047)
 optimization up to ...
pass 200: -208.4017   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0041)
 optimization up to ...
pass 210: -208.3980   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0037)
 optimization up to ...
pass 220: -208.3946   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0033)
 optimization up to ...
pass 230: -208.3916   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0030)
 optimization up to ...
pass 240: -208.3888   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0028)
 optimization up to ...
pass 250: -208.3863   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0025)
 optimization up to ...
pass 260: -208.3840   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0023)
 optimization up to ...
pass 270: -208.3819   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0021)
 optimization up to ...
pass 280: -208.3799   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0020)
 optimization up to ...
pass 290: -208.3781   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0018)
 optimization up to ...
pass 300: -208.3764   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0017)
 optimization up to ...
pass 310: -208.3749   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0015)
 optimization up to ...
pass 320: -208.3734   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0014)
 optimization up to ...
pass 330: -208.3721   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0014)
 optimization up to ...
pass 340: -208.3708   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0013)
 optimization up to ...
pass 350: -208.3696   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0012)
 optimization up to ...
pass 360: -208.3685   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0011)
 optimization up to ...
pass 370: -208.3674   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0011)
 optimization up to ...
pass 380: -208.3664   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0010)
 optimization up to ...
pass 390: -208.3655   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0009)
 optimization up to ...
pass 400: -208.3646   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0009)
 optimization up to ...
pass 410: -208.3638   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0008)
 optimization up to ...
pass 420: -208.3630   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0008)
 optimization up to ...
pass 430: -208.3623   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0008)
 optimization up to ...
pass 440: -208.3615   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0007)
 optimization up to ...
pass 450: -208.3608   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0007)
 optimization up to ...
pass 460: -208.3602   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0006)
 optimization up to ...
pass 470: -208.3596   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0006)
 optimization up to ...
pass 480: -208.3590   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0006)
 optimization up to ...
pass 490: -208.3586   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0003)
 optimization up to ...
pass 494: -208.3585   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0001)
Looking for minimum length branches...
Final score = -208.3585
Time used = 0 hours, 0 minutes and 9 seconds

MODEL REPORT - Parameter values are FINAL
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 121.821, AG = 187.997, AT = 6.950, CG = 204.113, CT = 194.212, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2225 0.2905 0.2035 0.2835 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      999.8998
    with an invariant (invariable) site category, proportion estimated
      0.2781
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.2781
      0.9601	0.1805
      0.9894	0.1805
      1.0100	0.1805
      1.0405	0.1805

NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    2 branches were collapsed.


#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -208.3585       

Parameter estimates:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
rep 1:   121.8    188   6.95  204.1  194.2      1 0.223 0.291 0.203 0.283 999.900 0.278

Treelengths:
          TL 
rep 1:  1.881

Saving final tree from best search rep (#1) to con.n.neg.const.best.tre
#######################################################
TREEFILES PASS
Running constraint test n.negBack.const
Running constraint test n.negBack.const
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./const/n.negBack.const.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  11 sequences.
	  11 constant characters.
	  17 parsimony-informative characters.
	  2 uninformative variable characters.
	  30 total characters.
	  25 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.4 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1-3

#######################################################
Loading constraints from file data/z.negBack.const.tre
All constraints are backbone
All constraints involve the same backbone set of taxa
Found 1 negatively (conversely) constrained bipartition
     Bipartition 1 (backbone): (1,2,3,5,8,9,10) | (4,11)
STARTING RUN
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2310 0.3201 0.1881 0.2607 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.0917
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0917
      0.0334	0.2271
      0.2519	0.2271
      0.8203	0.2271
      2.8944	0.2271

Starting with seed=1

creating likelihood stepwise addition starting tree (compatible with constraints)...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 0.005 lnL
Optimizing branchlengths... improved 0.292 lnL
 7  8  9  10  11 
Initial ln Likelihood: -238.2863
optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs...
pass 1:+    6.219 (branch=   2.07 scale=  0.00 alpha=  0.00 freqs=  1.61 rel rates=  2.53 pinv=  0.00)
pass 2:+    1.027 (branch=   0.47 scale=  0.00 alpha=  0.00 freqs=  0.55 rel rates=  0.00 pinv=  0.00)
pass 3:+    0.029 (branch=   0.00 scale=  0.00 alpha=  0.00 freqs=  0.02 rel rates=  0.00 pinv=  0.00)
lnL after optimization: -231.0119
gen      current_lnL    precision  last_tree_imp  
0        -231.0119        0.500           0 
500      -214.6598        0.500         276 
Optimization precision reduced 
   Optimizing parameters...    improved    1.751 lnL
   Optimizing branchlengths... improved    0.106 lnL
1000     -212.3291        0.010         825 
1500     -212.1959        0.010         825 
2000     -211.9101        0.010         825 
2500     -211.7710        0.010         825 
3000     -211.6572        0.010         825 
3500     -211.4394        0.010         825 
4000     -211.3138        0.010         825 
Reached termination condition!
last topological improvement at gen 825
Improvement over last 500 gen = 0.03817
Current score = -211.2856
Performing final optimizations...
pass 1 : -208.8370   (branch= 0.0000  alpha= 0.7695  pinv= 1.5819  eq freqs= 0.0061  rel rates= 0.0912)
pass 2 : -208.5500   (branch= 0.0559  alpha= 0.1910  pinv= 0.0000  eq freqs= 0.0115  rel rates= 0.0286)
pass 3 : -208.5121   (branch= 0.0133  alpha= 0.0021  pinv= 0.0028  eq freqs= 0.0015  rel rates= 0.0182)
pass 4 : -208.4860   (branch= 0.0045  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0007  rel rates= 0.0209)
pass 5 : -208.4643   (branch= 0.0019  alpha= 0.0007  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0191)
pass 6 : -208.4461   (branch= 0.0003  alpha= 0.0000  pinv= 0.0003  eq freqs= 0.0002  rel rates= 0.0175)
pass 7 : -208.4282   (branch= 0.0008  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0170)
pass 8 : -208.4134   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0146)
pass 9 : -208.3990   (branch= 0.0003  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0140)
pass 10: -208.3862   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0127)
pass 11: -208.3744   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0117)
pass 12: -208.3639   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0104)
pass 13: -208.3540   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0098)
pass 14: -208.3448   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0091)
pass 15: -208.3363   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0084)
pass 16: -208.3285   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0078)
pass 17: -208.3214   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0071)
pass 18: -208.3144   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0069)
pass 19: -208.3081   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0063)
pass 20: -208.3021   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0060)
 optimization up to ...
pass 30: -208.2576   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0444)
 optimization up to ...
pass 40: -208.2298   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0277)
 optimization up to ...
pass 50: -208.2109   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0189)
 optimization up to ...
pass 60: -208.1971   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0137)
 optimization up to ...
pass 70: -208.1867   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0104)
 optimization up to ...
pass 80: -208.1784   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0083)
 optimization up to ...
pass 90: -208.1717   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0067)
 optimization up to ...
pass 100: -208.1662   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0055)
 optimization up to ...
pass 110: -208.1615   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0046)
 optimization up to ...
pass 120: -208.1576   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0040)
 optimization up to ...
pass 130: -208.1542   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0034)
 optimization up to ...
pass 140: -208.1512   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0030)
 optimization up to ...
pass 150: -208.1485   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0026)
 optimization up to ...
pass 160: -208.1462   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0024)
 optimization up to ...
pass 170: -208.1441   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0021)
 optimization up to ...
pass 180: -208.1422   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0019)
 optimization up to ...
pass 190: -208.1404   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0017)
 optimization up to ...
pass 200: -208.1389   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0016)
 optimization up to ...
pass 210: -208.1375   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0014)
 optimization up to ...
pass 220: -208.1362   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0013)
 optimization up to ...
pass 230: -208.1349   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0012)
 optimization up to ...
pass 240: -208.1338   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0011)
 optimization up to ...
pass 250: -208.1328   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0010)
 optimization up to ...
pass 260: -208.1318   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0010)
 optimization up to ...
pass 270: -208.1309   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0009)
 optimization up to ...
pass 280: -208.1301   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0008)
 optimization up to ...
pass 290: -208.1293   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0008)
 optimization up to ...
pass 300: -208.1285   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0007)
 optimization up to ...
pass 310: -208.1278   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0007)
 optimization up to ...
pass 320: -208.1272   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0007)
 optimization up to ...
pass 330: -208.1266   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0006)
 optimization up to ...
pass 340: -208.1260   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0006)
 optimization up to ...
pass 350: -208.1254   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0006)
 optimization up to ...
pass 360: -208.1249   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0005)
 optimization up to ...
pass 370: -208.1244   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0005)
 optimization up to ...
pass 372: -208.1244   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
Looking for minimum length branches...
Final score = -208.1244
Time used = 0 hours, 0 minutes and 13 seconds

MODEL REPORT - Parameter values are FINAL
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 22.230, AG = 32.301, AT = 0.001, CG = 36.387, CT = 80.287, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2210 0.3445 0.2161 0.2184 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      999.9000
    with an invariant (invariable) site category, proportion estimated
      0.3383
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.3383
      0.9601	0.1654
      0.9894	0.1654
      1.0100	0.1654
      1.0405	0.1654

NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    1 branches were collapsed.


#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -208.1244       

Parameter estimates:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
rep 1:   22.23   32.3  0.001  36.39  80.29      1 0.221 0.344 0.216 0.218 999.900 0.338

Treelengths:
          TL 
rep 1:  2.421

Saving final tree from best search rep (#1) to con.n.negBack.const.best.tre
#######################################################
TREEFILES PASS
Running constraint test n.pos.const
Running constraint test n.pos.const
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./const/n.pos.const.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  11 sequences.
	  11 constant characters.
	  17 parsimony-informative characters.
	  2 uninformative variable characters.
	  30 total characters.
	  25 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.4 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1-5

#######################################################
Loading constraints from file data/z.pos.const.tre
Found 6 positively constrained bipartition(s)
     Bipartition 1: (1,2,3,5,6,7,8,9,10) | (4,11)
     Bipartition 2: (1,3,5,6,7,8,9,10) | (2,4,11)
     Bipartition 3: (1,5,6,7,8,9,10) | (2,3,4,11)
     Bipartition 4: (1,2,3,4,5,8,9,10,11) | (6,7)
     Bipartition 5: (1,2,3,4,5,8,9,11) | (6,7,10)
     Bipartition 6: (1,5) | (2,3,4,6,7,8,9,10,11)
STARTING RUN
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2310 0.3201 0.1881 0.2607 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.0917
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0917
      0.0334	0.2271
      0.2519	0.2271
      0.8203	0.2271
      2.8944	0.2271

Starting with seed=1

creating likelihood stepwise addition starting tree (compatible with constraints)...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 0.006 lnL
Optimizing branchlengths... improved 11.173 lnL
 7  8  9  10  11 
Initial ln Likelihood: -225.0726
optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs...
pass 1:+    5.893 (branch=   2.29 scale=  0.89 alpha=  0.00 freqs=  1.20 rel rates=  1.50 pinv=  0.00)
pass 2:+    0.035 (branch=   0.00 scale=  0.00 alpha=  0.00 freqs=  0.03 rel rates=  0.00 pinv=  0.00)
lnL after optimization: -219.1445
gen      current_lnL    precision  last_tree_imp  
0        -219.1445        0.500           0 
500      -216.3491        0.500         474 
1000     -215.0098        0.500         936 
1500     -213.9531        0.500         936 
Optimization precision reduced 
   Optimizing parameters...    improved    1.908 lnL
   Optimizing branchlengths... improved    0.702 lnL
2000     -210.9688        0.010        1502 
2500     -210.8711        0.010        1502 
3000     -210.7511        0.010        2883 
3500     -210.7006        0.010        2883 
4000     -210.6776        0.010        2883 
4500     -210.6277        0.010        2883 
5000     -210.5647        0.010        2883 
5500     -210.5012        0.010        2883 
6000     -210.3408        0.010        2883 
Reached termination condition!
last topological improvement at gen 2883
Improvement over last 500 gen = 0.04248
Current score = -210.3311
Performing final optimizations...
pass 1 : -209.7245   (branch= 0.0039  alpha= 0.2015  pinv= 0.3325  eq freqs= 0.0000  rel rates= 0.0687)
pass 2 : -209.3594   (branch= 0.0155  alpha= 0.2666  pinv= 0.0590  eq freqs= 0.0034  rel rates= 0.0207)
pass 3 : -209.2472   (branch= 0.0797  alpha= 0.0162  pinv= 0.0072  eq freqs= 0.0063  rel rates= 0.0029)
pass 4 : -209.1979   (branch= 0.0266  alpha= 0.0165  pinv= 0.0000  eq freqs= 0.0013  rel rates= 0.0050)
pass 5 : -209.1659   (branch= 0.0191  alpha= 0.0068  pinv= 0.0010  eq freqs= 0.0006  rel rates= 0.0045)
pass 6 : -209.1419   (branch= 0.0094  alpha= 0.0044  pinv= 0.0002  eq freqs= 0.0008  rel rates= 0.0091)
pass 7 : -209.1243   (branch= 0.0060  alpha= 0.0010  pinv= 0.0000  eq freqs= 0.0007  rel rates= 0.0100)
pass 8 : -209.1128   (branch= 0.0021  alpha= 0.0001  pinv= 0.0000  eq freqs= 0.0007  rel rates= 0.0086)
pass 9 : -209.1041   (branch= 0.0007  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0004  rel rates= 0.0076)
pass 10: -209.0965   (branch= 0.0004  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0002  rel rates= 0.0069)
pass 11: -209.0899   (branch= 0.0002  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0002  rel rates= 0.0062)
pass 12: -209.0839   (branch= 0.0002  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0057)
pass 13: -209.0784   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0053)
pass 14: -209.0732   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0050)
pass 15: -209.0681   (branch= 0.0002  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0049)
pass 16: -209.0626   (branch= 0.0004  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0050)
pass 17: -209.0567   (branch= 0.0006  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0052)
pass 18: -209.0503   (branch= 0.0008  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0056)
pass 19: -209.0432   (branch= 0.0010  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0058)
pass 20: -209.0353   (branch= 0.0013  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0002  rel rates= 0.0064)
 optimization up to ...
pass 30: -208.9014   (branch= 0.0269  alpha= 0.0000  pinv= 0.0010  eq freqs= 0.0054  rel rates= 0.1006)
 optimization up to ...
pass 40: -208.7354   (branch= 0.0207  alpha= 0.0000  pinv= 0.0018  eq freqs= 0.0076  rel rates= 0.1358)
 optimization up to ...
pass 50: -208.6460   (branch= 0.0024  alpha= 0.0000  pinv= 0.0004  eq freqs= 0.0014  rel rates= 0.0853)
 optimization up to ...
pass 60: -208.5896   (branch= 0.0004  alpha= 0.0000  pinv= 0.0001  eq freqs= 0.0003  rel rates= 0.0555)
 optimization up to ...
pass 70: -208.5497   (branch= 0.0002  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0396)
 optimization up to ...
pass 80: -208.5197   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0297)
 optimization up to ...
pass 90: -208.4966   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0230)
 optimization up to ...
pass 100: -208.4783   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0182)
 optimization up to ...
pass 110: -208.4634   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0148)
 optimization up to ...
pass 120: -208.4512   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0122)
 optimization up to ...
pass 130: -208.4408   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0103)
 optimization up to ...
pass 140: -208.4321   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0087)
 optimization up to ...
pass 150: -208.4246   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0074)
 optimization up to ...
pass 160: -208.4181   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0064)
 optimization up to ...
pass 170: -208.4125   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0056)
 optimization up to ...
pass 180: -208.4076   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0049)
 optimization up to ...
pass 190: -208.4032   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0043)
 optimization up to ...
pass 200: -208.3994   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0038)
 optimization up to ...
pass 210: -208.3959   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0035)
 optimization up to ...
pass 220: -208.3927   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0032)
 optimization up to ...
pass 230: -208.3898   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0029)
 optimization up to ...
pass 240: -208.3872   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0026)
 optimization up to ...
pass 250: -208.3848   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0024)
 optimization up to ...
pass 260: -208.3826   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0022)
 optimization up to ...
pass 270: -208.3806   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0020)
 optimization up to ...
pass 280: -208.3788   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0018)
 optimization up to ...
pass 290: -208.3770   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0017)
 optimization up to ...
pass 300: -208.3754   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0016)
 optimization up to ...
pass 310: -208.3740   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0015)
 optimization up to ...
pass 320: -208.3726   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0014)
 optimization up to ...
pass 330: -208.3713   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0013)
 optimization up to ...
pass 340: -208.3701   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0012)
 optimization up to ...
pass 350: -208.3689   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0011)
 optimization up to ...
pass 360: -208.3678   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0011)
 optimization up to ...
pass 370: -208.3668   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0010)
 optimization up to ...
pass 380: -208.3659   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0010)
 optimization up to ...
pass 390: -208.3650   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0009)
 optimization up to ...
pass 400: -208.3641   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0008)
 optimization up to ...
pass 410: -208.3633   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0008)
 optimization up to ...
pass 420: -208.3625   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0008)
 optimization up to ...
pass 430: -208.3618   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0007)
 optimization up to ...
pass 440: -208.3611   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0007)
 optimization up to ...
pass 450: -208.3604   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0007)
 optimization up to ...
pass 460: -208.3598   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0006)
 optimization up to ...
pass 470: -208.3592   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0006)
 optimization up to ...
pass 480: -208.3586   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0006)
 optimization up to ...
pass 488: -208.3584   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0002)
Looking for minimum length branches...
Final score = -208.3584
Time used = 0 hours, 0 minutes and 10 seconds

MODEL REPORT - Parameter values are FINAL
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 122.601, AG = 189.649, AT = 6.980, CG = 205.574, CT = 195.517, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2225 0.2906 0.2035 0.2834 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      999.9000
    with an invariant (invariable) site category, proportion estimated
      0.2781
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.2781
      0.9601	0.1805
      0.9894	0.1805
      1.0100	0.1805
      1.0405	0.1805

NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    2 branches were collapsed.


NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with
	a positive constraint, it is possible for a constrained branch itself to be collapsed.
	If you care, be careful to check whether this has happened or turn off branch collapsing.


#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -208.3584       

Parameter estimates:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
rep 1:   122.6  189.6   6.98  205.6  195.5      1 0.223 0.291 0.203 0.283 999.900 0.278

Treelengths:
          TL 
rep 1:  1.881

Saving final tree from best search rep (#1) to con.n.pos.const.best.tre
#######################################################
TREEFILES PASS
Running constraint test n.posBack.const
Running constraint test n.posBack.const
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./const/n.posBack.const.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  11 sequences.
	  11 constant characters.
	  17 parsimony-informative characters.
	  2 uninformative variable characters.
	  30 total characters.
	  25 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.4 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1 2

#######################################################
Loading constraints from file data/z.posBack.const.tre
All constraints are backbone
All constraints involve the same backbone set of taxa
Found 4 positively constrained bipartition(s)
     Bipartition 1 (backbone): (1,2,3,5,8,9,10) | (4,11)
     Bipartition 2 (backbone): (1,3,5,8,9,10) | (2,4,11)
     Bipartition 3 (backbone): (1,5,8,9,10) | (2,3,4,11)
     Bipartition 4 (backbone): (1,5) | (2,3,4,8,9,10,11)
STARTING RUN
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2310 0.3201 0.1881 0.2607 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.0917
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0917
      0.0334	0.2271
      0.2519	0.2271
      0.8203	0.2271
      2.8944	0.2271

Starting with seed=1

creating likelihood stepwise addition starting tree (compatible with constraints)...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 0.006 lnL
Optimizing branchlengths... improved 11.173 lnL
 7  8  9  10  11 
Initial ln Likelihood: -221.7983
optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs...
pass 1:+    5.406 (branch=   2.03 scale=  0.00 alpha=  0.00 freqs=  1.20 rel rates=  2.17 pinv=  0.00)
pass 2:+    0.072 (branch=   0.04 scale=  0.00 alpha=  0.00 freqs=  0.02 rel rates=  0.00 pinv=  0.00)
lnL after optimization: -216.3203
gen      current_lnL    precision  last_tree_imp  
0        -216.3203        0.500           0 
500      -213.9944        0.500         208 
1000     -213.0248        0.500         547 
Optimization precision reduced 
   Optimizing parameters...    improved    1.494 lnL
   Optimizing branchlengths... improved    0.350 lnL
1500     -210.9424        0.010        1230 
2000     -210.7769        0.010        1230 
2500     -210.6534        0.010        1230 
3000     -210.6127        0.010        1230 
Reached termination condition!
last topological improvement at gen 1230
Improvement over last 500 gen = 0.03867
Current score = -210.5967
Performing final optimizations...
pass 1 : -210.1948   (branch= 0.0000  alpha= 0.1301  pinv= 0.2110  eq freqs= 0.0000  rel rates= 0.0609)
pass 2 : -209.5594   (branch= 0.0039  alpha= 0.3421  pinv= 0.2529  eq freqs= 0.0036  rel rates= 0.0330)
pass 3 : -209.3328   (branch= 0.0569  alpha= 0.1302  pinv= 0.0195  eq freqs= 0.0092  rel rates= 0.0107)
pass 4 : -209.2518   (branch= 0.0540  alpha= 0.0194  pinv= 0.0013  eq freqs= 0.0022  rel rates= 0.0041)
pass 5 : -209.2022   (branch= 0.0348  alpha= 0.0091  pinv= 0.0010  eq freqs= 0.0004  rel rates= 0.0043)
pass 6 : -209.1701   (branch= 0.0178  alpha= 0.0057  pinv= 0.0003  eq freqs= 0.0011  rel rates= 0.0072)
pass 7 : -209.1440   (branch= 0.0102  alpha= 0.0039  pinv= 0.0002  eq freqs= 0.0006  rel rates= 0.0112)
pass 8 : -209.1243   (branch= 0.0067  alpha= 0.0015  pinv= 0.0000  eq freqs= 0.0009  rel rates= 0.0107)
pass 9 : -209.1109   (branch= 0.0029  alpha= 0.0001  pinv= 0.0000  eq freqs= 0.0007  rel rates= 0.0097)
pass 10: -209.1010   (branch= 0.0010  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0005  rel rates= 0.0084)
pass 11: -209.0929   (branch= 0.0005  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0003  rel rates= 0.0074)
pass 12: -209.0859   (branch= 0.0002  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0002  rel rates= 0.0065)
pass 13: -209.0797   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0060)
pass 14: -209.0741   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0054)
pass 15: -209.0688   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0051)
pass 16: -209.0639   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0048)
pass 17: -209.0591   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0047)
pass 18: -209.0542   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0047)
pass 19: -209.0490   (branch= 0.0003  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0049)
pass 20: -209.0434   (branch= 0.0004  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0051)
 optimization up to ...
pass 30: -208.9359   (branch= 0.0194  alpha= 0.0000  pinv= 0.0007  eq freqs= 0.0038  rel rates= 0.0836)
 optimization up to ...
pass 40: -208.7600   (branch= 0.0269  alpha= 0.0000  pinv= 0.0020  eq freqs= 0.0087  rel rates= 0.1383)
 optimization up to ...
pass 50: -208.6584   (branch= 0.0043  alpha= 0.0000  pinv= 0.0006  eq freqs= 0.0024  rel rates= 0.0944)
 optimization up to ...
pass 60: -208.5979   (branch= 0.0006  alpha= 0.0000  pinv= 0.0001  eq freqs= 0.0003  rel rates= 0.0595)
 optimization up to ...
pass 70: -208.5556   (branch= 0.0002  alpha= 0.0000  pinv= 0.0001  eq freqs= 0.0002  rel rates= 0.0419)
 optimization up to ...
pass 80: -208.5242   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0311)
 optimization up to ...
pass 90: -208.5002   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.0238)
 optimization up to ...
pass 100: -208.4812   (branch= 0.0001  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0189)
 optimization up to ...
pass 110: -208.4658   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0153)
 optimization up to ...
pass 120: -208.4532   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0126)
 optimization up to ...
pass 130: -208.4425   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0106)
 optimization up to ...
pass 140: -208.4334   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0090)
 optimization up to ...
pass 150: -208.4257   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0076)
 optimization up to ...
pass 160: -208.4192   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0065)
 optimization up to ...
pass 170: -208.4134   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0057)
 optimization up to ...
pass 180: -208.4084   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0050)
 optimization up to ...
pass 190: -208.4039   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0045)
 optimization up to ...
pass 200: -208.3999   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0040)
 optimization up to ...
pass 210: -208.3964   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0035)
 optimization up to ...
pass 220: -208.3932   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0032)
 optimization up to ...
pass 230: -208.3903   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0029)
 optimization up to ...
pass 240: -208.3876   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0026)
 optimization up to ...
pass 250: -208.3852   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0024)
 optimization up to ...
pass 260: -208.3830   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0022)
 optimization up to ...
pass 270: -208.3810   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0020)
 optimization up to ...
pass 280: -208.3791   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0019)
 optimization up to ...
pass 290: -208.3773   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0017)
 optimization up to ...
pass 300: -208.3757   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0016)
 optimization up to ...
pass 310: -208.3742   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0015)
 optimization up to ...
pass 320: -208.3728   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0014)
 optimization up to ...
pass 330: -208.3715   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0013)
 optimization up to ...
pass 340: -208.3703   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0012)
 optimization up to ...
pass 350: -208.3691   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0012)
 optimization up to ...
pass 360: -208.3680   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0011)
 optimization up to ...
pass 370: -208.3670   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0010)
 optimization up to ...
pass 380: -208.3660   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0010)
 optimization up to ...
pass 390: -208.3651   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0009)
 optimization up to ...
pass 400: -208.3643   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0009)
 optimization up to ...
pass 410: -208.3634   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0008)
 optimization up to ...
pass 420: -208.3627   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0008)
 optimization up to ...
pass 430: -208.3619   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0007)
 optimization up to ...
pass 440: -208.3612   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0007)
 optimization up to ...
pass 450: -208.3605   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0007)
 optimization up to ...
pass 460: -208.3599   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0006)
 optimization up to ...
pass 470: -208.3593   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0006)
 optimization up to ...
pass 480: -208.3588   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0005)
 optimization up to ...
pass 489: -208.3586   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0002)
Looking for minimum length branches...
Final score = -208.3586
Time used = 0 hours, 0 minutes and 11 seconds

MODEL REPORT - Parameter values are FINAL
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 121.696, AG = 187.808, AT = 6.943, CG = 203.906, CT = 194.015, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2225 0.2906 0.2035 0.2835 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      999.9000
    with an invariant (invariable) site category, proportion estimated
      0.2781
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.2781
      0.9601	0.1805
      0.9894	0.1805
      1.0100	0.1805
      1.0405	0.1805

NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    2 branches were collapsed.


NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with
	a positive constraint, it is possible for a constrained branch itself to be collapsed.
	If you care, be careful to check whether this has happened or turn off branch collapsing.


#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -208.3586       

Parameter estimates:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
rep 1:   121.7  187.8  6.943  203.9    194      1 0.223 0.291 0.203 0.283 999.900 0.278

Treelengths:
          TL 
rep 1:  1.881

Saving final tree from best search rep (#1) to con.n.posBack.const.best.tre
#######################################################
TREEFILES PASS
**************************
Running output tests ...
**************************
Running output test a.G3
Running output test a.G3
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./output/a.G3.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Amino acid data
WARNING: Not all amino acids were observed in this dataset.
	One pseudo-count will be added to each amino acid
	for calculation of the empirical frequencies. You
	should probably use a statefrequencies setting other 
	than emprical.

	Summary of data:
	  11 sequences.
	  3 constant characters.
	  6 parsimony-informative characters.
	  1 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.6 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1

#######################################################
STARTING RUN
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 20 (amino acid data)
  Amino Acid Rate Matrix: Jones
  Equilibrium State Frequencies: empirical (observed) values (+F)
    (ACDEFGHIKLMNPQRSTVWY)
    0.0165 0.0083 0.0496 0.0909 0.0909 
    0.0083 0.0744 0.0083 0.0083 0.1074 
    0.1157 0.0248 0.1240 0.0331 0.0083 
    0.0826 0.0496 0.0579 0.0083 0.0331 
  Rate Heterogeneity Model:
    3 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.0750
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0750
      0.0603	0.3083
      0.4894	0.3083
      2.4503	0.3083

Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 0.002 lnL
Optimizing branchlengths... improved 0.000 lnL
 7  8  9  10  11 
Initial ln Likelihood: -116.5267
optimizing: starting branch lengths, alpha shape, prop. invar...
pass 1:+    0.949 (branch=   0.95 scale=  0.00 alpha=  0.00 pinv=  0.00)
pass 2:+    0.099 (branch=   0.10 scale=  0.00 alpha=  0.00 pinv=  0.00)
lnL after optimization: -115.4785
gen      current_lnL    precision  last_tree_imp  
0        -115.4785        0.500           0 
NOTE: ****Specified generation limit (5) reached...

MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
Model 1
  Number of states = 20 (amino acid data)
  Amino Acid Rate Matrix: Jones
  Equilibrium State Frequencies: empirical (observed) values (+F)
    (ACDEFGHIKLMNPQRSTVWY)
    0.0165 0.0083 0.0496 0.0909 0.0909 
    0.0083 0.0744 0.0083 0.0083 0.1074 
    0.1157 0.0248 0.1240 0.0331 0.0083 
    0.0826 0.0496 0.0579 0.0083 0.0331 
  Rate Heterogeneity Model:
    3 discrete gamma distributed rate categories, alpha param estimated
      0.5015
    with an invariant (invariable) site category, proportion estimated
      0.0735
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0735
      0.0607	0.3088
      0.4905	0.3088
      2.4487	0.3088

NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    No branches were short enough to be collapsed.

Saving site likelihoods to file out.a.G3.sitelikes.log ...
WARNING: Site likelihoods being output on prematurely terminated search ...

NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -114.0488       

Parameter estimates:
        alpha  pinv
rep 1:  0.501 0.073

Treelengths:
          TL 
rep 1:  1.377

Saving final tree from best search rep (#1) to out.a.G3.best.tre
Inferring internal state probabilities on best tree... saving to file out.a.G3.internalstates.log

WARNING: Internal states inferred on tree from prematurely terminated search

#######################################################
[Reading test.out.a.G3.nex	 ]
Executing

Warning:  
 Expecting #NEXUS to be the first token in the file, but found 11 instead
at line 1, column (approximately) 4 (file position 3)

Warning:  
 A TAXA block should be read before the TREES block (but no TAXA block was found).  Taxa will be inferred from their usage in the TREES block.
at line 16, column (approximately) 1 (file position 470)
storing implied block: TAXA
storing read block: TREES
TREEFILES PASS
Running output test a.G4
Running output test a.G4
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./output/a.G4.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Amino acid data
WARNING: Not all amino acids were observed in this dataset.
	One pseudo-count will be added to each amino acid
	for calculation of the empirical frequencies. You
	should probably use a statefrequencies setting other 
	than emprical.

	Summary of data:
	  11 sequences.
	  3 constant characters.
	  6 parsimony-informative characters.
	  1 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.8 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1 2

#######################################################
STARTING RUN
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 20 (amino acid data)
  Amino Acid Rate Matrix: Jones
  Equilibrium State Frequencies: empirical (observed) values (+F)
    (ACDEFGHIKLMNPQRSTVWY)
    0.0165 0.0083 0.0496 0.0909 0.0909 
    0.0083 0.0744 0.0083 0.0083 0.1074 
    0.1157 0.0248 0.1240 0.0331 0.0083 
    0.0826 0.0496 0.0579 0.0083 0.0331 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.0750
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0750
      0.0334	0.2313
      0.2519	0.2313
      0.8203	0.2313
      2.8944	0.2313

Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 0.001 lnL
Optimizing branchlengths... improved 0.006 lnL
 7  8  9  10  11 
Initial ln Likelihood: -117.7431
optimizing: starting branch lengths, alpha shape, prop. invar...
pass 1:+    1.466 (branch=   1.13 scale=  0.33 alpha=  0.00 pinv=  0.00)
pass 2:+    0.134 (branch=   0.13 scale=  0.00 alpha=  0.00 pinv=  0.00)
lnL after optimization: -116.1434
gen      current_lnL    precision  last_tree_imp  
0        -116.1434        0.500           0 
NOTE: ****Specified generation limit (5) reached...

MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
Model 1
  Number of states = 20 (amino acid data)
  Amino Acid Rate Matrix: Jones
  Equilibrium State Frequencies: empirical (observed) values (+F)
    (ACDEFGHIKLMNPQRSTVWY)
    0.0165 0.0083 0.0496 0.0909 0.0909 
    0.0083 0.0744 0.0083 0.0083 0.1074 
    0.1157 0.0248 0.1240 0.0331 0.0083 
    0.0826 0.0496 0.0579 0.0083 0.0331 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5015
    with an invariant (invariable) site category, proportion estimated
      0.0735
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0735
      0.0337	0.2316
      0.2529	0.2316
      0.8214	0.2316
      2.8921	0.2316

NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    No branches were short enough to be collapsed.

Saving site likelihoods to file out.a.G4.sitelikes.log ...
WARNING: Site likelihoods being output on prematurely terminated search ...

NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -114.3787       

Parameter estimates:
        alpha  pinv
rep 1:  0.501 0.073

Treelengths:
          TL 
rep 1:  1.339

Saving final tree from best search rep (#1) to out.a.G4.best.tre
Inferring internal state probabilities on best tree... saving to file out.a.G4.internalstates.log

WARNING: Internal states inferred on tree from prematurely terminated search

#######################################################
[Reading test.out.a.G4.nex	 ]
Executing

Warning:  
 Expecting #NEXUS to be the first token in the file, but found 11 instead
at line 1, column (approximately) 4 (file position 3)

Warning:  
 A TAXA block should be read before the TREES block (but no TAXA block was found).  Taxa will be inferred from their usage in the TREES block.
at line 16, column (approximately) 1 (file position 470)
storing implied block: TAXA
storing read block: TREES
TREEFILES PASS
Running output test a
Running output test a
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./output/a.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.AA.fas as
	Fasta amino acid format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Amino acid data,
	modeled as Amino acid data
WARNING: Not all amino acids were observed in this dataset.
	One pseudo-count will be added to each amino acid
	for calculation of the empirical frequencies. You
	should probably use a statefrequencies setting other 
	than emprical.

	Summary of data:
	  11 sequences.
	  3 constant characters.
	  6 parsimony-informative characters.
	  1 uninformative variable characters.
	  1 characters were completely missing or ambiguous (removed).
	  10 total characters (11 before removing empty columns).
	  10 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.2 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1-3

#######################################################
STARTING RUN
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 20 (amino acid data)
  Amino Acid Rate Matrix: Jones
  Equilibrium State Frequencies: empirical (observed) values (+F)
    (ACDEFGHIKLMNPQRSTVWY)
    0.0165 0.0083 0.0496 0.0909 0.0909 
    0.0083 0.0744 0.0083 0.0083 0.1074 
    0.1157 0.0248 0.1240 0.0331 0.0083 
    0.0826 0.0496 0.0579 0.0083 0.0331 
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.121 lnL
 7  8  9  10  11 
NOTE: Model contains no mutable parameters!
Setting model mutation weight to zero.

Initial ln Likelihood: -117.7533
optimizing: starting branch lengths...
pass 1:+    0.632 (branch=   0.63 scale=  0.00)
pass 2:+    0.134 (branch=   0.13 scale=  0.00)
lnL after optimization: -116.9881
gen      current_lnL    precision  last_tree_imp  
0        -116.9881        0.500           0 
NOTE: ****Specified generation limit (5) reached...

MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
Model 1
  Number of states = 20 (amino acid data)
  Amino Acid Rate Matrix: Jones
  Equilibrium State Frequencies: empirical (observed) values (+F)
    (ACDEFGHIKLMNPQRSTVWY)
    0.0165 0.0083 0.0496 0.0909 0.0909 
    0.0083 0.0744 0.0083 0.0083 0.1074 
    0.1157 0.0248 0.1240 0.0331 0.0083 
    0.0826 0.0496 0.0579 0.0083 0.0331 
  Rate Heterogeneity Model:
    no rate heterogeneity

NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    No branches were short enough to be collapsed.

Saving site likelihoods to file out.a.sitelikes.log ...
WARNING: Site likelihoods being output on prematurely terminated search ...

NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -115.6197       

Parameter estimates:
	 Model contains no estimated parameters

Treelengths:
          TL 
rep 1:  2.324

Saving final tree from best search rep (#1) to out.a.best.tre
Inferring internal state probabilities on best tree... saving to file out.a.internalstates.log

WARNING: Internal states inferred on tree from prematurely terminated search

#######################################################
[Reading test.out.a.nex	 ]
Executing

Warning:  
 Expecting #NEXUS to be the first token in the file, but found > instead
at line 1, column (approximately) 2 (file position 1)

Warning:  
 A TAXA block should be read before the TREES block (but no TAXA block was found).  Taxa will be inferred from their usage in the TREES block.
at line 26, column (approximately) 1 (file position 310)
storing implied block: TAXA
storing read block: TREES
TREEFILES PASS
Running output test c.M3x2
Running output test c.M3x2
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./output/c.M3x2.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Codon data
Base usage at codon positions:
                A         C         G         T
 pos 1      0.27723   0.36634   0.21782   0.13861
 pos 2      0.30693   0.20792   0.07921   0.40594
 pos 3      0.10891   0.38614   0.26733   0.23762
 all pos    0.23102   0.32013   0.18812   0.26073

	Summary of data:
	  11 sequences.
	  0 constant characters.
	  9 parsimony-informative characters.
	  1 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 1.3 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1-5

#######################################################
STARTING RUN
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 61 (codon data, standard code)
  Nucleotide Relative Rate Matrix Assumed by Codon Model:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: 
    empirical values calculated by F3x4 method (fixed)
    (AAA, AAC, AAG, AAT, ACA, ... etc)
    0.0094 0.0334 0.0231 0.0206 0.0064 
    0.0226 0.0157 0.0139 0.0024 0.0086 
    0.0060 0.0053 0.0125 0.0442 0.0306 
    0.0272 0.0125 0.0442 0.0306 0.0272 
    0.0084 0.0299 0.0207 0.0184 0.0032 
    0.0114 0.0079 0.0070 0.0165 0.0584 
    0.0405 0.0360 0.0074 0.0263 0.0182 
    0.0162 0.0050 0.0178 0.0123 0.0110 
    0.0019 0.0068 0.0047 0.0042 0.0098 
    0.0347 0.0241 0.0214 0.0167 0.0103 
    0.0032 0.0113 0.0078 0.0070 0.0043 
    0.0030 0.0027 0.0062 0.0221 0.0153 
    0.0136 
  Rate Heterogeneity Model:
    2 nonsynonymous rate categories, rate and proportion of each estimated
     (this is effectively the M3 model of PAML)
      dN/dS	Proportion
      0.2500	0.5000
      0.5000	0.5000

Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 4.461 lnL
Optimizing branchlengths... improved 0.701 lnL
 7  8  9  10  11 
Initial ln Likelihood: -215.8071
optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters...
pass 1:+    6.388 (branch=   0.00 scale=  0.44 omega=  0.01 rel rates=  5.93)
pass 2:+    0.434 (branch=   0.00 scale=  0.00 omega=  0.01 rel rates=  0.42)
lnL after optimization: -208.9856
gen      current_lnL    precision  last_tree_imp  
0        -208.9856        0.500           0 
NOTE: ****Specified generation limit (5) reached...

MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
Model 1
  Number of states = 61 (codon data, standard code)
  Nucleotide Relative Rate Matrix Assumed by Codon Model:     6 rates 
    AC = 1.586, AG = 3.999, AT = 0.040, CG = 2.453, CT = 3.999, GT = 1.000
  Equilibrium State Frequencies: 
    empirical values calculated by F3x4 method (fixed)
    (AAA, AAC, AAG, AAT, ACA, ... etc)
    0.0094 0.0334 0.0231 0.0206 0.0064 
    0.0226 0.0157 0.0139 0.0024 0.0086 
    0.0060 0.0053 0.0125 0.0442 0.0306 
    0.0272 0.0125 0.0442 0.0306 0.0272 
    0.0084 0.0299 0.0207 0.0184 0.0032 
    0.0114 0.0079 0.0070 0.0165 0.0584 
    0.0405 0.0360 0.0074 0.0263 0.0182 
    0.0162 0.0050 0.0178 0.0123 0.0110 
    0.0019 0.0068 0.0047 0.0042 0.0098 
    0.0347 0.0241 0.0214 0.0167 0.0103 
    0.0032 0.0113 0.0078 0.0070 0.0043 
    0.0030 0.0027 0.0062 0.0221 0.0153 
    0.0136 
  Rate Heterogeneity Model:
    2 nonsynonymous rate categories, rate and proportion of each estimated
     (this is effectively the M3 model of PAML)
      dN/dS	Proportion
      0.0490	0.5030
      0.4995	0.4970

NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    No branches were short enough to be collapsed.

Saving site likelihoods to file out.c.M3x2.sitelikes.log ...
WARNING: Site likelihoods being output on prematurely terminated search ...

NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -208.2373       

Parameter estimates:
         w(0)  p(0)  w(1)  p(1)  r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT)
rep 1:  0.049 0.503 0.499 0.497  1.586  3.999   0.04  2.453  3.999      1

Treelengths:
          TL 
rep 1:  9.626

Saving final tree from best search rep (#1) to out.c.M3x2.best.tre
Inferring internal state probabilities on best tree... saving to file out.c.M3x2.internalstates.log

WARNING: Internal states inferred on tree from prematurely terminated search

#######################################################
[Reading test.out.c.M3x2.nex	 ]
Executing

Warning:  
 Expecting #NEXUS to be the first token in the file, but found 11 instead
at line 1, column (approximately) 4 (file position 3)

Warning:  
 A TAXA block should be read before the TREES block (but no TAXA block was found).  Taxa will be inferred from their usage in the TREES block.
at line 16, column (approximately) 1 (file position 470)
storing implied block: TAXA
storing read block: TREES
TREEFILES PASS
Running output test c
Running output test c
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./output/c.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Codon data
Base usage at codon positions:
                A         C         G         T
 pos 1      0.27723   0.36634   0.21782   0.13861
 pos 2      0.30693   0.20792   0.07921   0.40594
 pos 3      0.10891   0.38614   0.26733   0.23762
 all pos    0.23102   0.32013   0.18812   0.26073

	Summary of data:
	  11 sequences.
	  0 constant characters.
	  9 parsimony-informative characters.
	  1 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.6 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  5

#######################################################
STARTING RUN
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 61 (codon data, standard code)
  One estimated dN/dS ratio (aka omega) = 0.250000
  Nucleotide Relative Rate Matrix Assumed by Codon Model:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: 
    empirical values calculated by F3x4 method (fixed)
    (AAA, AAC, AAG, AAT, ACA, ... etc)
    0.0094 0.0334 0.0231 0.0206 0.0064 
    0.0226 0.0157 0.0139 0.0024 0.0086 
    0.0060 0.0053 0.0125 0.0442 0.0306 
    0.0272 0.0125 0.0442 0.0306 0.0272 
    0.0084 0.0299 0.0207 0.0184 0.0032 
    0.0114 0.0079 0.0070 0.0165 0.0584 
    0.0405 0.0360 0.0074 0.0263 0.0182 
    0.0162 0.0050 0.0178 0.0123 0.0110 
    0.0019 0.0068 0.0047 0.0042 0.0098 
    0.0347 0.0241 0.0214 0.0167 0.0103 
    0.0032 0.0113 0.0078 0.0070 0.0043 
    0.0030 0.0027 0.0062 0.0221 0.0153 
    0.0136 
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 0.001 lnL
Optimizing branchlengths... improved 0.000 lnL
 7  8  9  10  11 
Initial ln Likelihood: -225.6424
optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters...
pass 1:+   10.932 (branch=   2.26 scale=  0.50 omega=  0.00 rel rates=  8.17)
pass 2:+    0.925 (branch=   0.64 scale=  0.00 omega=  0.28 rel rates=  0.00)
pass 3:+    0.733 (branch=   0.04 scale=  0.68 omega=  0.01 rel rates=  0.00)
pass 4:+    0.015 (branch=   0.00 scale=  0.00 omega=  0.01 rel rates=  0.00)
lnL after optimization: -213.0377
gen      current_lnL    precision  last_tree_imp  
0        -213.0377        0.500           0 
NOTE: ****Specified generation limit (5) reached...

MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
Model 1
  Number of states = 61 (codon data, standard code)
  One estimated dN/dS ratio (aka omega) = 0.130452
  Nucleotide Relative Rate Matrix Assumed by Codon Model:     6 rates 
    AC = 2.468, AG = 4.008, AT = 0.588, CG = 2.683, CT = 2.283, GT = 1.000
  Equilibrium State Frequencies: 
    empirical values calculated by F3x4 method (fixed)
    (AAA, AAC, AAG, AAT, ACA, ... etc)
    0.0094 0.0334 0.0231 0.0206 0.0064 
    0.0226 0.0157 0.0139 0.0024 0.0086 
    0.0060 0.0053 0.0125 0.0442 0.0306 
    0.0272 0.0125 0.0442 0.0306 0.0272 
    0.0084 0.0299 0.0207 0.0184 0.0032 
    0.0114 0.0079 0.0070 0.0165 0.0584 
    0.0405 0.0360 0.0074 0.0263 0.0182 
    0.0162 0.0050 0.0178 0.0123 0.0110 
    0.0019 0.0068 0.0047 0.0042 0.0098 
    0.0347 0.0241 0.0214 0.0167 0.0103 
    0.0032 0.0113 0.0078 0.0070 0.0043 
    0.0030 0.0027 0.0062 0.0221 0.0153 
    0.0136 
  Rate Heterogeneity Model:
    no rate heterogeneity

NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    No branches were short enough to be collapsed.

Saving site likelihoods to file out.c.sitelikes.log ...
WARNING: Site likelihoods being output on prematurely terminated search ...

NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -210.2320       

Parameter estimates:
         w(0)  p(0)  r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT)
rep 1:  0.130 1.000  2.468  4.008  0.588  2.683  2.283      1

Treelengths:
          TL 
rep 1:  8.650

Saving final tree from best search rep (#1) to out.c.best.tre
Inferring internal state probabilities on best tree... saving to file out.c.internalstates.log

WARNING: Internal states inferred on tree from prematurely terminated search

#######################################################
[Reading test.out.c.nex	 ]
Executing

Warning:  
 Expecting #NEXUS to be the first token in the file, but found 11 instead
at line 1, column (approximately) 4 (file position 3)

Warning:  
 A TAXA block should be read before the TREES block (but no TAXA block was found).  Taxa will be inferred from their usage in the TREES block.
at line 16, column (approximately) 1 (file position 470)
storing implied block: TAXA
storing read block: TREES
TREEFILES PASS
Running output test n.G3
Running output test n.G3
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./output/n.G3.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  11 sequences.
	  11 constant characters.
	  17 parsimony-informative characters.
	  2 uninformative variable characters.
	  30 total characters.
	  25 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.3 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1

#######################################################
STARTING RUN
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2310 0.3201 0.1881 0.2607 
  Rate Heterogeneity Model:
    3 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.0917
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0917
      0.0603	0.3028
      0.4894	0.3028
      2.4503	0.3028

Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 0.004 lnL
Optimizing branchlengths... improved 0.000 lnL
 7  8  9  10  11 
Initial ln Likelihood: -226.8217
optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs...
pass 1:+    3.951 (branch=   0.75 scale=  0.00 alpha=  0.00 freqs=  1.76 rel rates=  1.44 pinv=  0.00)
pass 2:+    0.586 (branch=   0.56 scale=  0.00 alpha=  0.00 freqs=  0.03 rel rates=  0.00 pinv=  0.00)
pass 3:+    1.297 (branch=   0.66 scale=  0.00 alpha=  0.00 freqs=  0.03 rel rates=  0.61 pinv=  0.00)
pass 4:+    0.021 (branch=   0.00 scale=  0.00 alpha=  0.00 freqs=  0.02 rel rates=  0.00 pinv=  0.00)
lnL after optimization: -220.9660
gen      current_lnL    precision  last_tree_imp  
0        -220.9660        0.500           0 
NOTE: ****Specified generation limit (5) reached...

MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.002, AG = 3.998, AT = 0.998, CG = 2.322, CT = 3.998, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2184 0.3566 0.2049 0.2201 
  Rate Heterogeneity Model:
    3 discrete gamma distributed rate categories, alpha param estimated
      0.5025
    with an invariant (invariable) site category, proportion estimated
      0.0892
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0892
      0.0610	0.3036
      0.4913	0.3036
      2.4477	0.3036

NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    No branches were short enough to be collapsed.

Saving site likelihoods to file out.n.G3.sitelikes.log ...
WARNING: Site likelihoods being output on prematurely terminated search ...

NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -220.9571       

Parameter estimates:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
rep 1:   1.002  3.998  0.998  2.322  3.998      1 0.218 0.357 0.205 0.220 0.502 0.089

Treelengths:
          TL 
rep 1:  2.169

Saving final tree from best search rep (#1) to out.n.G3.best.tre
Inferring internal state probabilities on best tree... saving to file out.n.G3.internalstates.log

WARNING: Internal states inferred on tree from prematurely terminated search

#######################################################
[Reading test.out.n.G3.nex	 ]
Executing

Warning:  
 Expecting #NEXUS to be the first token in the file, but found 11 instead
at line 1, column (approximately) 4 (file position 3)

Warning:  
 A TAXA block should be read before the TREES block (but no TAXA block was found).  Taxa will be inferred from their usage in the TREES block.
at line 16, column (approximately) 1 (file position 470)
storing implied block: TAXA
storing read block: TREES
storing read block: PAUP
TREEFILES PASS
Running output test n.G4
Running output test n.G4
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./output/n.G4.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  11 sequences.
	  11 constant characters.
	  17 parsimony-informative characters.
	  2 uninformative variable characters.
	  30 total characters.
	  25 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.4 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1-4

#######################################################
STARTING RUN
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2310 0.3201 0.1881 0.2607 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.0917
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0917
      0.0334	0.2271
      0.2519	0.2271
      0.8203	0.2271
      2.8944	0.2271

Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 0.005 lnL
Optimizing branchlengths... improved 0.292 lnL
 7  8  9  10  11 
Initial ln Likelihood: -226.2799
optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs...
pass 1:+    5.831 (branch=   2.05 scale=  0.00 alpha=  0.00 freqs=  1.45 rel rates=  2.33 pinv=  0.00)
pass 2:+    0.107 (branch=   0.07 scale=  0.00 alpha=  0.00 freqs=  0.03 rel rates=  0.00 pinv=  0.00)
lnL after optimization: -220.3414
gen      current_lnL    precision  last_tree_imp  
0        -220.3414        0.500           0 
NOTE: ****Specified generation limit (5) reached...

MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.001, AG = 2.400, AT = 0.589, CG = 1.512, CT = 4.001, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2259 0.3629 0.1852 0.2261 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5015
    with an invariant (invariable) site category, proportion estimated
      0.0902
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0902
      0.0337	0.2275
      0.2529	0.2275
      0.8214	0.2275
      2.8921	0.2275

NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    No branches were short enough to be collapsed.

Saving site likelihoods to file out.n.G4.sitelikes.log ...
WARNING: Site likelihoods being output on prematurely terminated search ...

NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -217.4380       

Parameter estimates:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
rep 1:   1.001    2.4  0.589  1.512  4.001      1 0.226 0.363 0.185 0.226 0.501 0.090

Treelengths:
          TL 
rep 1:  1.694

Saving final tree from best search rep (#1) to out.n.G4.best.tre
Inferring internal state probabilities on best tree... saving to file out.n.G4.internalstates.log

WARNING: Internal states inferred on tree from prematurely terminated search

#######################################################
[Reading test.out.n.G4.nex	 ]
Executing

Warning:  
 Expecting #NEXUS to be the first token in the file, but found 11 instead
at line 1, column (approximately) 4 (file position 3)

Warning:  
 A TAXA block should be read before the TREES block (but no TAXA block was found).  Taxa will be inferred from their usage in the TREES block.
at line 16, column (approximately) 1 (file position 470)
storing implied block: TAXA
storing read block: TREES
storing read block: PAUP
TREEFILES PASS
Running output test n
Running output test n
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./output/n.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  11 sequences.
	  11 constant characters.
	  17 parsimony-informative characters.
	  2 uninformative variable characters.
	  30 total characters.
	  25 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.1 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  2 3

#######################################################
STARTING RUN
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2310 0.3201 0.1881 0.2607 
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 3.458 lnL
 7  8  9  10  11 
Initial ln Likelihood: -225.5327
optimizing: starting branch lengths, rel rates, eq freqs...
pass 1:+    7.466 (branch=   0.77 scale=  0.00 freqs=  0.02 rel rates=  6.68)
pass 2:+    0.468 (branch=   0.45 scale=  0.00 freqs=  0.02 rel rates=  0.00)
lnL after optimization: -217.5990
gen      current_lnL    precision  last_tree_imp  
0        -217.5990        0.500           0 
NOTE: ****Specified generation limit (5) reached...

MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.511, AG = 3.999, AT = 0.200, CG = 2.619, CT = 2.047, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2300 0.3205 0.1884 0.2611 
  Rate Heterogeneity Model:
    no rate heterogeneity

NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    No branches were short enough to be collapsed.

Saving site likelihoods to file out.n.sitelikes.log ...
WARNING: Site likelihoods being output on prematurely terminated search ...

NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -217.2394       

Parameter estimates:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T)
rep 1:   1.511  3.999 0.1995  2.619  2.047      1 0.230 0.321 0.188 0.261

Treelengths:
          TL 
rep 1:  1.686

Saving final tree from best search rep (#1) to out.n.best.tre
Inferring internal state probabilities on best tree... saving to file out.n.internalstates.log

WARNING: Internal states inferred on tree from prematurely terminated search

#######################################################
[Reading test.out.n.nex	 ]
Executing

Warning:  
 Expecting #NEXUS to be the first token in the file, but found 11 instead
at line 1, column (approximately) 4 (file position 3)

Warning:  
 A TAXA block should be read before the TREES block (but no TAXA block was found).  Taxa will be inferred from their usage in the TREES block.
at line 16, column (approximately) 1 (file position 470)
storing implied block: TAXA
storing read block: TREES
storing read block: PAUP
TREEFILES PASS
Running output test n.wackyNames
Running output test n.wackyNames
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./output/n.wackyNames.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/z.11x30.wackyNames.nex ...
Reading DATA block...storing implied block: TAXA
storing read block: DATA
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  11 sequences.
	  11 constant characters.
	  17 parsimony-informative characters.
	  2 uninformative variable characters.
	  30 total characters.
	  25 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.1 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1

#######################################################
STARTING RUN
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2310 0.3201 0.1881 0.2607 
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 3.458 lnL
 7  8  9  10  11 
Initial ln Likelihood: -225.5327
optimizing: starting branch lengths, rel rates, eq freqs...
pass 1:+    7.466 (branch=   0.77 scale=  0.00 freqs=  0.02 rel rates=  6.68)
pass 2:+    0.468 (branch=   0.45 scale=  0.00 freqs=  0.02 rel rates=  0.00)
lnL after optimization: -217.5990
gen      current_lnL    precision  last_tree_imp  
0        -217.5990        0.500           0 
NOTE: ****Specified generation limit (5) reached...

MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.511, AG = 3.999, AT = 0.200, CG = 2.619, CT = 2.047, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2300 0.3205 0.1884 0.2611 
  Rate Heterogeneity Model:
    no rate heterogeneity

NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    No branches were short enough to be collapsed.

Saving site likelihoods to file out.n.sitelikes.log ...
WARNING: Site likelihoods being output on prematurely terminated search ...

NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -217.2394       

Parameter estimates:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T)
rep 1:   1.511  3.999 0.1995  2.619  2.047      1 0.230 0.321 0.188 0.261

Treelengths:
          TL 
rep 1:  1.686

Saving final tree from best search rep (#1) to out.n.best.tre
#######################################################
cat: out.n.wackyNames.best.tre: No such file or directory
[Reading test.out.n.wackyNames.nex	 ]
Executing
storing implied block: TAXA
storing read block: DATA
TREEFILES PASS
Running output test p.3diff
Running output test p.3diff
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./output/p.3diff.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/z.byPos.11x2178.nex ...
Reading DATA block...storing implied block: TAXA
storing read block: DATA
 successful
Reading SETS block...storing read block: SETS
 successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS

CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY
	TO EACH DATA SUBSET (no linkage)

GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	CHARPARTITION subset #1 ("1stpos")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Excluded character numbers: 4
	
	Summary of data:
	  11 sequences.
	  441 constant characters.
	  171 parsimony-informative characters.
	  113 uninformative variable characters.
	  725 total characters.
	  237 unique patterns in compressed data matrix.
GARLI data subset 2
	CHARACTERS block #1 ("Untitled DATA Block 1")
	CHARPARTITION subset #2 ("2ndpos")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Excluded character numbers: 5
	
	Summary of data:
	  11 sequences.
	  527 constant characters.
	  90 parsimony-informative characters.
	  108 uninformative variable characters.
	  725 total characters.
	  158 unique patterns in compressed data matrix.
GARLI data subset 3
	CHARACTERS block #1 ("Untitled DATA Block 1")
	CHARPARTITION subset #3 ("3rdpos")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Excluded character numbers: 6
	
	Summary of data:
	  11 sequences.
	  102 constant characters.
	  507 parsimony-informative characters.
	  116 uninformative variable characters.
	  725 total characters.
	  548 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 11 MB
  good			approx 10 MB to 9 MB
  low			approx 8 MB to 5 MB
  very low		approx 4 MB to 4 MB
the minimum required availablememory is 4 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 16.0 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1 2

#######################################################
STARTING RUN
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix: 
    User specified matrix type: ( 0 1 2 2 3 4 ) 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.3150 0.1749 0.3006 0.2095 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    Substitution rate categories under this model:
      rate	proportion
      0.0334	0.2500
      0.2519	0.2500
      0.8203	0.2500
      2.8944	0.2500

Model 2
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix: 
    User specified matrix type: ( 0 1 2 1 0 3 ) 
    AC = 4.000, AG = 4.000, AT = 1.000, CG = 4.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2706 0.1568 0.1630 0.4096 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    Substitution rate categories under this model:
      rate	proportion
      0.0334	0.2500
      0.2519	0.2500
      0.8203	0.2500
      2.8944	0.2500

Model 3
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix: 
    User specified matrix type: ( 0 1 2 3 1 0 ) 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.1462 0.3614 0.2906 0.2018 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.0352
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0352
      0.0334	0.2412
      0.2519	0.2412
      0.8203	0.2412
      2.8944	0.2412

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 168.526 lnL
Optimizing branchlengths... improved 66.084 lnL
 7  8  9  10  11 
Initial ln Likelihood: -13699.7841
optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates...
pass 1:+  209.568 (branch=   7.95 scale=  0.00 alpha= 35.56 freqs= 28.70 rel rates= 62.31 pinv=  0.00 subset rates= 75.04)
pass 2:+   77.990 (branch=   2.27 scale=  0.00 alpha=  4.14 freqs= 11.22 rel rates=  3.32 pinv=  0.86 subset rates= 56.18)
pass 3:+   48.437 (branch=   6.88 scale=  0.73 alpha=  4.15 freqs=  1.22 rel rates=  1.34 pinv=  0.01 subset rates= 34.10)
pass 4:+   15.263 (branch=   0.00 scale=  0.79 alpha=  0.64 freqs=  1.21 rel rates=  0.57 pinv=  0.01 subset rates= 12.04)
pass 5:+    5.799 (branch=   0.00 scale=  0.00 alpha=  0.01 freqs=  0.10 rel rates=  0.77 pinv=  0.02 subset rates=  4.91)
pass 6:+    0.133 (branch=   0.00 scale=  0.00 alpha=  0.01 freqs=  0.10 rel rates=  0.01 pinv=  0.01 subset rates=  0.00)
lnL after optimization: -13342.5949
gen      current_lnL    precision  last_tree_imp  
0        -13342.5949      0.500           0 
NOTE: ****Specified generation limit (5) reached...

MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix: 
    User specified matrix type: ( 0 1 2 2 3 4 ) 
    AC = 1.951, AG = 2.401, AT = 1.336, CG = 1.336, CT = 3.999, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.3134 0.1755 0.2988 0.2122 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.3662
    Substitution rate categories under this model:
      rate	proportion
      0.0122	0.2500
      0.1561	0.2500
      0.6920	0.2500
      3.1397	0.2500

Model 2
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix: 
    User specified matrix type: ( 0 1 2 1 0 3 ) 
    AC = 3.969, AG = 6.053, AT = 1.216, CG = 6.053, CT = 3.969, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2816 0.1661 0.1574 0.3949 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.3384
    Substitution rate categories under this model:
      rate	proportion
      0.0089	0.2500
      0.1345	0.2500
      0.6550	0.2500
      3.2015	0.2500

Model 3
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix: 
    User specified matrix type: ( 0 1 2 3 1 0 ) 
    AC = 1.000, AG = 4.110, AT = 2.520, CG = 0.377, CT = 4.110, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.1591 0.3524 0.2842 0.2043 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      4.0328
    with an invariant (invariable) site category, proportion estimated
      0.0231
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0231
      0.4562	0.2442
      0.7763	0.2442
      1.0844	0.2442
      1.6831	0.2442

Subset rate multipliers:
    0.54  0.33  2.14
NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    No branches were short enough to be collapsed.

Saving site likelihoods to file out.p.3diff.sitelikes.log ...
WARNING: Site likelihoods being output on prematurely terminated search ...

NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -13324.2768       

Parameter estimates:

Partition model subset 1:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha
rep 1:   1.951  2.401  1.336  1.336  3.999      1 0.313 0.176 0.299 0.212 0.366

Partition model subset 2:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha
rep 1:   3.969  6.053  1.216  6.053  3.969      1 0.282 0.166 0.157 0.395 0.338

Partition model subset 3:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
rep 1:       1   4.11   2.52 0.3775   4.11      1 0.159 0.352 0.284 0.204 4.033 0.023

Treelengths and subset rate multipliers:
          TL   R(1)  R(2)  R(3)
rep 1:  1.695 0.538 0.326 2.137

Saving final tree from best search rep (#1) to out.p.3diff.best.tre
Inferring internal state probabilities on best tree... saving to file out.p.3diff.internalstates.log

WARNING: Internal states inferred on tree from prematurely terminated search

#######################################################
[Reading test.out.p.3diff.nex	 ]
Executing
storing implied block: TAXA
storing read block: DATA
storing read block: SETS
storing read block: ASSUMPTIONS
storing read block: TREES
TREEFILES PASS
Running output test p.mkvO.ssr
Running output test p.mkvO.ssr
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./output/p.mkvO.ssr.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard ordered k-state data, variable only,
	modeled as Standard ordered k-state data, variable only
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.6 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  5

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN

>>>Search rep 1 (of 5)<<<
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=1

Initial ln Likelihood: -637.9212
optimizing: starting branch lengths, subset rates...
pass 1:+  144.867 (branch= 134.40 scale=  0.48 subset rates=  9.98)
pass 2:+   12.967 (branch=   8.30 scale=  0.00 subset rates=  4.67)
pass 3:+    3.846 (branch=   2.24 scale=  0.02 subset rates=  1.58)
pass 4:+    1.162 (branch=   0.58 scale=  0.01 subset rates=  0.57)
pass 5:+    0.156 (branch=   0.12 scale=  0.00 subset rates=  0.03)
pass 6:+    0.044 (branch=   0.04 scale=  0.00 subset rates=  0.00)
pass 7:+    0.015 (branch=   0.02 scale=  0.00 subset rates=  0.00)
pass 8:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
lnL after optimization: -474.8632
gen      current_lnL    precision  last_tree_imp  
0        -474.8632        0.010           0 
NOTE: ****Specified generation limit (5) reached...

MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    0.60  2.02  2.82
NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    2 branches were collapsed.


NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 1 replicate search(es) (of 5).
Results:
Replicate 1 : -474.8624 (best)

Parameter estimates across search replicates:

Partition model subset 1:
	 Model contains no estimated parameters

Partition model subset 2:
	 Model contains no estimated parameters

Partition model subset 3:
	 Model contains no estimated parameters

Treelengths and subset rate multipliers:
          TL   R(1)  R(2)  R(3)
rep 1:  4.474 0.599 2.020 2.815

Saving final tree from best search rep (#1) to out.p.mkvO.ssr.best.tre
#######################################################

>>>Search rep 2 (of 5)<<<
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=1351934195

Initial ln Likelihood: -668.6258
optimizing: starting branch lengths, subset rates...
pass 1:+  167.892 (branch= 157.14 scale=  1.13 subset rates=  9.62)
pass 2:+   19.859 (branch=  15.03 scale=  0.02 subset rates=  4.81)
pass 3:+    5.107 (branch=   3.29 scale=  0.00 subset rates=  1.82)
pass 4:+    0.826 (branch=   0.20 scale=  0.00 subset rates=  0.62)
pass 5:+    0.065 (branch=   0.04 scale=  0.00 subset rates=  0.03)
pass 6:+    0.027 (branch=   0.03 scale=  0.00 subset rates=  0.00)
pass 7:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
lnL after optimization: -474.8510
gen      current_lnL    precision  last_tree_imp  
0        -474.8510        0.010           0 
NOTE: ****Specified generation limit (5) reached...

MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    0.60  2.01  2.84
NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    6 branches were collapsed.


NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 2 replicate search(es) (of 5).

NOTE: Unless the following output indicates that search replicates found the
	same topology, you should assume that they found different topologies.
Results:
Replicate 1 : -474.8624       
Replicate 2 : -474.8503 (best)

Parameter estimates across search replicates:

Partition model subset 1:
	 Model contains no estimated parameters

Partition model subset 2:
	 Model contains no estimated parameters

Partition model subset 3:
	 Model contains no estimated parameters

Treelengths and subset rate multipliers:
          TL   R(1)  R(2)  R(3)
rep 1:  4.474 0.599 2.020 2.815
rep 2:  4.516 0.599 2.013 2.840

Saving final trees from all search reps to out.p.mkvO.ssr.best.all.tre

Saving final tree from best search rep (#2) to out.p.mkvO.ssr.best.tre
#######################################################

>>>Search rep 3 (of 5)<<<
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=290145159

Initial ln Likelihood: -605.1903
optimizing: starting branch lengths, subset rates...
pass 1:+  116.111 (branch= 105.75 scale=  0.22 subset rates= 10.14)
pass 2:+   10.329 (branch=   5.57 scale=  0.02 subset rates=  4.75)
pass 3:+    2.693 (branch=   1.07 scale=  0.00 subset rates=  1.62)
pass 4:+    0.941 (branch=   0.38 scale=  0.00 subset rates=  0.56)
pass 5:+    0.205 (branch=   0.17 scale=  0.00 subset rates=  0.03)
pass 6:+    0.019 (branch=   0.02 scale=  0.00 subset rates=  0.00)
pass 7:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
lnL after optimization: -474.8930
gen      current_lnL    precision  last_tree_imp  
0        -474.8930        0.010           0 
NOTE: ****Specified generation limit (5) reached...

MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    0.60  2.01  2.83
NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    3 branches were collapsed.


NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 3 replicate search(es) (of 5).

NOTE: Unless the following output indicates that search replicates found the
	same topology, you should assume that they found different topologies.
Results:
Replicate 1 : -474.8624       
Replicate 2 : -474.8503 (best)
Replicate 3 : -474.8837       

Parameter estimates across search replicates:

Partition model subset 1:
	 Model contains no estimated parameters

Partition model subset 2:
	 Model contains no estimated parameters

Partition model subset 3:
	 Model contains no estimated parameters

Treelengths and subset rate multipliers:
          TL   R(1)  R(2)  R(3)
rep 1:  4.474 0.599 2.020 2.815
rep 2:  4.516 0.599 2.013 2.840
rep 3:  4.460 0.600 2.011 2.833

Saving final trees from all search reps to out.p.mkvO.ssr.best.all.tre

Saving final tree from best search rep (#2) to out.p.mkvO.ssr.best.tre
#######################################################

>>>Search rep 4 (of 5)<<<
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=2044747317

Initial ln Likelihood: -652.1691
optimizing: starting branch lengths, subset rates...
pass 1:+  155.944 (branch= 145.32 scale=  0.58 subset rates= 10.04)
pass 2:+   15.207 (branch=  10.68 scale=  0.00 subset rates=  4.52)
pass 3:+    3.711 (branch=   2.16 scale=  0.00 subset rates=  1.55)
pass 4:+    1.981 (branch=   1.40 scale=  0.00 subset rates=  0.58)
pass 5:+    0.365 (branch=   0.33 scale=  0.00 subset rates=  0.03)
pass 6:+    0.111 (branch=   0.11 scale=  0.00 subset rates=  0.00)
pass 7:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
lnL after optimization: -474.8509
gen      current_lnL    precision  last_tree_imp  
0        -474.8509        0.010           0 
NOTE: ****Specified generation limit (5) reached...

MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    0.60  2.01  2.86
NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    5 branches were collapsed.


NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 4 replicate search(es) (of 5).

NOTE: Unless the following output indicates that search replicates found the
	same topology, you should assume that they found different topologies.
Results:
Replicate 1 : -474.8624       
Replicate 2 : -474.8503       
Replicate 3 : -474.8837       
Replicate 4 : -474.8494 (best)

Parameter estimates across search replicates:

Partition model subset 1:
	 Model contains no estimated parameters

Partition model subset 2:
	 Model contains no estimated parameters

Partition model subset 3:
	 Model contains no estimated parameters

Treelengths and subset rate multipliers:
          TL   R(1)  R(2)  R(3)
rep 1:  4.474 0.599 2.020 2.815
rep 2:  4.516 0.599 2.013 2.840
rep 3:  4.460 0.600 2.011 2.833
rep 4:  4.504 0.598 2.009 2.858

Saving final trees from all search reps to out.p.mkvO.ssr.best.all.tre

Saving final tree from best search rep (#4) to out.p.mkvO.ssr.best.tre
#######################################################

>>>Search rep 5 (of 5)<<<
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=1380786643

Initial ln Likelihood: -628.4721
optimizing: starting branch lengths, subset rates...
pass 1:+  137.115 (branch= 125.84 scale=  0.86 subset rates= 10.41)
pass 2:+   12.972 (branch=   8.00 scale=  0.03 subset rates=  4.94)
pass 3:+    2.470 (branch=   0.79 scale=  0.00 subset rates=  1.68)
pass 4:+    0.825 (branch=   0.23 scale=  0.01 subset rates=  0.58)
pass 5:+    0.169 (branch=   0.13 scale=  0.00 subset rates=  0.04)
pass 6:+    0.011 (branch=   0.01 scale=  0.00 subset rates=  0.00)
pass 7:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
lnL after optimization: -474.9108
gen      current_lnL    precision  last_tree_imp  
0        -474.9108        0.010           0 
NOTE: ****Specified generation limit (5) reached...

MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    0.60  2.02  2.84
NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    4 branches were collapsed.


NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 5 replicate search(es) (of 5).

NOTE: Unless the following output indicates that search replicates found the
	same topology, you should assume that they found different topologies.
Results:
Replicate 1 : -474.8624       
Replicate 2 : -474.8503       
Replicate 3 : -474.8837       
Replicate 4 : -474.8494 (best)
Replicate 5 : -474.9075       

Parameter estimates across search replicates:

Partition model subset 1:
	 Model contains no estimated parameters

Partition model subset 2:
	 Model contains no estimated parameters

Partition model subset 3:
	 Model contains no estimated parameters

Treelengths and subset rate multipliers:
          TL   R(1)  R(2)  R(3)
rep 1:  4.474 0.599 2.020 2.815
rep 2:  4.516 0.599 2.013 2.840
rep 3:  4.460 0.600 2.011 2.833
rep 4:  4.504 0.598 2.009 2.858
rep 5:  4.499 0.597 2.020 2.843

Saving final trees from all search reps to out.p.mkvO.ssr.best.all.tre

Saving final tree from best search rep (#4) to out.p.mkvO.ssr.best.tre
#######################################################
[Reading test.out.p.mkvO.ssr.nex	 ]
Executing

Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
storing read block: ASSUMPTIONS
storing read block: TREES
TREEFILES PASS
**************************
Running checkpoint tests ...
**************************
Running checkpoint test ./check/a.G3.conf
Running checkpoint test ./check/a.G3.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./check/a.G3.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/z.11x30.stop.nex ...
Reading DATA block...storing implied block: TAXA
storing read block: DATA
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Amino acid data
Warning: stop codon TAA found at codon site 11 (nuc site 31) in taxon MorNa6.
	Treating as missing data because ignorestopcodons = 1 is set in configuration file.
Some sites treated as missing data for taxon MorNa6 due to ambiguity in translation.
	Aminoacids coded as missing for that taxon: 11 

Warning: stop codon TAA found at codon site 11 (nuc site 31) in taxon ClownNa6.
	Treating as missing data because ignorestopcodons = 1 is set in configuration file.
Some sites treated as missing data for taxon ClownNa6 due to ambiguity in translation.
	Aminoacids coded as missing for that taxon: 11 

WARNING: Not all amino acids were observed in this dataset.
	One pseudo-count will be added to each amino acid
	for calculation of the empirical frequencies. You
	should probably use a statefrequencies setting other 
	than emprical.

	Summary of data:
	  11 sequences.
	  3 constant characters.
	  6 parsimony-informative characters.
	  1 uninformative variable characters.
	  1 characters were completely missing or ambiguous (removed).
	  10 total characters (11 before removing empty columns).
	  10 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.6 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1 2

#######################################################
STARTING RUN

Bootstrap reweighting...
	Subset 1: Random seed for bootstrap reweighting: 42

>>>Bootstrap rep 1 (of 1) <<<
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 20 (amino acid data)
  Amino Acid Rate Matrix: Jones
  Equilibrium State Frequencies: empirical (observed) values (+F)
    (ACDEFGHIKLMNPQRSTVWY)
    0.0165 0.0083 0.0496 0.0909 0.0909 
    0.0083 0.0744 0.0083 0.0083 0.1074 
    0.1157 0.0248 0.1240 0.0331 0.0083 
    0.0826 0.0496 0.0579 0.0083 0.0331 
  Rate Heterogeneity Model:
    3 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.0750
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0750
      0.0603	0.3083
      0.4894	0.3083
      2.4503	0.3083

Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 0.001 lnL
Optimizing branchlengths... improved 0.178 lnL
 7  8  9  10  11 
Initial ln Likelihood: -94.5491
optimizing: starting branch lengths, alpha shape, prop. invar...
pass 1:+    1.029 (branch=   1.03 scale=  0.00 alpha=  0.00 pinv=  0.00)
pass 2:+    0.113 (branch=   0.11 scale=  0.00 alpha=  0.00 pinv=  0.00)
lnL after optimization: -93.4068
gen      current_lnL    precision  last_tree_imp  
0        -93.4068         0.500           0 
100      -93.0240         0.500           0 
200      -91.3705         0.500         199 
300      -90.7565         0.500         215 
NOTE: ****Specified time limit (5 seconds) reached...

NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
(set restart = 1 in the config file).  IF YOU WANT TO USE THE
PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
ADD "end;" TO THE TREE FILES.

Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./restart/a.G3.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/z.11x30.stop.nex ...
Reading DATA block...storing implied block: TAXA
storing read block: DATA
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Amino acid data
Warning: stop codon TAA found at codon site 11 (nuc site 31) in taxon MorNa6.
	Treating as missing data because ignorestopcodons = 1 is set in configuration file.
Some sites treated as missing data for taxon MorNa6 due to ambiguity in translation.
	Aminoacids coded as missing for that taxon: 11 

Warning: stop codon TAA found at codon site 11 (nuc site 31) in taxon ClownNa6.
	Treating as missing data because ignorestopcodons = 1 is set in configuration file.
Some sites treated as missing data for taxon ClownNa6 due to ambiguity in translation.
	Aminoacids coded as missing for that taxon: 11 

WARNING: Not all amino acids were observed in this dataset.
	One pseudo-count will be added to each amino acid
	for calculation of the empirical frequencies. You
	should probably use a statefrequencies setting other 
	than emprical.

	Summary of data:
	  11 sequences.
	  3 constant characters.
	  6 parsimony-informative characters.
	  1 uninformative variable characters.
	  1 characters were completely missing or ambiguous (removed).
	  10 total characters (11 before removing empty columns).
	  10 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.6 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1 2

#######################################################
STARTING RUN
	Subset 1: Random seed for bootstrap reweighting: 42

Restarting from checkpoint...
Bootstrap rep 1 (of 1)  generation 370, seed 1797603490, best lnL -90.631
gen      current_lnL    precision  last_tree_imp  
370      -90.6312         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 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./check/a.G4.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.AA.fas as
	Fasta amino acid format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Amino acid data,
	modeled as Amino acid data
WARNING: Not all amino acids were observed in this dataset.
	One pseudo-count will be added to each amino acid
	for calculation of the empirical frequencies. You
	should probably use a statefrequencies setting other 
	than emprical.

	Summary of data:
	  11 sequences.
	  3 constant characters.
	  6 parsimony-informative characters.
	  1 uninformative variable characters.
	  1 characters were completely missing or ambiguous (removed).
	  10 total characters (11 before removing empty columns).
	  10 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.8 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  2

#######################################################
STARTING RUN
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 20 (amino acid data)
  Amino Acid Rate Matrix: Jones
  Equilibrium State Frequencies: empirical (observed) values (+F)
    (ACDEFGHIKLMNPQRSTVWY)
    0.0165 0.0083 0.0496 0.0909 0.0909 
    0.0083 0.0744 0.0083 0.0083 0.1074 
    0.1157 0.0248 0.1240 0.0331 0.0083 
    0.0826 0.0496 0.0579 0.0083 0.0331 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.0750
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0750
      0.0334	0.2313
      0.2519	0.2313
      0.8203	0.2313
      2.8944	0.2313

Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 0.001 lnL
Optimizing branchlengths... improved 0.006 lnL
 7  8  9  10  11 
Initial ln Likelihood: -117.7431
optimizing: starting branch lengths, alpha shape, prop. invar...
pass 1:+    1.466 (branch=   1.13 scale=  0.33 alpha=  0.00 pinv=  0.00)
pass 2:+    0.134 (branch=   0.13 scale=  0.00 alpha=  0.00 pinv=  0.00)
lnL after optimization: -116.1434
gen      current_lnL    precision  last_tree_imp  
0        -116.1434        0.500           0 
100      -112.9555        0.500          84 
200      -112.4964        0.500          84 
NOTE: ****Specified time limit (5 seconds) reached...

NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
(set restart = 1 in the config file).  IF YOU WANT TO USE THE
PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
ADD "end;" TO THE TREE FILES.

Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./restart/a.G4.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.AA.fas as
	Fasta amino acid format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Amino acid data,
	modeled as Amino acid data
WARNING: Not all amino acids were observed in this dataset.
	One pseudo-count will be added to each amino acid
	for calculation of the empirical frequencies. You
	should probably use a statefrequencies setting other 
	than emprical.

	Summary of data:
	  11 sequences.
	  3 constant characters.
	  6 parsimony-informative characters.
	  1 uninformative variable characters.
	  1 characters were completely missing or ambiguous (removed).
	  10 total characters (11 before removing empty columns).
	  10 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.8 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  2

#######################################################
STARTING RUN

Restarting from checkpoint...
 generation 246, seed 1608648735, best lnL -112.441
gen      current_lnL    precision  last_tree_imp  
246      -112.4415        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     -110.5065        0.010         707 
NOTE: ****Specified generation limit (1000) reached...

MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
Model 1
  Number of states = 20 (amino acid data)
  Amino Acid Rate Matrix: Jones
  Equilibrium State Frequencies: empirical (observed) values (+F)
    (ACDEFGHIKLMNPQRSTVWY)
    0.0165 0.0083 0.0496 0.0909 0.0909 
    0.0083 0.0744 0.0083 0.0083 0.1074 
    0.1157 0.0248 0.1240 0.0331 0.0083 
    0.0826 0.0496 0.0579 0.0083 0.0331 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      1.3049
    with an invariant (invariable) site category, proportion estimated
      0.0988
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0988
      0.1936	0.2253
      0.5525	0.2253
      1.0366	0.2253
      2.2174	0.2253

NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    1 branches were collapsed.

Saving site likelihoods to file ch.a.G4.sitelikes.log ...
WARNING: Site likelihoods being output on prematurely terminated search ...

NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -110.5065       

Parameter estimates:
        alpha  pinv
rep 1:  1.305 0.099

Treelengths:
          TL 
rep 1:  2.534

Saving final tree from best search rep (#1) to ch.a.G4.best.tre
Inferring internal state probabilities on best tree... saving to file ch.a.G4.internalstates.log

WARNING: Internal states inferred on tree from prematurely terminated search

#######################################################
TREEFILES PASS
Running checkpoint test ./check/a.conf
Running checkpoint test ./check/a.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./check/a.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Amino acid data
WARNING: Not all amino acids were observed in this dataset.
	One pseudo-count will be added to each amino acid
	for calculation of the empirical frequencies. You
	should probably use a statefrequencies setting other 
	than emprical.

	Summary of data:
	  11 sequences.
	  3 constant characters.
	  6 parsimony-informative characters.
	  1 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.2 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  2

#######################################################
STARTING RUN
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 20 (amino acid data)
  Amino Acid Rate Matrix: Jones
  Equilibrium State Frequencies: empirical (observed) values (+F)
    (ACDEFGHIKLMNPQRSTVWY)
    0.0165 0.0083 0.0496 0.0909 0.0909 
    0.0083 0.0744 0.0083 0.0083 0.1074 
    0.1157 0.0248 0.1240 0.0331 0.0083 
    0.0826 0.0496 0.0579 0.0083 0.0331 
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 0.121 lnL
 7  8  9  10  11 
NOTE: Model contains no mutable parameters!
Setting model mutation weight to zero.

Initial ln Likelihood: -117.7533
optimizing: starting branch lengths...
pass 1:+    0.632 (branch=   0.63 scale=  0.00)
pass 2:+    0.134 (branch=   0.13 scale=  0.00)
lnL after optimization: -116.9881
gen      current_lnL    precision  last_tree_imp  
0        -116.9881        0.500           0 
100      -113.6842        0.500          91 
200      -112.5462        0.500         160 
300      -112.1250        0.500         160 
400      -111.8851        0.500         160 
500      -111.7755        0.500         160 
600      -111.6975        0.500         563 
700      -111.6876        0.500         563 
800      -111.6844        0.500         563 
900      -111.6835        0.500         563 
1000     -111.6829        0.500         563 
NOTE: ****Specified time limit (5 seconds) reached...

NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
(set restart = 1 in the config file).  IF YOU WANT TO USE THE
PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
ADD "end;" TO THE TREE FILES.

Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./restart/a.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Amino acid data
WARNING: Not all amino acids were observed in this dataset.
	One pseudo-count will be added to each amino acid
	for calculation of the empirical frequencies. You
	should probably use a statefrequencies setting other 
	than emprical.

	Summary of data:
	  11 sequences.
	  3 constant characters.
	  6 parsimony-informative characters.
	  1 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.2 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  2

#######################################################
STARTING RUN

Restarting from checkpoint...
 generation 1091, seed 462149512, best lnL -111.683
gen      current_lnL    precision  last_tree_imp  
1091     -111.6827        0.500         563 

MODEL REPORT - Parameter values are FINAL
Model 1
  Number of states = 20 (amino acid data)
  Amino Acid Rate Matrix: Jones
  Equilibrium State Frequencies: empirical (observed) values (+F)
    (ACDEFGHIKLMNPQRSTVWY)
    0.0165 0.0083 0.0496 0.0909 0.0909 
    0.0083 0.0744 0.0083 0.0083 0.1074 
    0.1157 0.0248 0.1240 0.0331 0.0083 
    0.0826 0.0496 0.0579 0.0083 0.0331 
  Rate Heterogeneity Model:
    no rate heterogeneity

NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    No branches were short enough to be collapsed.

Saving site likelihoods to file ch.a.sitelikes.log ...

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -111.6827       

Parameter estimates:
	 Model contains no estimated parameters

Treelengths:
          TL 
rep 1:  2.619

Saving final tree from best search rep (#1) to ch.a.best.tre
Inferring internal state probabilities on best tree... saving to file ch.a.internalstates.log

#######################################################
TREEFILES PASS
Running checkpoint test ./check/c.M3x2.conf
Running checkpoint test ./check/c.M3x2.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./check/c.M3x2.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Codon data
Base usage at codon positions:
                A         C         G         T
 pos 1      0.27723   0.36634   0.21782   0.13861
 pos 2      0.30693   0.20792   0.07921   0.40594
 pos 3      0.10891   0.38614   0.26733   0.23762
 all pos    0.23102   0.32013   0.18812   0.26073

	Summary of data:
	  11 sequences.
	  0 constant characters.
	  9 parsimony-informative characters.
	  1 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 1.3 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1

#######################################################
STARTING RUN
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 61 (codon data, standard code)
  Nucleotide Relative Rate Matrix Assumed by Codon Model:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: 
    empirical values calculated by F3x4 method (fixed)
    (AAA, AAC, AAG, AAT, ACA, ... etc)
    0.0094 0.0334 0.0231 0.0206 0.0064 
    0.0226 0.0157 0.0139 0.0024 0.0086 
    0.0060 0.0053 0.0125 0.0442 0.0306 
    0.0272 0.0125 0.0442 0.0306 0.0272 
    0.0084 0.0299 0.0207 0.0184 0.0032 
    0.0114 0.0079 0.0070 0.0165 0.0584 
    0.0405 0.0360 0.0074 0.0263 0.0182 
    0.0162 0.0050 0.0178 0.0123 0.0110 
    0.0019 0.0068 0.0047 0.0042 0.0098 
    0.0347 0.0241 0.0214 0.0167 0.0103 
    0.0032 0.0113 0.0078 0.0070 0.0043 
    0.0030 0.0027 0.0062 0.0221 0.0153 
    0.0136 
  Rate Heterogeneity Model:
    2 nonsynonymous rate categories, rate and proportion of each estimated
     (this is effectively the M3 model of PAML)
      dN/dS	Proportion
      0.2500	0.5000
      0.5000	0.5000

Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 4.461 lnL
Optimizing branchlengths... improved 0.701 lnL
 7  8  9  10  11 
Initial ln Likelihood: -215.8071
optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters...
pass 1:+    6.388 (branch=   0.00 scale=  0.44 omega=  0.01 rel rates=  5.93)
pass 2:+    0.434 (branch=   0.00 scale=  0.00 omega=  0.01 rel rates=  0.42)
lnL after optimization: -208.9856
gen      current_lnL    precision  last_tree_imp  
0        -208.9856        0.500           0 
10       -207.1401        0.500          10 
NOTE: ****Specified time limit (10 seconds) reached...

NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
(set restart = 1 in the config file).  IF YOU WANT TO USE THE
PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
ADD "end;" TO THE TREE FILES.

Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./restart/c.M3x2.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Codon data
Base usage at codon positions:
                A         C         G         T
 pos 1      0.27723   0.36634   0.21782   0.13861
 pos 2      0.30693   0.20792   0.07921   0.40594
 pos 3      0.10891   0.38614   0.26733   0.23762
 all pos    0.23102   0.32013   0.18812   0.26073

	Summary of data:
	  11 sequences.
	  0 constant characters.
	  9 parsimony-informative characters.
	  1 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 1.3 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1

#######################################################
STARTING RUN

Restarting from checkpoint...
 generation 13, seed 1603481258, best lnL -206.464
gen      current_lnL    precision  last_tree_imp  
13       -206.4639        0.500          13 
20       -205.6892        0.500          18 
30       -205.6499        0.500          18 
40       -205.6371        0.500          18 
50       -205.6175        0.500          18 
60       -205.5990        0.500          53 
70       -205.5741        0.500          53 
80       -205.4022        0.500          76 
90       -205.3871        0.500          76 
100      -205.3829        0.500          76 
NOTE: ****Specified generation limit (100) reached...

MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
Model 1
  Number of states = 61 (codon data, standard code)
  Nucleotide Relative Rate Matrix Assumed by Codon Model:     6 rates 
    AC = 1.586, AG = 3.999, AT = 0.040, CG = 2.453, CT = 3.968, GT = 1.000
  Equilibrium State Frequencies: 
    empirical values calculated by F3x4 method (fixed)
    (AAA, AAC, AAG, AAT, ACA, ... etc)
    0.0094 0.0334 0.0231 0.0206 0.0064 
    0.0226 0.0157 0.0139 0.0024 0.0086 
    0.0060 0.0053 0.0125 0.0442 0.0306 
    0.0272 0.0125 0.0442 0.0306 0.0272 
    0.0084 0.0299 0.0207 0.0184 0.0032 
    0.0114 0.0079 0.0070 0.0165 0.0584 
    0.0405 0.0360 0.0074 0.0263 0.0182 
    0.0162 0.0050 0.0178 0.0123 0.0110 
    0.0019 0.0068 0.0047 0.0042 0.0098 
    0.0347 0.0241 0.0214 0.0167 0.0103 
    0.0032 0.0113 0.0078 0.0070 0.0043 
    0.0030 0.0027 0.0062 0.0221 0.0153 
    0.0136 
  Rate Heterogeneity Model:
    2 nonsynonymous rate categories, rate and proportion of each estimated
     (this is effectively the M3 model of PAML)
      dN/dS	Proportion
      0.0490	0.5211
      0.4995	0.4789

NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    No branches were short enough to be collapsed.

Saving site likelihoods to file ch.c.M3x2.sitelikes.log ...
WARNING: Site likelihoods being output on prematurely terminated search ...

NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -205.3829       

Parameter estimates:
         w(0)  p(0)  w(1)  p(1)  r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT)
rep 1:  0.049 0.521 0.499 0.479  1.586  3.999   0.04  2.453  3.968      1

Treelengths:
          TL 
rep 1:  7.371

Saving final tree from best search rep (#1) to ch.c.M3x2.best.tre
Inferring internal state probabilities on best tree... saving to file ch.c.M3x2.internalstates.log

WARNING: Internal states inferred on tree from prematurely terminated search

#######################################################
TREEFILES PASS
Running checkpoint test ./check/c.conf
Running checkpoint test ./check/c.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./check/c.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Codon data
Base usage at codon positions:
                A         C         G         T
 pos 1      0.27723   0.36634   0.21782   0.13861
 pos 2      0.30693   0.20792   0.07921   0.40594
 pos 3      0.10891   0.38614   0.26733   0.23762
 all pos    0.23102   0.32013   0.18812   0.26073

	Summary of data:
	  11 sequences.
	  0 constant characters.
	  9 parsimony-informative characters.
	  1 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.6 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1 2

#######################################################
STARTING RUN

Bootstrap reweighting...
	Subset 1: Random seed for bootstrap reweighting: 42

>>>Bootstrap rep 1 (of 1) <<<
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 61 (codon data, standard code)
  One estimated dN/dS ratio (aka omega) = 0.250000
  Nucleotide Relative Rate Matrix Assumed by Codon Model:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: 
    empirical values calculated by F3x4 method (fixed)
    (AAA, AAC, AAG, AAT, ACA, ... etc)
    0.0094 0.0334 0.0231 0.0206 0.0064 
    0.0226 0.0157 0.0139 0.0024 0.0086 
    0.0060 0.0053 0.0125 0.0442 0.0306 
    0.0272 0.0125 0.0442 0.0306 0.0272 
    0.0084 0.0299 0.0207 0.0184 0.0032 
    0.0114 0.0079 0.0070 0.0165 0.0584 
    0.0405 0.0360 0.0074 0.0263 0.0182 
    0.0162 0.0050 0.0178 0.0123 0.0110 
    0.0019 0.0068 0.0047 0.0042 0.0098 
    0.0347 0.0241 0.0214 0.0167 0.0103 
    0.0032 0.0113 0.0078 0.0070 0.0043 
    0.0030 0.0027 0.0062 0.0221 0.0153 
    0.0136 
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 0.353 lnL
Optimizing branchlengths... improved 0.746 lnL
 7  8  9  10  11 
Initial ln Likelihood: -208.5106
optimizing: starting branch lengths, rel rates, dN/dS (aka omega) parameters...
pass 1:+   10.487 (branch=   0.90 scale=  0.55 omega=  0.01 rel rates=  9.03)
pass 2:+    2.529 (branch=   2.19 scale=  0.00 omega=  0.00 rel rates=  0.34)
pass 3:+    0.095 (branch=   0.02 scale=  0.00 omega=  0.00 rel rates=  0.07)
lnL after optimization: -195.4001
gen      current_lnL    precision  last_tree_imp  
0        -195.4001        0.500           0 
10       -195.3555        0.500           0 
NOTE: ****Specified time limit (5 seconds) reached...

NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
(set restart = 1 in the config file).  IF YOU WANT TO USE THE
PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
ADD "end;" TO THE TREE FILES.

Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./restart/c.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Codon data
Base usage at codon positions:
                A         C         G         T
 pos 1      0.27723   0.36634   0.21782   0.13861
 pos 2      0.30693   0.20792   0.07921   0.40594
 pos 3      0.10891   0.38614   0.26733   0.23762
 all pos    0.23102   0.32013   0.18812   0.26073

	Summary of data:
	  11 sequences.
	  0 constant characters.
	  9 parsimony-informative characters.
	  1 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.6 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1 2

#######################################################
STARTING RUN
	Subset 1: Random seed for bootstrap reweighting: 42

Restarting from checkpoint...
Bootstrap rep 1 (of 1)  generation 12, seed 1380786643, best lnL -195.348
gen      current_lnL    precision  last_tree_imp  
12       -195.3480        0.500           0 
20       -195.3342        0.500           0 
30       -195.2777        0.500           0 
40       -195.2556        0.500           0 
50       -195.2139        0.500           0 
60       -195.1631        0.500           0 
70       -195.0044        0.500           0 
80       -194.9480        0.500           0 
90       -194.9094        0.500           0 
100      -194.9094        0.500           0 
NOTE: ****Specified generation limit (100) reached...

MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
Model 1
  Number of states = 61 (codon data, standard code)
  One estimated dN/dS ratio (aka omega) = 0.120506
  Nucleotide Relative Rate Matrix Assumed by Codon Model:     6 rates 
    AC = 1.637, AG = 5.679, AT = 0.011, CG = 4.174, CT = 2.324, GT = 1.000
  Equilibrium State Frequencies: 
    empirical values calculated by F3x4 method (fixed)
    (AAA, AAC, AAG, AAT, ACA, ... etc)
    0.0094 0.0334 0.0231 0.0206 0.0064 
    0.0226 0.0157 0.0139 0.0024 0.0086 
    0.0060 0.0053 0.0125 0.0442 0.0306 
    0.0272 0.0125 0.0442 0.0306 0.0272 
    0.0084 0.0299 0.0207 0.0184 0.0032 
    0.0114 0.0079 0.0070 0.0165 0.0584 
    0.0405 0.0360 0.0074 0.0263 0.0182 
    0.0162 0.0050 0.0178 0.0123 0.0110 
    0.0019 0.0068 0.0047 0.0042 0.0098 
    0.0347 0.0241 0.0214 0.0167 0.0103 
    0.0032 0.0113 0.0078 0.0070 0.0043 
    0.0030 0.0027 0.0062 0.0221 0.0153 
    0.0136 
  Rate Heterogeneity Model:
    no rate heterogeneity

NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    No branches were short enough to be collapsed.


NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -194.9094       

Parameter estimates:
         w(0)  p(0)  r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT)
rep 1:  0.121 1.000  1.637  5.679 0.01146  4.174  2.324      1

Treelengths:
          TL 
rep 1:  9.255

Saving best tree to bootstrap file ch.c.boot.tre

WARNING: Tree from prematurely terminated search saved to bootstrap file
#######################################################
TREEFILES PASS
Running checkpoint test ./check/g.dnaBnoZ.conf
Running checkpoint test ./check/g.dnaBnoZ.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./check/g.dnaBnoZ.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/dnaGap.8x1K.nex ...
Reading TAXA block...storing read block: TAXA
 successful
Reading CHARACTERS block...storing read block: CHARACTERS
 found dna data... successful
Reading CHARACTERS block...storing read block: CHARACTERS
 found standard data... successful
Reading TREES block...storing read block: TREES
 successful

###################################################
PARTITIONING OF DATA AND MODELS

CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY
	TO EACH DATA SUBSET (no linkage)

GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1GapsAsMissing")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  8 sequences.
	  428 constant characters.
	  129 parsimony-informative characters.
	  100 uninformative variable characters.
	  343 characters were completely missing or ambiguous (removed).
	  657 total characters (1000 before removing empty columns).
	  239 unique patterns in compressed data matrix.
GARLI data subset 2
	CHARACTERS block #2 ("Untitled DATA Block 1GapsAsBinary")
	Data read as Binary data, no constant state 0 chars,
	modeled as Binary data, no constant state 0 chars
	NOTE: entirely missing characters removed from matrix:  1 25 29-34 36 37 52-54 61 67-69 84 85 87 95 96 99 106 110-116 125 138-145 163-165 167 169-177 188 197-199 202-210 213 216-218 228-231 233-236 238-240 247 249 256 257 260 266-270 \ 2 271-277 281-285 290-294 298-300 311 312 322 325 331 332 336-338 344 359 369 373-378 397 404-406 413 416 417 420-426 439-442 450-454 \ 2 455-460 462 471 474-479 487-490 492 494 495 497 502-506 510 521-526 532 533 538-541 544 547 551-553 562 570-572 577 579 609 610 614 615 622 624-626 639 640 647-650 653 655-660 667 668 673-676 679 680 685 695 696 701-705 708-713 716 717 731 742-749 751-755 762 763 770 771 783 788 791-793 804 806-808 813 821-825 827 830-832 840 842 843 845 850 851 856-865 886-894 896 897 903-905 913 914 924 927 948-956 963-971 976-981 991-993 996
	Subset of data with 2 states:
	  chars 1-1000
	Summary of data:
	  8 sequences.
	  502 constant characters.
	  39 parsimony-informative characters.
	  116 uninformative variable characters.
	  343 characters were completely missing or ambiguous (removed).
	  657 total characters (1000 before removing empty columns).
	  24 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 2 MB
  good			approx 2 MB to 2 MB
  low			approx 2 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 2.8 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1

#######################################################
STARTING RUN

>>>Search rep 1 (of 2)<<<
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.3220 0.2180 0.1602 0.2999 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.1629
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.1629
      0.0334	0.2093
      0.2519	0.2093
      0.8203	0.2093
      2.8944	0.2093

Model 2
  Number of states = 2 (binary data)
  Character change matrix:
    Binary, no all-zero columns (2-state symmetric one rate model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00
Starting with seed=1

Initial ln Likelihood: -4043.7391
optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates...
pass 1:+  532.047 (branch= 438.84 scale=  6.77 alpha= 15.79 freqs=  3.30 rel rates=  8.48 pinv=  0.00 subset rates= 58.86)
pass 2:+   88.209 (branch=  42.39 scale=  0.83 alpha=  0.82 freqs=  0.72 rel rates=  0.01 pinv=  0.00 subset rates= 43.45)
pass 3:+   34.899 (branch=   0.70 scale=  2.02 alpha=  1.89 freqs=  0.04 rel rates=  0.72 pinv=  0.00 subset rates= 29.52)
pass 4:+   17.437 (branch=   4.66 scale=  2.38 alpha=  1.70 freqs=  0.05 rel rates=  0.01 pinv=  0.00 subset rates=  8.64)
pass 5:+   10.201 (branch=   4.19 scale=  1.64 alpha=  0.69 freqs=  0.05 rel rates=  2.14 pinv=  0.00 subset rates=  1.49)
pass 6:+    1.986 (branch=   0.00 scale=  1.92 alpha=  0.00 freqs=  0.06 rel rates=  0.01 pinv=  0.00 subset rates=  0.00)
pass 7:+    0.532 (branch=   0.47 scale=  0.00 alpha=  0.00 freqs=  0.06 rel rates=  0.01 pinv=  0.00 subset rates=  0.00)
pass 8:+    0.057 (branch=   0.00 scale=  0.00 alpha=  0.00 freqs=  0.05 rel rates=  0.01 pinv=  0.00 subset rates=  0.00)
lnL after optimization: -3358.3708
gen      current_lnL    precision  last_tree_imp  
0        -3358.3708       0.500           0 
100      -3357.1202       0.500           0 
200      -3356.8081       0.500           0 
300      -3356.5910       0.500           0 
400      -3355.9752       0.500           0 
500      -3355.8101       0.500           0 
Optimization precision reduced 
   Optimizing parameters...    improved    0.940 lnL
   Optimizing branchlengths... improved    0.000 lnL
600      -3354.6612       0.255           0 
700      -3354.3974       0.255           0 
800      -3354.0880       0.255           0 
900      -3353.8938       0.255           0 
1000     -3353.6942       0.255           0 
Optimization precision reduced 
   Optimizing parameters...    improved    0.833 lnL
   Optimizing branchlengths... improved    0.085 lnL
NOTE: ****Specified time limit (5 seconds) reached...

NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
(set restart = 1 in the config file).  IF YOU WANT TO USE THE
PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
ADD "end;" TO THE TREE FILES.

Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./restart/g.dnaBnoZ.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/dnaGap.8x1K.nex ...
Reading TAXA block...storing read block: TAXA
 successful
Reading CHARACTERS block...storing read block: CHARACTERS
 found dna data... successful
Reading CHARACTERS block...storing read block: CHARACTERS
 found standard data... successful
Reading TREES block...storing read block: TREES
 successful

###################################################
PARTITIONING OF DATA AND MODELS

CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY
	TO EACH DATA SUBSET (no linkage)

GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1GapsAsMissing")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  8 sequences.
	  428 constant characters.
	  129 parsimony-informative characters.
	  100 uninformative variable characters.
	  343 characters were completely missing or ambiguous (removed).
	  657 total characters (1000 before removing empty columns).
	  239 unique patterns in compressed data matrix.
GARLI data subset 2
	CHARACTERS block #2 ("Untitled DATA Block 1GapsAsBinary")
	Data read as Binary data, no constant state 0 chars,
	modeled as Binary data, no constant state 0 chars
	NOTE: entirely missing characters removed from matrix:  1 25 29-34 36 37 52-54 61 67-69 84 85 87 95 96 99 106 110-116 125 138-145 163-165 167 169-177 188 197-199 202-210 213 216-218 228-231 233-236 238-240 247 249 256 257 260 266-270 \ 2 271-277 281-285 290-294 298-300 311 312 322 325 331 332 336-338 344 359 369 373-378 397 404-406 413 416 417 420-426 439-442 450-454 \ 2 455-460 462 471 474-479 487-490 492 494 495 497 502-506 510 521-526 532 533 538-541 544 547 551-553 562 570-572 577 579 609 610 614 615 622 624-626 639 640 647-650 653 655-660 667 668 673-676 679 680 685 695 696 701-705 708-713 716 717 731 742-749 751-755 762 763 770 771 783 788 791-793 804 806-808 813 821-825 827 830-832 840 842 843 845 850 851 856-865 886-894 896 897 903-905 913 914 924 927 948-956 963-971 976-981 991-993 996
	Subset of data with 2 states:
	  chars 1-1000
	Summary of data:
	  8 sequences.
	  502 constant characters.
	  39 parsimony-informative characters.
	  116 uninformative variable characters.
	  343 characters were completely missing or ambiguous (removed).
	  657 total characters (1000 before removing empty columns).
	  24 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 2 MB
  good			approx 2 MB to 2 MB
  low			approx 2 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 2.8 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1

#######################################################
STARTING RUN

Restarting from checkpoint...
Search rep 1 (of 2) generation 1050, seed 1689402887, best lnL -3352.754
gen      current_lnL    precision  last_tree_imp  
1050     -3352.7536       0.010           0 
1100     -3352.7168       0.010           0 
1200     -3352.6373       0.010           0 
1300     -3352.5144       0.010           0 
1400     -3352.4046       0.010           0 
1500     -3352.3996       0.010           0 
1600     -3352.2933       0.010           0 
1700     -3352.2857       0.010           0 
1800     -3352.2040       0.010           0 
NOTE: ****Specified time limit (5 seconds) reached...
Current score = -3352.0486
Performing final optimizations...
pass 1 : -3351.7984   (branch= 0.0075  alpha= 0.0156  pinv= 0.0206  eq freqs= 0.0127  rel rates= 0.1846  subset rates= 0.0092)
pass 2 : -3351.5648   (branch= 0.0159  alpha= 0.0110  pinv= 0.0186  eq freqs= 0.0066  rel rates= 0.1798  subset rates= 0.0016)
pass 3 : -3351.3672   (branch= 0.0083  alpha= 0.0170  pinv= 0.0161  eq freqs= 0.0088  rel rates= 0.1463  subset rates= 0.0011)
pass 4 : -3351.2022   (branch= 0.0091  alpha= 0.0137  pinv= 0.0152  eq freqs= 0.0013  rel rates= 0.1237  subset rates= 0.0021)
pass 5 : -3351.0655   (branch= 0.0092  alpha= 0.0130  pinv= 0.0143  eq freqs= 0.0004  rel rates= 0.0977  subset rates= 0.0021)
pass 6 : -3350.9493   (branch= 0.0060  alpha= 0.0117  pinv= 0.0135  eq freqs= 0.0005  rel rates= 0.0829  subset rates= 0.0017)
pass 7 : -3350.8512   (branch= 0.0036  alpha= 0.0109  pinv= 0.0124  eq freqs= 0.0002  rel rates= 0.0696  subset rates= 0.0013)
pass 8 : -3350.7661   (branch= 0.0027  alpha= 0.0103  pinv= 0.0114  eq freqs= 0.0001  rel rates= 0.0596  subset rates= 0.0010)
pass 9 : -3350.6938   (branch= 0.0019  alpha= 0.0097  pinv= 0.0105  eq freqs= 0.0001  rel rates= 0.0501  subset rates= 0.0000)
pass 10: -3350.6289   (branch= 0.0005  alpha= 0.0093  pinv= 0.0101  eq freqs= 0.0001  rel rates= 0.0438  subset rates= 0.0011)
pass 11: -3350.5747   (branch= 0.0009  alpha= 0.0088  pinv= 0.0085  eq freqs= 0.0001  rel rates= 0.0358  subset rates= 0.0000)
pass 12: -3350.5289   (branch= 0.0002  alpha= 0.0081  pinv= 0.0077  eq freqs= 0.0001  rel rates= 0.0297  subset rates= 0.0000)
pass 13: -3350.4890   (branch= 0.0001  alpha= 0.0076  pinv= 0.0069  eq freqs= 0.0001  rel rates= 0.0252  subset rates= 0.0000)
pass 14: -3350.4544   (branch= 0.0000  alpha= 0.0069  pinv= 0.0062  eq freqs= 0.0001  rel rates= 0.0214  subset rates= 0.0000)
pass 15: -3350.4246   (branch= 0.0000  alpha= 0.0062  pinv= 0.0056  eq freqs= 0.0001  rel rates= 0.0180  subset rates= 0.0000)
pass 16: -3350.3987   (branch= 0.0000  alpha= 0.0055  pinv= 0.0050  eq freqs= 0.0000  rel rates= 0.0153  subset rates= 0.0000)
pass 17: -3350.3763   (branch= 0.0000  alpha= 0.0049  pinv= 0.0044  eq freqs= 0.0000  rel rates= 0.0130  subset rates= 0.0000)
pass 18: -3350.3570   (branch= 0.0000  alpha= 0.0044  pinv= 0.0039  eq freqs= 0.0000  rel rates= 0.0110  subset rates= 0.0000)
pass 19: -3350.3403   (branch= 0.0000  alpha= 0.0038  pinv= 0.0035  eq freqs= 0.0000  rel rates= 0.0094  subset rates= 0.0000)
pass 20: -3350.3258   (branch= 0.0000  alpha= 0.0034  pinv= 0.0031  eq freqs= 0.0000  rel rates= 0.0080  subset rates= 0.0000)
 optimization up to ...
pass 30: -3350.2547   (branch= 0.0000  alpha= 0.0172  pinv= 0.0156  eq freqs= 0.0001  rel rates= 0.0382  subset rates= 0.0000)
 optimization up to ...
pass 40: -3350.2384   (branch= 0.0000  alpha= 0.0038  pinv= 0.0035  eq freqs= 0.0000  rel rates= 0.0089  subset rates= 0.0000)
 optimization up to ...
pass 50: -3350.2348   (branch= 0.0000  alpha= 0.0007  pinv= 0.0007  eq freqs= 0.0000  rel rates= 0.0023  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= 0.0006  subset rates= 0.0000)
 optimization up to ...
pass 70: -3350.2337   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0002  subset rates= 0.0000)
 optimization up to ...
pass 71: -3350.2337   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000  subset rates= 0.0000)
Looking for minimum length branches...
Final score = -3350.2338
Time used so far = 0 hours, 0 minutes and 13 seconds

MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 3.112, AG = 10.402, AT = 2.687, CG = 0.001, CT = 21.855, 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
      0.5793
    with an invariant (invariable) site category, proportion estimated
      0.3662
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.3662
      0.0489	0.1585
      0.3006	0.1585
      0.8704	0.1585
      2.7801	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:   3.112   10.4  2.687  0.001  21.85      1 0.333 0.222 0.157 0.288 0.579 0.366

Partition model subset 2:
	 Model contains no estimated parameters

Treelengths and subset rate multipliers:
          TL   R(1)  R(2)
rep 1:  0.787 1.820 0.180

Saving final tree from best search rep (#1) to ch.g.dnaBnoZ.best.tre
#######################################################
TREEFILES PASS
Running checkpoint test ./check/g.dnaMix.conf
Running checkpoint test ./check/g.dnaMix.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./check/g.dnaMix.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/dnaGap.8x1K.nex ...
Reading TAXA block...storing read block: TAXA
 successful
Reading CHARACTERS block...storing read block: CHARACTERS
 found dna data... successful
Reading CHARACTERS block...storing read block: CHARACTERS
 found standard data... successful
Reading TREES block...storing read block: TREES
 successful

###################################################
PARTITIONING OF DATA AND MODELS

CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY
	TO EACH DATA SUBSET (no linkage)

GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1GapsAsMissing")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  8 sequences.
	  428 constant characters.
	  129 parsimony-informative characters.
	  100 uninformative variable characters.
	  343 characters were completely missing or ambiguous (removed).
	  657 total characters (1000 before removing empty columns).
	  239 unique patterns in compressed data matrix.
GARLI data subset 2
	CHARACTERS block #2 ("Untitled DATA Block 1GapsAsBinary")
	Data read as Gap-coded data, oriented with respect to time,
	modeled as Gap-coded data, oriented with respect to time
	Summary of data:
	  8 sequences.
	  502 constant characters.
	  39 parsimony-informative characters.
	  116 uninformative variable characters.
	  343 characters were completely missing or ambiguous (removed).
	  657 total characters (1000 before removing empty columns).
	  24 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 2 MB
  good			approx 2 MB to 2 MB
  low			approx 2 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 3.2 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
WARNING - specified outgroup (1) being ignored due to inference of a rooted true

#######################################################
STARTING RUN

>>>Search rep 1 (of 2)<<<
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.3220 0.2180 0.1602 0.2999 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.1629
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.1629
      0.0334	0.2093
      0.2519	0.2093
      0.8203	0.2093
      2.8944	0.2093

Model 2
  Number of states = 2 (0/1 coding of gaps)
  Character change matrix: irreversible matrix
    deletion rate parameter only estimated if using a partitioned
    model without subset rates
    deletion rate = 1.000
  Equilibrium State Frequencies: proportion of inserted sites parameter
    insert proportion = 0.500
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

Initial ln Likelihood: -4257.0961
optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, ins rate, del rate...
pass 1:+  640.405 (branch= 431.06 scale=  2.03 alpha=  9.92 freqs=  3.07 rel rates=  7.29 pinv=  0.00 ins/del=187.03)
pass 2:+  169.102 (branch=  75.12 scale=  1.32 alpha=  0.88 freqs=  0.65 rel rates=  0.01 pinv=  0.00 ins/del= 91.12)
pass 3:+   55.144 (branch=   7.14 scale=  1.85 alpha=  1.09 freqs=  0.05 rel rates=  0.90 pinv=  0.00 ins/del= 44.12)
pass 4:+   25.231 (branch=   7.02 scale=  1.52 alpha=  0.69 freqs=  0.06 rel rates=  0.01 pinv=  0.00 ins/del= 15.94)
pass 5:+   14.361 (branch=   7.97 scale=  1.87 alpha=  0.01 freqs=  0.05 rel rates=  2.45 pinv=  0.00 ins/del=  2.01)
pass 6:+   10.438 (branch=   7.36 scale=  2.34 alpha=  0.01 freqs=  0.07 rel rates=  0.00 pinv=  0.00 ins/del=  0.66)
pass 7:+    6.158 (branch=   5.23 scale=  0.83 alpha=  0.01 freqs=  0.06 rel rates=  0.00 pinv=  0.00 ins/del=  0.03)
pass 8:+    3.640 (branch=   2.31 scale=  0.00 alpha=  0.00 freqs=  0.05 rel rates=  0.60 pinv=  0.00 ins/del=  0.67)
pass 9:+    0.148 (branch=   0.08 scale=  0.00 alpha=  0.00 freqs=  0.06 rel rates=  0.00 pinv=  0.00 ins/del=  0.00)
lnL after optimization: -3332.4700
gen      current_lnL    precision  last_tree_imp  
0        -3332.4700       0.500           0 
100      -3324.9856       0.500           1 
200      -3324.7543       0.500           1 
NOTE: ****Specified time limit (5 seconds) reached...

NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
(set restart = 1 in the config file).  IF YOU WANT TO USE THE
PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
ADD "end;" TO THE TREE FILES.

Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./restart/g.dnaMix.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/dnaGap.8x1K.nex ...
Reading TAXA block...storing read block: TAXA
 successful
Reading CHARACTERS block...storing read block: CHARACTERS
 found dna data... successful
Reading CHARACTERS block...storing read block: CHARACTERS
 found standard data... successful
Reading TREES block...storing read block: TREES
 successful

###################################################
PARTITIONING OF DATA AND MODELS

CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY
	TO EACH DATA SUBSET (no linkage)

GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1GapsAsMissing")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  8 sequences.
	  428 constant characters.
	  129 parsimony-informative characters.
	  100 uninformative variable characters.
	  343 characters were completely missing or ambiguous (removed).
	  657 total characters (1000 before removing empty columns).
	  239 unique patterns in compressed data matrix.
GARLI data subset 2
	CHARACTERS block #2 ("Untitled DATA Block 1GapsAsBinary")
	Data read as Gap-coded data, oriented with respect to time,
	modeled as Gap-coded data, oriented with respect to time
	Summary of data:
	  8 sequences.
	  502 constant characters.
	  39 parsimony-informative characters.
	  116 uninformative variable characters.
	  343 characters were completely missing or ambiguous (removed).
	  657 total characters (1000 before removing empty columns).
	  24 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 2 MB
  good			approx 2 MB to 2 MB
  low			approx 2 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 3.2 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
WARNING - specified outgroup (1) being ignored due to inference of a rooted true

#######################################################
STARTING RUN

Restarting from checkpoint...
Search rep 1 (of 2) generation 259, seed 526245243, best lnL -3324.603
gen      current_lnL    precision  last_tree_imp  
259      -3324.6034       0.500           1 
300      -3324.3007       0.500           1 
400      -3323.9848       0.500           1 
500      -3323.6818       0.500           1 
NOTE: ****Specified time limit (5 seconds) reached...
Current score = -3323.3791
Performing final optimizations...
pass 1 : -3321.1625   (branch= 0.0809  alpha= 0.0053  pinv= 0.0162  eq freqs= 0.0760  rel rates= 0.6741  ins/del rates= 1.3641)
pass 2 : -3320.4671   (branch= 0.1141  alpha= 0.0000  pinv= 0.0300  eq freqs= 0.0144  rel rates= 0.5069  ins/del rates= 0.0299)
pass 3 : -3319.9579   (branch= 0.0614  alpha= 0.0048  pinv= 0.0162  eq freqs= 0.0150  rel rates= 0.3871  ins/del rates= 0.0246)
pass 4 : -3319.5645   (branch= 0.0361  alpha= 0.0091  pinv= 0.0153  eq freqs= 0.0039  rel rates= 0.3142  ins/del rates= 0.0147)
pass 5 : -3319.2468   (branch= 0.0239  alpha= 0.0102  pinv= 0.0145  eq freqs= 0.0021  rel rates= 0.2576  ins/del rates= 0.0094)
pass 6 : -3318.9921   (branch= 0.0149  alpha= 0.0098  pinv= 0.0140  eq freqs= 0.0008  rel rates= 0.2091  ins/del rates= 0.0061)
pass 7 : -3318.7934   (branch= 0.0094  alpha= 0.0104  pinv= 0.0131  eq freqs= 0.0008  rel rates= 0.1612  ins/del rates= 0.0039)
pass 8 : -3318.6302   (branch= 0.0060  alpha= 0.0102  pinv= 0.0122  eq freqs= 0.0006  rel rates= 0.1315  ins/del rates= 0.0026)
pass 9 : -3318.4984   (branch= 0.0040  alpha= 0.0099  pinv= 0.0113  eq freqs= 0.0004  rel rates= 0.1045  ins/del rates= 0.0017)
pass 10: -3318.3897   (branch= 0.0026  alpha= 0.0095  pinv= 0.0111  eq freqs= 0.0003  rel rates= 0.0841  ins/del rates= 0.0011)
pass 11: -3318.3003   (branch= 0.0017  alpha= 0.0090  pinv= 0.0095  eq freqs= 0.0002  rel rates= 0.0681  ins/del rates= 0.0008)
pass 12: -3318.2263   (branch= 0.0011  alpha= 0.0084  pinv= 0.0087  eq freqs= 0.0002  rel rates= 0.0550  ins/del rates= 0.0005)
pass 13: -3318.1643   (branch= 0.0008  alpha= 0.0078  pinv= 0.0079  eq freqs= 0.0001  rel rates= 0.0450  ins/del rates= 0.0003)
pass 14: -3318.1116   (branch= 0.0005  alpha= 0.0072  pinv= 0.0072  eq freqs= 0.0001  rel rates= 0.0374  ins/del rates= 0.0002)
pass 15: -3318.0670   (branch= 0.0003  alpha= 0.0068  pinv= 0.0065  eq freqs= 0.0001  rel rates= 0.0307  ins/del rates= 0.0001)
pass 16: -3318.0292   (branch= 0.0002  alpha= 0.0061  pinv= 0.0059  eq freqs= 0.0001  rel rates= 0.0254  ins/del rates= 0.0001)
pass 17: -3317.9966   (branch= 0.0001  alpha= 0.0056  pinv= 0.0053  eq freqs= 0.0001  rel rates= 0.0215  ins/del rates= 0.0000)
pass 18: -3317.9685   (branch= 0.0001  alpha= 0.0050  pinv= 0.0047  eq freqs= 0.0000  rel rates= 0.0182  ins/del rates= 0.0000)
pass 19: -3317.9442   (branch= 0.0001  alpha= 0.0045  pinv= 0.0042  eq freqs= 0.0000  rel rates= 0.0155  ins/del rates= 0.0000)
pass 20: -3317.9231   (branch= 0.0000  alpha= 0.0040  pinv= 0.0037  eq freqs= 0.0000  rel rates= 0.0132  ins/del rates= 0.0000)
 optimization up to ...
pass 30: -3317.8190   (branch= 0.0001  alpha= 0.0217  pinv= 0.0200  eq freqs= 0.0001  rel rates= 0.0622  ins/del rates= 0.0000)
 optimization up to ...
pass 40: -3317.7943   (branch= 0.0001  alpha= 0.0054  pinv= 0.0050  eq freqs= 0.0000  rel rates= 0.0142  ins/del rates= 0.0000)
 optimization up to ...
pass 50: -3317.7887   (branch= 0.0000  alpha= 0.0012  pinv= 0.0010  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 74: -3317.7871   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000  ins/del rates= 0.0000)
Looking for minimum length branches...
Final score = -3317.7871
Time used so far = 0 hours, 0 minutes and 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 = 3.066, AG = 10.265, AT = 2.655, CG = 0.001, CT = 21.537, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.3328 0.2223 0.1567 0.2882 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5751
    with an invariant (invariable) site category, proportion estimated
      0.3614
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.3614
      0.0480	0.1596
      0.2981	0.1596
      0.8680	0.1596
      2.7858	0.1596

Model 2
  Number of states = 2 (0/1 coding of gaps)
  Character change matrix: irreversible matrix
    deletion rate parameter only estimated if using a partitioned
    model without subset rates
    deletion rate = 0.158
  Equilibrium State Frequencies: proportion of inserted sites parameter
    insert proportion = 0.036
  Rate Heterogeneity Model:
    no rate heterogeneity

NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    No branches were short enough to be collapsed.

>>>Terminated Search rep 1 (of 2)<<<

NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 1 replicate search(es) (of 2).
Results:
Replicate 1 : -3317.7871 (best) (TERMINATED PREMATURELY) 

Parameter estimates across search replicates:

Partition model subset 1:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
rep 1:   3.066  10.26  2.655  0.001  21.54      1 0.333 0.222 0.157 0.288 0.575 0.361

Partition model subset 2:
          ins   del
rep 1:  0.036 0.158
	 **ins = proportion of columns that experienced an insertion
	 **del = deletion rate relative to nucleotide substitution rate

Treelengths:
          TL 
rep 1:  1.418

Saving final tree from best search rep (#1) to ch.g.dnaMix.best.tre
#######################################################
TREEFILES PASS
Running checkpoint test ./check/n.G3.conf
Running checkpoint test ./check/n.G3.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./check/n.G3.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  11 sequences.
	  11 constant characters.
	  17 parsimony-informative characters.
	  2 uninformative variable characters.
	  30 total characters.
	  25 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.3 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1

#######################################################
STARTING RUN
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2310 0.3201 0.1881 0.2607 
  Rate Heterogeneity Model:
    3 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.0917
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0917
      0.0603	0.3028
      0.4894	0.3028
      2.4503	0.3028

Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 0.004 lnL
Optimizing branchlengths... improved 0.000 lnL
 7  8  9  10  11 
Initial ln Likelihood: -226.8217
optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs...
pass 1:+    3.951 (branch=   0.75 scale=  0.00 alpha=  0.00 freqs=  1.76 rel rates=  1.44 pinv=  0.00)
pass 2:+    0.586 (branch=   0.56 scale=  0.00 alpha=  0.00 freqs=  0.03 rel rates=  0.00 pinv=  0.00)
pass 3:+    1.297 (branch=   0.66 scale=  0.00 alpha=  0.00 freqs=  0.03 rel rates=  0.61 pinv=  0.00)
pass 4:+    0.021 (branch=   0.00 scale=  0.00 alpha=  0.00 freqs=  0.02 rel rates=  0.00 pinv=  0.00)
lnL after optimization: -220.9660
gen      current_lnL    precision  last_tree_imp  
0        -220.9660        0.500           0 
200      -214.6292        0.500         192 
400      -213.8826        0.500         231 
600      -213.2669        0.500         572 
800      -213.0149        0.500         572 
1000     -212.8168        0.500         572 
Optimization precision reduced 
   Optimizing parameters...    improved    1.264 lnL
   Optimizing branchlengths... improved    0.275 lnL
1200     -211.1653        0.010        1104 
1400     -211.1319        0.010        1104 
1600     -211.0218        0.010        1104 
1800     -210.9997        0.010        1104 
2000     -210.9460        0.010        1104 
2200     -210.8946        0.010        1104 
2400     -210.8863        0.010        1104 
2600     -210.8436        0.010        1104 
2800     -210.8250        0.010        1104 
3000     -210.8188        0.010        1104 
3200     -210.7905        0.010        1104 
3400     -210.7553        0.010        1104 
3600     -210.7287        0.010        1104 
NOTE: ****Specified time limit (5 seconds) reached...

NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
(set restart = 1 in the config file).  IF YOU WANT TO USE THE
PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
ADD "end;" TO THE TREE FILES.

Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./restart/n.G3.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  11 sequences.
	  11 constant characters.
	  17 parsimony-informative characters.
	  2 uninformative variable characters.
	  30 total characters.
	  25 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.3 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1

#######################################################
STARTING RUN

Restarting from checkpoint...
 generation 3766, seed 1263385291, best lnL -210.709
gen      current_lnL    precision  last_tree_imp  
3766     -210.7094        0.010        1104 
3800     -210.7083        0.010        1104 
3900     -210.7020        0.010        1104 
4000     -210.6946        0.010        1104 
Reached termination condition!
last topological improvement at gen 1104
Improvement over last 500 gen = 0.03869

MODEL REPORT - Parameter values are FINAL
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 2.570, AG = 4.854, AT = 0.222, CG = 4.460, CT = 6.971, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2329 0.3364 0.2106 0.2201 
  Rate Heterogeneity Model:
    3 discrete gamma distributed rate categories, alpha param estimated
      1.1902
    with an invariant (invariable) site category, proportion estimated
      0.1105
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.1105
      0.2293	0.2965
      0.7543	0.2965
      2.0164	0.2965

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.G3.sitelikes.log ...

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -210.6946       

Parameter estimates:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
rep 1:    2.57  4.854 0.2216   4.46  6.971      1 0.233 0.336 0.211 0.220 1.190 0.110

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 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./check/n.G4.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  11 sequences.
	  11 constant characters.
	  17 parsimony-informative characters.
	  2 uninformative variable characters.
	  30 total characters.
	  25 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.4 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1

#######################################################
STARTING RUN

Bootstrap reweighting...
	Subset 1: Random seed for bootstrap reweighting: 42

>>>Bootstrap rep 1 (of 1) <<<
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2310 0.3201 0.1881 0.2607 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.0917
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0917
      0.0334	0.2271
      0.2519	0.2271
      0.8203	0.2271
      2.8944	0.2271

Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 0.004 lnL
Optimizing branchlengths... improved 0.786 lnL
 7  8  9  10  11 
Initial ln Likelihood: -178.2162
optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs...
pass 1:+    5.336 (branch=   0.56 scale=  1.69 alpha=  0.00 freqs=  1.38 rel rates=  1.70 pinv=  0.00)
pass 2:+    0.075 (branch=   0.04 scale=  0.00 alpha=  0.00 freqs=  0.03 rel rates=  0.00 pinv=  0.00)
lnL after optimization: -172.8046
gen      current_lnL    precision  last_tree_imp  
0        -172.8046        0.500           0 
200      -171.4789        0.500         172 
400      -170.7806        0.500         296 
600      -170.2707        0.500         296 
800      -169.9099        0.500         296 
Optimization precision reduced 
   Optimizing parameters...    improved    2.192 lnL
   Optimizing branchlengths... improved    0.320 lnL
1000     -167.2068        0.010         843 
1200     -167.1476        0.010         843 
1400     -167.0487        0.010         843 
1600     -166.9641        0.010         843 
1800     -166.8222        0.010         843 
2000     -166.6788        0.010         843 
2200     -166.5887        0.010         843 
2400     -166.4579        0.010         843 
2600     -166.3862        0.010         843 
2800     -166.3657        0.010         843 
3000     -166.3070        0.010         843 
3200     -166.2787        0.010         843 
3400     -166.2099        0.010         843 
3600     -166.0618        0.010         843 
3800     -165.9521        0.010         843 
4000     -165.9340        0.010         843 
4200     -165.8876        0.010         843 
4400     -165.8800        0.010         843 
NOTE: ****Specified time limit (5 seconds) reached...

NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
(set restart = 1 in the config file).  IF YOU WANT TO USE THE
PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
ADD "end;" TO THE TREE FILES.

Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./restart/n.G4.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  11 sequences.
	  11 constant characters.
	  17 parsimony-informative characters.
	  2 uninformative variable characters.
	  30 total characters.
	  25 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.4 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1

#######################################################
STARTING RUN
	Subset 1: Random seed for bootstrap reweighting: 42

Restarting from checkpoint...
Bootstrap rep 1 (of 1)  generation 4471, seed 234127599, best lnL -165.855
gen      current_lnL    precision  last_tree_imp  
4471     -165.8546        0.010         843 
4500     -165.8545        0.010         843 
4600     -165.7809        0.010         843 
4700     -165.7799        0.010         843 
4800     -165.7682        0.010         843 
4900     -165.6827        0.010         843 
5000     -165.6807        0.010         843 
5100     -165.6632        0.010         843 
5200     -165.6629        0.010         843 
5300     -165.6249        0.010         843 
5400     -165.5966        0.010         843 
5500     -165.5256        0.010         843 
5600     -165.4767        0.010         843 
5700     -165.4334        0.010         843 
5800     -165.3754        0.010         843 
5900     -165.3476        0.010         843 
6000     -165.2856        0.010         843 
6100     -165.2630        0.010        6021 
6200     -165.2442        0.010        6021 
6300     -165.1487        0.010        6021 
6400     -165.1354        0.010        6021 
6500     -165.1254        0.010        6021 
6600     -165.0479        0.010        6021 
6700     -165.0438        0.010        6021 
6800     -165.0428        0.010        6021 
6900     -164.8438        0.010        6021 
7000     -164.8383        0.010        6021 
7100     -164.7890        0.010        6021 
7200     -164.6664        0.010        6021 
7300     -164.6617        0.010        6021 
7400     -164.6478        0.010        6021 
7500     -164.6472        0.010        6021 
7600     -164.5352        0.010        7573 
7700     -164.4035        0.010        7573 
7800     -164.3902        0.010        7573 
7900     -164.3595        0.010        7573 
8000     -164.3323        0.010        7573 
8100     -164.1711        0.010        7573 
8200     -164.1537        0.010        7573 
8300     -164.0538        0.010        7573 
8400     -164.0465        0.010        7573 
8500     -164.0049        0.010        7573 
8600     -163.9411        0.010        7573 
8700     -163.8406        0.010        7573 
8800     -163.8133        0.010        7573 
8900     -163.8024        0.010        7573 
9000     -163.7249        0.010        7573 
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 = 0.785, AG = 10.958, AT = 2.211, CG = 4.183, CT = 36.394, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.1255 0.4233 0.2365 0.2147 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      3.0988
    with an invariant (invariable) site category, proportion estimated
      0.3385
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.3385
      0.3968	0.1654
      0.7369	0.1654
      1.0830	0.1654
      1.7834	0.1654

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 : -163.7242        (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:  0.7848  10.96  2.211  4.183  36.39      1 0.126 0.423 0.236 0.215 3.099 0.338

Treelengths:
          TL 
rep 1:  3.159

Saving best tree to bootstrap file ch.n.G4.boot.tre

WARNING: Tree from prematurely terminated search saved to bootstrap file
#######################################################
TREEFILES PASS
Running checkpoint test ./check/n.conf
Running checkpoint test ./check/n.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./check/n.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  11 sequences.
	  11 constant characters.
	  17 parsimony-informative characters.
	  2 uninformative variable characters.
	  30 total characters.
	  25 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.1 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1

#######################################################
STARTING RUN
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2310 0.3201 0.1881 0.2607 
  Rate Heterogeneity Model:
    no rate heterogeneity

Starting with seed=1

creating likelihood stepwise addition starting tree...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 0.000 lnL
Optimizing branchlengths... improved 3.458 lnL
 7  8  9  10  11 
Initial ln Likelihood: -225.5327
optimizing: starting branch lengths, rel rates, eq freqs...
pass 1:+    7.466 (branch=   0.77 scale=  0.00 freqs=  0.02 rel rates=  6.68)
pass 2:+    0.468 (branch=   0.45 scale=  0.00 freqs=  0.02 rel rates=  0.00)
lnL after optimization: -217.5990
gen      current_lnL    precision  last_tree_imp  
0        -217.5990        0.500           0 
200      -215.8307        0.500         188 
400      -214.8938        0.500         276 
600      -214.3966        0.500         530 
800      -214.1704        0.500         530 
1000     -214.0528        0.500         530 
Optimization precision reduced 
   Optimizing parameters...    improved    0.223 lnL
   Optimizing branchlengths... improved    0.080 lnL
1200     -213.6191        0.010         530 
1400     -213.5800        0.010         530 
1600     -213.5575        0.010         530 
1800     -213.3951        0.010         530 
2000     -213.3646        0.010         530 
2200     -213.3318        0.010         530 
2400     -213.2446        0.010         530 
2600     -213.2282        0.010         530 
2800     -213.2194        0.010         530 
3000     -213.2002        0.010         530 
3200     -213.1946        0.010         530 
3400     -213.1682        0.010         530 
3600     -213.1582        0.010         530 
3800     -213.0252        0.010        3769 
4000     -212.9704        0.010        3769 
4200     -212.9483        0.010        3769 
4400     -212.9234        0.010        3769 
4600     -212.8794        0.010        3769 
4800     -212.8766        0.010        3769 
5000     -212.8761        0.010        3769 
5200     -212.8556        0.010        3769 
5400     -212.8534        0.010        3769 
5600     -212.8186        0.010        3769 
5800     -212.7686        0.010        3769 
6000     -212.7264        0.010        3769 
6200     -212.7248        0.010        3769 
6400     -212.7245        0.010        3769 
6600     -212.7155        0.010        3769 
6800     -212.7057        0.010        3769 
7000     -212.7025        0.010        3769 
7200     -212.7020        0.010        3769 
7400     -212.6750        0.010        3769 
NOTE: ****Specified time limit (5 seconds) reached...

NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
(set restart = 1 in the config file).  IF YOU WANT TO USE THE
PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
ADD "end;" TO THE TREE FILES.

Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./restart/n.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  11 sequences.
	  11 constant characters.
	  17 parsimony-informative characters.
	  2 uninformative variable characters.
	  30 total characters.
	  25 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.1 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1

#######################################################
STARTING RUN

Restarting from checkpoint...
 generation 7598, seed 440755700, best lnL -212.670
gen      current_lnL    precision  last_tree_imp  
7598     -212.6702        0.010        3769 
7600     -212.6702        0.010        3769 
Reached termination condition!
last topological improvement at gen 3769
Improvement over last 500 gen = 0.03227

MODEL REPORT - Parameter values are FINAL
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 5.420, AG = 10.376, AT = 0.430, CG = 10.468, CT = 6.838, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2205 0.2887 0.1831 0.3078 
  Rate Heterogeneity Model:
    no rate heterogeneity

NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    1 branches were collapsed.

Saving site likelihoods to file ch.n.sitelikes.log ...

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -212.6702       

Parameter estimates:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T)
rep 1:    5.42  10.38 0.4295  10.47  6.838      1 0.220 0.289 0.183 0.308

Treelengths:
          TL 
rep 1:  1.728

Saving final tree from best search rep (#1) to ch.n.best.tre
Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log

#######################################################
TREEFILES PASS
Running checkpoint test ./check/n.const.conf
Running checkpoint test ./check/n.const.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./check/n.const.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  11 sequences.
	  11 constant characters.
	  17 parsimony-informative characters.
	  2 uninformative variable characters.
	  30 total characters.
	  25 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.4 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1

#######################################################
Loading constraints from file data/z.pos.const.tre
Found 6 positively constrained bipartition(s)
     Bipartition 1: (1,2,3,5,6,7,8,9,10) | (4,11)
     Bipartition 2: (1,3,5,6,7,8,9,10) | (2,4,11)
     Bipartition 3: (1,5,6,7,8,9,10) | (2,3,4,11)
     Bipartition 4: (1,2,3,4,5,8,9,10,11) | (6,7)
     Bipartition 5: (1,2,3,4,5,8,9,11) | (6,7,10)
     Bipartition 6: (1,5) | (2,3,4,6,7,8,9,10,11)
STARTING RUN
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 1.000, AG = 4.000, AT = 1.000, CG = 1.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2310 0.3201 0.1881 0.2607 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.0917
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0917
      0.0334	0.2271
      0.2519	0.2271
      0.8203	0.2271
      2.8944	0.2271

Starting with seed=1

creating likelihood stepwise addition starting tree (compatible with constraints)...
number of taxa added:
 4  5  6 
Optimizing parameters... improved 0.006 lnL
Optimizing branchlengths... improved 11.173 lnL
 7  8  9  10  11 
Initial ln Likelihood: -225.0726
optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs...
pass 1:+    5.893 (branch=   2.29 scale=  0.89 alpha=  0.00 freqs=  1.20 rel rates=  1.50 pinv=  0.00)
pass 2:+    0.035 (branch=   0.00 scale=  0.00 alpha=  0.00 freqs=  0.03 rel rates=  0.00 pinv=  0.00)
lnL after optimization: -219.1445
gen      current_lnL    precision  last_tree_imp  
0        -219.1445        0.500           0 
200      -217.4629        0.500          32 
400      -216.6525        0.500         363 
600      -216.1293        0.500         474 
800      -215.4112        0.500         669 
1000     -215.0098        0.500         936 
1200     -214.3654        0.500         936 
1400     -214.0189        0.500         936 
Optimization precision reduced 
   Optimizing parameters...    improved    1.908 lnL
   Optimizing branchlengths... improved    0.702 lnL
1600     -211.2006        0.010        1502 
1800     -211.0868        0.010        1502 
2000     -210.9688        0.010        1502 
2200     -210.8961        0.010        1502 
2400     -210.8906        0.010        1502 
2600     -210.8173        0.010        1502 
2800     -210.7848        0.010        1502 
3000     -210.7511        0.010        2883 
3200     -210.7243        0.010        2883 
3400     -210.7006        0.010        2883 
3600     -210.6993        0.010        2883 
3800     -210.6779        0.010        2883 
4000     -210.6776        0.010        2883 
4200     -210.6505        0.010        2883 
4400     -210.6306        0.010        2883 
4600     -210.6208        0.010        2883 
4800     -210.5769        0.010        2883 
5000     -210.5647        0.010        2883 
5200     -210.5368        0.010        2883 
NOTE: ****Specified time limit (5 seconds) reached...

NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
(set restart = 1 in the config file).  IF YOU WANT TO USE THE
PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
ADD "end;" TO THE TREE FILES.

Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./restart/n.const.conf
###################################################
READING OF DATA
Attempting to read data file data/z.11x30.phy as
	relaxed Phylip DNA format (using NCL) ...
storing implied block: TAXA
storing read block: DATA

Data read successfully.

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Summary of data:
	  11 sequences.
	  11 constant characters.
	  17 parsimony-informative characters.
	  2 uninformative variable characters.
	  30 total characters.
	  25 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.4 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Found outgroup specification:  1

#######################################################
Loading constraints from file data/z.pos.const.tre
Found 6 positively constrained bipartition(s)
     Bipartition 1: (1,2,3,5,6,7,8,9,10) | (4,11)
     Bipartition 2: (1,3,5,6,7,8,9,10) | (2,4,11)
     Bipartition 3: (1,5,6,7,8,9,10) | (2,3,4,11)
     Bipartition 4: (1,2,3,4,5,8,9,10,11) | (6,7)
     Bipartition 5: (1,2,3,4,5,8,9,11) | (6,7,10)
     Bipartition 6: (1,5) | (2,3,4,6,7,8,9,10,11)
STARTING RUN

Restarting from checkpoint...
 generation 5329, seed 612164611, best lnL -210.512
gen      current_lnL    precision  last_tree_imp  
5329     -210.5122        0.010        2883 
5400     -210.5093        0.010        2883 
5500     -210.5012        0.010        2883 
5600     -210.4832        0.010        2883 
5700     -210.4040        0.010        2883 
5800     -210.3736        0.010        2883 
5900     -210.3639        0.010        2883 
6000     -210.3408        0.010        2883 
6100     -210.3320        0.010        2883 
6200     -210.3319        0.010        2883 
6300     -210.3311        0.010        2883 
Reached termination condition!
last topological improvement at gen 2883
Improvement over last 500 gen = 0.04248

MODEL REPORT - Parameter values are FINAL
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix:     6 rates 
    AC = 2.168, AG = 4.001, AT = 0.207, CG = 3.857, CT = 7.381, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2427 0.3358 0.2126 0.2089 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      1.4302
    with an invariant (invariable) site category, proportion estimated
      0.1984
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.1984
      0.2143	0.2004
      0.5765	0.2004
      1.0460	0.2004
      2.1631	0.2004

NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    No branches were short enough to be collapsed.


NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with
	a positive constraint, it is possible for a constrained branch itself to be collapsed.
	If you care, be careful to check whether this has happened or turn off branch collapsing.

Saving site likelihoods to file ch.n.const.sitelikes.log ...

#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -210.3311       

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:   2.168  4.001 0.2071  3.857  7.381      1 0.243 0.336 0.213 0.209 1.430 0.198

Treelengths:
          TL 
rep 1:  2.397

Saving final tree from best search rep (#1) to ch.n.const.best.tre
Inferring internal state probabilities on best tree... saving to file ch.n.const.internalstates.log

#######################################################
TREEFILES PASS
Running checkpoint test ./check/p.3diff.conf
Running checkpoint test ./check/p.3diff.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./check/p.3diff.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/z.byPos.11x2178.nex ...
Reading DATA block...storing implied block: TAXA
storing read block: DATA
 successful
Reading SETS block...storing read block: SETS
 successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS

CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY
	TO EACH DATA SUBSET (no linkage)

GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	CHARPARTITION subset #1 ("1stpos")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Excluded character numbers: 4
	
	Summary of data:
	  11 sequences.
	  441 constant characters.
	  171 parsimony-informative characters.
	  113 uninformative variable characters.
	  725 total characters.
	  237 unique patterns in compressed data matrix.
GARLI data subset 2
	CHARACTERS block #1 ("Untitled DATA Block 1")
	CHARPARTITION subset #2 ("2ndpos")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Excluded character numbers: 5
	
	Summary of data:
	  11 sequences.
	  527 constant characters.
	  90 parsimony-informative characters.
	  108 uninformative variable characters.
	  725 total characters.
	  158 unique patterns in compressed data matrix.
GARLI data subset 3
	CHARACTERS block #1 ("Untitled DATA Block 1")
	CHARPARTITION subset #3 ("3rdpos")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Excluded character numbers: 6
	
	Summary of data:
	  11 sequences.
	  102 constant characters.
	  507 parsimony-informative characters.
	  116 uninformative variable characters.
	  725 total characters.
	  548 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 11 MB
  good			approx 10 MB to 9 MB
  low			approx 8 MB to 5 MB
  very low		approx 4 MB to 4 MB
the minimum required availablememory is 4 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 16.0 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Loading starting model and/or tree from file data/p.3diff.start
Reading TREES block...storing read block: TREES
 successful
Reading GARLI block...storing read block: GARLI
 successful
STARTING RUN

Bootstrap reweighting...
	Subset 1: Random seed for bootstrap reweighting: 42
	Subset 2: Random seed for bootstrap reweighting: 655766889
	Subset 3: Random seed for bootstrap reweighting: 486988955

>>>Bootstrap rep 1 (of 1) <<<
Obtained starting tree 1 from Nexus
Obtained starting or fixed model parameter values from Nexus:
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix: 
    User specified matrix type: ( 0 1 2 2 3 4 ) 
    AC = 1.000, AG = 10.000, AT = 2.000, CG = 2.000, CT = 0.010, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.3150 0.1749 0.3006 0.2095 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.6000
    Substitution rate categories under this model:
      rate	proportion
      0.0531	0.2500
      0.3123	0.2500
      0.8813	0.2500
      2.7533	0.2500

Model 2
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix: 
    User specified matrix type: ( 0 1 2 1 0 3 ) 
    AC = 4.000, AG = 4.000, AT = 1.000, CG = 4.000, CT = 4.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.1000 0.2000 0.3000 0.4000 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.4000
    Substitution rate categories under this model:
      rate	proportion
      0.0167	0.2500
      0.1818	0.2500
      0.7313	0.2500
      3.0702	0.2500

Model 3
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix: 
    User specified matrix type: ( 0 1 2 3 1 0 ) 
    AC = 1.000, AG = 2.000, AT = 3.000, CG = 5.000, CT = 2.000, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.4000 0.2000 0.3000 0.1000 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.5000
    with an invariant (invariable) site category, proportion estimated
      0.0100
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0100
      0.0334	0.2475
      0.2519	0.2475
      0.8203	0.2475
      2.8944	0.2475

Subset rate multipliers:
    0.54  0.30  2.16
Starting with seed=1

Initial ln Likelihood: -17331.1409
optimizing: starting branch lengths, alpha shape, prop. invar, rel rates, eq freqs, subset rates...
pass 1:+ 3336.674 (branch=2061.91 scale= 45.13 alpha=125.85 freqs=435.78 rel rates=661.66 pinv=  0.00 subset rates=  6.34)
pass 2:+  338.355 (branch=  41.98 scale=  1.04 alpha= 22.50 freqs=192.29 rel rates= 77.24 pinv=  2.39 subset rates=  0.92)
pass 3:+  222.683 (branch=   0.46 scale=  0.67 alpha=  8.57 freqs= 98.23 rel rates=113.31 pinv=  0.80 subset rates=  0.64)
pass 4:+   44.580 (branch=   0.51 scale=  0.00 alpha=  1.57 freqs= 22.89 rel rates= 19.62 pinv=  0.00 subset rates=  0.00)
pass 5:+    8.682 (branch=   0.00 scale=  0.00 alpha=  0.01 freqs=  4.12 rel rates=  4.53 pinv=  0.02 subset rates=  0.00)
pass 6:+    1.298 (branch=   0.59 scale=  0.00 alpha=  0.01 freqs=  0.65 rel rates=  0.01 pinv=  0.03 subset rates=  0.00)
pass 7:+    1.354 (branch=   0.00 scale=  0.49 alpha=  0.72 freqs=  0.12 rel rates=  0.02 pinv=  0.01 subset rates=  0.00)
pass 8:+    0.126 (branch=   0.00 scale=  0.00 alpha=  0.01 freqs=  0.09 rel rates=  0.02 pinv=  0.01 subset rates=  0.00)
lnL after optimization: -13377.3893
gen      current_lnL    precision  last_tree_imp  
0        -13377.3893      0.500           0 
100      -13375.8793      0.500           0 
200      -13373.8435      0.500           0 
300      -13372.9677      0.500           0 
400      -13371.8985      0.500           0 
500      -13371.5864      0.500           0 
Optimization precision reduced 
   Optimizing parameters...    improved    0.048 lnL
   Optimizing branchlengths... improved    0.000 lnL
NOTE: ****Specified time limit (5 seconds) reached...

NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
(set restart = 1 in the config file).  IF YOU WANT TO USE THE
PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
ADD "end;" TO THE TREE FILES.

Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./restart/p.3diff.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/z.byPos.11x2178.nex ...
Reading DATA block...storing implied block: TAXA
storing read block: DATA
 successful
Reading SETS block...storing read block: SETS
 successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS

CHECK: DIFFERENT MODEL TYPES AND MODEL PARAMETERS APPLY
	TO EACH DATA SUBSET (no linkage)

GARLI data subset 1
	CHARACTERS block #1 ("Untitled DATA Block 1")
	CHARPARTITION subset #1 ("1stpos")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Excluded character numbers: 4
	
	Summary of data:
	  11 sequences.
	  441 constant characters.
	  171 parsimony-informative characters.
	  113 uninformative variable characters.
	  725 total characters.
	  237 unique patterns in compressed data matrix.
GARLI data subset 2
	CHARACTERS block #1 ("Untitled DATA Block 1")
	CHARPARTITION subset #2 ("2ndpos")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Excluded character numbers: 5
	
	Summary of data:
	  11 sequences.
	  527 constant characters.
	  90 parsimony-informative characters.
	  108 uninformative variable characters.
	  725 total characters.
	  158 unique patterns in compressed data matrix.
GARLI data subset 3
	CHARACTERS block #1 ("Untitled DATA Block 1")
	CHARPARTITION subset #3 ("3rdpos")
	Data read as Nucleotide data,
	modeled as Nucleotide data
	Excluded character numbers: 6
	
	Summary of data:
	  11 sequences.
	  102 constant characters.
	  507 parsimony-informative characters.
	  116 uninformative variable characters.
	  725 total characters.
	  548 unique patterns in compressed data matrix.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 11 MB
  good			approx 10 MB to 9 MB
  low			approx 8 MB to 5 MB
  very low		approx 4 MB to 4 MB
the minimum required availablememory is 4 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 16.0 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Loading starting model and/or tree from file data/p.3diff.start
Reading TREES block...storing read block: TREES
 successful
Reading GARLI block...storing read block: GARLI
 successful
STARTING RUN
	Subset 1: Random seed for bootstrap reweighting: 42
	Subset 2: Random seed for bootstrap reweighting: 655766889
	Subset 3: Random seed for bootstrap reweighting: 486988955

Restarting from checkpoint...
Bootstrap rep 1 (of 1)  generation 532, seed 1053527202, best lnL -13371.442
gen      current_lnL    precision  last_tree_imp  
532      -13371.4417      0.402           0 
600      -13371.2064      0.402           0 
700      -13371.0754      0.402           0 
800      -13370.9489      0.402           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 = 1.413, AG = 2.328, AT = 1.077, CG = 1.077, CT = 3.707, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.3111 0.1852 0.3053 0.1984 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.3534
    Substitution rate categories under this model:
      rate	proportion
      0.0106	0.2500
      0.1462	0.2500
      0.6755	0.2500
      3.1677	0.2500

Model 2
  Number of states = 4 (nucleotide data)
  Nucleotide Relative Rate Matrix: 
    User specified matrix type: ( 0 1 2 1 0 3 ) 
    AC = 2.627, AG = 4.236, AT = 0.821, CG = 4.236, CT = 2.627, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.2812 0.1777 0.1599 0.3811 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      0.2463
    Substitution rate categories under this model:
      rate	proportion
      0.0019	0.2500
      0.0640	0.2500
      0.4936	0.2500
      3.4404	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 = 5.382, AT = 4.420, CG = 0.634, CT = 5.382, GT = 1.000
  Equilibrium State Frequencies: estimated
    (ACGT) 0.1554 0.3450 0.2777 0.2219 
  Rate Heterogeneity Model:
    4 discrete gamma distributed rate categories, alpha param estimated
      4.1086
    with an invariant (invariable) site category, proportion estimated
      0.0475
    Substitution rate categories under this model:
      rate	proportion
      0.0000	0.0475
      0.4602	0.2381
      0.7789	0.2381
      1.0844	0.2381
      1.6765	0.2381

Subset rate multipliers:
    0.53  0.29  2.18
NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    No branches were short enough to be collapsed.

>>>Terminated Bootstrap rep 1 (of 1) <<<

NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 1 replicate search(es) (of 1).
Results:
Replicate 1 : -13370.9488        (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:   1.413  2.328  1.077  1.077  3.707      1 0.311 0.185 0.305 0.198 0.353

Partition model subset 2:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha
rep 1:   2.627  4.236 0.8209  4.236  2.627      1 0.281 0.178 0.160 0.381 0.246

Partition model subset 3:
         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
rep 1:       1  5.382   4.42 0.6343  5.382      1 0.155 0.345 0.278 0.222 4.109 0.047

Treelengths and subset rate multipliers:
          TL   R(1)  R(2)  R(3)
rep 1:  1.772 0.530 0.285 2.185

Saving best tree to bootstrap file ch.p.3diff.boot.tre

WARNING: Tree from prematurely terminated search saved to bootstrap file
#######################################################
TREEFILES PASS
Running checkpoint test ./check/p.mk.ssr.conf
Running checkpoint test ./check/p.mk.ssr.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./check/p.mk.ssr.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard k-state data,
	modeled as Standard k-state data
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.5 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN

>>>Search rep 1 (of 5)<<<
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=1

Initial ln Likelihood: -609.1934
optimizing: starting branch lengths, subset rates...
pass 1:+  130.207 (branch= 124.97 scale=  0.94 subset rates=  4.29)
pass 2:+    9.055 (branch=   8.14 scale=  0.00 subset rates=  0.91)
pass 3:+    1.801 (branch=   1.66 scale=  0.02 subset rates=  0.12)
pass 4:+    0.304 (branch=   0.30 scale=  0.00 subset rates=  0.00)
pass 5:+    0.012 (branch=   0.01 scale=  0.00 subset rates=  0.00)
pass 6:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
lnL after optimization: -467.8138
gen      current_lnL    precision  last_tree_imp  
0        -467.8138        0.010           0 
100      -467.7847        0.010          76 
200      -467.7757        0.010          76 
300      -467.7641        0.010          76 
400      -467.7601        0.010          76 
500      -467.7562        0.010          76 
600      -467.7484        0.010          76 
700      -467.7453        0.010          76 
800      -467.7426        0.010          76 
900      -467.7420        0.010          76 
1000     -467.7408        0.010          76 
1100     -467.7395        0.010          76 
1200     -467.7384        0.010          76 
1300     -467.7383        0.010          76 
1400     -467.7371        0.010          76 
1500     -467.7350        0.010          76 
1600     -467.7322        0.010          76 
1700     -467.7288        0.010          76 
1800     -467.7270        0.010          76 
1900     -467.7270        0.010          76 
2000     -467.7247        0.010          76 
2100     -467.7240        0.010          76 
2200     -467.7237        0.010          76 
2300     -467.7235        0.010          76 
2400     -467.7217        0.010          76 
2500     -467.7212        0.010          76 
2600     -467.7209        0.010          76 
2700     -467.7204        0.010          76 
2800     -467.7202        0.010          76 
2900     -467.7200        0.010          76 
3000     -467.7200        0.010          76 
3100     -467.7184        0.010          76 
3200     -467.7183        0.010          76 
3300     -467.7165        0.010          76 
3400     -467.7165        0.010          76 
NOTE: ****Specified time limit (5 seconds) reached...

NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
(set restart = 1 in the config file).  IF YOU WANT TO USE THE
PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
ADD "end;" TO THE TREE FILES.

Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./restart/p.mk.ssr.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard k-state data,
	modeled as Standard k-state data
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.5 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN

Restarting from checkpoint...
Search rep 1 (of 5) generation 3461, seed 271493482, best lnL -467.716
gen      current_lnL    precision  last_tree_imp  
3461     -467.7164        0.010          76 
3500     -467.7162        0.010          76 
3600     -467.7160        0.010          76 
3700     -467.7160        0.010          76 
3800     -467.7159        0.010          76 
Reached termination condition!
last topological improvement at gen 76
Improvement over last 500 gen = 0.00059
Current score = -467.7159
Performing final optimizations...
pass 1 : -467.7120   (branch= 0.0000  subset rates= 0.0039)
pass 2 : -467.6911   (branch= 0.0209  subset rates= 0.0000)
pass 3 : -467.6869   (branch= 0.0042  subset rates= 0.0000)
pass 4 : -467.6843   (branch= 0.0026  subset rates= 0.0000)
pass 5 : -467.6817   (branch= 0.0026  subset rates= 0.0000)
pass 6 : -467.6803   (branch= 0.0014  subset rates= 0.0000)
pass 7 : -467.6795   (branch= 0.0007  subset rates= 0.0001)
pass 8 : -467.6788   (branch= 0.0007  subset rates= 0.0000)
pass 9 : -467.6786   (branch= 0.0002  subset rates= 0.0000)
pass 10: -467.6784   (branch= 0.0002  subset rates= 0.0000)
pass 11: -467.6783   (branch= 0.0001  subset rates= 0.0000)
pass 12: -467.6783   (branch= 0.0000  subset rates= 0.0000)
pass 13: -467.6783   (branch= 0.0000  subset rates= 0.0000)
pass 14: -467.6783   (branch= 0.0000  subset rates= 0.0000)
Looking for minimum length branches...
Final score = -467.6782
Time used so far = 0 hours, 0 minutes and 6 seconds

MODEL REPORT - Parameter values are FINAL
Model 1
  Number of states = 2 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    0.79  1.48  2.18
NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    8 branches were collapsed.

>>>Completed Search rep 1 (of 5)<<<

>>>Search rep 2 (of 5)<<<
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=1831048457

Initial ln Likelihood: -637.1584
optimizing: starting branch lengths, subset rates...
pass 1:+  151.120 (branch= 144.13 scale=  2.32 subset rates=  4.67)
pass 2:+   14.959 (branch=  13.95 scale=  0.00 subset rates=  1.01)
pass 3:+    2.985 (branch=   2.78 scale=  0.01 subset rates=  0.19)
pass 4:+    0.213 (branch=   0.21 scale=  0.00 subset rates=  0.00)
pass 5:+    0.015 (branch=   0.02 scale=  0.00 subset rates=  0.00)
pass 6:+    0.025 (branch=   0.03 scale=  0.00 subset rates=  0.00)
pass 7:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
lnL after optimization: -467.8409
gen      current_lnL    precision  last_tree_imp  
0        -467.8409        0.010           0 
100      -467.8006        0.010          88 
200      -467.7829        0.010          88 
300      -467.7645        0.010          88 
400      -467.7572        0.010          88 
500      -467.7508        0.010          88 
600      -467.7420        0.010          88 
700      -467.7377        0.010          88 
800      -467.7326        0.010          88 
900      -467.7300        0.010          88 
1000     -467.7251        0.010          88 
1100     -467.7186        0.010          88 
1200     -467.7174        0.010          88 
1300     -467.7143        0.010          88 
1400     -467.7139        0.010          88 
1500     -467.7130        0.010          88 
1600     -467.7128        0.010          88 
1700     -467.7101        0.010          88 
1800     -467.7076        0.010          88 
1900     -467.7072        0.010          88 
2000     -467.7065        0.010          88 
2100     -467.7061        0.010          88 
2200     -467.7057        0.010          88 
2300     -467.7052        0.010          88 
2400     -467.7043        0.010          88 
2500     -467.7039        0.010          88 
2600     -467.7039        0.010          88 
2700     -467.7038        0.010          88 
2800     -467.7036        0.010          88 
2900     -467.7035        0.010          88 
Reached termination condition!
last topological improvement at gen 88
Improvement over last 500 gen = 0.00077
Current score = -467.7035
Performing final optimizations...
pass 1 : -467.7035   (branch= 0.0000  subset rates= 0.0001)
pass 2 : -467.6923   (branch= 0.0112  subset rates= 0.0000)
pass 3 : -467.6861   (branch= 0.0060  subset rates= 0.0001)
pass 4 : -467.6835   (branch= 0.0027  subset rates= 0.0000)
pass 5 : -467.6821   (branch= 0.0013  subset rates= 0.0000)
pass 6 : -467.6810   (branch= 0.0011  subset rates= 0.0000)
pass 7 : -467.6801   (branch= 0.0009  subset rates= 0.0000)
pass 8 : -467.6795   (branch= 0.0006  subset rates= 0.0000)
pass 9 : -467.6792   (branch= 0.0003  subset rates= 0.0000)
pass 10: -467.6789   (branch= 0.0002  subset rates= 0.0001)
pass 11: -467.6788   (branch= 0.0002  subset rates= 0.0000)
pass 12: -467.6787   (branch= 0.0001  subset rates= 0.0000)
pass 13: -467.6787   (branch= 0.0000  subset rates= 0.0000)
pass 14: -467.6787   (branch= 0.0000  subset rates= 0.0000)
Looking for minimum length branches...
Final score = -467.6787
Time used so far = 0 hours, 0 minutes and 11 seconds

MODEL REPORT - Parameter values are FINAL
Model 1
  Number of states = 2 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    0.79  1.47  2.18
NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    8 branches were collapsed.

>>>Completed Search rep 2 (of 5)<<<

>>>Search rep 3 (of 5)<<<
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=387765568

Initial ln Likelihood: -629.3844
optimizing: starting branch lengths, subset rates...
pass 1:+  145.913 (branch= 138.38 scale=  3.36 subset rates=  4.18)
pass 2:+   12.537 (branch=  11.64 scale=  0.00 subset rates=  0.90)
pass 3:+    2.852 (branch=   2.62 scale=  0.06 subset rates=  0.18)
pass 4:+    0.211 (branch=   0.21 scale=  0.00 subset rates=  0.00)
pass 5:+    0.034 (branch=   0.03 scale=  0.00 subset rates=  0.00)
pass 6:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
lnL after optimization: -467.8378
gen      current_lnL    precision  last_tree_imp  
0        -467.8378        0.010           0 
100      -467.8202        0.010           0 
NOTE: ****Specified time limit (5 seconds) reached...
Current score = -467.8202
Performing final optimizations...
pass 1 : -467.7839   (branch= 0.0363  subset rates= 0.0000)
pass 2 : -467.7382   (branch= 0.0457  subset rates= 0.0000)
pass 3 : -467.7045   (branch= 0.0327  subset rates= 0.0011)
pass 4 : -467.6883   (branch= 0.0154  subset rates= 0.0008)
pass 5 : -467.6838   (branch= 0.0045  subset rates= 0.0000)
pass 6 : -467.6818   (branch= 0.0020  subset rates= 0.0000)
pass 7 : -467.6799   (branch= 0.0016  subset rates= 0.0003)
pass 8 : -467.6791   (branch= 0.0008  subset rates= 0.0000)
pass 9 : -467.6788   (branch= 0.0004  subset rates= 0.0000)
pass 10: -467.6787   (branch= 0.0001  subset rates= 0.0000)
pass 11: -467.6786   (branch= 0.0000  subset rates= 0.0000)
pass 12: -467.6786   (branch= 0.0000  subset rates= 0.0000)
pass 13: -467.6786   (branch= 0.0000  subset rates= 0.0000)
pass 14: -467.6785   (branch= 0.0000  subset rates= 0.0000)
pass 15: -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  2.17
NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    8 branches were collapsed.

>>>Terminated Search rep 3 (of 5)<<<

NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 3 replicate search(es) (of 5).

NOTE: Unless the following output indicates that search replicates found the
	same topology, you should assume that they found different topologies.
Results:
Replicate 1 : -467.6782 (best)
Replicate 2 : -467.6787        (same topology as 1)
Replicate 3 : -467.6785        (same topology as 1) (TERMINATED PREMATURELY) 

Parameter estimates across search replicates:

Partition model subset 1:
	 Model contains no estimated parameters

Partition model subset 2:
	 Model contains no estimated parameters

Partition model subset 3:
	 Model contains no estimated parameters

Treelengths and subset rate multipliers:
          TL   R(1)  R(2)  R(3)
rep 1:  3.844 0.786 1.480 2.180
rep 2:  3.839 0.788 1.472 2.178
rep 3:  3.840 0.788 1.476 2.170

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 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./check/p.mkO.ssr.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard ordered k-state data,
	modeled as Standard ordered k-state data
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.5 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN

>>>Search rep 1 (of 5)<<<
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=1

Initial ln Likelihood: -641.9257
optimizing: starting branch lengths, subset rates...
pass 1:+  147.096 (branch= 136.58 scale=  0.83 subset rates=  9.68)
pass 2:+   12.451 (branch=   8.46 scale=  0.00 subset rates=  3.99)
pass 3:+    3.549 (branch=   2.32 scale=  0.03 subset rates=  1.20)
pass 4:+    0.759 (branch=   0.51 scale=  0.00 subset rates=  0.25)
pass 5:+    0.120 (branch=   0.11 scale=  0.00 subset rates=  0.01)
pass 6:+    0.011 (branch=   0.01 scale=  0.00 subset rates=  0.00)
pass 7:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
lnL after optimization: -477.9402
gen      current_lnL    precision  last_tree_imp  
0        -477.9402        0.010           0 
100      -477.8625        0.010          76 
200      -477.8283        0.010         152 
300      -477.7511        0.010         215 
400      -477.5621        0.010         373 
500      -477.5385        0.010         373 
600      -477.5298        0.010         373 
700      -477.5290        0.010         373 
800      -477.5213        0.010         373 
900      -477.5166        0.010         373 
1000     -477.5163        0.010         373 
1100     -477.5124        0.010         373 
1200     -477.5109        0.010         373 
1300     -477.5098        0.010         373 
1400     -477.4981        0.010         373 
1500     -477.4922        0.010         373 
1600     -477.4850        0.010         373 
1700     -477.4817        0.010         373 
1800     -477.4773        0.010         373 
1900     -477.4761        0.010         373 
2000     -477.4748        0.010         373 
2100     -477.4739        0.010         373 
2200     -477.4732        0.010         373 
2300     -477.4729        0.010         373 
2400     -477.4726        0.010         373 
2500     -477.4723        0.010         373 
2600     -477.4711        0.010         373 
2700     -477.4707        0.010         373 
2800     -477.4706        0.010         373 
2900     -477.4705        0.010         373 
3000     -477.4702        0.010         373 
3100     -477.4701        0.010         373 
Reached termination condition!
last topological improvement at gen 373
Improvement over last 500 gen = 0.00099
Current score = -477.4701
Performing final optimizations...
pass 1 : -477.4701   (branch= 0.0000  subset rates= 0.0000)
pass 2 : -477.4430   (branch= 0.0269  subset rates= 0.0002)
pass 3 : -477.4394   (branch= 0.0036  subset rates= 0.0000)
pass 4 : -477.4366   (branch= 0.0027  subset rates= 0.0000)
pass 5 : -477.4354   (branch= 0.0013  subset rates= 0.0000)
pass 6 : -477.4347   (branch= 0.0007  subset rates= 0.0000)
pass 7 : -477.4334   (branch= 0.0013  subset rates= 0.0000)
pass 8 : -477.4324   (branch= 0.0010  subset rates= 0.0000)
pass 9 : -477.4321   (branch= 0.0004  subset rates= 0.0000)
pass 10: -477.4319   (branch= 0.0002  subset rates= 0.0000)
pass 11: -477.4318   (branch= 0.0001  subset rates= 0.0000)
pass 12: -477.4316   (branch= 0.0001  subset rates= 0.0001)
pass 13: -477.4316   (branch= 0.0000  subset rates= 0.0000)
pass 14: -477.4316   (branch= 0.0000  subset rates= 0.0000)
Looking for minimum length branches...
Final score = -477.4316
Time used so far = 0 hours, 0 minutes and 5 seconds

MODEL REPORT - Parameter values are FINAL
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    0.63  1.92  2.74
NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    7 branches were collapsed.

>>>Completed Search rep 1 (of 5)<<<

>>>Search rep 2 (of 5)<<<
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=200420059

Initial ln Likelihood: -656.4902
optimizing: starting branch lengths, subset rates...
pass 1:+  148.906 (branch= 137.62 scale=  1.92 subset rates=  9.37)
pass 2:+   19.722 (branch=  15.83 scale=  0.00 subset rates=  3.89)
pass 3:+    3.562 (branch=   2.11 scale=  0.00 subset rates=  1.45)
pass 4:+    2.460 (branch=   2.02 scale=  0.00 subset rates=  0.44)
pass 5:+    3.227 (branch=   3.23 scale=  0.00 subset rates=  0.00)
pass 6:+    0.745 (branch=   0.71 scale=  0.01 subset rates=  0.02)
pass 7:+    0.015 (branch=   0.02 scale=  0.00 subset rates=  0.00)
pass 8:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
lnL after optimization: -477.8527
gen      current_lnL    precision  last_tree_imp  
0        -477.8527        0.010           0 
NOTE: ****Specified time limit (5 seconds) reached...

NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
(set restart = 1 in the config file).  IF YOU WANT TO USE THE
PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
ADD "end;" TO THE TREE FILES.

Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./restart/p.mkO.ssr.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard ordered k-state data,
	modeled as Standard ordered k-state data
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.5 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN

Restarting from checkpoint...
Search rep 2 (of 5) generation 1, seed 1140057502, best lnL -477.853
gen      current_lnL    precision  last_tree_imp  
1        -477.8527        0.010           0 
100      -477.7879        0.010          74 
200      -477.7665        0.010          74 
300      -477.7486        0.010          74 
400      -477.7424        0.010          74 
500      -477.7295        0.010          74 
600      -477.7267        0.010          74 
700      -477.7205        0.010          74 
800      -477.7194        0.010          74 
900      -477.7186        0.010          74 
1000     -477.7135        0.010          74 
1100     -477.7094        0.010          74 
1200     -477.7090        0.010          74 
1300     -477.7060        0.010          74 
1400     -477.7036        0.010          74 
1500     -477.7019        0.010          74 
1600     -477.7004        0.010          74 
1700     -477.6994        0.010          74 
1800     -477.6984        0.010          74 
1900     -477.6977        0.010          74 
2000     -477.6953        0.010          74 
2100     -477.3774        0.010        2081 
2200     -477.3631        0.010        2170 
2300     -477.3559        0.010        2170 
2400     -477.3497        0.010        2170 
2500     -477.3452        0.010        2170 
2600     -477.3293        0.010        2170 
2700     -477.3261        0.010        2170 
2800     -477.3186        0.010        2170 
2900     -477.3149        0.010        2170 
3000     -477.3144        0.010        2170 
3100     -477.3140        0.010        2170 
3200     -477.3125        0.010        2170 
3300     -477.3125        0.010        2170 
NOTE: ****Specified time limit (5 seconds) reached...
Current score = -477.3125
Performing final optimizations...
pass 1 : -477.2438   (branch= 0.0000  subset rates= 0.0687)
pass 2 : -477.2269   (branch= 0.0113  subset rates= 0.0056)
pass 3 : -477.2182   (branch= 0.0087  subset rates= 0.0000)
pass 4 : -477.2113   (branch= 0.0069  subset rates= 0.0000)
pass 5 : -477.2078   (branch= 0.0035  subset rates= 0.0000)
pass 6 : -477.2064   (branch= 0.0009  subset rates= 0.0005)
pass 7 : -477.2052   (branch= 0.0012  subset rates= 0.0000)
pass 8 : -477.2046   (branch= 0.0006  subset rates= 0.0000)
pass 9 : -477.2045   (branch= 0.0002  subset rates= 0.0000)
pass 10: -477.2044   (branch= 0.0001  subset rates= 0.0000)
pass 11: -477.2044   (branch= 0.0000  subset rates= 0.0000)
pass 12: -477.2044   (branch= 0.0000  subset rates= 0.0000)
pass 13: -477.2043   (branch= 0.0000  subset rates= 0.0000)
Looking for minimum length branches...
Final score = -477.2043
Time used so far = 0 hours, 0 minutes and 12 seconds

MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mk model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    0.63  1.94  2.63
NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    8 branches were collapsed.

>>>Terminated Search rep 2 (of 5)<<<

NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 2 replicate search(es) (of 5).

NOTE: Unless the following output indicates that search replicates found the
	same topology, you should assume that they found different topologies.
Results:
Replicate 1 : -477.4316       
Replicate 2 : -477.2043 (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:  4.930 0.631 1.917 2.740
rep 2:  4.699 0.634 1.939 2.635

Saving final tree from best search rep (#2) to ch.p.mkO.ssr.best.tre
#######################################################
TREEFILES PASS
Running checkpoint test ./check/p.mkv.ssr.conf
Running checkpoint test ./check/p.mkv.ssr.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./check/p.mkv.ssr.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard k-state data, variable only,
	modeled as Standard k-state data, variable only
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.6 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN

Bootstrap reweighting...
	Subset 1: Random seed for bootstrap reweighting: 42
	Subset 2: Random seed for bootstrap reweighting: 1339106791
	Subset 3: Random seed for bootstrap reweighting: 974568031

>>>Bootstrap rep 1 (of 1) Search rep 1 (of 5)<<<
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=1

Initial ln Likelihood: -602.2288
optimizing: starting branch lengths, subset rates...
pass 1:+  152.798 (branch= 152.15 scale=  0.58 subset rates=  0.07)
pass 2:+    9.798 (branch=   9.63 scale=  0.00 subset rates=  0.16)
pass 3:+    0.369 (branch=   0.35 scale=  0.00 subset rates=  0.02)
pass 4:+    0.040 (branch=   0.04 scale=  0.00 subset rates=  0.00)
pass 5:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
lnL after optimization: -439.2244
gen      current_lnL    precision  last_tree_imp  
0        -439.2244        0.010           0 
100      -430.2535        0.010          92 
200      -427.7092        0.010         179 
300      -426.9758        0.010         293 
400      -425.6931        0.010         365 
500      -425.6675        0.010         365 
600      -425.6508        0.010         365 
700      -425.6316        0.010         365 
800      -425.6209        0.010         365 
900      -425.6123        0.010         365 
1000     -425.6089        0.010         365 
1100     -425.6081        0.010         365 
1200     -425.6057        0.010         365 
1300     -425.6039        0.010         365 
1400     -425.6034        0.010         365 
1500     -425.6029        0.010         365 
1600     -425.6020        0.010         365 
1700     -425.6018        0.010         365 
1800     -425.6014        0.010         365 
1900     -425.6001        0.010         365 
2000     -425.5991        0.010         365 
2100     -425.5979        0.010         365 
2200     -425.5930        0.010         365 
2300     -425.5915        0.010         365 
2400     -425.5913        0.010         365 
2500     -425.5897        0.010         365 
2600     -425.5895        0.010         365 
2700     -425.5894        0.010         365 
2800     -425.5890        0.010         365 
2900     -425.5876        0.010         365 
3000     -425.5875        0.010         365 
3100     -425.5854        0.010         365 
NOTE: ****Specified time limit (5 seconds) reached...

NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
(set restart = 1 in the config file).  IF YOU WANT TO USE THE
PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
ADD "end;" TO THE TREE FILES.

Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./restart/p.mkv.ssr.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard k-state data, variable only,
	modeled as Standard k-state data, variable only
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.6 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN
	Subset 1: Random seed for bootstrap reweighting: 42
	Subset 2: Random seed for bootstrap reweighting: 1339106791
	Subset 3: Random seed for bootstrap reweighting: 974568031

Restarting from checkpoint...
Bootstrap rep 1 (of 1) Search rep 1 (of 5) generation 3102, seed 169259964, best lnL -425.585
gen      current_lnL    precision  last_tree_imp  
3102     -425.5854        0.010         365 
3200     -425.5852        0.010         365 
3300     -425.5851        0.010         365 
3400     -425.5828        0.010         365 
3500     -425.5828        0.010         365 
3600     -425.5827        0.010         365 
3700     -425.5827        0.010         365 
3800     -425.5826        0.010         365 
3900     -425.5824        0.010         365 
Reached termination condition!
last topological improvement at gen 365
Improvement over last 500 gen = 0.00046
Current score = -425.5824
Performing final optimizations...
pass 1 : -425.5752   (branch= 0.0000  subset rates= 0.0071)
pass 2 : -425.5571   (branch= 0.0147  subset rates= 0.0034)
pass 3 : -425.5512   (branch= 0.0059  subset rates= 0.0000)
pass 4 : -425.5505   (branch= 0.0007  subset rates= 0.0000)
pass 5 : -425.5501   (branch= 0.0004  subset rates= 0.0000)
pass 6 : -425.5497   (branch= 0.0004  subset rates= 0.0000)
pass 7 : -425.5493   (branch= 0.0004  subset rates= 0.0000)
pass 8 : -425.5490   (branch= 0.0003  subset rates= 0.0000)
pass 9 : -425.5487   (branch= 0.0003  subset rates= 0.0000)
pass 10: -425.5487   (branch= 0.0000  subset rates= 0.0000)
pass 11: -425.5487   (branch= 0.0000  subset rates= 0.0000)
pass 12: -425.5486   (branch= 0.0000  subset rates= 0.0000)
pass 13: -425.5486   (branch= 0.0000  subset rates= 0.0000)
Looking for minimum length branches...
Final score = -425.5486
Time used so far = 0 hours, 0 minutes and 7 seconds

MODEL REPORT - Parameter values are FINAL
Model 1
  Number of states = 2 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    0.87  1.53  1.12
NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    9 branches were collapsed.

>>>Completed Bootstrap rep 1 (of 1) Search rep 1 (of 5)<<<

>>>Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<<
Obtained starting tree 1 from Nexus
Starting with seed=255600397

Initial ln Likelihood: -577.2924
optimizing: starting branch lengths, subset rates...
pass 1:+  121.000 (branch= 120.23 scale=  0.75 subset rates=  0.02)
pass 2:+   14.984 (branch=  14.74 scale=  0.04 subset rates=  0.20)
pass 3:+    1.951 (branch=   1.90 scale=  0.00 subset rates=  0.05)
pass 4:+    0.046 (branch=   0.05 scale=  0.00 subset rates=  0.00)
pass 5:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
lnL after optimization: -439.3118
gen      current_lnL    precision  last_tree_imp  
0        -439.3118        0.010           0 
100      -428.8361        0.010          97 
200      -428.0348        0.010         163 
300      -425.9017        0.010         248 
400      -425.7902        0.010         327 
500      -425.7309        0.010         411 
600      -425.6571        0.010         523 
700      -425.6380        0.010         523 
800      -425.6343        0.010         523 
900      -425.6312        0.010         523 
1000     -425.6253        0.010         523 
1100     -425.6236        0.010         523 
1200     -425.6180        0.010         523 
1300     -425.6157        0.010         523 
1400     -425.6057        0.010         523 
1500     -425.6031        0.010         523 
1600     -425.5999        0.010         523 
1700     -425.5980        0.010         523 
1800     -425.5977        0.010         523 
1900     -425.5940        0.010         523 
2000     -425.5929        0.010         523 
2100     -425.5928        0.010         523 
2200     -425.5912        0.010         523 
2300     -425.5897        0.010         523 
2400     -425.5887        0.010         523 
NOTE: ****Specified time limit (5 seconds) reached...
Current score = -425.5885
Performing final optimizations...
pass 1 : -425.5777   (branch= 0.0000  subset rates= 0.0108)
pass 2 : -425.5573   (branch= 0.0204  subset rates= 0.0000)
pass 3 : -425.5560   (branch= 0.0013  subset rates= 0.0000)
pass 4 : -425.5517   (branch= 0.0043  subset rates= 0.0000)
pass 5 : -425.5512   (branch= 0.0005  subset rates= 0.0000)
pass 6 : -425.5503   (branch= 0.0009  subset rates= 0.0000)
pass 7 : -425.5495   (branch= 0.0008  subset rates= 0.0000)
pass 8 : -425.5490   (branch= 0.0005  subset rates= 0.0000)
pass 9 : -425.5489   (branch= 0.0001  subset rates= 0.0000)
pass 10: -425.5489   (branch= 0.0000  subset rates= 0.0000)
pass 11: -425.5488   (branch= 0.0001  subset rates= 0.0000)
pass 12: -425.5488   (branch= 0.0000  subset rates= 0.0000)
pass 13: -425.5488   (branch= 0.0000  subset rates= 0.0000)
pass 14: -425.5488   (branch= 0.0000  subset rates= 0.0000)
Looking for minimum length branches...
Final score = -425.5488
Time used so far = 0 hours, 0 minutes and 12 seconds

MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT
Model 1
  Number of states = 2 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (standard data)
  Character change matrix:
    One rate (symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    0.87  1.52  1.12
NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    9 branches were collapsed.

>>>Terminated Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<<

NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 2 replicate search(es) (of 5).

NOTE: Unless the following output indicates that search replicates found the
	same topology, you should assume that they found different topologies.
Results:
Replicate 1 : -425.5486 (best)
Replicate 2 : -425.5488        (same topology as 1) (TERMINATED PREMATURELY) 

Parameter estimates across search replicates:

Partition model subset 1:
	 Model contains no estimated parameters

Partition model subset 2:
	 Model contains no estimated parameters

Partition model subset 3:
	 Model contains no estimated parameters

Treelengths and subset rate multipliers:
          TL   R(1)  R(2)  R(3)
rep 1:  3.037 0.868 1.530 1.116
rep 2:  3.039 0.869 1.525 1.119

Saving tree from best search rep (#1) to bootstrap file ch.p.mkv.ssr.boot.tre

#######################################################
TREEFILES PASS
Running checkpoint test ./check/p.mkvO.ssr.conf
Running checkpoint test ./check/p.mkvO.ssr.conf
Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./check/p.mkvO.ssr.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard ordered k-state data, variable only,
	modeled as Standard ordered k-state data, variable only
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.6 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN

>>>Search rep 1 (of 5)<<<
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=1

Initial ln Likelihood: -637.9212
optimizing: starting branch lengths, subset rates...
pass 1:+  144.867 (branch= 134.40 scale=  0.48 subset rates=  9.98)
pass 2:+   12.967 (branch=   8.30 scale=  0.00 subset rates=  4.67)
pass 3:+    3.846 (branch=   2.24 scale=  0.02 subset rates=  1.58)
pass 4:+    1.162 (branch=   0.58 scale=  0.01 subset rates=  0.57)
pass 5:+    0.156 (branch=   0.12 scale=  0.00 subset rates=  0.03)
pass 6:+    0.044 (branch=   0.04 scale=  0.00 subset rates=  0.00)
pass 7:+    0.015 (branch=   0.02 scale=  0.00 subset rates=  0.00)
pass 8:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
lnL after optimization: -474.8632
gen      current_lnL    precision  last_tree_imp  
0        -474.8632        0.010           0 
100      -474.7514        0.010          68 
200      -474.7186        0.010          68 
300      -474.6982        0.010          68 
400      -474.6395        0.010         329 
500      -474.1549        0.010         455 
600      -474.1345        0.010         560 
700      -474.0337        0.010         653 
800      -474.0224        0.010         653 
900      -474.0129        0.010         653 
1000     -474.0072        0.010         653 
1100     -474.0048        0.010         653 
1200     -474.0017        0.010         653 
1300     -473.9998        0.010         653 
1400     -473.9960        0.010         653 
1500     -473.9930        0.010         653 
1600     -473.9888        0.010         653 
1700     -473.9875        0.010         653 
1800     -473.9857        0.010         653 
1900     -473.9846        0.010         653 
2000     -473.9839        0.010         653 
2100     -473.9834        0.010         653 
2200     -473.9820        0.010         653 
2300     -473.9814        0.010         653 
2400     -473.9804        0.010         653 
2500     -473.9804        0.010         653 
NOTE: ****Specified time limit (5 seconds) reached...

NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
(set restart = 1 in the config file).  IF YOU WANT TO USE THE
PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
ADD "end;" TO THE TREE FILES.

Running GARLI Version 2.1. ()
->Single processor version for 32-bit OS<-
##############################################################
 This is GARLI 2.1: maximum likelihood phylogenetic inference
 using nucleotide, amino acid, codon and morphology-like data,
             as well as partitioned models.
   General program usage is extensively documented here:
            http://www.nescent.org/wg/garli/
   See this page for details on partitioned model usage:
  http://www.nescent.org/wg_garli/Using_partitioned_models
   and this page for details on Mkv mophology model usage:
    http://www.nescent.org/wg_garli/Mkv_morphology_model
         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
                garli.support@gmail.com
##############################################################
Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 14.2.0
Using NCL version 2.1.17

#######################################################
Reading config file ./restart/p.mkvO.ssr.conf
###################################################
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
	data/L2001.30x52.nex ...
Reading CHARACTERS block...
Warning:  
 Skipping command: OPTIONS
at line 23, column (approximately) 9 (file position 611)
storing implied block: TAXA
storing read block: CHARACTERS
 found standard data... successful
Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
 successful

###################################################
PARTITIONING OF DATA AND MODELS
GARLI data subset 1
	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
	Data read as Standard ordered k-state data, variable only,
	modeled as Standard ordered k-state data, variable only
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 2 states:
	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  39 parsimony-informative characters.
	  0 uninformative variable characters.
	  39 total characters.
	  39 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
	  char  90 
	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
	  char  90 
	Subset of data with 3 states:
	  chars 54 61 62 64 71 72 83 90-102 \ 6
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  10 parsimony-informative characters.
	  0 uninformative variable characters.
	  10 total characters.
	  10 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
	Subset of data with 4 states:
	  chars 52 59 73
	Summary of data:
	  30 sequences.
	  0 constant characters.
	  0 parsimony-informative characters.
	  3 uninformative variable characters.
	  3 total characters.
	  3 unique patterns in compressed data matrix.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 5 observed states.
NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
	
NOTE: No characters found with 6 observed states.

###################################################
NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user.
(This comes from the availablememory setting in the configuration file.
Availablememory should NOT be set to more than the actual amount of 
physical memory that your computer has installed)

For this dataset:
 Mem level		availablememory setting
  great			    >= 1 MB
  good			approx 0 MB to 1 MB
  low			approx 0 MB to 1 MB
  very low		approx 0 MB to 1 MB
the minimum required availablememory is 1 MB

You specified that Garli should use at most 512.0 MB of memory.

Garli will actually use approx. 0.6 MB of memory
**Your memory level is: great (you don't need to change anything)**

#######################################################
Loading starting model and/or tree from file data/L.start
Reading TREES block...storing read block: TREES
 successful
STARTING RUN

Restarting from checkpoint...
Search rep 1 (of 5) generation 2500, seed 988000168, best lnL -473.980
gen      current_lnL    precision  last_tree_imp  
2500     -473.9804        0.010         653 
2600     -473.9801        0.010         653 
2700     -473.9793        0.010         653 
2800     -473.9779        0.010         653 
2900     -473.9777        0.010         653 
3000     -473.9777        0.010         653 
3100     -473.9773        0.010         653 
3200     -473.9772        0.010         653 
3300     -473.9770        0.010         653 
Reached termination condition!
last topological improvement at gen 653
Improvement over last 500 gen = 0.00088
Current score = -473.9770
Performing final optimizations...
pass 1 : -473.9770   (branch= 0.0000  subset rates= 0.0000)
pass 2 : -473.9587   (branch= 0.0183  subset rates= 0.0000)
pass 3 : -473.9587   (branch= 0.0000  subset rates= 0.0000)
pass 4 : -473.9562   (branch= 0.0011  subset rates= 0.0014)
pass 5 : -473.9537   (branch= 0.0013  subset rates= 0.0013)
pass 6 : -473.9523   (branch= 0.0010  subset rates= 0.0003)
pass 7 : -473.9516   (branch= 0.0008  subset rates= 0.0000)
pass 8 : -473.9511   (branch= 0.0004  subset rates= 0.0001)
pass 9 : -473.9509   (branch= 0.0002  subset rates= 0.0000)
pass 10: -473.9508   (branch= 0.0000  subset rates= 0.0000)
pass 11: -473.9508   (branch= 0.0001  subset rates= 0.0000)
pass 12: -473.9508   (branch= 0.0000  subset rates= 0.0000)
pass 13: -473.9507   (branch= 0.0000  subset rates= 0.0000)
Looking for minimum length branches...
Final score = -473.9507
Time used so far = 0 hours, 0 minutes and 12 seconds

MODEL REPORT - Parameter values are FINAL
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    0.59  2.07  2.80
NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    8 branches were collapsed.

>>>Completed Search rep 1 (of 5)<<<

>>>Search rep 2 (of 5)<<<
Obtained starting tree 1 from Nexus
MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    1.00  1.00  1.00
Starting with seed=2125680066

Initial ln Likelihood: -649.8224
optimizing: starting branch lengths, subset rates...
pass 1:+  148.288 (branch= 136.88 scale=  0.96 subset rates= 10.45)
pass 2:+   18.126 (branch=  13.41 scale=  0.03 subset rates=  4.69)
pass 3:+    5.650 (branch=   3.93 scale=  0.00 subset rates=  1.72)
pass 4:+    2.345 (branch=   1.67 scale=  0.00 subset rates=  0.67)
pass 5:+    0.473 (branch=   0.43 scale=  0.01 subset rates=  0.03)
pass 6:+    0.134 (branch=   0.13 scale=  0.00 subset rates=  0.00)
pass 7:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
lnL after optimization: -474.8071
gen      current_lnL    precision  last_tree_imp  
0        -474.8071        0.010           0 
100      -474.7912        0.010           0 
200      -474.7021        0.010         123 
300      -474.5642        0.010         272 
400      -474.5190        0.010         272 
500      -474.5075        0.010         272 
600      -474.5034        0.010         272 
700      -474.4997        0.010         272 
NOTE: ****Specified time limit (5 seconds) reached...
Current score = -474.4967
Performing final optimizations...
pass 1 : -474.4798   (branch= 0.0169  subset rates= 0.0000)
pass 2 : -474.4499   (branch= 0.0299  subset rates= 0.0000)
pass 3 : -474.4433   (branch= 0.0066  subset rates= 0.0000)
pass 4 : -474.4354   (branch= 0.0077  subset rates= 0.0002)
pass 5 : -474.4316   (branch= 0.0038  subset rates= 0.0000)
pass 6 : -474.4307   (branch= 0.0009  subset rates= 0.0000)
pass 7 : -474.4301   (branch= 0.0006  subset rates= 0.0000)
pass 8 : -474.4294   (branch= 0.0007  subset rates= 0.0000)
pass 9 : -474.4289   (branch= 0.0005  subset rates= 0.0000)
pass 10: -474.4287   (branch= 0.0002  subset rates= 0.0000)
pass 11: -474.4286   (branch= 0.0001  subset rates= 0.0000)
pass 12: -474.4286   (branch= 0.0001  subset rates= 0.0000)
pass 13: -474.4285   (branch= 0.0000  subset rates= 0.0000)
pass 14: -474.4285   (branch= 0.0000  subset rates= 0.0000)
pass 15: -474.4285   (branch= 0.0000  subset rates= 0.0000)
Looking for minimum length branches...
Final score = -474.4285
Time used so far = 0 hours, 0 minutes and 14 seconds

MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT
Model 1
  Number of states = 2 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.50, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 2
  Number of states = 3 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.33, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Model 3
  Number of states = 4 (ordered standard data)
  Character change matrix:
    One rate (ordered symmetric one rate Mkv model)
  Equilibrium State Frequencies: equal (0.25, fixed)
  Rate Heterogeneity Model:
    no rate heterogeneity

Subset rate multipliers:
    0.59  2.03  2.91
NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
    7 branches were collapsed.

>>>Terminated Search rep 2 (of 5)<<<

NOTE: ***Search was terminated before full auto-termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***


#######################################################

Completed 2 replicate search(es) (of 5).

NOTE: Unless the following output indicates that search replicates found the
	same topology, you should assume that they found different topologies.
Results:
Replicate 1 : -473.9507 (best)
Replicate 2 : -474.4285        (TERMINATED PREMATURELY) 

Parameter estimates across search replicates:

Partition model subset 1:
	 Model contains no estimated parameters

Partition model subset 2:
	 Model contains no estimated parameters

Partition model subset 3:
	 Model contains no estimated parameters

Treelengths and subset rate multipliers:
          TL   R(1)  R(2)  R(3)
rep 1:  4.349 0.588 2.066 2.804
rep 2:  4.597 0.589 2.028 2.912

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 -j3 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
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 from: /lib/ld-linux-armhf.so.3
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 from: /lib/ld-linux-armhf.so.3
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged
dpkg-shlibdeps: warning: debian/garli/usr/lib/garli/bin/Garli-2.1 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/garli-mpi/usr/lib/garli/bin/Garli-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
   dh_installdeb
   dh_gencontrol
   dh_md5sums
   dh_builddeb
dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-9_armhf.deb'.
dpkg-deb: building package 'garli' in '../garli_2.1-9_armhf.deb'.
dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-9_all.deb'.
dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-9_armhf.deb'.
dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-9_armhf.deb'.
 dpkg-genbuildinfo --build=binary -O../garli_2.1-9_armhf.buildinfo
 dpkg-genchanges --build=binary -O../garli_2.1-9_armhf.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env 
I: removing directory /srv/workspace/pbuilder/32626 and its subdirectories
I: Current time: Sat Jan 11 17:53:57 -12 2025
I: pbuilder-time-stamp: 1736661237
Sun Jan 12 05:54:38 UTC 2025  I: 1st build successful. Starting 2nd build on remote node virt32c-armhf-rb.debian.net.
Sun Jan 12 05:54:38 UTC 2025  I: Preparing to do remote build '2' on virt32c-armhf-rb.debian.net.
Sun Jan 12 06:28:47 UTC 2025  I: Deleting $TMPDIR on virt32c-armhf-rb.debian.net.
Sun Jan 12 06:28:50 UTC 2025  I: garli_2.1-9_armhf.changes:
Format: 1.8
Date: Thu, 19 Dec 2024 20:44:33 +0100
Source: garli
Binary: garli garli-dbgsym garli-examples garli-mpi garli-mpi-dbgsym
Architecture: armhf all
Version: 2.1-9
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
 garli      - phylogenetic analysis of molecular sequence data using maximum-li
 garli-examples - phylogenetic analysis of molecular sequence data (examples)
 garli-mpi  - phylogenetic analysis of molecular sequence data using maximum-li
Changes:
 garli (2.1-9) unstable; urgency=medium
 .
   * Team upload.
   * d/rules: skip tests on armel: too heavy.
   * d/t/control: skip autopkgtest on armel: too heavy.
Checksums-Sha1:
 30f0293b8a73def885bf5915669d0d2780dfb4b6 5005208 garli-dbgsym_2.1-9_armhf.deb
 9190fdad700fcdc0fc9fe53c5c92c112dc23d533 103464 garli-examples_2.1-9_all.deb
 8793d97e122265a73a0748ed0e944e957a51617e 5040836 garli-mpi-dbgsym_2.1-9_armhf.deb
 b819cc0134f74852ff6d6538b7750f85618f3664 509284 garli-mpi_2.1-9_armhf.deb
 1a71648d15e08b16d4456942465336bfb2ce5b66 6268 garli_2.1-9_armhf.buildinfo
 3c51f39c5907b0d7f7be30e63e2d85647184d452 532156 garli_2.1-9_armhf.deb
Checksums-Sha256:
 4fa9938be931bd07eff81a14f41266fad3e164208916223fe4a8dfca83432698 5005208 garli-dbgsym_2.1-9_armhf.deb
 932b8ad8935349f05f0abbf62fbba0c7f312a7d912d9bc30ec9287833081b095 103464 garli-examples_2.1-9_all.deb
 076d825cfde75732f1ea84f54feb0936ac6c3d5d41e5eb6a0ede973d5f134c1b 5040836 garli-mpi-dbgsym_2.1-9_armhf.deb
 97952b6ed59ec6788f1f184950651aa5ad4d18cf670bc4ab394469de7e389346 509284 garli-mpi_2.1-9_armhf.deb
 50a5062fb725b54dd20b0f3739eeb8627744a8f9d20c155a023339c58856d1b4 6268 garli_2.1-9_armhf.buildinfo
 a7a2b37fa43fa765b4825758ac46a200fde1efe84b2c664bef2c77f8a95ca169 532156 garli_2.1-9_armhf.deb
Files:
 aa95629ee0ee07a08295b9d99193d9d2 5005208 debug optional garli-dbgsym_2.1-9_armhf.deb
 d7e71d1f8908fce11e935020473b4b15 103464 science optional garli-examples_2.1-9_all.deb
 a06e31de55978b51f7fa13eb11bdfc38 5040836 debug optional garli-mpi-dbgsym_2.1-9_armhf.deb
 887f949d5e73d05f64ee126e1cd07ebd 509284 science optional garli-mpi_2.1-9_armhf.deb
 5d5932260492346cb85d7907bef0317f 6268 science optional garli_2.1-9_armhf.buildinfo
 48bceb3b83bfb3110596fa62a3db46fa 532156 science optional garli_2.1-9_armhf.deb
Sun Jan 12 06:28:51 UTC 2025  I: diffoscope 284 will be used to compare the two builds:
Running as unit: rb-diffoscope-armhf_32-23626.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.HHFUF2XE/garli_2.1-9.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.HHFUF2XE/garli_2.1-9.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.HHFUF2XE/garli_2.1-9.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.HHFUF2XE/b1/garli_2.1-9_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.HHFUF2XE/b2/garli_2.1-9_armhf.changes

## command (total time: 0.000s)
       0.000s      1 call     cmp (internal)

## has_same_content_as (total time: 0.000s)
       0.000s      1 call     abc.DotChangesFile

## main (total time: 0.420s)
       0.420s      2 calls    outputs
       0.000s      1 call     cleanup

## recognizes (total time: 0.111s)
       0.111s     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: 710ms
CPU time consumed: 707ms
Sun Jan 12 06:28:52 UTC 2025  I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists.
Sun Jan 12 06:28:52 UTC 2025  I: garli from trixie built successfully and reproducibly on armhf.
Sun Jan 12 06:28:53 UTC 2025  I: Submitting .buildinfo files to external archives:
Sun Jan 12 06:28:53 UTC 2025  I: Submitting 8.0K	b1/garli_2.1-9_armhf.buildinfo.asc
Sun Jan 12 06:28:54 UTC 2025  I: Submitting 8.0K	b2/garli_2.1-9_armhf.buildinfo.asc
Sun Jan 12 06:28:55 UTC 2025  I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sun Jan 12 06:28:55 UTC 2025  I: Done submitting .buildinfo files.
Sun Jan 12 06:28:55 UTC 2025  I: Removing signed garli_2.1-9_armhf.buildinfo.asc files:
removed './b1/garli_2.1-9_armhf.buildinfo.asc'
removed './b2/garli_2.1-9_armhf.buildinfo.asc'