Thu Jul 2 10:36:53 UTC 2020 I: starting to build tree-puzzle/buster/armhf on jenkins on '2020-07-02 10:36' Thu Jul 2 10:36:53 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_14/4824/console.log Thu Jul 2 10:36:53 UTC 2020 I: Downloading source for buster/tree-puzzle=5.2-11 --2020-07-02 10:36:53-- http://deb.debian.org/debian/pool/main/t/tree-puzzle/tree-puzzle_5.2-11.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2137 (2.1K) Saving to: ‘tree-puzzle_5.2-11.dsc’ 0K .. 100% 240M=0s 2020-07-02 10:36:53 (240 MB/s) - ‘tree-puzzle_5.2-11.dsc’ saved [2137/2137] Thu Jul 2 10:36:53 UTC 2020 I: tree-puzzle_5.2-11.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: tree-puzzle Binary: tree-puzzle, tree-ppuzzle, tree-puzzle-doc Architecture: any all Version: 5.2-11 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Charles Plessy Homepage: http://www.tree-puzzle.de Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/tree-puzzle Vcs-Git: https://salsa.debian.org/med-team/tree-puzzle.git Build-Depends: debhelper (>= 11~), libopenmpi-dev, libsprng2-dev Package-List: tree-ppuzzle deb science optional arch=any tree-puzzle deb science optional arch=any tree-puzzle-doc deb doc optional arch=all Checksums-Sha1: fd52a9f04dc871b765d9f7464f68bdb8edc22e37 875142 tree-puzzle_5.2.orig.tar.gz ea4dd9256880f32c8eb246a43462220f71d387a6 67040 tree-puzzle_5.2-11.debian.tar.xz Checksums-Sha256: 3396d3b80b03b0600afb479dc33f0bd3e5631298337295a4fa454211ac44c3fb 875142 tree-puzzle_5.2.orig.tar.gz f0e786507c3fdcc5c6650a517548515d947a9c6e001eab5f6b9f2dfb27958133 67040 tree-puzzle_5.2-11.debian.tar.xz Files: 20fa9606434ddc789670e681d98fe68f 875142 tree-puzzle_5.2.orig.tar.gz 6b64109d321dcecce5cb5eeec408e613 67040 tree-puzzle_5.2-11.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlvFqzwRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFzJw/+JvW6xyLIofVKBChqCwWyPJcvgDUJO44F LVwKIaA6Z4acSFxdbQLyyPm1WgJ8XTaf8mSsA3Lk/HH5UjVyupPOM50S/FM5YBEm zeBY9+Ev2oghMJWgUWK8i+v9BQss19ILmaA0ihxEM2364e81I3cuIkOR83bcmqUT BLAi59j/bTwtOvjQsx30HNMrb/KYUOxqXi6N1nLTU0+rhRJRIEJsBpWyA66ZKKRp 8sY2D1ambdzmOTTjTntdQb4JySxmzcVBY8jtMbhKvIqDzH1RCHXHqf5E6r2cFu/5 R6hZu/EKe9277UI8jnVedJZ3tlSEcrWmxmlESEFKD8G7tXUnmXcO92FgYborOq4l spYHRO3C6dn72Oprd4bfL7n6DMUwgiFbswmSshqG4DgyvvjeeOc6lRn9TKzGr+bA 6JgB1XYBfAkq0Idj7YsCyuTqC9XvqlMPNldYqLcixbSnr1MkMxcih71DsGQR6d5D 0b4N1j+6BhHJ+OfFgFrA0r6wPP64VVWqOoi4xFTNriD6KCpn/v4OioQrZ5oki67o yGVNaDWBFpMDQV2JDd90M1HN7wnI+7KySPlbmluScldTNPMcKkjjq4wjqdbsSohs rnRNzTEhKNAYbyf5Uq1eYOw+njDCqBW34erBy0u7GldUqvAqNp8odhzTjAcs0J/Z KUoRYmMizsQ= =YrzR -----END PGP SIGNATURE----- Thu Jul 2 10:36:53 UTC 2020 I: Checking whether the package is not for us Thu Jul 2 10:36:53 UTC 2020 I: Starting 1st build on remote node ff2b-armhf-rb.debian.net. Thu Jul 2 10:36:53 UTC 2020 I: Preparing to do remote build '1' on ff2b-armhf-rb.debian.net. Thu Jul 2 10:39:40 UTC 2020 I: Deleting $TMPDIR on ff2b-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Jul 1 22:37:02 -12 2020 I: pbuilder-time-stamp: 1593686222 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [tree-puzzle_5.2-11.dsc] I: copying [./tree-puzzle_5.2.orig.tar.gz] I: copying [./tree-puzzle_5.2-11.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Mon Oct 15 21:11:24 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./tree-puzzle_5.2-11.dsc dpkg-source: info: extracting tree-puzzle in tree-puzzle-5.2 dpkg-source: info: unpacking tree-puzzle_5.2.orig.tar.gz dpkg-source: info: unpacking tree-puzzle_5.2-11.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 20_no_copy_of_sprng.patch dpkg-source: info: applying tests-need-bash.patch dpkg-source: info: applying spelling.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/16100/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='23ad42966672430c91a5fc49162cc7db' 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='16100' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.riEdOoUizN/pbuilderrc_MOEg --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.riEdOoUizN/b1 --logfile b1/build.log tree-puzzle_5.2-11.dsc' SUDO_GID='114' SUDO_UID='109' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux ff2b 4.19.0-9-armmp-lpae #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) armv7l GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 22432 Feb 28 2019 cat -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash -rwxr-xr-x 1 root root 71648 Feb 28 2019 date -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd -rwxr-xr-x 1 root root 55672 Feb 28 2019 df -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir -rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 22364 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 18260 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 124508 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln -rwxr-xr-x 1 root root 34932 Jul 26 2018 login -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 9 2019 more -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 84284 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jun 30 20:25 sh -> dash -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty -rwsr-xr-x 1 root root 42472 Jan 9 2019 su -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch -rwxr-xr-x 1 root root 18260 Feb 28 2019 true -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir -rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/16100/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), libopenmpi-dev, libsprng2-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18932 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 (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libopenmpi-dev; however: Package libopenmpi-dev is not installed. pbuilder-satisfydepends-dummy depends on libsprng2-dev; however: Package libsprng2-dev 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} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libedit2{a} libelf1{a} libevent-2.1-6{a} libevent-core-2.1-6{a} libevent-pthreads-2.1-6{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libgmp-dev{a} libgmpxx4ldbl{a} libgssapi-krb5-2{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc5{a} libibverbs-dev{a} libibverbs1{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libopenmpi-dev{a} libopenmpi3{a} libpciaccess0{a} libpipeline1{a} libpmix2{a} libsigsegv2{a} libsprng2{a} libsprng2-dev{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libglib2.0-data libgpm2 libmail-sendmail-perl lynx shared-mime-info wget xauth xdg-user-dirs 0 packages upgraded, 68 newly installed, 0 to remove and 0 not upgraded. Need to get 27.5 MB of archives. After unpacking 90.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 10 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 11 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 12 http://deb.debian.org/debian buster/main armhf libedit2 armhf 3.1-20181209-1 [79.5 kB] Get: 13 http://deb.debian.org/debian buster/main armhf libkeyutils1 armhf 1.6-6 [13.9 kB] Get: 14 http://deb.debian.org/debian buster/main armhf libkrb5support0 armhf 1.17-3 [62.3 kB] Get: 15 http://deb.debian.org/debian buster/main armhf libk5crypto3 armhf 1.17-3 [119 kB] Get: 16 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u3 [1299 kB] Get: 17 http://deb.debian.org/debian buster/main armhf libkrb5-3 armhf 1.17-3 [323 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libgssapi-krb5-2 armhf 1.17-3 [137 kB] Get: 19 http://deb.debian.org/debian buster/main armhf openssh-client armhf 1:7.9p1-10+deb10u2 [704 kB] Get: 20 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 21 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 22 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 23 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 24 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 25 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 26 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 27 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 29 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 30 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 31 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 32 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 33 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 34 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 35 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 36 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 37 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 38 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 39 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 40 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 41 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 42 http://deb.debian.org/debian buster/main armhf libnl-3-200 armhf 3.4.0-1 [55.6 kB] Get: 43 http://deb.debian.org/debian buster/main armhf libnl-route-3-200 armhf 3.4.0-1 [136 kB] Get: 44 http://deb.debian.org/debian buster/main armhf libibverbs1 armhf 22.1-1 [44.1 kB] Get: 45 http://deb.debian.org/debian buster/main armhf ibverbs-providers armhf 22.1-1 [20.2 kB] Get: 46 http://deb.debian.org/debian buster/main armhf libevent-2.1-6 armhf 2.1.8-stable-4 [159 kB] Get: 47 http://deb.debian.org/debian buster/main armhf libevent-core-2.1-6 armhf 2.1.8-stable-4 [118 kB] Get: 48 http://deb.debian.org/debian buster/main armhf libevent-pthreads-2.1-6 armhf 2.1.8-stable-4 [47.6 kB] Get: 49 http://deb.debian.org/debian buster/main armhf libgfortran5 armhf 8.3.0-6 [213 kB] Get: 50 http://deb.debian.org/debian buster/main armhf libgmpxx4ldbl armhf 2:6.1.2+dfsg-4 [21.7 kB] Get: 51 http://deb.debian.org/debian buster/main armhf libgmp-dev armhf 2:6.1.2+dfsg-4 [581 kB] Get: 52 http://deb.debian.org/debian buster/main armhf libltdl7 armhf 2.4.6-9 [387 kB] Get: 53 http://deb.debian.org/debian buster/main armhf libhwloc5 armhf 1.11.12-3 [87.6 kB] Get: 54 http://deb.debian.org/debian buster/main armhf libltdl-dev armhf 2.4.6-9 [160 kB] Get: 55 http://deb.debian.org/debian buster/main armhf libhwloc-dev armhf 1.11.12-3 [153 kB] Get: 56 http://deb.debian.org/debian buster/main armhf libpciaccess0 armhf 0.14-1 [51.0 kB] Get: 57 http://deb.debian.org/debian buster/main armhf ocl-icd-libopencl1 armhf 2.2.12-2 [35.6 kB] Get: 58 http://deb.debian.org/debian buster/main armhf libhwloc-plugins armhf 1.11.12-3 [15.7 kB] Get: 59 http://deb.debian.org/debian buster/main armhf libnl-3-dev armhf 3.4.0-1 [96.9 kB] Get: 60 http://deb.debian.org/debian buster/main armhf libnl-route-3-dev armhf 3.4.0-1 [162 kB] Get: 61 http://deb.debian.org/debian buster/main armhf libibverbs-dev armhf 22.1-1 [151 kB] Get: 62 http://deb.debian.org/debian buster/main armhf libpmix2 armhf 3.1.2-3 [449 kB] Get: 63 http://deb.debian.org/debian buster/main armhf libopenmpi3 armhf 3.1.3-11 [1890 kB] Get: 64 http://deb.debian.org/debian buster/main armhf openmpi-common all 3.1.3-11 [165 kB] Get: 65 http://deb.debian.org/debian buster/main armhf openmpi-bin armhf 3.1.3-11 [198 kB] Get: 66 http://deb.debian.org/debian buster/main armhf libopenmpi-dev armhf 3.1.3-11 [964 kB] Get: 67 http://deb.debian.org/debian buster/main armhf libsprng2 armhf 2.0a-12 [75.2 kB] Get: 68 http://deb.debian.org/debian buster/main armhf libsprng2-dev armhf 2.0a-12 [76.6 kB] Fetched 27.5 MB in 4s (6535 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ... Unpacking libuchardet0:armhf (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_armhf.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../04-libpipeline1_1.5.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_armhf.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic1:armhf (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_armhf.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libedit2:armhf. Preparing to unpack .../11-libedit2_3.1-20181209-1_armhf.deb ... Unpacking libedit2:armhf (3.1-20181209-1) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../12-libkeyutils1_1.6-6_armhf.deb ... Unpacking libkeyutils1:armhf (1.6-6) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../13-libkrb5support0_1.17-3_armhf.deb ... Unpacking libkrb5support0:armhf (1.17-3) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../14-libk5crypto3_1.17-3_armhf.deb ... Unpacking libk5crypto3:armhf (1.17-3) ... Selecting previously unselected package libssl1.1:armhf. Preparing to unpack .../15-libssl1.1_1.1.1d-0+deb10u3_armhf.deb ... Unpacking libssl1.1:armhf (1.1.1d-0+deb10u3) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../16-libkrb5-3_1.17-3_armhf.deb ... Unpacking libkrb5-3:armhf (1.17-3) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../17-libgssapi-krb5-2_1.17-3_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.17-3) ... Selecting previously unselected package openssh-client. Preparing to unpack .../18-openssh-client_1%3a7.9p1-10+deb10u2_armhf.deb ... Unpacking openssh-client (1:7.9p1-10+deb10u2) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../19-libsigsegv2_2.12-2_armhf.deb ... Unpacking libsigsegv2:armhf (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../20-m4_1.4.18-2_armhf.deb ... Unpacking m4 (1.4.18-2) ... 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Selecting previously unselected package libicu63:armhf. Preparing to unpack .../33-libicu63_63.1-6+deb10u1_armhf.deb ... Unpacking libicu63:armhf (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../34-libxml2_2.9.4+dfsg1-7+b3_armhf.deb ... Unpacking libxml2:armhf (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:armhf. Preparing to unpack .../35-libcroco3_0.6.12-3_armhf.deb ... Unpacking libcroco3:armhf (0.6.12-3) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../36-libncurses6_6.1+20181013-2+deb10u2_armhf.deb ... Unpacking libncurses6:armhf (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../37-gettext_0.19.8.1-9_armhf.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../38-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../39-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../40-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package libnl-3-200:armhf. Preparing to unpack .../41-libnl-3-200_3.4.0-1_armhf.deb ... Unpacking libnl-3-200:armhf (3.4.0-1) ... Selecting previously unselected package libnl-route-3-200:armhf. Preparing to unpack .../42-libnl-route-3-200_3.4.0-1_armhf.deb ... Unpacking libnl-route-3-200:armhf (3.4.0-1) ... Selecting previously unselected package libibverbs1:armhf. Preparing to unpack .../43-libibverbs1_22.1-1_armhf.deb ... Unpacking libibverbs1:armhf (22.1-1) ... Selecting previously unselected package ibverbs-providers:armhf. Preparing to unpack .../44-ibverbs-providers_22.1-1_armhf.deb ... Unpacking ibverbs-providers:armhf (22.1-1) ... Selecting previously unselected package libevent-2.1-6:armhf. Preparing to unpack .../45-libevent-2.1-6_2.1.8-stable-4_armhf.deb ... Unpacking libevent-2.1-6:armhf (2.1.8-stable-4) ... Selecting previously unselected package libevent-core-2.1-6:armhf. Preparing to unpack .../46-libevent-core-2.1-6_2.1.8-stable-4_armhf.deb ... Unpacking libevent-core-2.1-6:armhf (2.1.8-stable-4) ... Selecting previously unselected package libevent-pthreads-2.1-6:armhf. Preparing to unpack .../47-libevent-pthreads-2.1-6_2.1.8-stable-4_armhf.deb ... Unpacking libevent-pthreads-2.1-6:armhf (2.1.8-stable-4) ... Selecting previously unselected package libgfortran5:armhf. Preparing to unpack .../48-libgfortran5_8.3.0-6_armhf.deb ... Unpacking libgfortran5:armhf (8.3.0-6) ... Selecting previously unselected package libgmpxx4ldbl:armhf. Preparing to unpack .../49-libgmpxx4ldbl_2%3a6.1.2+dfsg-4_armhf.deb ... Unpacking libgmpxx4ldbl:armhf (2:6.1.2+dfsg-4) ... Selecting previously unselected package libgmp-dev:armhf. Preparing to unpack .../50-libgmp-dev_2%3a6.1.2+dfsg-4_armhf.deb ... Unpacking libgmp-dev:armhf (2:6.1.2+dfsg-4) ... Selecting previously unselected package libltdl7:armhf. Preparing to unpack .../51-libltdl7_2.4.6-9_armhf.deb ... Unpacking libltdl7:armhf (2.4.6-9) ... Selecting previously unselected package libhwloc5:armhf. Preparing to unpack .../52-libhwloc5_1.11.12-3_armhf.deb ... Unpacking libhwloc5:armhf (1.11.12-3) ... Selecting previously unselected package libltdl-dev:armhf. Preparing to unpack .../53-libltdl-dev_2.4.6-9_armhf.deb ... Unpacking libltdl-dev:armhf (2.4.6-9) ... Selecting previously unselected package libhwloc-dev:armhf. Preparing to unpack .../54-libhwloc-dev_1.11.12-3_armhf.deb ... Unpacking libhwloc-dev:armhf (1.11.12-3) ... Selecting previously unselected package libpciaccess0:armhf. Preparing to unpack .../55-libpciaccess0_0.14-1_armhf.deb ... Unpacking libpciaccess0:armhf (0.14-1) ... Selecting previously unselected package ocl-icd-libopencl1:armhf. Preparing to unpack .../56-ocl-icd-libopencl1_2.2.12-2_armhf.deb ... Unpacking ocl-icd-libopencl1:armhf (2.2.12-2) ... Selecting previously unselected package libhwloc-plugins:armhf. Preparing to unpack .../57-libhwloc-plugins_1.11.12-3_armhf.deb ... Unpacking libhwloc-plugins:armhf (1.11.12-3) ... Selecting previously unselected package libnl-3-dev:armhf. Preparing to unpack .../58-libnl-3-dev_3.4.0-1_armhf.deb ... Unpacking libnl-3-dev:armhf (3.4.0-1) ... Selecting previously unselected package libnl-route-3-dev:armhf. Preparing to unpack .../59-libnl-route-3-dev_3.4.0-1_armhf.deb ... Unpacking libnl-route-3-dev:armhf (3.4.0-1) ... Selecting previously unselected package libibverbs-dev:armhf. Preparing to unpack .../60-libibverbs-dev_22.1-1_armhf.deb ... Unpacking libibverbs-dev:armhf (22.1-1) ... Selecting previously unselected package libpmix2:armhf. Preparing to unpack .../61-libpmix2_3.1.2-3_armhf.deb ... Unpacking libpmix2:armhf (3.1.2-3) ... Selecting previously unselected package libopenmpi3:armhf. Preparing to unpack .../62-libopenmpi3_3.1.3-11_armhf.deb ... Unpacking libopenmpi3:armhf (3.1.3-11) ... Selecting previously unselected package openmpi-common. Preparing to unpack .../63-openmpi-common_3.1.3-11_all.deb ... Unpacking openmpi-common (3.1.3-11) ... Selecting previously unselected package openmpi-bin. Preparing to unpack .../64-openmpi-bin_3.1.3-11_armhf.deb ... Unpacking openmpi-bin (3.1.3-11) ... Selecting previously unselected package libopenmpi-dev:armhf. Preparing to unpack .../65-libopenmpi-dev_3.1.3-11_armhf.deb ... Unpacking libopenmpi-dev:armhf (3.1.3-11) ... Selecting previously unselected package libsprng2. Preparing to unpack .../66-libsprng2_2.0a-12_armhf.deb ... Unpacking libsprng2 (2.0a-12) ... Selecting previously unselected package libsprng2-dev. Preparing to unpack .../67-libsprng2-dev_2.0a-12_armhf.deb ... Unpacking libsprng2-dev (2.0a-12) ... Setting up libpipeline1:armhf (1.5.1-2) ... Setting up libpciaccess0:armhf (0.14-1) ... Setting up libkeyutils1:armhf (1.6-6) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:armhf (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libssl1.1:armhf (1.1.1d-0+deb10u3) ... Setting up libmagic1:armhf (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libicu63:armhf (63.1-6+deb10u1) ... Setting up libkrb5support0:armhf (1.17-3) ... Setting up autotools-dev (20180224.1) ... Setting up libgmpxx4ldbl:armhf (2:6.1.2+dfsg-4) ... Setting up libncurses6:armhf (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libk5crypto3:armhf (1.17-3) ... Setting up libltdl7:armhf (2.4.6-9) ... Setting up libevent-core-2.1-6:armhf (2.1.8-stable-4) ... Setting up libgfortran5:armhf (8.3.0-6) ... Setting up libevent-2.1-6:armhf (2.1.8-stable-4) ... Setting up sensible-utils (0.0.12) ... Setting up ocl-icd-libopencl1:armhf (2.2.12-2) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up libnl-3-200:armhf (3.4.0-1) ... Setting up openmpi-common (3.1.3-11) ... Setting up libkrb5-3:armhf (1.17-3) ... Setting up libbsd0:armhf (0.9.1-2) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up libxml2:armhf (2.9.4+dfsg1-7+b3) ... Setting up libsprng2 (2.0a-12) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libevent-pthreads-2.1-6:armhf (2.1.8-stable-4) ... Setting up libgmp-dev:armhf (2:6.1.2+dfsg-4) ... Setting up libtool (2.4.6-9) ... Setting up libhwloc5:armhf (1.11.12-3) ... Setting up libedit2:armhf (3.1-20181209-1) ... Setting up m4 (1.4.18-2) ... Setting up libhwloc-plugins:armhf (1.11.12-3) ... Setting up libnl-route-3-200:armhf (3.4.0-1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:armhf (1.17-3) ... Setting up libcroco3:armhf (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up libnl-3-dev:armhf (3.4.0-1) ... Setting up groff-base (1.22.4-3) ... Setting up libsprng2-dev (2.0a-12) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libibverbs1:armhf (22.1-1) ... Setting up gettext (0.19.8.1-9) ... Setting up libpmix2:armhf (3.1.2-3) ... Setting up ibverbs-providers:armhf (22.1-1) ... Setting up openssh-client (1:7.9p1-10+deb10u2) ... Setting up libopenmpi3:armhf (3.1.3-11) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libnl-route-3-dev:armhf (3.4.0-1) ... Setting up libltdl-dev:armhf (2.4.6-9) ... Setting up libhwloc-dev:armhf (1.11.12-3) ... Setting up openmpi-bin (3.1.3-11) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up po-debconf (1.0.21) ... Setting up libibverbs-dev:armhf (22.1-1) ... Setting up libopenmpi-dev:armhf (3.1.3-11) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/tree-puzzle-5.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package tree-puzzle dpkg-buildpackage: info: source version 5.2-11 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean --no-parallel dh_auto_clean -O--no-parallel dh_autoreconf_clean -O--no-parallel dh_clean -O--no-parallel debian/rules build dh build --no-parallel dh_update_autotools_config -O--no-parallel dh_autoreconf -O--no-parallel configure.ac:27: warning: underquoted definition of AC_TEST_MPICC configure.ac:27: run info Automake 'Extending aclocal' configure.ac:27: or see https://www.gnu.org/software/automake/manual/automake.html#Extending-aclocal configure.ac:11: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated. For more info, see: configure.ac:11: https://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_005fINIT_005fAUTOMAKE-invocation configure.ac:17: installing './compile' src/Makefile.am:45: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') parallel-tests: installing './test-driver' dh_auto_configure -O--no-parallel ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking target system type... arm-unknown-linux-gnueabihf checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking whether gcc and cc understand -c and -o together... yes checking whether make sets $(MAKE)... (cached) yes checking for mpcc... no checking for hcc... no checking for mpicc... /usr/bin/mpicc checking for mpicc_lam... no checking for mpicc_mpich... no checking for cc... /usr/bin/cc checking whether /usr/bin/mpicc works as MPI compiler... yes checking whether /usr/bin/mpicc handles quotes correctly... yes checking whether gcc handles quotes correctly... yes checking for main in -lm... yes checking for main in -lsprng... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for an ANSI C-conforming const... yes checking for size_t... 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 doc/Makefile config.status: creating data/Makefile config.status: creating tests/Makefile config.status: creating src/config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build -O--no-parallel make -j1 make[1]: Entering directory '/build/tree-puzzle-5.2' Making all in src make[2]: Entering directory '/build/tree-puzzle-5.2/src' make all-am make[3]: Entering directory '/build/tree-puzzle-5.2/src' gcc -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./gamma.c && mv gamma.o sgamma.o gcc -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./ml1.c && mv ml1.o sml1.o gcc -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./ml2.c && mv ml2.o sml2.o gcc -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./mlparam.c && mv mlparam.o smlparam.o gcc -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./model1.c && mv model1.o smodel1.o gcc -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./model2.c && mv model2.o smodel2.o gcc -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./puzzle1.c && mv puzzle1.o spuzzle1.o ./puzzle1.c: In function 'readallquarts': ./puzzle1.c:294:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(ifp, "TREE-PUZZLE\n"); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:295:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(ifp, "%s\n\n", dummyversion); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:297:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(ifp, "species: %d\n", &dummynspec); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:298:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(ifp, "quartets: %lu\n", &dummynquart); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:299:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(ifp, "bytes: %lu\n\n", &dummyblocklen); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:322:6: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(ifp, "%s\n", dummyname); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:335:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(quartetinfo[0]), sizeof(char), blocklen, ifp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c: In function 'setoptions': ./puzzle1.c:718:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%d", &locroot); ^~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:776:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", &fracinv); ^~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:795:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", &Geta); ^~~~~~~~~~~~~~~~~~~ ./puzzle1.c:813:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%d", &numcats); ^~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:915:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%d", &numclust); ^~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1115:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", &(Freqtpm[i])); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1149:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lu", &Numtrial); ^~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1164:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lu", &lmqts); ^~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1181:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%d", &outgroup); ^~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1449:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", &TSparam); ^~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1478:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", &YRparam); ^~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1502:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", &tstvf84); ^~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1515:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", >R_ACrate); ^~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1524:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", >R_AGrate); ^~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1533:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", >R_ATrate); ^~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1542:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", >R_CGrate); ^~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1551:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", >R_CTrate); ^~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1560:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", >R_GTrate); ^~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c: In function 'setfilenames': ./puzzle1.c:5283:28: warning: '%s' directive writing 6 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(OUTFILE ,"%s.%s", FILEPREFIX, OUTFILEEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 8 and 2055 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5284:28: warning: '%s' directive writing 4 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(TREEFILE ,"%s.%s", FILEPREFIX, TREEFILEEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 6 and 2053 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5285:28: warning: '%s' directive writing 4 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(DISTANCES ,"%s.%s", FILEPREFIX, DISTANCESEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 6 and 2053 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5286:28: warning: '%s' directive writing 3 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(TRIANGLE ,"%s.%s", FILEPREFIX, TRIANGLEEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 5 and 2052 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5287:28: warning: '%s' directive writing 5 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(UNRESOLVED ,"%s.%s", FILEPREFIX, UNRESOLVEDEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 2054 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5288:28: warning: '%s' directive writing 8 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(ALLQUART ,"%s.%s", FILEPREFIX, ALLQUARTEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 2057 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5289:28: warning: '%s' directive writing 10 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(ALLQUARTLH ,"%s.%s", FILEPREFIX, ALLQUARTLHEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 12 and 2059 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5290:28: warning: '%s' directive writing 6 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(SITELH ,"%s.%s", FILEPREFIX, SITELHEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 8 and 2055 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5291:28: warning: '%s' directive writing 7 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(SITELHB ,"%s.%s", FILEPREFIX, SITELHBEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 9 and 2056 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5292:28: warning: '%s' directive writing 8 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(SITERATE ,"%s.%s", FILEPREFIX, SITERATEEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 2057 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5293:28: warning: '%s' directive writing 9 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(SITERATEB ,"%s.%s", FILEPREFIX, SITERATEBEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 11 and 2058 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5294:28: warning: '%s' directive writing 5 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(OUTPARAM ,"%s.%s", FILEPREFIX, OUTPARAMEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 2054 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5295:28: warning: '%s' directive writing 10 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(SUBSET ,"%s.%s", FILEPREFIX, SUBSETEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 12 and 2059 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5296:28: warning: '%s' directive writing 5 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(OUTPTLIST ,"%s.%s", FILEPREFIX, OUTPTLISTEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 2054 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5297:28: warning: '%s' directive writing 7 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(OUTPTORDER ,"%s.%s", FILEPREFIX, OUTPTORDEREXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 9 and 2056 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./puzzle2.c && mv puzzle2.o spuzzle2.o gcc -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./pstep.c && mv pstep.o spstep.o gcc -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./util.c && mv util.o sutil.o gcc -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./consensus.c && mv consensus.o sconsensus.o gcc -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./treesort.c && mv treesort.o streesort.o gcc -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./treetest.c && mv treetest.o streetest.o gcc -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now sgamma.o sml1.o sml2.o smlparam.o smodel1.o smodel2.o spuzzle1.o spuzzle2.o spstep.o sutil.o sconsensus.o streesort.o streetest.o -lsprng -lm -o puzzle /usr/bin/mpicc -DPARALLEL -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./gamma.c && mv gamma.o pgamma.o /usr/bin/mpicc -DPARALLEL -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./ml1.c && mv ml1.o pml1.o /usr/bin/mpicc -DPARALLEL -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./ml2.c && mv ml2.o pml2.o /usr/bin/mpicc -DPARALLEL -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./mlparam.c && mv mlparam.o pmlparam.o /usr/bin/mpicc -DPARALLEL -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./model1.c && mv model1.o pmodel1.o /usr/bin/mpicc -DPARALLEL -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./model2.c && mv model2.o pmodel2.o /usr/bin/mpicc -DPARALLEL -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./puzzle1.c && mv puzzle1.o ppuzzle1.o ./puzzle1.c: In function 'readallquarts': ./puzzle1.c:294:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(ifp, "TREE-PUZZLE\n"); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:295:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(ifp, "%s\n\n", dummyversion); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:297:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(ifp, "species: %d\n", &dummynspec); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:298:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(ifp, "quartets: %lu\n", &dummynquart); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:299:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(ifp, "bytes: %lu\n\n", &dummyblocklen); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:322:6: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(ifp, "%s\n", dummyname); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:335:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(quartetinfo[0]), sizeof(char), blocklen, ifp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c: In function 'setoptions': ./puzzle1.c:718:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%d", &locroot); ^~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:776:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", &fracinv); ^~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:795:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", &Geta); ^~~~~~~~~~~~~~~~~~~ ./puzzle1.c:813:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%d", &numcats); ^~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:915:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%d", &numclust); ^~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1115:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", &(Freqtpm[i])); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1149:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lu", &Numtrial); ^~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1164:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lu", &lmqts); ^~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1181:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%d", &outgroup); ^~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1449:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", &TSparam); ^~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1478:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", &YRparam); ^~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1502:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", &tstvf84); ^~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1515:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", >R_ACrate); ^~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1524:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", >R_AGrate); ^~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1533:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", >R_ATrate); ^~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1542:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", >R_CGrate); ^~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1551:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", >R_CTrate); ^~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:1560:8: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%lf", >R_GTrate); ^~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c: In function 'setfilenames': ./puzzle1.c:5283:28: warning: '%s' directive writing 6 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(OUTFILE ,"%s.%s", FILEPREFIX, OUTFILEEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 8 and 2055 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5284:28: warning: '%s' directive writing 4 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(TREEFILE ,"%s.%s", FILEPREFIX, TREEFILEEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 6 and 2053 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5285:28: warning: '%s' directive writing 4 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(DISTANCES ,"%s.%s", FILEPREFIX, DISTANCESEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 6 and 2053 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5286:28: warning: '%s' directive writing 3 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(TRIANGLE ,"%s.%s", FILEPREFIX, TRIANGLEEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 5 and 2052 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5287:28: warning: '%s' directive writing 5 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(UNRESOLVED ,"%s.%s", FILEPREFIX, UNRESOLVEDEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 2054 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5288:28: warning: '%s' directive writing 8 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(ALLQUART ,"%s.%s", FILEPREFIX, ALLQUARTEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 2057 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5289:28: warning: '%s' directive writing 10 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(ALLQUARTLH ,"%s.%s", FILEPREFIX, ALLQUARTLHEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 12 and 2059 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5290:28: warning: '%s' directive writing 6 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(SITELH ,"%s.%s", FILEPREFIX, SITELHEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 8 and 2055 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5291:28: warning: '%s' directive writing 7 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(SITELHB ,"%s.%s", FILEPREFIX, SITELHBEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 9 and 2056 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5292:28: warning: '%s' directive writing 8 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(SITERATE ,"%s.%s", FILEPREFIX, SITERATEEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 2057 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5293:28: warning: '%s' directive writing 9 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(SITERATEB ,"%s.%s", FILEPREFIX, SITERATEBEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 11 and 2058 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5294:28: warning: '%s' directive writing 5 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(OUTPARAM ,"%s.%s", FILEPREFIX, OUTPARAMEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 2054 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5295:28: warning: '%s' directive writing 10 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(SUBSET ,"%s.%s", FILEPREFIX, SUBSETEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 12 and 2059 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5296:28: warning: '%s' directive writing 5 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(OUTPTLIST ,"%s.%s", FILEPREFIX, OUTPTLISTEXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 2054 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./puzzle1.c:5297:28: warning: '%s' directive writing 7 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] sprintf(OUTPTORDER ,"%s.%s", FILEPREFIX, OUTPTORDEREXT); ^~ In file included from /usr/include/stdio.h:873, from ./puzzle.h:32, from ./puzzle1.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 9 and 2056 bytes into a destination of size 2048 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/mpicc -DPARALLEL -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./puzzle2.c && mv puzzle2.o ppuzzle2.o /usr/bin/mpicc -DPARALLEL -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./pstep.c && mv pstep.o ppstep.o /usr/bin/mpicc -DPARALLEL -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./sched.c && mv sched.o psched.o /usr/bin/mpicc -DPARALLEL -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./util.c && mv util.o putil.o /usr/bin/mpicc -DPARALLEL -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./consensus.c && mv consensus.o pconsensus.o /usr/bin/mpicc -DPARALLEL -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./treesort.c && mv treesort.o ptreesort.o /usr/bin/mpicc -DPARALLEL -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./treetest.c && mv treetest.o ptreetest.o /usr/bin/mpicc -DPARALLEL -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -c ./ppuzzle.c ./ppuzzle.c: In function 'PP_Update_EEI': ./ppuzzle.c:300:2: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Eval[0]), &(Dtypeaddr[0])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:302:2: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Evec[0][0]), &(Dtypeaddr[1])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:304:2: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Ievc[0][0]), &(Dtypeaddr[2])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:306:2: warning: 'MPI_Type_struct' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(3, Dtypelens, Dtypeaddr, Dtypes, &PP_Data); ^~~~~~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1801:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ ./ppuzzle.c: In function 'PP_Final_Update': ./ppuzzle.c:344:2: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(DMVector[0]), &(Dtypeaddr[0])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:346:2: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Rates[0]), &(Dtypeaddr[1])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:348:2: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(fracinv), &(Dtypeaddr[2])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:350:2: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Eval[0]), &(Dtypeaddr[3])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:352:2: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Evec[0][0]), &(Dtypeaddr[4])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:354:2: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Ievc[0][0]), &(Dtypeaddr[5])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:356:2: warning: 'MPI_Type_struct' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(6, Dtypelens, Dtypeaddr, Dtypes, &PP_Data); ^~~~~~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1801:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ ./ppuzzle.c: In function 'PP_SendSizes': ./ppuzzle.c:722:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(ints, Dtypeaddr); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:723:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(doubles, (Dtypeaddr+1)); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:725:3: warning: 'MPI_Type_struct' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Sizes); ^~~~~~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1801:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ ./ppuzzle.c: In function 'PP_RecvSizes': ./ppuzzle.c:800:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(ints, Dtypeaddr); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:801:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(doubles, (Dtypeaddr+1)); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:803:3: warning: 'MPI_Type_struct' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Sizes); ^~~~~~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1801:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ ./ppuzzle.c: In function 'PP_RecvData': ./ppuzzle.c:892:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Seqpat[0][0]), &(Dtypeaddr[0])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:894:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Alias[0]), &(Dtypeaddr[1])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:896:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Weight[0]), &(Dtypeaddr[2])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:898:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(constpat[0]), &(Dtypeaddr[3])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:900:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Rates[0]), &(Dtypeaddr[4])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:902:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Eval[0]), &(Dtypeaddr[5])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:904:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Freqtpm[0]), &(Dtypeaddr[6])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:906:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Evec[0][0]), &(Dtypeaddr[7])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:908:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Ievc[0][0]), &(Dtypeaddr[8])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:910:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(iexp[0][0]), &(Dtypeaddr[9])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:912:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Distanmat[0][0]), &(Dtypeaddr[10])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:914:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(ltprobr[0][0][0]), &(Dtypeaddr[11])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:916:3: warning: 'MPI_Type_struct' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(12, Dtypelens, Dtypeaddr, Dtypes, &PP_Data); ^~~~~~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1801:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ ./ppuzzle.c: In function 'PP_SendData': ./ppuzzle.c:987:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Seqpat[0][0]), &(Dtypeaddr[0])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:989:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Alias[0]), &(Dtypeaddr[1])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:991:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Weight[0]), &(Dtypeaddr[2])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:993:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(constpat[0]), &(Dtypeaddr[3])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:995:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Rates[0]), &(Dtypeaddr[4])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:997:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Eval[0]), &(Dtypeaddr[5])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:999:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Freqtpm[0]), &(Dtypeaddr[6])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1001:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Evec[0][0]), &(Dtypeaddr[7])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1003:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Ievc[0][0]), &(Dtypeaddr[8])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1005:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(iexp[0][0]), &(Dtypeaddr [9])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1007:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(Distanmat[0][0]), &(Dtypeaddr[10])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1009:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(ltprobr[0][0][0]), &(Dtypeaddr[11])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1011:3: warning: 'MPI_Type_struct' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(12, Dtypelens, Dtypeaddr, Dtypes, &PP_Data); ^~~~~~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1801:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ ./ppuzzle.c: In function 'PP_SendQuart': ./ppuzzle.c:1153:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(ints, Dtypeaddr); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1154:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(doubles, (Dtypeaddr+1)); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1156:3: warning: 'MPI_Type_struct' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Quart); ^~~~~~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1801:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ ./ppuzzle.c: In function 'PP_RecvQuart': ./ppuzzle.c:1204:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(ints, Dtypeaddr); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1205:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(doubles, (Dtypeaddr+1)); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1207:3: warning: 'MPI_Type_struct' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Quart); ^~~~~~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1801:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ ./ppuzzle.c: In function 'PP_SendQuartBlock': ./ppuzzle.c:1371:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(ulis, Dtypeaddr); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1372:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(ints, (Dtypeaddr+1)); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1374:3: warning: 'MPI_Type_struct' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_QBlockSpecs); ^~~~~~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1801:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ ./ppuzzle.c:1387:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(trueaddr, DtypeaddrRes); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1390:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(bq, (DtypeaddrRes + 1)); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1392:3: warning: 'MPI_Type_struct' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(2, DtypelensRes, DtypeaddrRes, DtypesRes, &PP_QBlockRes); ^~~~~~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1801:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ ./ppuzzle.c: In function 'PP_RecvQuartBlock': ./ppuzzle.c:1458:2: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(ulis, Dtypeaddr); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1459:2: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(ints, (Dtypeaddr+1)); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1461:2: warning: 'MPI_Type_struct' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_QBlockSpecs); ^~~~~~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1801:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ ./ppuzzle.c:1489:2: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(trueaddr, DtypeaddrRes); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1494:2: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(bq, (DtypeaddrRes+1)); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1495:2: warning: 'MPI_Type_struct' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(2, DtypelensRes, DtypeaddrRes, DtypesRes, &PP_QBlockRes); ^~~~~~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1801:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ ./ppuzzle.c: In function 'PP_SendAllQuarts': ./ppuzzle.c:1640:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(quartetinfo[0]), Dtypeaddr); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1641:3: warning: 'MPI_Type_struct' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(1, Dtypelens, Dtypeaddr, Dtypes, &PP_AllQuarts); ^~~~~~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1801:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ ./ppuzzle.c: In function 'PP_RecvAllQuarts': ./ppuzzle.c:1689:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(quartetinfo[0]), Dtypeaddr); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1690:3: warning: 'MPI_Type_struct' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(1, Dtypelens, Dtypeaddr, Dtypes, &PP_AllQuarts); ^~~~~~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1801:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ ./ppuzzle.c: In function 'PP_SendSplitsBlock': ./ppuzzle.c:1751:5: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(biparts[n][0][0]), &(Dtypeaddr[n])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1757:5: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address((*pstptr).tree, &(Dtypeaddr[(int)blocksize + n])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1767:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(pstnumarr[0]), &(Dtypeaddr[((int)blocksize + pstnum)])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1769:3: warning: 'MPI_Type_struct' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(((int)blocksize + pstnum + 1), Dtypelens, Dtypeaddr, Dtypes, &PP_Biparts); ^~~~~~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1801:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ ./ppuzzle.c: In function 'PP_RecvSplitsBlock': ./ppuzzle.c:1846:5: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&((*bip)[n][0][0]), &(Dtypeaddr[n])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1852:5: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(pstarr[n][0]), &(Dtypeaddr[(int)*blocksize + n])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1857:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&(pstnumarr[0]), &(Dtypeaddr[(int)*blocksize + pstlistnum])); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:1859:3: warning: 'MPI_Type_struct' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(((int)*blocksize + pstlistnum + 1), Dtypelens, Dtypeaddr, Dtypes, &PP_Biparts); ^~~~~~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1801:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ ./ppuzzle.c: In function 'PP_SendDone': ./ppuzzle.c:2056:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(ints, Dtypeaddr); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:2057:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(doubles, (Dtypeaddr+1)); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:2059:3: warning: 'MPI_Type_struct' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Stats); ^~~~~~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1801:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ ./ppuzzle.c: In function 'PP_RecvDone': ./ppuzzle.c:2176:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(ints, Dtypeaddr); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:2177:3: warning: 'MPI_Address' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(doubles, (Dtypeaddr+1)); ^~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ ./ppuzzle.c:2179:3: warning: 'MPI_Type_struct' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Stats); ^~~~~~~~~~~~~~~ In file included from ./ppuzzle.c:25: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1801:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ /usr/bin/mpicc -g -O2 -ffile-prefix-map=/build/tree-puzzle-5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now pgamma.o pml1.o pml2.o pmlparam.o pmodel1.o pmodel2.o ppuzzle1.o ppuzzle2.o ppstep.o psched.o putil.o pconsensus.o ptreesort.o ptreetest.o ppuzzle.o -lsprng -lm -o ppuzzle make[3]: Leaving directory '/build/tree-puzzle-5.2/src' make[2]: Leaving directory '/build/tree-puzzle-5.2/src' Making all in doc make[2]: Entering directory '/build/tree-puzzle-5.2/doc' make[3]: Entering directory '/build/tree-puzzle-5.2/doc' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/tree-puzzle-5.2/doc' make[2]: Leaving directory '/build/tree-puzzle-5.2/doc' Making all in data make[2]: Entering directory '/build/tree-puzzle-5.2/data' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/tree-puzzle-5.2/data' Making all in tests make[2]: Entering directory '/build/tree-puzzle-5.2/tests' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/tree-puzzle-5.2/tests' make[2]: Entering directory '/build/tree-puzzle-5.2' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/tree-puzzle-5.2' make[1]: Leaving directory '/build/tree-puzzle-5.2' debian/rules override_dh_auto_test make[1]: Entering directory '/build/tree-puzzle-5.2' # unfortunately most tests are failing for the moment # the issue is documented in # debian/patches/patch_test_results.patch # and needs to be discussed with upstream dh_auto_test || true make -j1 check VERBOSE=1 make[2]: Entering directory '/build/tree-puzzle-5.2' Making check in src make[3]: Entering directory '/build/tree-puzzle-5.2/src' make[3]: Leaving directory '/build/tree-puzzle-5.2/src' Making check in doc make[3]: Entering directory '/build/tree-puzzle-5.2/doc' make[4]: Entering directory '/build/tree-puzzle-5.2/doc' make[4]: Nothing to be done for 'check-am'. make[4]: Leaving directory '/build/tree-puzzle-5.2/doc' make[3]: Leaving directory '/build/tree-puzzle-5.2/doc' Making check in data make[3]: Entering directory '/build/tree-puzzle-5.2/data' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/tree-puzzle-5.2/data' Making check in tests make[3]: Entering directory '/build/tree-puzzle-5.2/tests' make check-TESTS make[4]: Entering directory '/build/tree-puzzle-5.2/tests' make[5]: Entering directory '/build/tree-puzzle-5.2/tests' SKIP: build-puzzle FAIL: qp-pure-bin.test FAIL: qp-pure-nucl.test FAIL: qp-tn-nucl.test FAIL: qp-hky-clock-nucl.test FAIL: qp-hky-rhet-nucl.test FAIL: qp-hky-rhet-clock-nucl.test FAIL: qp-pure-prot.test FAIL: qp-mtrev-prot.test FAIL: qp-vt-prot.test FAIL: qp-wag-prot.test FAIL: qp-clock.test FAIL: qp-jtt-prot.test FAIL: qp-jtt-rhet-prot.test FAIL: qp-jtt-rhet-clock-prot.test FAIL: lm-pure-prot.test FAIL: ut-pure-prot.test FAIL: cons-pure-prot.test SKIP: build-remark ============================ : tests/test-suite.log ============================ # TOTAL: 19 # PASS: 0 # SKIP: 2 # XFAIL: 0 # FAIL: 17 # XPASS: 0 # ERROR: 0 .. contents:: :depth: 2 SKIP: build-puzzle ================== SKIP build-puzzle (exit status: 77) FAIL: qp-pure-bin ================= Testing: binary data, quartet puzzling (qp-pure-bin) ./qp-pure-bin.test: line 181: 18674 Segmentation fault ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 cat: qp-pure-bin.bin.puzzle: No such file or directory 0a1,214 > TREE-PUZZLE > > Input file name: qp-pure-bin.bin > Type of analysis: tree reconstruction > Parameter estimation: approximate (faster) > Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) > > Standard errors (S.E.) are obtained by the curvature method. > The upper and lower bounds of an approximate 95% confidence interval > for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. > > > SEQUENCE ALIGNMENT > > Input data: 5 sequences with 895 binary state sites > Number of constant sites: 825 (= 92.2% of all sites) > Number of site patterns: 16 > Number of constant site patterns: 2 (= 12.5% of all site patterns) > > > SUBSTITUTION PROCESS > > Model of substitution: Two-state model (Felsenstein 1981) > Binary state frequencies (estimated from data set): > > pi(0) = 41.8% > pi(1) = 58.2% > > > AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) > > gaps wildcards sum % sequence > Gibbon 0 0 0 0.00% > Human 0 0 0 0.00% > Chimpanzee 0 0 0 0.00% > Gorilla 0 0 0 0.00% > Orangutan 0 0 0 0.00% > ------------------------------------------------------- > Sum 0 0 0 0.00% > > > The table above shows the amount of gaps ('-') and other 'wildcard' > characters ('X', '?', etc.) and their percentage of the 895 columns > in the alignment. > Sequences with more than 50% ambiguous characters are marked with a '!' and > should be checked, whether they have sufficient overlap to other sequences. > Sequences with 100% ambiguous characters do not hold any phylogenetic > information and had to be discarded from the analysis. > > > > SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) > > 5% chi-square test p-value > Gibbon passed 41.61% > Human passed 73.47% > Chimpanzee passed 68.43% > Gorilla passed 94.60% > Orangutan passed 100.00% > > The chi-square tests compares the binary state composition of each sequence > to the frequency distribution assumed in the maximum likelihood model. > > > IDENTICAL SEQUENCES > > The sequences in each of the following groups are all identical. To speed > up computation please remove all but one of each group from the data set. > > All sequences are unique. > > > MAXIMUM LIKELIHOOD DISTANCES > > Maximum likelihood distances are computed using the selected model of > substitution and rate heterogeneity. > > 5 > Gibbon 0.00000 0.05300 0.05176 0.05295 0.06171 > Human 0.05300 0.00000 0.00563 0.00903 0.04081 > Chimpanzee 0.05176 0.00563 0.00000 0.01018 0.03960 > Gorilla 0.05295 0.00903 0.01018 0.00000 0.03835 > Orangutan 0.06171 0.04081 0.03960 0.03835 0.00000 > > Average distance (over all possible pairs of sequences): 0.03630 > minimum : 0.00563, maximum : 0.06171 > variance : 0.00043, std.dev. : 0.02066 > > > RATE HETEROGENEITY > > Model of rate heterogeneity: uniform rate > > > QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) > > > name | resolved | partly resolved | unresolved | sum > -------------------------------------------------------------------------- > Gibbon 4 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 4 > Human 4 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 4 > Chimpanzee 4 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 4 > Gorilla 4 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 4 > Orangutan 4 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 4 > -------------------------------------------------------------------------- > #quartets : 5 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 5 > > The table shows the occurrences of fully resolved, partially, and > completely unresolved quartets for each sequence and their percentage > relative to the number of times the sequence occurs in the list of > quartets (i.e. 4 quartets out of 5 in total). > In fully resolved quartet one single topology is supported, while for > partially resolved quartets two and for completely unresolved quartets > none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. > Note: Because 4 sequences are involved in one quartet numbers add up > to a four-fold of the existing quartets. > > Hint: The overall numbers in the last row give information about the > phylogenetic content of the dataset. The higher the percentage of partially > and unresolved quartets, the lower the content of phylogenetic information. > This can be visualized in more detail by likelihood mapping analysis. > > > > TREE SEARCH > > Quartet puzzling is used to choose from the possible tree topologies > and to simultaneously infer support values for internal branches. > > Number of puzzling steps: 1000 > Analysed quartets: 5 > Fully resolved quartets: 5 (= 100.0%) > Partly resolved quartets: 0 (= 0.0%) > Unresolved quartets: 0 (= 0.0%) > > Quartet trees are based on exact maximum likelihood values > using the selected model of substitution and rate heterogeneity. > > > QUARTET PUZZLING TREE > > Support for the internal branches of the unrooted quartet puzzling > tree topology is shown in percent. > > This quartet puzzling tree is completely resolved. > > > :---Human > :100: > :100: :---Chimpanzee > : : > : :-------Gorilla > : > :-----------Orangutan > : > :-----------Gibbon > > > Quartet puzzling tree (in CLUSTAL W notation): > > (Gibbon,((Human,Chimpanzee)100,Gorilla)100,Orangutan); > > > BIPARTITIONS > > The following bipartitions occured at least once in all intermediate > trees that have been generated in the 1000 puzzling steps. > Bipartitions included in the quartet puzzling tree: > (bipartition with sequences in input order : number of times seen) > > *..** : 1000 > *...* : 1000 > > Congruent bipartitions occurred in 50% or less, not included in > the consensus tree: > (bipartition with sequences in input order : number of times seen) > > None (all bipartitions are included) > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > > :-2 Human > :--6 > : :-3 Chimpanzee > :---7 > : :-4 Gorilla > : > :---5 Orangutan > : > :----1 Gibbon > > > branch length S.E. branch length S.E. > Gibbon 1 0.03803 0.00691 6 0.00339 0.00199 > Human 2 0.00240 0.00170 7 0.01106 0.00384 > Chimpanzee 3 0.00323 0.00196 > Gorilla 4 0.00353 0.00206 5 iterations until convergence > Orangutan 5 0.02357 0.00543 log L: -968.78 > > > Consensus tree with maximum likelihood branch lengths > (in CLUSTAL W notation): > > (Gibbon:0.03803,((Human:0.00240,Chimpanzee:0.00323)100:0.00339,Gorilla:0.00353) > 100:0.01106,Orangutan:0.02357); > > > TIME STAMP > FAIL qp-pure-bin.test (exit status: 1) FAIL: qp-pure-nucl ================== Testing: nucleotide data, default model, quartet puzzling (qp-pure-nucl) ./qp-pure-nucl.test: line 181: 18693 Segmentation fault ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 cat: qp-pure-nucl.nucl.puzzle: No such file or directory 0a1,295 > TREE-PUZZLE > > Input file name: qp-pure-nucl.nucl > Type of analysis: tree reconstruction > Parameter estimation: approximate (faster) > Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) > > Standard errors (S.E.) are obtained by the curvature method. > The upper and lower bounds of an approximate 95% confidence interval > for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. > > > SEQUENCE ALIGNMENT > > Input data: 8 sequences with 116 nucleotide sites > Number of constant sites: 66 (= 56.9% of all sites) > Number of site patterns: 54 > Number of constant site patterns: 4 (= 7.4% of all site patterns) > > > SUBSTITUTION PROCESS > > Model of substitution: HKY (Hasegawa et al. 1985) > Transition/transversion parameter (estimated from data set): 1.51 (S.E. 0.28) > > Rate matrix R (parameters restricted to selected model): > > A-C rate: 1.00000 > A-G rate: 2.98614 > A-T rate: 1.00000 > C-G rate: 1.00000 > C-T rate: 2.98614 > G-T rate: 1.00000 > > Nucleotide frequencies (estimated from data set): > > pi(A) = 26.6% > pi(C) = 30.6% > pi(G) = 12.0% > pi(T) = 30.7% > > Expected transition/transversion ratio: 1.60 > Expected pyrimidine transition/purine transition ratio: 2.95 > > > AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) > > gaps wildcards sum % sequence > Thylacinus 0 0 0 0.00% > Sarcophilu 0 0 0 0.00% > Dasyurus 0 1 1 0.86% > Echymipera 0 0 0 0.00% > Trichosuru 0 0 0 0.00% > Phalanger 0 0 0 0.00% > Philander 0 0 0 0.00% > Bos 0 0 0 0.00% > ------------------------------------------------------- > Sum 0 1 1 0.11% > > > The table above shows the amount of gaps ('-') and other 'wildcard' > characters ('X', '?', etc.) and their percentage of the 116 columns > in the alignment. > Sequences with more than 50% ambiguous characters are marked with a '!' and > should be checked, whether they have sufficient overlap to other sequences. > Sequences with 100% ambiguous characters do not hold any phylogenetic > information and had to be discarded from the analysis. > > > > SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) > > 5% chi-square test p-value > Thylacinus passed 90.89% > Sarcophilu passed 93.32% > Dasyurus passed 98.01% > Echymipera passed 92.83% > Trichosuru passed 90.41% > Phalanger passed 86.09% > Philander passed 66.19% > Bos passed 60.02% > > The chi-square tests compares the nucleotide composition of each sequence > to the frequency distribution assumed in the maximum likelihood model. > > > IDENTICAL SEQUENCES > > The sequences in each of the following groups are all identical. To speed > up computation please remove all but one of each group from the data set. > > All sequences are unique. > > > MAXIMUM LIKELIHOOD DISTANCES > > Maximum likelihood distances are computed using the selected model of > substitution and rate heterogeneity. > > 8 > Thylacinus 0.00000 0.25562 0.22032 0.24509 0.26007 0.24938 0.22246 > 0.23734 > Sarcophilu 0.25562 0.00000 0.13169 0.26969 0.28414 0.32680 0.26008 > 0.29786 > Dasyurus 0.22032 0.13169 0.00000 0.20032 0.24821 0.25234 0.17801 > 0.23883 > Echymipera 0.24509 0.26969 0.20032 0.00000 0.29531 0.33871 0.23041 > 0.27215 > Trichosuru 0.26007 0.28414 0.24821 0.29531 0.00000 0.21136 0.28562 > 0.27148 > Phalanger 0.24938 0.32680 0.25234 0.33871 0.21136 0.00000 0.29036 > 0.33042 > Philander 0.22246 0.26008 0.17801 0.23041 0.28562 0.29036 0.00000 > 0.22452 > Bos 0.23734 0.29786 0.23883 0.27215 0.27148 0.33042 0.22452 > 0.00000 > > Average distance (over all possible pairs of sequences): 0.25459 > minimum : 0.13169, maximum : 0.33871 > variance : 0.00207, std.dev. : 0.04544 > > > RATE HETEROGENEITY > > Model of rate heterogeneity: uniform rate > > > QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) > > > name | resolved | partly resolved | unresolved | sum > -------------------------------------------------------------------------- > Thylacinus 22 [ 62.86%] 4 [ 11.43%] 9 [ 25.71%] 35 > Sarcophilu 27 [ 77.14%] 1 [ 2.86%] 7 [ 20.00%] 35 > Dasyurus 27 [ 77.14%] 4 [ 11.43%] 4 [ 11.43%] 35 > Echymipera 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 > Trichosuru 27 [ 77.14%] 2 [ 5.71%] 6 [ 17.14%] 35 > Phalanger 28 [ 80.00%] 3 [ 8.57%] 4 [ 11.43%] 35 > Philander 25 [ 71.43%] 6 [ 17.14%] 4 [ 11.43%] 35 > Bos 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 > -------------------------------------------------------------------------- > #quartets : 49 [ 70.00%] 7 [ 10.00%] 14 [ 20.00%] 70 > > The table shows the occurrences of fully resolved, partially, and > completely unresolved quartets for each sequence and their percentage > relative to the number of times the sequence occurs in the list of > quartets (i.e. 35 quartets out of 70 in total). > In fully resolved quartet one single topology is supported, while for > partially resolved quartets two and for completely unresolved quartets > none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. > Note: Because 4 sequences are involved in one quartet numbers add up > to a four-fold of the existing quartets. > > Hint: The overall numbers in the last row give information about the > phylogenetic content of the dataset. The higher the percentage of partially > and unresolved quartets, the lower the content of phylogenetic information. > This can be visualized in more detail by likelihood mapping analysis. > > > > TREE SEARCH > > Quartet puzzling is used to choose from the possible tree topologies > and to simultaneously infer support values for internal branches. > > Number of puzzling steps: 1000 > Analysed quartets: 70 > Fully resolved quartets: 49 (= 70.0%) > Partly resolved quartets: 7 (= 10.0%) > Unresolved quartets: 14 (= 20.0%) > > Quartet trees are based on approximate maximum likelihood values > using the selected model of substitution and rate heterogeneity. > > > QUARTET PUZZLING TREE > > Support for the internal branches of the unrooted quartet puzzling > tree topology is shown in percent. > > This quartet puzzling tree is not completely resolved! > > > :---Trichosuru > :-----97: > : :---Phalanger > : > : :---Sarcophilu > : :-98: > : : :---Dasyurus > : : > :-71: :---Philander > : :-65: > : : :---Bos > : : > : :-------Echymipera > : > :-----------Thylacinus > > > Quartet puzzling tree (in CLUSTAL W notation): > > (Thylacinus,(Trichosuru,Phalanger)97,((Sarcophilu,Dasyurus)98, > (Philander,Bos)65,Echymipera)71); > > > BIPARTITIONS > > The following bipartitions occured at least once in all intermediate > trees that have been generated in the 1000 puzzling steps. > Bipartitions included in the quartet puzzling tree: > (bipartition with sequences in input order : number of times seen) > > *..***** : 981 > ****..** : 971 > *...**.. : 713 > ******.. : 649 > > Congruent bipartitions occurred in 50% or less, not included in > the consensus tree: > (bipartition with sequences in input order : number of times seen) > > *...**** : 426 > > Incongruent bipartitions not included in the consensus tree: > (bipartition with sequences in input order : number of times seen) > > ***.**.. : 347 > ***.**.* : 150 > *...**.* : 131 > *..***.. : 87 > *..*..** : 81 > *.....** : 72 > ****..*. : 55 > ***.***. : 37 > ****.... : 36 > *..***.* : 36 > ***..... : 31 > *.....*. : 28 > *...***. : 27 > *......* : 27 > *....*.. : 26 > *..*.... : 21 > **..**** : 16 > ***...** : 14 > *..*..*. : 13 > *..****. : 12 > > (6 other less frequent bipartitions not shown) > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > > :---------5 Trichosuru > :------9 > : :----------6 Phalanger > : > : :-----------2 Sarcophilu > : :-------10 > : : :-3 Dasyurus > :-----12 > : : :--------7 Philander > : :----11 > : : :-----------8 Bos > : : > : :------------4 Echymipera > : > :---------1 Thylacinus > > > branch length S.E. branch length S.E. > Thylacinus 1 0.11024 0.03812 9 0.05953 0.03382 > Sarcophilu 2 0.13180 0.03734 10 0.08585 0.03452 > Dasyurus 3 0.00572 0.01273 11 0.04220 0.02513 > Echymipera 4 0.13997 0.04108 12 0.05457 0.02998 > Trichosuru 5 0.10654 0.03770 > Phalanger 6 0.12258 0.04064 > Philander 7 0.08995 0.03428 8 iterations until convergence > Bos 8 0.13479 0.04095 log L: -603.37 > > > Consensus tree with maximum likelihood branch lengths > (in CLUSTAL W notation): > > (Thylacinus:0.11024,(Trichosuru:0.10654,Phalanger:0.12258)97:0.05953, > ((Sarcophilu:0.13180,Dasyurus:0.00572)98:0.08585,(Philander:0.08995, > Bos:0.13479)65:0.04220,Echymipera:0.13997)71:0.05457); > > > TIME STAMP > FAIL qp-pure-nucl.test (exit status: 1) FAIL: qp-tn-nucl ================ Testing: nucleotide data, TN, quartet puzzling (qp-tn-nucl) ./qp-tn-nucl.test: line 181: 18712 Segmentation fault ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 cat: qp-tn-nucl.nucl.puzzle: No such file or directory 0a1,296 > TREE-PUZZLE > > Input file name: qp-tn-nucl.nucl > Type of analysis: tree reconstruction > Parameter estimation: approximate (faster) > Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) > > Standard errors (S.E.) are obtained by the curvature method. > The upper and lower bounds of an approximate 95% confidence interval > for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. > > > SEQUENCE ALIGNMENT > > Input data: 8 sequences with 116 nucleotide sites > Number of constant sites: 66 (= 56.9% of all sites) > Number of site patterns: 54 > Number of constant site patterns: 4 (= 7.4% of all site patterns) > > > SUBSTITUTION PROCESS > > Model of substitution: TN (Tamura-Nei 1993) > Transition/transversion parameter (estimated from data set): 1.24 (S.E. 0.61) > Y/R transition parameter (estimated from data set): 2.27 (S.E. 0.65) > > Rate matrix R (parameters restricted to selected model): > > A-C rate: 1.00000 > A-G rate: 1.52641 > A-T rate: 1.00000 > C-G rate: 1.00000 > C-T rate: 3.42338 > G-T rate: 1.00000 > > Nucleotide frequencies (estimated from data set): > > pi(A) = 26.6% > pi(C) = 30.6% > pi(G) = 12.0% > pi(T) = 30.7% > > Expected transition/transversion ratio: 1.57 > Expected pyrimidine transition/purine transition ratio: 6.69 > > > AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) > > gaps wildcards sum % sequence > Thylacinus 0 0 0 0.00% > Sarcophilu 0 0 0 0.00% > Dasyurus 0 1 1 0.86% > Echymipera 0 0 0 0.00% > Trichosuru 0 0 0 0.00% > Phalanger 0 0 0 0.00% > Philander 0 0 0 0.00% > Bos 0 0 0 0.00% > ------------------------------------------------------- > Sum 0 1 1 0.11% > > > The table above shows the amount of gaps ('-') and other 'wildcard' > characters ('X', '?', etc.) and their percentage of the 116 columns > in the alignment. > Sequences with more than 50% ambiguous characters are marked with a '!' and > should be checked, whether they have sufficient overlap to other sequences. > Sequences with 100% ambiguous characters do not hold any phylogenetic > information and had to be discarded from the analysis. > > > > SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) > > 5% chi-square test p-value > Thylacinus passed 90.89% > Sarcophilu passed 93.32% > Dasyurus passed 98.01% > Echymipera passed 92.83% > Trichosuru passed 90.41% > Phalanger passed 86.09% > Philander passed 66.19% > Bos passed 60.02% > > The chi-square tests compares the nucleotide composition of each sequence > to the frequency distribution assumed in the maximum likelihood model. > > > IDENTICAL SEQUENCES > > The sequences in each of the following groups are all identical. To speed > up computation please remove all but one of each group from the data set. > > All sequences are unique. > > > MAXIMUM LIKELIHOOD DISTANCES > > Maximum likelihood distances are computed using the selected model of > substitution and rate heterogeneity. > > 8 > Thylacinus 0.00000 0.25968 0.22378 0.25026 0.26619 0.25302 0.22610 > 0.24162 > Sarcophilu 0.25968 0.00000 0.13240 0.27376 0.28965 0.33121 0.26282 > 0.30169 > Dasyurus 0.22378 0.13240 0.00000 0.20328 0.25274 0.25432 0.17972 > 0.24235 > Echymipera 0.25026 0.27376 0.20328 0.00000 0.30289 0.34430 0.23479 > 0.27773 > Trichosuru 0.26619 0.28965 0.25274 0.30289 0.00000 0.21414 0.29157 > 0.27782 > Phalanger 0.25302 0.33121 0.25432 0.34430 0.21414 0.00000 0.29425 > 0.33582 > Philander 0.22610 0.26282 0.17972 0.23479 0.29157 0.29425 0.00000 > 0.22749 > Bos 0.24162 0.30169 0.24235 0.27773 0.27782 0.33582 0.22749 > 0.00000 > > Average distance (over all possible pairs of sequences): 0.25876 > minimum : 0.13240, maximum : 0.34430 > variance : 0.00217, std.dev. : 0.04653 > > > RATE HETEROGENEITY > > Model of rate heterogeneity: uniform rate > > > QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) > > > name | resolved | partly resolved | unresolved | sum > -------------------------------------------------------------------------- > Thylacinus 21 [ 60.00%] 4 [ 11.43%] 10 [ 28.57%] 35 > Sarcophilu 26 [ 74.29%] 1 [ 2.86%] 8 [ 22.86%] 35 > Dasyurus 27 [ 77.14%] 2 [ 5.71%] 6 [ 17.14%] 35 > Echymipera 19 [ 54.29%] 3 [ 8.57%] 13 [ 37.14%] 35 > Trichosuru 25 [ 71.43%] 4 [ 11.43%] 6 [ 17.14%] 35 > Phalanger 28 [ 80.00%] 1 [ 2.86%] 6 [ 17.14%] 35 > Philander 23 [ 65.71%] 5 [ 14.29%] 7 [ 20.00%] 35 > Bos 19 [ 54.29%] 4 [ 11.43%] 12 [ 34.29%] 35 > -------------------------------------------------------------------------- > #quartets : 47 [ 67.14%] 6 [ 8.57%] 17 [ 24.29%] 70 > > The table shows the occurrences of fully resolved, partially, and > completely unresolved quartets for each sequence and their percentage > relative to the number of times the sequence occurs in the list of > quartets (i.e. 35 quartets out of 70 in total). > In fully resolved quartet one single topology is supported, while for > partially resolved quartets two and for completely unresolved quartets > none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. > Note: Because 4 sequences are involved in one quartet numbers add up > to a four-fold of the existing quartets. > > Hint: The overall numbers in the last row give information about the > phylogenetic content of the dataset. The higher the percentage of partially > and unresolved quartets, the lower the content of phylogenetic information. > This can be visualized in more detail by likelihood mapping analysis. > > > > TREE SEARCH > > Quartet puzzling is used to choose from the possible tree topologies > and to simultaneously infer support values for internal branches. > > Number of puzzling steps: 1000 > Analysed quartets: 70 > Fully resolved quartets: 47 (= 67.1%) > Partly resolved quartets: 6 (= 8.6%) > Unresolved quartets: 17 (= 24.3%) > > Quartet trees are based on approximate maximum likelihood values > using the selected model of substitution and rate heterogeneity. > > > QUARTET PUZZLING TREE > > Support for the internal branches of the unrooted quartet puzzling > tree topology is shown in percent. > > This quartet puzzling tree is not completely resolved! > > > :---Trichosuru > :-----94: > : :---Phalanger > : > : :---Sarcophilu > : :-98: > : : :---Dasyurus > : : > :-63: :---Philander > : :-67: > : : :---Bos > : : > : :-------Echymipera > : > :-----------Thylacinus > > > Quartet puzzling tree (in CLUSTAL W notation): > > (Thylacinus,(Trichosuru,Phalanger)94,((Sarcophilu,Dasyurus)98, > (Philander,Bos)67,Echymipera)63); > > > BIPARTITIONS > > The following bipartitions occured at least once in all intermediate > trees that have been generated in the 1000 puzzling steps. > Bipartitions included in the quartet puzzling tree: > (bipartition with sequences in input order : number of times seen) > > *..***** : 979 > ****..** : 935 > ******.. : 666 > *...**.. : 629 > > Congruent bipartitions occurred in 50% or less, not included in > the consensus tree: > (bipartition with sequences in input order : number of times seen) > > *...**** : 422 > > Incongruent bipartitions not included in the consensus tree: > (bipartition with sequences in input order : number of times seen) > > ***.**.. : 271 > *..***.. : 132 > *...**.* : 122 > ***.**.* : 112 > *..*..** : 94 > *.....** : 88 > ****.... : 83 > ****..*. : 79 > *..*.... : 65 > *....*.. : 56 > *..***.* : 49 > ***.***. : 40 > ***..... : 36 > **..**** : 21 > *..*..*. : 21 > *.....*. : 20 > *......* : 19 > *...***. : 17 > ***...** : 13 > ****.**. : 7 > > (9 other less frequent bipartitions not shown) > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > > :---------5 Trichosuru > :------9 > : :----------6 Phalanger > : > : :----------2 Sarcophilu > : :-------10 > : : :-3 Dasyurus > :-----12 > : : :-------7 Philander > : :----11 > : : :-----------8 Bos > : : > : :------------4 Echymipera > : > :---------1 Thylacinus > > > branch length S.E. branch length S.E. > Thylacinus 1 0.11472 0.03957 9 0.05924 0.03453 > Sarcophilu 2 0.12889 0.03726 10 0.08141 0.03441 > Dasyurus 3 0.00946 0.01286 11 0.04411 0.02610 > Echymipera 4 0.14312 0.04216 12 0.05429 0.03071 > Trichosuru 5 0.10849 0.03850 > Phalanger 6 0.12332 0.04128 > Philander 7 0.09008 0.03478 7 iterations until convergence > Bos 8 0.13724 0.04194 log L: -600.80 > > > Consensus tree with maximum likelihood branch lengths > (in CLUSTAL W notation): > > (Thylacinus:0.11472,(Trichosuru:0.10849,Phalanger:0.12332)94:0.05924, > ((Sarcophilu:0.12889,Dasyurus:0.00946)98:0.08141,(Philander:0.09008, > Bos:0.13724)67:0.04411,Echymipera:0.14312)63:0.05429); > > > TIME STAMP > FAIL qp-tn-nucl.test (exit status: 1) FAIL: qp-hky-clock-nucl ======================= Testing: nucleotide data, HKY, clock, quartet puzzling (qp-hky-clock-nucl) ./qp-hky-clock-nucl.test: line 181: 18731 Segmentation fault ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 cat: qp-hky-clock-nucl.nucl.puzzle: No such file or directory 0a1,368 > TREE-PUZZLE > > Input file name: qp-hky-clock-nucl.nucl > Type of analysis: tree reconstruction > Parameter estimation: approximate (faster) > Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) > > Standard errors (S.E.) are obtained by the curvature method. > The upper and lower bounds of an approximate 95% confidence interval > for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. > > > SEQUENCE ALIGNMENT > > Input data: 8 sequences with 116 nucleotide sites > Number of constant sites: 66 (= 56.9% of all sites) > Number of site patterns: 54 > Number of constant site patterns: 4 (= 7.4% of all site patterns) > > > SUBSTITUTION PROCESS > > Model of substitution: HKY (Hasegawa et al. 1985) > Transition/transversion parameter (estimated from data set): 1.51 (S.E. 0.28) > > Rate matrix R (parameters restricted to selected model): > > A-C rate: 1.00000 > A-G rate: 2.98614 > A-T rate: 1.00000 > C-G rate: 1.00000 > C-T rate: 2.98614 > G-T rate: 1.00000 > > Nucleotide frequencies (estimated from data set): > > pi(A) = 26.6% > pi(C) = 30.6% > pi(G) = 12.0% > pi(T) = 30.7% > > Expected transition/transversion ratio: 1.60 > Expected pyrimidine transition/purine transition ratio: 2.95 > > > AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) > > gaps wildcards sum % sequence > Thylacinus 0 0 0 0.00% > Sarcophilu 0 0 0 0.00% > Dasyurus 0 1 1 0.86% > Echymipera 0 0 0 0.00% > Trichosuru 0 0 0 0.00% > Phalanger 0 0 0 0.00% > Philander 0 0 0 0.00% > Bos 0 0 0 0.00% > ------------------------------------------------------- > Sum 0 1 1 0.11% > > > The table above shows the amount of gaps ('-') and other 'wildcard' > characters ('X', '?', etc.) and their percentage of the 116 columns > in the alignment. > Sequences with more than 50% ambiguous characters are marked with a '!' and > should be checked, whether they have sufficient overlap to other sequences. > Sequences with 100% ambiguous characters do not hold any phylogenetic > information and had to be discarded from the analysis. > > > > SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) > > 5% chi-square test p-value > Thylacinus passed 90.89% > Sarcophilu passed 93.32% > Dasyurus passed 98.01% > Echymipera passed 92.83% > Trichosuru passed 90.41% > Phalanger passed 86.09% > Philander passed 66.19% > Bos passed 60.02% > > The chi-square tests compares the nucleotide composition of each sequence > to the frequency distribution assumed in the maximum likelihood model. > > > IDENTICAL SEQUENCES > > The sequences in each of the following groups are all identical. To speed > up computation please remove all but one of each group from the data set. > > All sequences are unique. > > > MAXIMUM LIKELIHOOD DISTANCES > > Maximum likelihood distances are computed using the selected model of > substitution and rate heterogeneity. > > 8 > Thylacinus 0.00000 0.25562 0.22032 0.24509 0.26007 0.24938 0.22246 > 0.23734 > Sarcophilu 0.25562 0.00000 0.13169 0.26969 0.28414 0.32680 0.26008 > 0.29786 > Dasyurus 0.22032 0.13169 0.00000 0.20032 0.24821 0.25234 0.17801 > 0.23883 > Echymipera 0.24509 0.26969 0.20032 0.00000 0.29531 0.33871 0.23041 > 0.27215 > Trichosuru 0.26007 0.28414 0.24821 0.29531 0.00000 0.21136 0.28562 > 0.27148 > Phalanger 0.24938 0.32680 0.25234 0.33871 0.21136 0.00000 0.29036 > 0.33042 > Philander 0.22246 0.26008 0.17801 0.23041 0.28562 0.29036 0.00000 > 0.22452 > Bos 0.23734 0.29786 0.23883 0.27215 0.27148 0.33042 0.22452 > 0.00000 > > Average distance (over all possible pairs of sequences): 0.25459 > minimum : 0.13169, maximum : 0.33871 > variance : 0.00207, std.dev. : 0.04544 > > > RATE HETEROGENEITY > > Model of rate heterogeneity: uniform rate > > > QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) > > > name | resolved | partly resolved | unresolved | sum > -------------------------------------------------------------------------- > Thylacinus 22 [ 62.86%] 4 [ 11.43%] 9 [ 25.71%] 35 > Sarcophilu 27 [ 77.14%] 1 [ 2.86%] 7 [ 20.00%] 35 > Dasyurus 27 [ 77.14%] 4 [ 11.43%] 4 [ 11.43%] 35 > Echymipera 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 > Trichosuru 27 [ 77.14%] 2 [ 5.71%] 6 [ 17.14%] 35 > Phalanger 28 [ 80.00%] 3 [ 8.57%] 4 [ 11.43%] 35 > Philander 25 [ 71.43%] 6 [ 17.14%] 4 [ 11.43%] 35 > Bos 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 > -------------------------------------------------------------------------- > #quartets : 49 [ 70.00%] 7 [ 10.00%] 14 [ 20.00%] 70 > > The table shows the occurrences of fully resolved, partially, and > completely unresolved quartets for each sequence and their percentage > relative to the number of times the sequence occurs in the list of > quartets (i.e. 35 quartets out of 70 in total). > In fully resolved quartet one single topology is supported, while for > partially resolved quartets two and for completely unresolved quartets > none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. > Note: Because 4 sequences are involved in one quartet numbers add up > to a four-fold of the existing quartets. > > Hint: The overall numbers in the last row give information about the > phylogenetic content of the dataset. The higher the percentage of partially > and unresolved quartets, the lower the content of phylogenetic information. > This can be visualized in more detail by likelihood mapping analysis. > > > > TREE SEARCH > > Quartet puzzling is used to choose from the possible tree topologies > and to simultaneously infer support values for internal branches. > > Number of puzzling steps: 1000 > Analysed quartets: 70 > Fully resolved quartets: 49 (= 70.0%) > Partly resolved quartets: 7 (= 10.0%) > Unresolved quartets: 14 (= 20.0%) > > Quartet trees are based on approximate maximum likelihood values > using the selected model of substitution and rate heterogeneity. > > > QUARTET PUZZLING TREE > > Support for the internal branches of the unrooted quartet puzzling > tree topology is shown in percent. > > This quartet puzzling tree is not completely resolved! > > > :---Trichosuru > :-----97: > : :---Phalanger > : > : :---Sarcophilu > : :-98: > : : :---Dasyurus > : : > :-71: :---Philander > : :-65: > : : :---Bos > : : > : :-------Echymipera > : > :-----------Thylacinus > > > Quartet puzzling tree (in CLUSTAL W notation): > > (Thylacinus,(Trichosuru,Phalanger)97,((Sarcophilu,Dasyurus)98, > (Philander,Bos)65,Echymipera)71); > > > BIPARTITIONS > > The following bipartitions occured at least once in all intermediate > trees that have been generated in the 1000 puzzling steps. > Bipartitions included in the quartet puzzling tree: > (bipartition with sequences in input order : number of times seen) > > *..***** : 981 > ****..** : 971 > *...**.. : 713 > ******.. : 649 > > Congruent bipartitions occurred in 50% or less, not included in > the consensus tree: > (bipartition with sequences in input order : number of times seen) > > *...**** : 426 > > Incongruent bipartitions not included in the consensus tree: > (bipartition with sequences in input order : number of times seen) > > ***.**.. : 347 > ***.**.* : 150 > *...**.* : 131 > *..***.. : 87 > *..*..** : 81 > *.....** : 72 > ****..*. : 55 > ***.***. : 37 > ****.... : 36 > *..***.* : 36 > ***..... : 31 > *.....*. : 28 > *...***. : 27 > *......* : 27 > *....*.. : 26 > *..*.... : 21 > **..**** : 16 > ***...** : 14 > *..*..*. : 13 > *..****. : 12 > > (6 other less frequent bipartitions not shown) > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > > :---------5 Trichosuru > :------9 > : :----------6 Phalanger > : > : :-----------2 Sarcophilu > : :-------10 > : : :-3 Dasyurus > :-----12 > : : :--------7 Philander > : :----11 > : : :-----------8 Bos > : : > : :------------4 Echymipera > : > :---------1 Thylacinus > > > branch length S.E. branch length S.E. > Thylacinus 1 0.11024 0.03812 9 0.05953 0.03382 > Sarcophilu 2 0.13180 0.03734 10 0.08585 0.03452 > Dasyurus 3 0.00572 0.01273 11 0.04220 0.02513 > Echymipera 4 0.13997 0.04108 12 0.05457 0.02998 > Trichosuru 5 0.10654 0.03770 > Phalanger 6 0.12258 0.04064 > Philander 7 0.08995 0.03428 8 iterations until convergence > Bos 8 0.13479 0.04095 log L: -603.37 > > > Consensus tree with maximum likelihood branch lengths > (in CLUSTAL W notation): > > (Thylacinus:0.11024,(Trichosuru:0.10654,Phalanger:0.12258)97:0.05953, > ((Sarcophilu:0.13180,Dasyurus:0.00572)98:0.08585,(Philander:0.08995, > Bos:0.13479)65:0.04220,Echymipera:0.13997)71:0.05457); > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > Root located at branch: 1 "Thylacinus" (automatic search) > > If the automatic search misplaces the root please rerun the analysis > (rename "outtree" to "intree") and select location of root manually! > > > :---------5 Trichosuru > :-----9 > : :---------6 Phalanger > : > : :-----2 Sarcophilu > : :------10 > : : :-----3 Dasyurus > :--12 > : : :--------7 Philander > : :---11 > : : :--------8 Bos > : : > : :-----------4 Echymipera > : > :------------1 Thylacinus > > > Tree drawn as unrooted tree for better comparison with non-clock tree! > > branch length nc/c branch length nc/c (= non-clock/clock) > Thylacinus 1 0.14706 0.750 9 0.04504 1.322 > Sarcophilu 2 0.06189 2.130 10 0.06663 1.288 > Dasyurus 3 0.06189 0.092 11 0.03304 1.277 > Echymipera 4 0.12852 1.089 12 0.01851 2.948 > Trichosuru 5 0.10199 1.045 > Phalanger 6 0.10199 1.202 > Philander 7 0.09549 0.942 6 iterations until convergence > Bos 8 0.09549 1.412 log L: -610.75 > > height S.E. of node common to branches > 0.10199 0.01922 9 5 6 > 0.06189 0.01495 10 2 3 > 0.09549 0.01498 11 7 8 > 0.12852 0.01108 12 10 11 4 > 0.14704 0.01235 1 9 12 > 0.14705 0.02366 of root at branch 1 > > > Rooted consensus tree with clocklike maximum likelihood branch lengths > (in CLUSTAL W notation): > > (Thylacinus:0.14705,((Trichosuru:0.10199,Phalanger:0.10199)97:0.04504 > ,((Sarcophilu:0.06189,Dasyurus:0.06189)98:0.06663,(Philander:0.09549, > Bos:0.09549)65:0.03304,Echymipera:0.12852)71:0.01851):0.00001); > > > MOLECULAR CLOCK LIKELIHOOD RATIO TEST > > log L without clock: -603.37 (independent branch parameters: 12) > log L with clock: -610.75 (independent branch parameters: 6) > > Likelihood ratio test statistic delta: 14.77 > Degress of freedom of chi-square distribution: 6 > Critical significance level: 2.22% > > The simpler (clocklike) tree is rejected on a significance level > of 5%. The log-likelihood of the more complex (no clock) tree is > significantly increased. > > Please take care that the correct root is used! > > > TIME STAMP > FAIL qp-hky-clock-nucl.test (exit status: 1) FAIL: qp-hky-rhet-nucl ====================== Testing: nucleotide data, HKY, rate heterogeneity, quartet puzzling (qp-hky-rhet-nucl) ./qp-hky-rhet-nucl.test: line 181: 18750 Segmentation fault ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 cat: qp-hky-rhet-nucl.nucl.puzzle: No such file or directory 0a1,321 > TREE-PUZZLE > > Input file name: qp-hky-rhet-nucl.nucl > Type of analysis: tree reconstruction > Parameter estimation: approximate (faster) > Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) > > Standard errors (S.E.) are obtained by the curvature method. > The upper and lower bounds of an approximate 95% confidence interval > for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. > > > SEQUENCE ALIGNMENT > > Input data: 8 sequences with 116 nucleotide sites > Number of constant sites: 66 (= 56.9% of all sites) > Number of site patterns: 54 > Number of constant site patterns: 4 (= 7.4% of all site patterns) > > > SUBSTITUTION PROCESS > > Model of substitution: HKY (Hasegawa et al. 1985) > Transition/transversion parameter (estimated from data set): 2.95 (S.E. 0.84) > > Rate matrix R (parameters restricted to selected model): > > A-C rate: 1.00000 > A-G rate: 5.85063 > A-T rate: 1.00000 > C-G rate: 1.00000 > C-T rate: 5.85063 > G-T rate: 1.00000 > > Nucleotide frequencies (estimated from data set): > > pi(A) = 26.6% > pi(C) = 30.6% > pi(G) = 12.0% > pi(T) = 30.7% > > Expected transition/transversion ratio: 3.14 > Expected pyrimidine transition/purine transition ratio: 2.95 > > > AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) > > gaps wildcards sum % sequence > Thylacinus 0 0 0 0.00% > Sarcophilu 0 0 0 0.00% > Dasyurus 0 1 1 0.86% > Echymipera 0 0 0 0.00% > Trichosuru 0 0 0 0.00% > Phalanger 0 0 0 0.00% > Philander 0 0 0 0.00% > Bos 0 0 0 0.00% > ------------------------------------------------------- > Sum 0 1 1 0.11% > > > The table above shows the amount of gaps ('-') and other 'wildcard' > characters ('X', '?', etc.) and their percentage of the 116 columns > in the alignment. > Sequences with more than 50% ambiguous characters are marked with a '!' and > should be checked, whether they have sufficient overlap to other sequences. > Sequences with 100% ambiguous characters do not hold any phylogenetic > information and had to be discarded from the analysis. > > > > SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) > > 5% chi-square test p-value > Thylacinus passed 90.89% > Sarcophilu passed 93.32% > Dasyurus passed 98.01% > Echymipera passed 92.83% > Trichosuru passed 90.41% > Phalanger passed 86.09% > Philander passed 66.19% > Bos passed 60.02% > > The chi-square tests compares the nucleotide composition of each sequence > to the frequency distribution assumed in the maximum likelihood model. > > > IDENTICAL SEQUENCES > > The sequences in each of the following groups are all identical. To speed > up computation please remove all but one of each group from the data set. > > All sequences are unique. > > > MAXIMUM LIKELIHOOD DISTANCES > > Maximum likelihood distances are computed using the selected model of > substitution and rate heterogeneity. > > 8 > Thylacinus 0.00000 0.52940 0.37900 0.52236 0.58922 0.56150 0.43932 > 0.55291 > Sarcophilu 0.52940 0.00000 0.17837 0.62532 0.69892 0.93602 0.62327 > 0.78596 > Dasyurus 0.37900 0.17837 0.00000 0.39032 0.53431 0.60369 0.31919 > 0.56220 > Echymipera 0.52236 0.62532 0.39032 0.00000 0.70229 0.94283 0.42016 > 0.66063 > Trichosuru 0.58922 0.69892 0.53431 0.70229 0.00000 0.39416 0.70017 > 0.62697 > Phalanger 0.56150 0.93602 0.60369 0.94283 0.39416 0.00000 0.78658 > 0.98921 > Philander 0.43932 0.62327 0.31919 0.42016 0.70017 0.78658 0.00000 > 0.49264 > Bos 0.55291 0.78596 0.56220 0.66063 0.62697 0.98921 0.49264 > 0.00000 > > Average distance (over all possible pairs of sequences): 0.59096 > minimum : 0.17837, maximum : 0.98921 > variance : 0.03581, std.dev. : 0.18924 > > > RATE HETEROGENEITY > > Model of rate heterogeneity: Gamma distributed rates > Gamma distribution parameter alpha (estimated from data set): 0.25 (S.E. 0.05) > Number of Gamma rate categories: 8 > > Rates and their respective probabilities used in the likelihood function: > > Category Relative rate Probability > 1 0.0000 0.1250 > 2 0.0031 0.1250 > 3 0.0262 0.1250 > 4 0.1071 0.1250 > 5 0.3140 0.1250 > 6 0.7768 0.1250 > 7 1.8180 0.1250 > 8 4.9547 0.1250 > > Categories 1-8 approximate a continous Gamma-distribution with expectation 1 > and variance 3.94. > > Combination of categories that contributes the most to the likelihood > (computation done without clock assumption assuming quartet-puzzling tree): > > 7 1 1 7 1 1 8 1 1 8 7 1 7 6 1 6 1 1 7 8 1 8 1 1 1 7 1 1 7 5 > 8 6 1 8 1 1 1 1 1 5 6 1 8 1 1 6 1 1 7 7 1 1 1 1 7 7 1 1 1 1 > 7 1 1 6 1 1 7 1 1 5 1 1 8 6 1 8 1 1 6 1 1 6 8 7 7 1 1 8 1 1 > 8 1 1 7 1 1 8 1 1 8 5 1 8 5 1 7 1 1 7 1 1 6 1 5 7 1 > > > QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) > > > name | resolved | partly resolved | unresolved | sum > -------------------------------------------------------------------------- > Thylacinus 15 [ 42.86%] 0 [ 0.00%] 20 [ 57.14%] 35 > Sarcophilu 16 [ 45.71%] 1 [ 2.86%] 18 [ 51.43%] 35 > Dasyurus 19 [ 54.29%] 3 [ 8.57%] 13 [ 37.14%] 35 > Echymipera 12 [ 34.29%] 0 [ 0.00%] 23 [ 65.71%] 35 > Trichosuru 16 [ 45.71%] 2 [ 5.71%] 17 [ 48.57%] 35 > Phalanger 20 [ 57.14%] 2 [ 5.71%] 13 [ 37.14%] 35 > Philander 13 [ 37.14%] 1 [ 2.86%] 21 [ 60.00%] 35 > Bos 9 [ 25.71%] 3 [ 8.57%] 23 [ 65.71%] 35 > -------------------------------------------------------------------------- > #quartets : 30 [ 42.86%] 3 [ 4.29%] 37 [ 52.86%] 70 > > The table shows the occurrences of fully resolved, partially, and > completely unresolved quartets for each sequence and their percentage > relative to the number of times the sequence occurs in the list of > quartets (i.e. 35 quartets out of 70 in total). > In fully resolved quartet one single topology is supported, while for > partially resolved quartets two and for completely unresolved quartets > none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. > Note: Because 4 sequences are involved in one quartet numbers add up > to a four-fold of the existing quartets. > > Hint: The overall numbers in the last row give information about the > phylogenetic content of the dataset. The higher the percentage of partially > and unresolved quartets, the lower the content of phylogenetic information. > This can be visualized in more detail by likelihood mapping analysis. > > > > TREE SEARCH > > Quartet puzzling is used to choose from the possible tree topologies > and to simultaneously infer support values for internal branches. > > Number of puzzling steps: 1000 > Analysed quartets: 70 > Fully resolved quartets: 30 (= 42.9%) > Partly resolved quartets: 3 (= 4.3%) > Unresolved quartets: 37 (= 52.9%) > > Quartet trees are based on approximate maximum likelihood values > using the selected model of substitution and rate heterogeneity. > > > QUARTET PUZZLING TREE > > Support for the internal branches of the unrooted quartet puzzling > tree topology is shown in percent. > > This quartet puzzling tree is not completely resolved! > > > :---Sarcophilu > :-90: > : :---Dasyurus > : > : :---Trichosuru > :-87: > : :---Phalanger > : > :-------Echymipera > : > :-------Philander > : > :-------Bos > : > :-------Thylacinus > > > Quartet puzzling tree (in CLUSTAL W notation): > > (Thylacinus,(Sarcophilu,Dasyurus)90,(Trichosuru,Phalanger)87, > Echymipera,Philander,Bos); > > > BIPARTITIONS > > The following bipartitions occured at least once in all intermediate > trees that have been generated in the 1000 puzzling steps. > Bipartitions included in the quartet puzzling tree: > (bipartition with sequences in input order : number of times seen) > > *..***** : 904 > ****..** : 872 > > Congruent bipartitions occurred in 50% or less, not included in > the consensus tree: > (bipartition with sequences in input order : number of times seen) > > *...**.. : 377 > ******.. : 357 > > Incongruent bipartitions not included in the consensus tree: > (bipartition with sequences in input order : number of times seen) > > ***.**.* : 220 > ***.**.. : 218 > *...**** : 205 > ***.***. : 145 > *......* : 135 > *..*..** : 129 > *...**.* : 124 > *.....** : 106 > *..*.... : 102 > *..***.* : 92 > *..***.. : 91 > ***..... : 86 > *.....*. : 71 > ***...** : 70 > *..****. : 67 > ****..*. : 67 > *....*.. : 64 > *...***. : 54 > ****.... : 52 > *..*...* : 47 > > (49 other less frequent bipartitions not shown) > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > > :------2 Sarcophilu > :-------9 > : :-3 Dasyurus > : > : :-----5 Trichosuru > :-------10 > : :--------6 Phalanger > : > :--------4 Echymipera > : > :-------7 Philander > : > :-----------8 Bos > : > :-------1 Thylacinus > > > branch length S.E. branch length S.E. > Thylacinus 1 0.23363 0.10248 9 0.19927 0.09576 > Sarcophilu 2 0.18905 0.06712 10 0.22291 0.13093 > Dasyurus 3 0.00001 0.00200 > Echymipera 4 0.27841 0.11691 > Trichosuru 5 0.17822 0.10160 > Phalanger 6 0.27519 0.12613 > Philander 7 0.22533 0.10269 10 iterations until convergence > Bos 8 0.38507 0.14566 log L: -570.33 > > WARNING --- at least one branch length is close to an internal boundary! > > > Consensus tree with maximum likelihood branch lengths > (in CLUSTAL W notation): > > (Thylacinus:0.23363,(Sarcophilu:0.18905,Dasyurus:0.00001)90:0.19927, > (Trichosuru:0.17822,Phalanger:0.27519)87:0.22291,Echymipera:0.27841, > Philander:0.22533,Bos:0.38507); > > > TIME STAMP > FAIL qp-hky-rhet-nucl.test (exit status: 1) FAIL: qp-hky-rhet-clock-nucl ============================ Testing: nucleotide data, HKY, clock, rate heterogeneity, quartet puzzling (qp-hky-rhet-clock-nucl) ./qp-hky-rhet-clock-nucl.test: line 181: 18769 Segmentation fault ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 cat: qp-hky-rhet-clock-nucl.nucl.puzzle: No such file or directory 0a1,392 > TREE-PUZZLE > > Input file name: qp-hky-rhet-clock-nucl.nucl > Type of analysis: tree reconstruction > Parameter estimation: approximate (faster) > Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) > > Standard errors (S.E.) are obtained by the curvature method. > The upper and lower bounds of an approximate 95% confidence interval > for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. > > > SEQUENCE ALIGNMENT > > Input data: 8 sequences with 116 nucleotide sites > Number of constant sites: 66 (= 56.9% of all sites) > Number of site patterns: 54 > Number of constant site patterns: 4 (= 7.4% of all site patterns) > > > SUBSTITUTION PROCESS > > Model of substitution: HKY (Hasegawa et al. 1985) > Transition/transversion parameter (estimated from data set): 2.95 (S.E. 0.84) > > Rate matrix R (parameters restricted to selected model): > > A-C rate: 1.00000 > A-G rate: 5.85063 > A-T rate: 1.00000 > C-G rate: 1.00000 > C-T rate: 5.85063 > G-T rate: 1.00000 > > Nucleotide frequencies (estimated from data set): > > pi(A) = 26.6% > pi(C) = 30.6% > pi(G) = 12.0% > pi(T) = 30.7% > > Expected transition/transversion ratio: 3.14 > Expected pyrimidine transition/purine transition ratio: 2.95 > > > AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) > > gaps wildcards sum % sequence > Thylacinus 0 0 0 0.00% > Sarcophilu 0 0 0 0.00% > Dasyurus 0 1 1 0.86% > Echymipera 0 0 0 0.00% > Trichosuru 0 0 0 0.00% > Phalanger 0 0 0 0.00% > Philander 0 0 0 0.00% > Bos 0 0 0 0.00% > ------------------------------------------------------- > Sum 0 1 1 0.11% > > > The table above shows the amount of gaps ('-') and other 'wildcard' > characters ('X', '?', etc.) and their percentage of the 116 columns > in the alignment. > Sequences with more than 50% ambiguous characters are marked with a '!' and > should be checked, whether they have sufficient overlap to other sequences. > Sequences with 100% ambiguous characters do not hold any phylogenetic > information and had to be discarded from the analysis. > > > > SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) > > 5% chi-square test p-value > Thylacinus passed 90.89% > Sarcophilu passed 93.32% > Dasyurus passed 98.01% > Echymipera passed 92.83% > Trichosuru passed 90.41% > Phalanger passed 86.09% > Philander passed 66.19% > Bos passed 60.02% > > The chi-square tests compares the nucleotide composition of each sequence > to the frequency distribution assumed in the maximum likelihood model. > > > IDENTICAL SEQUENCES > > The sequences in each of the following groups are all identical. To speed > up computation please remove all but one of each group from the data set. > > All sequences are unique. > > > MAXIMUM LIKELIHOOD DISTANCES > > Maximum likelihood distances are computed using the selected model of > substitution and rate heterogeneity. > > 8 > Thylacinus 0.00000 0.52940 0.37900 0.52236 0.58922 0.56150 0.43932 > 0.55291 > Sarcophilu 0.52940 0.00000 0.17837 0.62532 0.69892 0.93602 0.62327 > 0.78596 > Dasyurus 0.37900 0.17837 0.00000 0.39032 0.53431 0.60369 0.31919 > 0.56220 > Echymipera 0.52236 0.62532 0.39032 0.00000 0.70229 0.94283 0.42016 > 0.66063 > Trichosuru 0.58922 0.69892 0.53431 0.70229 0.00000 0.39416 0.70017 > 0.62697 > Phalanger 0.56150 0.93602 0.60369 0.94283 0.39416 0.00000 0.78658 > 0.98921 > Philander 0.43932 0.62327 0.31919 0.42016 0.70017 0.78658 0.00000 > 0.49264 > Bos 0.55291 0.78596 0.56220 0.66063 0.62697 0.98921 0.49264 > 0.00000 > > Average distance (over all possible pairs of sequences): 0.59096 > minimum : 0.17837, maximum : 0.98921 > variance : 0.03581, std.dev. : 0.18924 > > > RATE HETEROGENEITY > > Model of rate heterogeneity: Gamma distributed rates > Gamma distribution parameter alpha (estimated from data set): 0.25 (S.E. 0.05) > Number of Gamma rate categories: 8 > > Rates and their respective probabilities used in the likelihood function: > > Category Relative rate Probability > 1 0.0000 0.1250 > 2 0.0031 0.1250 > 3 0.0262 0.1250 > 4 0.1071 0.1250 > 5 0.3140 0.1250 > 6 0.7768 0.1250 > 7 1.8180 0.1250 > 8 4.9547 0.1250 > > Categories 1-8 approximate a continous Gamma-distribution with expectation 1 > and variance 3.94. > > Combination of categories that contributes the most to the likelihood > (computation done without clock assumption assuming quartet-puzzling tree): > > 7 1 1 7 1 1 8 1 1 8 7 1 7 6 1 6 1 1 7 8 1 8 1 1 1 7 1 1 7 5 > 8 6 1 8 1 1 1 1 1 5 6 1 8 1 1 6 1 1 7 7 1 1 1 1 7 7 1 1 1 1 > 7 1 1 6 1 1 7 1 1 5 1 1 8 6 1 8 1 1 6 1 1 6 8 7 7 1 1 8 1 1 > 8 1 1 7 1 1 8 1 1 8 5 1 8 5 1 7 1 1 7 1 1 6 1 5 7 1 > > > QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) > > > name | resolved | partly resolved | unresolved | sum > -------------------------------------------------------------------------- > Thylacinus 15 [ 42.86%] 0 [ 0.00%] 20 [ 57.14%] 35 > Sarcophilu 16 [ 45.71%] 1 [ 2.86%] 18 [ 51.43%] 35 > Dasyurus 19 [ 54.29%] 3 [ 8.57%] 13 [ 37.14%] 35 > Echymipera 12 [ 34.29%] 0 [ 0.00%] 23 [ 65.71%] 35 > Trichosuru 16 [ 45.71%] 2 [ 5.71%] 17 [ 48.57%] 35 > Phalanger 20 [ 57.14%] 2 [ 5.71%] 13 [ 37.14%] 35 > Philander 13 [ 37.14%] 1 [ 2.86%] 21 [ 60.00%] 35 > Bos 9 [ 25.71%] 3 [ 8.57%] 23 [ 65.71%] 35 > -------------------------------------------------------------------------- > #quartets : 30 [ 42.86%] 3 [ 4.29%] 37 [ 52.86%] 70 > > The table shows the occurrences of fully resolved, partially, and > completely unresolved quartets for each sequence and their percentage > relative to the number of times the sequence occurs in the list of > quartets (i.e. 35 quartets out of 70 in total). > In fully resolved quartet one single topology is supported, while for > partially resolved quartets two and for completely unresolved quartets > none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. > Note: Because 4 sequences are involved in one quartet numbers add up > to a four-fold of the existing quartets. > > Hint: The overall numbers in the last row give information about the > phylogenetic content of the dataset. The higher the percentage of partially > and unresolved quartets, the lower the content of phylogenetic information. > This can be visualized in more detail by likelihood mapping analysis. > > > > TREE SEARCH > > Quartet puzzling is used to choose from the possible tree topologies > and to simultaneously infer support values for internal branches. > > Number of puzzling steps: 1000 > Analysed quartets: 70 > Fully resolved quartets: 30 (= 42.9%) > Partly resolved quartets: 3 (= 4.3%) > Unresolved quartets: 37 (= 52.9%) > > Quartet trees are based on approximate maximum likelihood values > using the selected model of substitution and rate heterogeneity. > > > QUARTET PUZZLING TREE > > Support for the internal branches of the unrooted quartet puzzling > tree topology is shown in percent. > > This quartet puzzling tree is not completely resolved! > > > :---Sarcophilu > :-90: > : :---Dasyurus > : > : :---Trichosuru > :-87: > : :---Phalanger > : > :-------Echymipera > : > :-------Philander > : > :-------Bos > : > :-------Thylacinus > > > Quartet puzzling tree (in CLUSTAL W notation): > > (Thylacinus,(Sarcophilu,Dasyurus)90,(Trichosuru,Phalanger)87, > Echymipera,Philander,Bos); > > > BIPARTITIONS > > The following bipartitions occured at least once in all intermediate > trees that have been generated in the 1000 puzzling steps. > Bipartitions included in the quartet puzzling tree: > (bipartition with sequences in input order : number of times seen) > > *..***** : 904 > ****..** : 872 > > Congruent bipartitions occurred in 50% or less, not included in > the consensus tree: > (bipartition with sequences in input order : number of times seen) > > *...**.. : 377 > ******.. : 357 > > Incongruent bipartitions not included in the consensus tree: > (bipartition with sequences in input order : number of times seen) > > ***.**.* : 220 > ***.**.. : 218 > *...**** : 205 > ***.***. : 145 > *......* : 135 > *..*..** : 129 > *...**.* : 124 > *.....** : 106 > *..*.... : 102 > *..***.* : 92 > *..***.. : 91 > ***..... : 86 > *.....*. : 71 > ***...** : 70 > *..****. : 67 > ****..*. : 67 > *....*.. : 64 > *...***. : 54 > ****.... : 52 > *..*...* : 47 > > (49 other less frequent bipartitions not shown) > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > > :------2 Sarcophilu > :-------9 > : :-3 Dasyurus > : > : :-----5 Trichosuru > :-------10 > : :--------6 Phalanger > : > :--------4 Echymipera > : > :-------7 Philander > : > :-----------8 Bos > : > :-------1 Thylacinus > > > branch length S.E. branch length S.E. > Thylacinus 1 0.23363 0.10248 9 0.19927 0.09576 > Sarcophilu 2 0.18905 0.06712 10 0.22291 0.13093 > Dasyurus 3 0.00001 0.00200 > Echymipera 4 0.27841 0.11691 > Trichosuru 5 0.17822 0.10160 > Phalanger 6 0.27519 0.12613 > Philander 7 0.22533 0.10269 10 iterations until convergence > Bos 8 0.38507 0.14566 log L: -570.33 > > WARNING --- at least one branch length is close to an internal boundary! > > > Consensus tree with maximum likelihood branch lengths > (in CLUSTAL W notation): > > (Thylacinus:0.23363,(Sarcophilu:0.18905,Dasyurus:0.00001)90:0.19927, > (Trichosuru:0.17822,Phalanger:0.27519)87:0.22291,Echymipera:0.27841, > Philander:0.22533,Bos:0.38507); > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > Root located at branch: 10 "internal branch" (automatic search) > > If the automatic search misplaces the root please rerun the analysis > (rename "outtree" to "intree") and select location of root manually! > > > :---2 Sarcophilu > :-------9 > : :---3 Dasyurus > : > : :-------5 Trichosuru > :-------10 > : :-------6 Phalanger > : > :---------4 Echymipera > : > :---------7 Philander > : > :---------8 Bos > : > :---------1 Thylacinus > > > Tree drawn as unrooted tree for better comparison with non-clock tree! > > branch length nc/c branch length nc/c (= non-clock/clock) > Thylacinus 1 0.29776 0.785 9 0.20356 0.979 > Sarcophilu 2 0.09420 2.007 10 0.22846 0.976 > Dasyurus 3 0.09420 0.000 > Echymipera 4 0.29776 0.935 > Trichosuru 5 0.23472 0.759 > Phalanger 6 0.23472 1.172 > Philander 7 0.29776 0.757 16 iterations until convergence > Bos 8 0.29776 1.293 log L: -573.89 > > height S.E. of node common to branches > 0.23472 0.07631 10 5 6 > 0.09420 0.03153 9 2 3 > 0.29776 0.05401 10 4 7 8 1 9 > 0.38047 0.07031 of root at branch 10 > > > Rooted consensus tree with clocklike maximum likelihood branch lengths > (in CLUSTAL W notation): > > ((Trichosuru:0.23472,Phalanger:0.23472)87:0.14575,(Echymipera:0.29776, > Philander:0.29776,Bos:0.29776,Thylacinus:0.29776,(Sarcophilu:0.09420, > Dasyurus:0.09420)90:0.20356):0.08271); > > > MOLECULAR CLOCK LIKELIHOOD RATIO TEST > > log L without clock: -570.33 (independent branch parameters: 10) > log L with clock: -573.89 (independent branch parameters: 4) > > Likelihood ratio test statistic delta: 7.12 > Degress of freedom of chi-square distribution: 6 > Critical significance level: 30.97% > > The simpler (clocklike) tree can not be rejected on a significance > level of 5%. The log-likelihood of the more complex (no clock) tree > is not significantly increased. > > Please take care that the correct root is used! > > > TIME STAMP > FAIL qp-hky-rhet-clock-nucl.test (exit status: 1) FAIL: qp-pure-prot ================== Testing: protein data, default model, quartet puzzling (qp-pure-prot) ./qp-pure-prot.test: line 181: 18788 Segmentation fault ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 cat: qp-pure-prot.prot.puzzle: No such file or directory 0a1,263 > TREE-PUZZLE > > Input file name: qp-pure-prot.prot > Type of analysis: tree reconstruction > Parameter estimation: approximate (faster) > Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) > > Standard errors (S.E.) are obtained by the curvature method. > The upper and lower bounds of an approximate 95% confidence interval > for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. > > > SEQUENCE ALIGNMENT > > Input data: 7 sequences with 128 amino acid sites > Number of constant sites: 7 (= 5.5% of all sites) > Number of site patterns: 125 > Number of constant site patterns: 5 (= 4.0% of all site patterns) > > > SUBSTITUTION PROCESS > > Model of substitution: Dayhoff (Dayhoff et al. 1978) > Amino acid frequencies (estimated from data set): > > pi(A) = 12.2% > pi(R) = 2.3% > pi(N) = 3.0% > pi(D) = 4.9% > pi(C) = 0.7% > pi(Q) = 2.3% > pi(E) = 5.4% > pi(G) = 6.0% > pi(H) = 5.8% > pi(I) = 2.7% > pi(L) = 12.5% > pi(K) = 9.3% > pi(M) = 1.3% > pi(F) = 4.9% > pi(P) = 2.6% > pi(S) = 6.7% > pi(T) = 4.5% > pi(W) = 1.3% > pi(Y) = 2.2% > pi(V) = 9.4% > > > AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) > > gaps wildcards sum % sequence > HBB_HUMAN 0 0 0 0.00% > HBB_HORSE 0 0 0 0.00% > HBA_HUMAN 0 0 0 0.00% > HBA_HORSE 0 0 0 0.00% > MYG_PHYCA 0 0 0 0.00% > GLB5_PETMA 0 0 0 0.00% > LGB2_LUPLU 0 0 0 0.00% > ------------------------------------------------------- > Sum 0 0 0 0.00% > > > The table above shows the amount of gaps ('-') and other 'wildcard' > characters ('X', '?', etc.) and their percentage of the 128 columns > in the alignment. > Sequences with more than 50% ambiguous characters are marked with a '!' and > should be checked, whether they have sufficient overlap to other sequences. > Sequences with 100% ambiguous characters do not hold any phylogenetic > information and had to be discarded from the analysis. > > > > SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) > > 5% chi-square test p-value > HBB_HUMAN passed 92.31% > HBB_HORSE passed 79.58% > HBA_HUMAN passed 93.09% > HBA_HORSE passed 81.20% > MYG_PHYCA passed 33.23% > GLB5_PETMA passed 19.11% > LGB2_LUPLU passed 41.67% > > The chi-square tests compares the amino acid composition of each sequence > to the frequency distribution assumed in the maximum likelihood model. > > WARNING: Result of chi-square test may not be valid because of small > maximum likelihood frequencies and short sequence length! > > > IDENTICAL SEQUENCES > > The sequences in each of the following groups are all identical. To speed > up computation please remove all but one of each group from the data set. > > All sequences are unique. > > > MAXIMUM LIKELIHOOD DISTANCES > > Maximum likelihood distances are computed using the selected model of > substitution and rate heterogeneity. > > 7 > HBB_HUMAN 0.00000 0.17425 0.96068 0.99267 2.12932 1.77231 2.78644 > HBB_HORSE 0.17425 0.00000 1.01062 1.02118 2.09456 1.78465 2.86187 > HBA_HUMAN 0.96068 1.01062 0.00000 0.12147 1.93540 1.30123 2.54730 > HBA_HORSE 0.99267 1.02118 0.12147 0.00000 2.00515 1.39193 2.51172 > MYG_PHYCA 2.12932 2.09456 1.93540 2.00515 0.00000 2.12347 2.79386 > GLB5_PETMA 1.77231 1.78465 1.30123 1.39193 2.12347 0.00000 2.18272 > LGB2_LUPLU 2.78644 2.86187 2.54730 2.51172 2.79386 2.18272 0.00000 > > Average distance (over all possible pairs of sequences): 1.73823 > minimum : 0.12147, maximum : 2.86187 > variance : 0.65214, std.dev. : 0.80755 > > > RATE HETEROGENEITY > > Model of rate heterogeneity: uniform rate > > > QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) > > > name | resolved | partly resolved | unresolved | sum > -------------------------------------------------------------------------- > HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 > HBB_HORSE 20 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 20 > HBA_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 > HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 > MYG_PHYCA 17 [ 85.00%] 0 [ 0.00%] 3 [ 15.00%] 20 > GLB5_PETMA 17 [ 85.00%] 0 [ 0.00%] 3 [ 15.00%] 20 > LGB2_LUPLU 17 [ 85.00%] 0 [ 0.00%] 3 [ 15.00%] 20 > -------------------------------------------------------------------------- > #quartets : 32 [ 91.43%] 0 [ 0.00%] 3 [ 8.57%] 35 > > The table shows the occurrences of fully resolved, partially, and > completely unresolved quartets for each sequence and their percentage > relative to the number of times the sequence occurs in the list of > quartets (i.e. 20 quartets out of 35 in total). > In fully resolved quartet one single topology is supported, while for > partially resolved quartets two and for completely unresolved quartets > none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. > Note: Because 4 sequences are involved in one quartet numbers add up > to a four-fold of the existing quartets. > > Hint: The overall numbers in the last row give information about the > phylogenetic content of the dataset. The higher the percentage of partially > and unresolved quartets, the lower the content of phylogenetic information. > This can be visualized in more detail by likelihood mapping analysis. > > > > TREE SEARCH > > Quartet puzzling is used to choose from the possible tree topologies > and to simultaneously infer support values for internal branches. > > Number of puzzling steps: 1000 > Analysed quartets: 35 > Fully resolved quartets: 32 (= 91.4%) > Partly resolved quartets: 0 (= 0.0%) > Unresolved quartets: 3 (= 8.6%) > > Quartet trees are based on approximate maximum likelihood values > using the selected model of substitution and rate heterogeneity. > > > QUARTET PUZZLING TREE > > Support for the internal branches of the unrooted quartet puzzling > tree topology is shown in percent. > > This quartet puzzling tree is completely resolved. > > > :---HBA_HUMAN > :----100: > : :---HBA_HORSE > :100: > : : :---GLB5_PETMA > : : :-54: > : :100: :---LGB2_LUPLU > : : > : :-------MYG_PHYCA > : > :---------------HBB_HORSE > : > :---------------HBB_HUMAN > > > Quartet puzzling tree (in CLUSTAL W notation): > > (HBB_HUMAN,((HBA_HUMAN,HBA_HORSE)100,((GLB5_PETMA,LGB2_LUPLU)54, > MYG_PHYCA)100)100,HBB_HORSE); > > > BIPARTITIONS > > The following bipartitions occured at least once in all intermediate > trees that have been generated in the 1000 puzzling steps. > Bipartitions included in the quartet puzzling tree: > (bipartition with sequences in input order : number of times seen) > > **..... : 1000 > **..*** : 1000 > ****... : 1000 > *****.. : 544 > > Congruent bipartitions occurred in 50% or less, not included in > the consensus tree: > (bipartition with sequences in input order : number of times seen) > > None (No congruent split not included) > > Incongruent bipartitions not included in the consensus tree: > (bipartition with sequences in input order : number of times seen) > > ****.*. : 234 > ****..* : 222 > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > > :-3 HBA_HUMAN > :----8 > : :-4 HBA_HORSE > :------11 > : : :------6 GLB5_PETMA > : : :---9 > : : : :----------------7 LGB2_LUPLU > : :----10 > : :-------------5 MYG_PHYCA > : > :--2 HBB_HORSE > : > :-1 HBB_HUMAN > > > branch length S.E. branch length S.E. > HBB_HUMAN 1 0.04915 0.03158 8 0.28345 0.08777 > HBB_HORSE 2 0.12603 0.03871 9 0.18154 0.13086 > HBA_HUMAN 3 0.02555 0.02185 10 0.34694 0.12552 > HBA_HORSE 4 0.09542 0.03153 11 0.60239 0.11261 > MYG_PHYCA 5 1.33166 0.21117 > GLB5_PETMA 6 0.57466 0.13843 10 iterations until convergence > LGB2_LUPLU 7 1.71333 0.27645 log L: -1699.00 > > > Consensus tree with maximum likelihood branch lengths > (in CLUSTAL W notation): > > (HBB_HUMAN:0.04915,((HBA_HUMAN:0.02555,HBA_HORSE:0.09542)100:0.28345, > ((GLB5_PETMA:0.57466,LGB2_LUPLU:1.71333)54:0.18154,MYG_PHYCA:1.33166) > 100:0.34694)100:0.60239,HBB_HORSE:0.12603); > > > TIME STAMP > FAIL qp-pure-prot.test (exit status: 1) FAIL: qp-mtrev-prot =================== Testing: protein data, mtREV, quartet puzzling (qp-mtrev-prot) ./qp-mtrev-prot.test: line 181: 18807 Segmentation fault ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 cat: qp-mtrev-prot.prot.puzzle: No such file or directory 0a1,265 > TREE-PUZZLE > > Input file name: qp-mtrev-prot.prot > Type of analysis: tree reconstruction > Parameter estimation: approximate (faster) > Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) > > Standard errors (S.E.) are obtained by the curvature method. > The upper and lower bounds of an approximate 95% confidence interval > for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. > > > SEQUENCE ALIGNMENT > > Input data: 7 sequences with 128 amino acid sites > Number of constant sites: 7 (= 5.5% of all sites) > Number of site patterns: 125 > Number of constant site patterns: 5 (= 4.0% of all site patterns) > > > SUBSTITUTION PROCESS > > Model of substitution: mtREV24 (Adachi-Hasegawa 1996) > Amino acid frequencies (estimated from data set): > > pi(A) = 12.2% > pi(R) = 2.3% > pi(N) = 3.0% > pi(D) = 4.9% > pi(C) = 0.7% > pi(Q) = 2.3% > pi(E) = 5.4% > pi(G) = 6.0% > pi(H) = 5.8% > pi(I) = 2.7% > pi(L) = 12.5% > pi(K) = 9.3% > pi(M) = 1.3% > pi(F) = 4.9% > pi(P) = 2.6% > pi(S) = 6.7% > pi(T) = 4.5% > pi(W) = 1.3% > pi(Y) = 2.2% > pi(V) = 9.4% > > > AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) > > gaps wildcards sum % sequence > HBB_HUMAN 0 0 0 0.00% > HBB_HORSE 0 0 0 0.00% > HBA_HUMAN 0 0 0 0.00% > HBA_HORSE 0 0 0 0.00% > MYG_PHYCA 0 0 0 0.00% > GLB5_PETMA 0 0 0 0.00% > LGB2_LUPLU 0 0 0 0.00% > ------------------------------------------------------- > Sum 0 0 0 0.00% > > > The table above shows the amount of gaps ('-') and other 'wildcard' > characters ('X', '?', etc.) and their percentage of the 128 columns > in the alignment. > Sequences with more than 50% ambiguous characters are marked with a '!' and > should be checked, whether they have sufficient overlap to other sequences. > Sequences with 100% ambiguous characters do not hold any phylogenetic > information and had to be discarded from the analysis. > > > > SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) > > 5% chi-square test p-value > HBB_HUMAN passed 92.31% > HBB_HORSE passed 79.58% > HBA_HUMAN passed 93.09% > HBA_HORSE passed 81.20% > MYG_PHYCA passed 33.23% > GLB5_PETMA passed 19.11% > LGB2_LUPLU passed 41.67% > > The chi-square tests compares the amino acid composition of each sequence > to the frequency distribution assumed in the maximum likelihood model. > > WARNING: Result of chi-square test may not be valid because of small > maximum likelihood frequencies and short sequence length! > > > IDENTICAL SEQUENCES > > The sequences in each of the following groups are all identical. To speed > up computation please remove all but one of each group from the data set. > > All sequences are unique. > > > MAXIMUM LIKELIHOOD DISTANCES > > Maximum likelihood distances are computed using the selected model of > substitution and rate heterogeneity. > > 7 > HBB_HUMAN 0.00000 0.19615 1.12348 1.16856 2.59690 2.15305 3.47989 > HBB_HORSE 0.19615 0.00000 1.17857 1.20524 2.74793 2.18071 3.63316 > HBA_HUMAN 1.12348 1.17857 0.00000 0.13144 2.41361 1.43785 3.06000 > HBA_HORSE 1.16856 1.20524 0.13144 0.00000 2.44163 1.55582 3.05140 > MYG_PHYCA 2.59690 2.74793 2.41361 2.44163 0.00000 2.62256 3.47779 > GLB5_PETMA 2.15305 2.18071 1.43785 1.55582 2.62256 0.00000 2.97722 > LGB2_LUPLU 3.47989 3.63316 3.06000 3.05140 3.47779 2.97722 0.00000 > > Average distance (over all possible pairs of sequences): 2.13490 > minimum : 0.13144, maximum : 3.63316 > variance : 1.07966, std.dev. : 1.03906 > > > RATE HETEROGENEITY > > Model of rate heterogeneity: uniform rate > > > QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) > > > name | resolved | partly resolved | unresolved | sum > -------------------------------------------------------------------------- > HBB_HUMAN 18 [ 90.00%] 1 [ 5.00%] 1 [ 5.00%] 20 > HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 > HBA_HUMAN 19 [ 95.00%] 1 [ 5.00%] 0 [ 0.00%] 20 > HBA_HORSE 18 [ 90.00%] 2 [ 10.00%] 0 [ 0.00%] 20 > MYG_PHYCA 15 [ 75.00%] 3 [ 15.00%] 2 [ 10.00%] 20 > GLB5_PETMA 15 [ 75.00%] 3 [ 15.00%] 2 [ 10.00%] 20 > LGB2_LUPLU 16 [ 80.00%] 2 [ 10.00%] 2 [ 10.00%] 20 > -------------------------------------------------------------------------- > #quartets : 30 [ 85.71%] 3 [ 8.57%] 2 [ 5.71%] 35 > > The table shows the occurrences of fully resolved, partially, and > completely unresolved quartets for each sequence and their percentage > relative to the number of times the sequence occurs in the list of > quartets (i.e. 20 quartets out of 35 in total). > In fully resolved quartet one single topology is supported, while for > partially resolved quartets two and for completely unresolved quartets > none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. > Note: Because 4 sequences are involved in one quartet numbers add up > to a four-fold of the existing quartets. > > Hint: The overall numbers in the last row give information about the > phylogenetic content of the dataset. The higher the percentage of partially > and unresolved quartets, the lower the content of phylogenetic information. > This can be visualized in more detail by likelihood mapping analysis. > > > > TREE SEARCH > > Quartet puzzling is used to choose from the possible tree topologies > and to simultaneously infer support values for internal branches. > > Number of puzzling steps: 1000 > Analysed quartets: 35 > Fully resolved quartets: 30 (= 85.7%) > Partly resolved quartets: 3 (= 8.6%) > Unresolved quartets: 2 (= 5.7%) > > Quartet trees are based on approximate maximum likelihood values > using the selected model of substitution and rate heterogeneity. > > > QUARTET PUZZLING TREE > > Support for the internal branches of the unrooted quartet puzzling > tree topology is shown in percent. > > This quartet puzzling tree is not completely resolved! > > > :---HBA_HUMAN > :100: > : :---HBA_HORSE > :100: > : : :---MYG_PHYCA > : : : > : :-97:---GLB5_PETMA > : : > : :---LGB2_LUPLU > : > :-----------HBB_HORSE > : > :-----------HBB_HUMAN > > > Quartet puzzling tree (in CLUSTAL W notation): > > (HBB_HUMAN,((HBA_HUMAN,HBA_HORSE)100,(MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)97)100, > HBB_HORSE); > > > BIPARTITIONS > > The following bipartitions occured at least once in all intermediate > trees that have been generated in the 1000 puzzling steps. > Bipartitions included in the quartet puzzling tree: > (bipartition with sequences in input order : number of times seen) > > **..... : 1000 > **..*** : 1000 > ****... : 971 > > Congruent bipartitions occurred in 50% or less, not included in > the consensus tree: > (bipartition with sequences in input order : number of times seen) > > ****.*. : 462 > > Incongruent bipartitions not included in the consensus tree: > (bipartition with sequences in input order : number of times seen) > > *****.. : 436 > ****..* : 100 > **..*.* : 15 > **..*.. : 14 > **....* : 2 > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > > :-3 HBA_HUMAN > :----8 > : :-4 HBA_HORSE > :------10 > : : :------------5 MYG_PHYCA > : :----9 > : :-------6 GLB5_PETMA > : : > : :----------------7 LGB2_LUPLU > : > :--2 HBB_HORSE > : > :-1 HBB_HUMAN > > > branch length S.E. branch length S.E. > HBB_HUMAN 1 0.03472 0.03059 8 0.30126 0.09575 > HBB_HORSE 2 0.16246 0.04359 9 0.34149 0.13763 > HBA_HUMAN 3 0.04636 0.02527 10 0.70896 0.13056 > HBA_HORSE 4 0.08355 0.03082 > MYG_PHYCA 5 1.58550 0.26736 > GLB5_PETMA 6 0.88663 0.17157 10 iterations until convergence > LGB2_LUPLU 7 2.13259 0.35215 log L: -1736.55 > > > Consensus tree with maximum likelihood branch lengths > (in CLUSTAL W notation): > > (HBB_HUMAN:0.03472,((HBA_HUMAN:0.04636,HBA_HORSE:0.08355)100:0.30126, > (MYG_PHYCA:1.58550,GLB5_PETMA:0.88663,LGB2_LUPLU:2.13259)97:0.34149) > 100:0.70896,HBB_HORSE:0.16246); > > > TIME STAMP > FAIL qp-mtrev-prot.test (exit status: 1) FAIL: qp-vt-prot ================ Testing: protein data, VT, quartet puzzling (qp-vt-prot) ./qp-vt-prot.test: line 181: 18826 Segmentation fault ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 cat: qp-vt-prot.prot.puzzle: No such file or directory 0a1,262 > TREE-PUZZLE > > Input file name: qp-vt-prot.prot > Type of analysis: tree reconstruction > Parameter estimation: approximate (faster) > Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) > > Standard errors (S.E.) are obtained by the curvature method. > The upper and lower bounds of an approximate 95% confidence interval > for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. > > > SEQUENCE ALIGNMENT > > Input data: 7 sequences with 128 amino acid sites > Number of constant sites: 7 (= 5.5% of all sites) > Number of site patterns: 125 > Number of constant site patterns: 5 (= 4.0% of all site patterns) > > > SUBSTITUTION PROCESS > > Model of substitution: VT (Mueller-Vingron 2000) > Amino acid frequencies (estimated from data set): > > pi(A) = 12.2% > pi(R) = 2.3% > pi(N) = 3.0% > pi(D) = 4.9% > pi(C) = 0.7% > pi(Q) = 2.3% > pi(E) = 5.4% > pi(G) = 6.0% > pi(H) = 5.8% > pi(I) = 2.7% > pi(L) = 12.5% > pi(K) = 9.3% > pi(M) = 1.3% > pi(F) = 4.9% > pi(P) = 2.6% > pi(S) = 6.7% > pi(T) = 4.5% > pi(W) = 1.3% > pi(Y) = 2.2% > pi(V) = 9.4% > > > AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) > > gaps wildcards sum % sequence > HBB_HUMAN 0 0 0 0.00% > HBB_HORSE 0 0 0 0.00% > HBA_HUMAN 0 0 0 0.00% > HBA_HORSE 0 0 0 0.00% > MYG_PHYCA 0 0 0 0.00% > GLB5_PETMA 0 0 0 0.00% > LGB2_LUPLU 0 0 0 0.00% > ------------------------------------------------------- > Sum 0 0 0 0.00% > > > The table above shows the amount of gaps ('-') and other 'wildcard' > characters ('X', '?', etc.) and their percentage of the 128 columns > in the alignment. > Sequences with more than 50% ambiguous characters are marked with a '!' and > should be checked, whether they have sufficient overlap to other sequences. > Sequences with 100% ambiguous characters do not hold any phylogenetic > information and had to be discarded from the analysis. > > > > SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) > > 5% chi-square test p-value > HBB_HUMAN passed 92.31% > HBB_HORSE passed 79.58% > HBA_HUMAN passed 93.09% > HBA_HORSE passed 81.20% > MYG_PHYCA passed 33.23% > GLB5_PETMA passed 19.11% > LGB2_LUPLU passed 41.67% > > The chi-square tests compares the amino acid composition of each sequence > to the frequency distribution assumed in the maximum likelihood model. > > WARNING: Result of chi-square test may not be valid because of small > maximum likelihood frequencies and short sequence length! > > > IDENTICAL SEQUENCES > > The sequences in each of the following groups are all identical. To speed > up computation please remove all but one of each group from the data set. > > All sequences are unique. > > > MAXIMUM LIKELIHOOD DISTANCES > > Maximum likelihood distances are computed using the selected model of > substitution and rate heterogeneity. > > 7 > HBB_HUMAN 0.00000 0.16783 0.85204 0.87347 1.69056 1.50964 2.05575 > HBB_HORSE 0.16783 0.00000 0.87363 0.87544 1.67978 1.52916 2.09374 > HBA_HUMAN 0.85204 0.87363 0.00000 0.11958 1.58540 1.13053 2.11864 > HBA_HORSE 0.87347 0.87544 0.11958 0.00000 1.64085 1.18694 2.01999 > MYG_PHYCA 1.69056 1.67978 1.58540 1.64085 0.00000 1.63531 2.09093 > GLB5_PETMA 1.50964 1.52916 1.13053 1.18694 1.63531 0.00000 1.84636 > LGB2_LUPLU 2.05575 2.09374 2.11864 2.01999 2.09093 1.84636 0.00000 > > Average distance (over all possible pairs of sequences): 1.40836 > minimum : 0.11958, maximum : 2.11864 > variance : 0.36159, std.dev. : 0.60133 > > > RATE HETEROGENEITY > > Model of rate heterogeneity: uniform rate > > > QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) > > > name | resolved | partly resolved | unresolved | sum > -------------------------------------------------------------------------- > HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 > HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 > HBA_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 > HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 > MYG_PHYCA 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 > GLB5_PETMA 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 > LGB2_LUPLU 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 > -------------------------------------------------------------------------- > #quartets : 31 [ 88.57%] 0 [ 0.00%] 4 [ 11.43%] 35 > > The table shows the occurrences of fully resolved, partially, and > completely unresolved quartets for each sequence and their percentage > relative to the number of times the sequence occurs in the list of > quartets (i.e. 20 quartets out of 35 in total). > In fully resolved quartet one single topology is supported, while for > partially resolved quartets two and for completely unresolved quartets > none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. > Note: Because 4 sequences are involved in one quartet numbers add up > to a four-fold of the existing quartets. > > Hint: The overall numbers in the last row give information about the > phylogenetic content of the dataset. The higher the percentage of partially > and unresolved quartets, the lower the content of phylogenetic information. > This can be visualized in more detail by likelihood mapping analysis. > > > > TREE SEARCH > > Quartet puzzling is used to choose from the possible tree topologies > and to simultaneously infer support values for internal branches. > > Number of puzzling steps: 1000 > Analysed quartets: 35 > Fully resolved quartets: 31 (= 88.6%) > Partly resolved quartets: 0 (= 0.0%) > Unresolved quartets: 4 (= 11.4%) > > Quartet trees are based on approximate maximum likelihood values > using the selected model of substitution and rate heterogeneity. > > > QUARTET PUZZLING TREE > > Support for the internal branches of the unrooted quartet puzzling > tree topology is shown in percent. > > This quartet puzzling tree is not completely resolved! > > > :---MYG_PHYCA > : > :100:---GLB5_PETMA > : : > :100: :---LGB2_LUPLU > : : > : : :---HBA_HUMAN > : :100: > : :---HBA_HORSE > : > :-----------HBB_HORSE > : > :-----------HBB_HUMAN > > > Quartet puzzling tree (in CLUSTAL W notation): > > (HBB_HUMAN,((MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)100,(HBA_HUMAN, > HBA_HORSE)100)100,HBB_HORSE); > > > BIPARTITIONS > > The following bipartitions occured at least once in all intermediate > trees that have been generated in the 1000 puzzling steps. > Bipartitions included in the quartet puzzling tree: > (bipartition with sequences in input order : number of times seen) > > ****... : 1000 > **..... : 1000 > **..*** : 1000 > > Congruent bipartitions occurred in 50% or less, not included in > the consensus tree: > (bipartition with sequences in input order : number of times seen) > > *****.. : 347 > > Incongruent bipartitions not included in the consensus tree: > (bipartition with sequences in input order : number of times seen) > > ****..* : 331 > ****.*. : 322 > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > > :-------------5 MYG_PHYCA > :-------8 > : :--------6 GLB5_PETMA > : : > : :------------------7 LGB2_LUPLU > :-------10 > : : :-3 HBA_HUMAN > : :-----9 > : :--4 HBA_HORSE > : > :--2 HBB_HORSE > : > :-1 HBB_HUMAN > > > branch length S.E. branch length S.E. > HBB_HUMAN 1 0.04599 0.03062 8 0.42025 0.11481 > HBB_HORSE 2 0.12231 0.03740 9 0.25241 0.08069 > HBA_HUMAN 3 0.03150 0.02213 10 0.54296 0.10035 > HBA_HORSE 4 0.08803 0.03011 > MYG_PHYCA 5 1.02811 0.16334 > GLB5_PETMA 6 0.60661 0.11823 12 iterations until convergence > LGB2_LUPLU 7 1.38558 0.20879 log L: -1703.59 > > > Consensus tree with maximum likelihood branch lengths > (in CLUSTAL W notation): > > (HBB_HUMAN:0.04599,((MYG_PHYCA:1.02811,GLB5_PETMA:0.60661,LGB2_LUPLU:1.38558) > 100:0.42025,(HBA_HUMAN:0.03150,HBA_HORSE:0.08803)100:0.25241)100:0.54296, > HBB_HORSE:0.12231); > > > TIME STAMP > FAIL qp-vt-prot.test (exit status: 1) FAIL: qp-wag-prot ================= Testing: protein data, WAG, quartet puzzling (qp-wag-prot) ./qp-wag-prot.test: line 181: 18845 Segmentation fault ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 cat: qp-wag-prot.prot.puzzle: No such file or directory 0a1,262 > TREE-PUZZLE > > Input file name: qp-wag-prot.prot > Type of analysis: tree reconstruction > Parameter estimation: approximate (faster) > Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) > > Standard errors (S.E.) are obtained by the curvature method. > The upper and lower bounds of an approximate 95% confidence interval > for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. > > > SEQUENCE ALIGNMENT > > Input data: 7 sequences with 128 amino acid sites > Number of constant sites: 7 (= 5.5% of all sites) > Number of site patterns: 125 > Number of constant site patterns: 5 (= 4.0% of all site patterns) > > > SUBSTITUTION PROCESS > > Model of substitution: WAG (Whelan-Goldman 2000) > Amino acid frequencies (estimated from data set): > > pi(A) = 12.2% > pi(R) = 2.3% > pi(N) = 3.0% > pi(D) = 4.9% > pi(C) = 0.7% > pi(Q) = 2.3% > pi(E) = 5.4% > pi(G) = 6.0% > pi(H) = 5.8% > pi(I) = 2.7% > pi(L) = 12.5% > pi(K) = 9.3% > pi(M) = 1.3% > pi(F) = 4.9% > pi(P) = 2.6% > pi(S) = 6.7% > pi(T) = 4.5% > pi(W) = 1.3% > pi(Y) = 2.2% > pi(V) = 9.4% > > > AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) > > gaps wildcards sum % sequence > HBB_HUMAN 0 0 0 0.00% > HBB_HORSE 0 0 0 0.00% > HBA_HUMAN 0 0 0 0.00% > HBA_HORSE 0 0 0 0.00% > MYG_PHYCA 0 0 0 0.00% > GLB5_PETMA 0 0 0 0.00% > LGB2_LUPLU 0 0 0 0.00% > ------------------------------------------------------- > Sum 0 0 0 0.00% > > > The table above shows the amount of gaps ('-') and other 'wildcard' > characters ('X', '?', etc.) and their percentage of the 128 columns > in the alignment. > Sequences with more than 50% ambiguous characters are marked with a '!' and > should be checked, whether they have sufficient overlap to other sequences. > Sequences with 100% ambiguous characters do not hold any phylogenetic > information and had to be discarded from the analysis. > > > > SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) > > 5% chi-square test p-value > HBB_HUMAN passed 92.31% > HBB_HORSE passed 79.58% > HBA_HUMAN passed 93.09% > HBA_HORSE passed 81.20% > MYG_PHYCA passed 33.23% > GLB5_PETMA passed 19.11% > LGB2_LUPLU passed 41.67% > > The chi-square tests compares the amino acid composition of each sequence > to the frequency distribution assumed in the maximum likelihood model. > > WARNING: Result of chi-square test may not be valid because of small > maximum likelihood frequencies and short sequence length! > > > IDENTICAL SEQUENCES > > The sequences in each of the following groups are all identical. To speed > up computation please remove all but one of each group from the data set. > > All sequences are unique. > > > MAXIMUM LIKELIHOOD DISTANCES > > Maximum likelihood distances are computed using the selected model of > substitution and rate heterogeneity. > > 7 > HBB_HUMAN 0.00000 0.16900 0.89717 0.92939 1.84037 1.59398 2.23038 > HBB_HORSE 0.16900 0.00000 0.92202 0.93317 1.80081 1.60452 2.27765 > HBA_HUMAN 0.89717 0.92202 0.00000 0.12400 1.71106 1.17087 2.28564 > HBA_HORSE 0.92939 0.93317 0.12400 0.00000 1.77692 1.23977 2.22372 > MYG_PHYCA 1.84037 1.80081 1.71106 1.77692 0.00000 1.72932 2.25004 > GLB5_PETMA 1.59398 1.60452 1.17087 1.23977 1.72932 0.00000 1.91159 > LGB2_LUPLU 2.23038 2.27765 2.28564 2.22372 2.25004 1.91159 0.00000 > > Average distance (over all possible pairs of sequences): 1.50578 > minimum : 0.12400, maximum : 2.28564 > variance : 0.42979, std.dev. : 0.65558 > > > RATE HETEROGENEITY > > Model of rate heterogeneity: uniform rate > > > QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) > > > name | resolved | partly resolved | unresolved | sum > -------------------------------------------------------------------------- > HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 > HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 > HBA_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 > HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 > MYG_PHYCA 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 > GLB5_PETMA 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 > LGB2_LUPLU 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 > -------------------------------------------------------------------------- > #quartets : 31 [ 88.57%] 0 [ 0.00%] 4 [ 11.43%] 35 > > The table shows the occurrences of fully resolved, partially, and > completely unresolved quartets for each sequence and their percentage > relative to the number of times the sequence occurs in the list of > quartets (i.e. 20 quartets out of 35 in total). > In fully resolved quartet one single topology is supported, while for > partially resolved quartets two and for completely unresolved quartets > none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. > Note: Because 4 sequences are involved in one quartet numbers add up > to a four-fold of the existing quartets. > > Hint: The overall numbers in the last row give information about the > phylogenetic content of the dataset. The higher the percentage of partially > and unresolved quartets, the lower the content of phylogenetic information. > This can be visualized in more detail by likelihood mapping analysis. > > > > TREE SEARCH > > Quartet puzzling is used to choose from the possible tree topologies > and to simultaneously infer support values for internal branches. > > Number of puzzling steps: 1000 > Analysed quartets: 35 > Fully resolved quartets: 31 (= 88.6%) > Partly resolved quartets: 0 (= 0.0%) > Unresolved quartets: 4 (= 11.4%) > > Quartet trees are based on approximate maximum likelihood values > using the selected model of substitution and rate heterogeneity. > > > QUARTET PUZZLING TREE > > Support for the internal branches of the unrooted quartet puzzling > tree topology is shown in percent. > > This quartet puzzling tree is not completely resolved! > > > :---MYG_PHYCA > : > :100:---GLB5_PETMA > : : > :100: :---LGB2_LUPLU > : : > : : :---HBA_HUMAN > : :100: > : :---HBA_HORSE > : > :-----------HBB_HORSE > : > :-----------HBB_HUMAN > > > Quartet puzzling tree (in CLUSTAL W notation): > > (HBB_HUMAN,((MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)100,(HBA_HUMAN, > HBA_HORSE)100)100,HBB_HORSE); > > > BIPARTITIONS > > The following bipartitions occured at least once in all intermediate > trees that have been generated in the 1000 puzzling steps. > Bipartitions included in the quartet puzzling tree: > (bipartition with sequences in input order : number of times seen) > > ****... : 1000 > **..... : 1000 > **..*** : 1000 > > Congruent bipartitions occurred in 50% or less, not included in > the consensus tree: > (bipartition with sequences in input order : number of times seen) > > *****.. : 347 > > Incongruent bipartitions not included in the consensus tree: > (bipartition with sequences in input order : number of times seen) > > ****..* : 331 > ****.*. : 322 > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > > :-------------5 MYG_PHYCA > :-------8 > : :-------6 GLB5_PETMA > : : > : :------------------7 LGB2_LUPLU > :-------10 > : : :-3 HBA_HUMAN > : :-----9 > : :--4 HBA_HORSE > : > :--2 HBB_HORSE > : > :-1 HBB_HUMAN > > > branch length S.E. branch length S.E. > HBB_HUMAN 1 0.05028 0.03102 8 0.44299 0.11946 > HBB_HORSE 2 0.11946 0.03740 9 0.25788 0.08204 > HBA_HUMAN 3 0.02934 0.02189 10 0.57110 0.10504 > HBA_HORSE 4 0.09430 0.03146 > MYG_PHYCA 5 1.11230 0.17628 > GLB5_PETMA 6 0.59340 0.11994 11 iterations until convergence > LGB2_LUPLU 7 1.46501 0.22199 log L: -1699.78 > > > Consensus tree with maximum likelihood branch lengths > (in CLUSTAL W notation): > > (HBB_HUMAN:0.05028,((MYG_PHYCA:1.11230,GLB5_PETMA:0.59340,LGB2_LUPLU:1.46501) > 100:0.44299,(HBA_HUMAN:0.02934,HBA_HORSE:0.09430)100:0.25788)100:0.57110, > HBB_HORSE:0.11946); > > > TIME STAMP > FAIL qp-wag-prot.test (exit status: 1) FAIL: qp-clock ============== Testing: default data, default model, clock, quartet puzzling (qp-clock) ./qp-clock.test: line 181: 18864 Segmentation fault ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 cat: qp-clock.nucl.puzzle: No such file or directory 0a1,368 > TREE-PUZZLE > > Input file name: qp-clock.nucl > Type of analysis: tree reconstruction > Parameter estimation: approximate (faster) > Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) > > Standard errors (S.E.) are obtained by the curvature method. > The upper and lower bounds of an approximate 95% confidence interval > for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. > > > SEQUENCE ALIGNMENT > > Input data: 8 sequences with 116 nucleotide sites > Number of constant sites: 66 (= 56.9% of all sites) > Number of site patterns: 54 > Number of constant site patterns: 4 (= 7.4% of all site patterns) > > > SUBSTITUTION PROCESS > > Model of substitution: HKY (Hasegawa et al. 1985) > Transition/transversion parameter (estimated from data set): 1.51 (S.E. 0.28) > > Rate matrix R (parameters restricted to selected model): > > A-C rate: 1.00000 > A-G rate: 2.98614 > A-T rate: 1.00000 > C-G rate: 1.00000 > C-T rate: 2.98614 > G-T rate: 1.00000 > > Nucleotide frequencies (estimated from data set): > > pi(A) = 26.6% > pi(C) = 30.6% > pi(G) = 12.0% > pi(T) = 30.7% > > Expected transition/transversion ratio: 1.60 > Expected pyrimidine transition/purine transition ratio: 2.95 > > > AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) > > gaps wildcards sum % sequence > Thylacinus 0 0 0 0.00% > Sarcophilu 0 0 0 0.00% > Dasyurus 0 1 1 0.86% > Echymipera 0 0 0 0.00% > Trichosuru 0 0 0 0.00% > Phalanger 0 0 0 0.00% > Philander 0 0 0 0.00% > Bos 0 0 0 0.00% > ------------------------------------------------------- > Sum 0 1 1 0.11% > > > The table above shows the amount of gaps ('-') and other 'wildcard' > characters ('X', '?', etc.) and their percentage of the 116 columns > in the alignment. > Sequences with more than 50% ambiguous characters are marked with a '!' and > should be checked, whether they have sufficient overlap to other sequences. > Sequences with 100% ambiguous characters do not hold any phylogenetic > information and had to be discarded from the analysis. > > > > SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) > > 5% chi-square test p-value > Thylacinus passed 90.89% > Sarcophilu passed 93.32% > Dasyurus passed 98.01% > Echymipera passed 92.83% > Trichosuru passed 90.41% > Phalanger passed 86.09% > Philander passed 66.19% > Bos passed 60.02% > > The chi-square tests compares the nucleotide composition of each sequence > to the frequency distribution assumed in the maximum likelihood model. > > > IDENTICAL SEQUENCES > > The sequences in each of the following groups are all identical. To speed > up computation please remove all but one of each group from the data set. > > All sequences are unique. > > > MAXIMUM LIKELIHOOD DISTANCES > > Maximum likelihood distances are computed using the selected model of > substitution and rate heterogeneity. > > 8 > Thylacinus 0.00000 0.25562 0.22032 0.24509 0.26007 0.24938 0.22246 > 0.23734 > Sarcophilu 0.25562 0.00000 0.13169 0.26969 0.28414 0.32680 0.26008 > 0.29786 > Dasyurus 0.22032 0.13169 0.00000 0.20032 0.24821 0.25234 0.17801 > 0.23883 > Echymipera 0.24509 0.26969 0.20032 0.00000 0.29531 0.33871 0.23041 > 0.27215 > Trichosuru 0.26007 0.28414 0.24821 0.29531 0.00000 0.21136 0.28562 > 0.27148 > Phalanger 0.24938 0.32680 0.25234 0.33871 0.21136 0.00000 0.29036 > 0.33042 > Philander 0.22246 0.26008 0.17801 0.23041 0.28562 0.29036 0.00000 > 0.22452 > Bos 0.23734 0.29786 0.23883 0.27215 0.27148 0.33042 0.22452 > 0.00000 > > Average distance (over all possible pairs of sequences): 0.25459 > minimum : 0.13169, maximum : 0.33871 > variance : 0.00207, std.dev. : 0.04544 > > > RATE HETEROGENEITY > > Model of rate heterogeneity: uniform rate > > > QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) > > > name | resolved | partly resolved | unresolved | sum > -------------------------------------------------------------------------- > Thylacinus 22 [ 62.86%] 4 [ 11.43%] 9 [ 25.71%] 35 > Sarcophilu 27 [ 77.14%] 1 [ 2.86%] 7 [ 20.00%] 35 > Dasyurus 27 [ 77.14%] 4 [ 11.43%] 4 [ 11.43%] 35 > Echymipera 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 > Trichosuru 27 [ 77.14%] 2 [ 5.71%] 6 [ 17.14%] 35 > Phalanger 28 [ 80.00%] 3 [ 8.57%] 4 [ 11.43%] 35 > Philander 25 [ 71.43%] 6 [ 17.14%] 4 [ 11.43%] 35 > Bos 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 > -------------------------------------------------------------------------- > #quartets : 49 [ 70.00%] 7 [ 10.00%] 14 [ 20.00%] 70 > > The table shows the occurrences of fully resolved, partially, and > completely unresolved quartets for each sequence and their percentage > relative to the number of times the sequence occurs in the list of > quartets (i.e. 35 quartets out of 70 in total). > In fully resolved quartet one single topology is supported, while for > partially resolved quartets two and for completely unresolved quartets > none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. > Note: Because 4 sequences are involved in one quartet numbers add up > to a four-fold of the existing quartets. > > Hint: The overall numbers in the last row give information about the > phylogenetic content of the dataset. The higher the percentage of partially > and unresolved quartets, the lower the content of phylogenetic information. > This can be visualized in more detail by likelihood mapping analysis. > > > > TREE SEARCH > > Quartet puzzling is used to choose from the possible tree topologies > and to simultaneously infer support values for internal branches. > > Number of puzzling steps: 1000 > Analysed quartets: 70 > Fully resolved quartets: 49 (= 70.0%) > Partly resolved quartets: 7 (= 10.0%) > Unresolved quartets: 14 (= 20.0%) > > Quartet trees are based on approximate maximum likelihood values > using the selected model of substitution and rate heterogeneity. > > > QUARTET PUZZLING TREE > > Support for the internal branches of the unrooted quartet puzzling > tree topology is shown in percent. > > This quartet puzzling tree is not completely resolved! > > > :---Trichosuru > :-----97: > : :---Phalanger > : > : :---Sarcophilu > : :-98: > : : :---Dasyurus > : : > :-71: :---Philander > : :-65: > : : :---Bos > : : > : :-------Echymipera > : > :-----------Thylacinus > > > Quartet puzzling tree (in CLUSTAL W notation): > > (Thylacinus,(Trichosuru,Phalanger)97,((Sarcophilu,Dasyurus)98, > (Philander,Bos)65,Echymipera)71); > > > BIPARTITIONS > > The following bipartitions occured at least once in all intermediate > trees that have been generated in the 1000 puzzling steps. > Bipartitions included in the quartet puzzling tree: > (bipartition with sequences in input order : number of times seen) > > *..***** : 981 > ****..** : 971 > *...**.. : 713 > ******.. : 649 > > Congruent bipartitions occurred in 50% or less, not included in > the consensus tree: > (bipartition with sequences in input order : number of times seen) > > *...**** : 426 > > Incongruent bipartitions not included in the consensus tree: > (bipartition with sequences in input order : number of times seen) > > ***.**.. : 347 > ***.**.* : 150 > *...**.* : 131 > *..***.. : 87 > *..*..** : 81 > *.....** : 72 > ****..*. : 55 > ***.***. : 37 > ****.... : 36 > *..***.* : 36 > ***..... : 31 > *.....*. : 28 > *...***. : 27 > *......* : 27 > *....*.. : 26 > *..*.... : 21 > **..**** : 16 > ***...** : 14 > *..*..*. : 13 > *..****. : 12 > > (6 other less frequent bipartitions not shown) > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > > :---------5 Trichosuru > :------9 > : :----------6 Phalanger > : > : :-----------2 Sarcophilu > : :-------10 > : : :-3 Dasyurus > :-----12 > : : :--------7 Philander > : :----11 > : : :-----------8 Bos > : : > : :------------4 Echymipera > : > :---------1 Thylacinus > > > branch length S.E. branch length S.E. > Thylacinus 1 0.11024 0.03812 9 0.05953 0.03382 > Sarcophilu 2 0.13180 0.03734 10 0.08585 0.03452 > Dasyurus 3 0.00572 0.01273 11 0.04220 0.02513 > Echymipera 4 0.13997 0.04108 12 0.05457 0.02998 > Trichosuru 5 0.10654 0.03770 > Phalanger 6 0.12258 0.04064 > Philander 7 0.08995 0.03428 8 iterations until convergence > Bos 8 0.13479 0.04095 log L: -603.37 > > > Consensus tree with maximum likelihood branch lengths > (in CLUSTAL W notation): > > (Thylacinus:0.11024,(Trichosuru:0.10654,Phalanger:0.12258)97:0.05953, > ((Sarcophilu:0.13180,Dasyurus:0.00572)98:0.08585,(Philander:0.08995, > Bos:0.13479)65:0.04220,Echymipera:0.13997)71:0.05457); > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > Root located at branch: 1 "Thylacinus" (automatic search) > > If the automatic search misplaces the root please rerun the analysis > (rename "outtree" to "intree") and select location of root manually! > > > :---------5 Trichosuru > :-----9 > : :---------6 Phalanger > : > : :-----2 Sarcophilu > : :------10 > : : :-----3 Dasyurus > :--12 > : : :--------7 Philander > : :---11 > : : :--------8 Bos > : : > : :-----------4 Echymipera > : > :------------1 Thylacinus > > > Tree drawn as unrooted tree for better comparison with non-clock tree! > > branch length nc/c branch length nc/c (= non-clock/clock) > Thylacinus 1 0.14706 0.750 9 0.04504 1.322 > Sarcophilu 2 0.06189 2.130 10 0.06663 1.288 > Dasyurus 3 0.06189 0.092 11 0.03304 1.277 > Echymipera 4 0.12852 1.089 12 0.01851 2.948 > Trichosuru 5 0.10199 1.045 > Phalanger 6 0.10199 1.202 > Philander 7 0.09549 0.942 6 iterations until convergence > Bos 8 0.09549 1.412 log L: -610.75 > > height S.E. of node common to branches > 0.10199 0.01922 9 5 6 > 0.06189 0.01495 10 2 3 > 0.09549 0.01498 11 7 8 > 0.12852 0.01108 12 10 11 4 > 0.14704 0.01235 1 9 12 > 0.14705 0.02366 of root at branch 1 > > > Rooted consensus tree with clocklike maximum likelihood branch lengths > (in CLUSTAL W notation): > > (Thylacinus:0.14705,((Trichosuru:0.10199,Phalanger:0.10199)97:0.04504 > ,((Sarcophilu:0.06189,Dasyurus:0.06189)98:0.06663,(Philander:0.09549, > Bos:0.09549)65:0.03304,Echymipera:0.12852)71:0.01851):0.00001); > > > MOLECULAR CLOCK LIKELIHOOD RATIO TEST > > log L without clock: -603.37 (independent branch parameters: 12) > log L with clock: -610.75 (independent branch parameters: 6) > > Likelihood ratio test statistic delta: 14.77 > Degress of freedom of chi-square distribution: 6 > Critical significance level: 2.22% > > The simpler (clocklike) tree is rejected on a significance level > of 5%. The log-likelihood of the more complex (no clock) tree is > significantly increased. > > Please take care that the correct root is used! > > > TIME STAMP > FAIL qp-clock.test (exit status: 1) FAIL: qp-jtt-prot ================= Testing: protein data, JTT, quartet puzzling (qp-jtt-prot) ./qp-jtt-prot.test: line 181: 18883 Segmentation fault ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 cat: qp-jtt-prot.prot.puzzle: No such file or directory 0a1,262 > TREE-PUZZLE > > Input file name: qp-jtt-prot.prot > Type of analysis: tree reconstruction > Parameter estimation: approximate (faster) > Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) > > Standard errors (S.E.) are obtained by the curvature method. > The upper and lower bounds of an approximate 95% confidence interval > for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. > > > SEQUENCE ALIGNMENT > > Input data: 7 sequences with 128 amino acid sites > Number of constant sites: 7 (= 5.5% of all sites) > Number of site patterns: 125 > Number of constant site patterns: 5 (= 4.0% of all site patterns) > > > SUBSTITUTION PROCESS > > Model of substitution: JTT (Jones et al. 1992) > Amino acid frequencies (estimated from data set): > > pi(A) = 12.2% > pi(R) = 2.3% > pi(N) = 3.0% > pi(D) = 4.9% > pi(C) = 0.7% > pi(Q) = 2.3% > pi(E) = 5.4% > pi(G) = 6.0% > pi(H) = 5.8% > pi(I) = 2.7% > pi(L) = 12.5% > pi(K) = 9.3% > pi(M) = 1.3% > pi(F) = 4.9% > pi(P) = 2.6% > pi(S) = 6.7% > pi(T) = 4.5% > pi(W) = 1.3% > pi(Y) = 2.2% > pi(V) = 9.4% > > > AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) > > gaps wildcards sum % sequence > HBB_HUMAN 0 0 0 0.00% > HBB_HORSE 0 0 0 0.00% > HBA_HUMAN 0 0 0 0.00% > HBA_HORSE 0 0 0 0.00% > MYG_PHYCA 0 0 0 0.00% > GLB5_PETMA 0 0 0 0.00% > LGB2_LUPLU 0 0 0 0.00% > ------------------------------------------------------- > Sum 0 0 0 0.00% > > > The table above shows the amount of gaps ('-') and other 'wildcard' > characters ('X', '?', etc.) and their percentage of the 128 columns > in the alignment. > Sequences with more than 50% ambiguous characters are marked with a '!' and > should be checked, whether they have sufficient overlap to other sequences. > Sequences with 100% ambiguous characters do not hold any phylogenetic > information and had to be discarded from the analysis. > > > > SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) > > 5% chi-square test p-value > HBB_HUMAN passed 92.31% > HBB_HORSE passed 79.58% > HBA_HUMAN passed 93.09% > HBA_HORSE passed 81.20% > MYG_PHYCA passed 33.23% > GLB5_PETMA passed 19.11% > LGB2_LUPLU passed 41.67% > > The chi-square tests compares the amino acid composition of each sequence > to the frequency distribution assumed in the maximum likelihood model. > > WARNING: Result of chi-square test may not be valid because of small > maximum likelihood frequencies and short sequence length! > > > IDENTICAL SEQUENCES > > The sequences in each of the following groups are all identical. To speed > up computation please remove all but one of each group from the data set. > > All sequences are unique. > > > MAXIMUM LIKELIHOOD DISTANCES > > Maximum likelihood distances are computed using the selected model of > substitution and rate heterogeneity. > > 7 > HBB_HUMAN 0.00000 0.17343 0.93732 0.96340 2.06393 1.74159 2.60857 > HBB_HORSE 0.17343 0.00000 0.97297 0.97742 2.03298 1.75271 2.65715 > HBA_HUMAN 0.93732 0.97297 0.00000 0.12200 1.93956 1.25126 2.51688 > HBA_HORSE 0.96340 0.97742 0.12200 0.00000 1.99570 1.34817 2.47562 > MYG_PHYCA 2.06393 2.03298 1.93956 1.99570 0.00000 2.04426 2.69086 > GLB5_PETMA 1.74159 1.75271 1.25126 1.34817 2.04426 0.00000 2.23399 > LGB2_LUPLU 2.60857 2.65715 2.51688 2.47562 2.69086 2.23399 0.00000 > > Average distance (over all possible pairs of sequences): 1.69047 > minimum : 0.12200, maximum : 2.69086 > variance : 0.60537, std.dev. : 0.77805 > > > RATE HETEROGENEITY > > Model of rate heterogeneity: uniform rate > > > QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) > > > name | resolved | partly resolved | unresolved | sum > -------------------------------------------------------------------------- > HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 > HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 > HBA_HUMAN 19 [ 95.00%] 1 [ 5.00%] 0 [ 0.00%] 20 > HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 > MYG_PHYCA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 > GLB5_PETMA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 > LGB2_LUPLU 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 > -------------------------------------------------------------------------- > #quartets : 31 [ 88.57%] 1 [ 2.86%] 3 [ 8.57%] 35 > > The table shows the occurrences of fully resolved, partially, and > completely unresolved quartets for each sequence and their percentage > relative to the number of times the sequence occurs in the list of > quartets (i.e. 20 quartets out of 35 in total). > In fully resolved quartet one single topology is supported, while for > partially resolved quartets two and for completely unresolved quartets > none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. > Note: Because 4 sequences are involved in one quartet numbers add up > to a four-fold of the existing quartets. > > Hint: The overall numbers in the last row give information about the > phylogenetic content of the dataset. The higher the percentage of partially > and unresolved quartets, the lower the content of phylogenetic information. > This can be visualized in more detail by likelihood mapping analysis. > > > > TREE SEARCH > > Quartet puzzling is used to choose from the possible tree topologies > and to simultaneously infer support values for internal branches. > > Number of puzzling steps: 1000 > Analysed quartets: 35 > Fully resolved quartets: 31 (= 88.6%) > Partly resolved quartets: 1 (= 2.9%) > Unresolved quartets: 3 (= 8.6%) > > Quartet trees are based on approximate maximum likelihood values > using the selected model of substitution and rate heterogeneity. > > > QUARTET PUZZLING TREE > > Support for the internal branches of the unrooted quartet puzzling > tree topology is shown in percent. > > This quartet puzzling tree is not completely resolved! > > > :---MYG_PHYCA > : > :100:---GLB5_PETMA > : : > :100: :---LGB2_LUPLU > : : > : : :---HBA_HUMAN > : :100: > : :---HBA_HORSE > : > :-----------HBB_HORSE > : > :-----------HBB_HUMAN > > > Quartet puzzling tree (in CLUSTAL W notation): > > (HBB_HUMAN,((MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)100,(HBA_HUMAN, > HBA_HORSE)100)100,HBB_HORSE); > > > BIPARTITIONS > > The following bipartitions occured at least once in all intermediate > trees that have been generated in the 1000 puzzling steps. > Bipartitions included in the quartet puzzling tree: > (bipartition with sequences in input order : number of times seen) > > ****... : 1000 > **..... : 1000 > **..*** : 1000 > > Congruent bipartitions occurred in 50% or less, not included in > the consensus tree: > (bipartition with sequences in input order : number of times seen) > > *****.. : 393 > > Incongruent bipartitions not included in the consensus tree: > (bipartition with sequences in input order : number of times seen) > > ****.*. : 380 > ****..* : 227 > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > > :--------------5 MYG_PHYCA > :------8 > : :-------6 GLB5_PETMA > : : > : :------------------7 LGB2_LUPLU > :-------10 > : : :-3 HBA_HUMAN > : :----9 > : :-4 HBA_HORSE > : > :--2 HBB_HORSE > : > :-1 HBB_HUMAN > > > branch length S.E. branch length S.E. > HBB_HUMAN 1 0.04638 0.03177 8 0.42254 0.12722 > HBB_HORSE 2 0.12734 0.03889 9 0.25371 0.08572 > HBA_HUMAN 3 0.02556 0.02189 10 0.61836 0.11268 > HBA_HORSE 4 0.09595 0.03156 > MYG_PHYCA 5 1.31230 0.21006 > GLB5_PETMA 6 0.68479 0.13678 12 iterations until convergence > LGB2_LUPLU 7 1.72936 0.26616 log L: -1707.74 > > > Consensus tree with maximum likelihood branch lengths > (in CLUSTAL W notation): > > (HBB_HUMAN:0.04638,((MYG_PHYCA:1.31230,GLB5_PETMA:0.68479,LGB2_LUPLU:1.72936) > 100:0.42254,(HBA_HUMAN:0.02556,HBA_HORSE:0.09595)100:0.25371)100:0.61836, > HBB_HORSE:0.12734); > > > TIME STAMP > FAIL qp-jtt-prot.test (exit status: 1) FAIL: qp-jtt-rhet-prot ====================== Testing: protein data, JTT, rate heterogeneity, quartet puzzling (qp-jtt-rhet-prot) ./qp-jtt-rhet-prot.test: line 181: 18902 Segmentation fault ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 cat: qp-jtt-rhet-prot.prot.puzzle: No such file or directory 0a1,288 > TREE-PUZZLE > > Input file name: qp-jtt-rhet-prot.prot > Type of analysis: tree reconstruction > Parameter estimation: approximate (faster) > Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) > > Standard errors (S.E.) are obtained by the curvature method. > The upper and lower bounds of an approximate 95% confidence interval > for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. > > > SEQUENCE ALIGNMENT > > Input data: 7 sequences with 128 amino acid sites > Number of constant sites: 7 (= 5.5% of all sites) > Number of site patterns: 125 > Number of constant site patterns: 5 (= 4.0% of all site patterns) > > > SUBSTITUTION PROCESS > > Model of substitution: JTT (Jones et al. 1992) > Amino acid frequencies (estimated from data set): > > pi(A) = 12.2% > pi(R) = 2.3% > pi(N) = 3.0% > pi(D) = 4.9% > pi(C) = 0.7% > pi(Q) = 2.3% > pi(E) = 5.4% > pi(G) = 6.0% > pi(H) = 5.8% > pi(I) = 2.7% > pi(L) = 12.5% > pi(K) = 9.3% > pi(M) = 1.3% > pi(F) = 4.9% > pi(P) = 2.6% > pi(S) = 6.7% > pi(T) = 4.5% > pi(W) = 1.3% > pi(Y) = 2.2% > pi(V) = 9.4% > > > AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) > > gaps wildcards sum % sequence > HBB_HUMAN 0 0 0 0.00% > HBB_HORSE 0 0 0 0.00% > HBA_HUMAN 0 0 0 0.00% > HBA_HORSE 0 0 0 0.00% > MYG_PHYCA 0 0 0 0.00% > GLB5_PETMA 0 0 0 0.00% > LGB2_LUPLU 0 0 0 0.00% > ------------------------------------------------------- > Sum 0 0 0 0.00% > > > The table above shows the amount of gaps ('-') and other 'wildcard' > characters ('X', '?', etc.) and their percentage of the 128 columns > in the alignment. > Sequences with more than 50% ambiguous characters are marked with a '!' and > should be checked, whether they have sufficient overlap to other sequences. > Sequences with 100% ambiguous characters do not hold any phylogenetic > information and had to be discarded from the analysis. > > > > SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) > > 5% chi-square test p-value > HBB_HUMAN passed 92.31% > HBB_HORSE passed 79.58% > HBA_HUMAN passed 93.09% > HBA_HORSE passed 81.20% > MYG_PHYCA passed 33.23% > GLB5_PETMA passed 19.11% > LGB2_LUPLU passed 41.67% > > The chi-square tests compares the amino acid composition of each sequence > to the frequency distribution assumed in the maximum likelihood model. > > WARNING: Result of chi-square test may not be valid because of small > maximum likelihood frequencies and short sequence length! > > > IDENTICAL SEQUENCES > > The sequences in each of the following groups are all identical. To speed > up computation please remove all but one of each group from the data set. > > All sequences are unique. > > > MAXIMUM LIKELIHOOD DISTANCES > > Maximum likelihood distances are computed using the selected model of > substitution and rate heterogeneity. > > 7 > HBB_HUMAN 0.00000 0.17887 1.04805 1.08480 2.52050 2.10945 3.26098 > HBB_HORSE 0.17887 0.00000 1.09690 1.10752 2.49215 2.12870 3.34229 > HBA_HUMAN 1.04805 1.09690 0.00000 0.12538 2.35997 1.45565 3.24727 > HBA_HORSE 1.08480 1.10752 0.12538 0.00000 2.43814 1.57611 3.14845 > MYG_PHYCA 2.52050 2.49215 2.35997 2.43814 0.00000 2.54103 3.42222 > GLB5_PETMA 2.10945 2.12870 1.45565 1.57611 2.54103 0.00000 2.84131 > LGB2_LUPLU 3.26098 3.34229 3.24727 3.14845 3.42222 2.84131 0.00000 > > Average distance (over all possible pairs of sequences): 2.07265 > minimum : 0.12538, maximum : 3.42222 > variance : 1.03523, std.dev. : 1.01746 > > > RATE HETEROGENEITY > > Model of rate heterogeneity: Gamma distributed rates > Gamma distribution parameter alpha (estimated from data set): 2.85 (S.E. 1.58) > Number of Gamma rate categories: 8 > > Rates and their respective probabilities used in the likelihood function: > > Category Relative rate Probability > 1 0.2882 0.1250 > 2 0.4879 0.1250 > 3 0.6513 0.1250 > 4 0.8135 0.1250 > 5 0.9910 0.1250 > 6 1.2042 0.1250 > 7 1.4978 0.1250 > 8 2.0662 0.1250 > > Categories 1-8 approximate a continous Gamma-distribution with expectation 1 > and variance 0.35. > > Combination of categories that contributes the most to the likelihood > (computation done without clock assumption assuming quartet-puzzling tree): > > 8 1 1 8 3 2 6 4 8 1 8 2 4 1 8 4 1 8 8 8 6 6 1 8 3 3 1 4 1 6 > 2 8 5 8 1 8 1 4 4 7 1 8 8 1 4 2 1 6 6 1 4 4 2 2 8 1 2 7 3 1 > 8 8 2 5 8 8 2 4 8 4 8 3 7 6 8 8 7 1 4 8 1 1 7 8 1 2 8 1 7 6 > 1 1 8 1 1 6 4 2 5 7 4 1 6 8 1 2 4 8 7 4 1 5 8 6 2 8 6 6 8 3 > 6 6 7 2 6 4 3 1 > > > QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) > > > name | resolved | partly resolved | unresolved | sum > -------------------------------------------------------------------------- > HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 > HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 > HBA_HUMAN 19 [ 95.00%] 1 [ 5.00%] 0 [ 0.00%] 20 > HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 > MYG_PHYCA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 > GLB5_PETMA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 > LGB2_LUPLU 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 > -------------------------------------------------------------------------- > #quartets : 31 [ 88.57%] 1 [ 2.86%] 3 [ 8.57%] 35 > > The table shows the occurrences of fully resolved, partially, and > completely unresolved quartets for each sequence and their percentage > relative to the number of times the sequence occurs in the list of > quartets (i.e. 20 quartets out of 35 in total). > In fully resolved quartet one single topology is supported, while for > partially resolved quartets two and for completely unresolved quartets > none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. > Note: Because 4 sequences are involved in one quartet numbers add up > to a four-fold of the existing quartets. > > Hint: The overall numbers in the last row give information about the > phylogenetic content of the dataset. The higher the percentage of partially > and unresolved quartets, the lower the content of phylogenetic information. > This can be visualized in more detail by likelihood mapping analysis. > > > > TREE SEARCH > > Quartet puzzling is used to choose from the possible tree topologies > and to simultaneously infer support values for internal branches. > > Number of puzzling steps: 1000 > Analysed quartets: 35 > Fully resolved quartets: 31 (= 88.6%) > Partly resolved quartets: 1 (= 2.9%) > Unresolved quartets: 3 (= 8.6%) > > Quartet trees are based on approximate maximum likelihood values > using the selected model of substitution and rate heterogeneity. > > > QUARTET PUZZLING TREE > > Support for the internal branches of the unrooted quartet puzzling > tree topology is shown in percent. > > This quartet puzzling tree is not completely resolved! > > > :---MYG_PHYCA > : > :100:---GLB5_PETMA > : : > :100: :---LGB2_LUPLU > : : > : : :---HBA_HUMAN > : :100: > : :---HBA_HORSE > : > :-----------HBB_HORSE > : > :-----------HBB_HUMAN > > > Quartet puzzling tree (in CLUSTAL W notation): > > (HBB_HUMAN,((MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)100,(HBA_HUMAN, > HBA_HORSE)100)100,HBB_HORSE); > > > BIPARTITIONS > > The following bipartitions occured at least once in all intermediate > trees that have been generated in the 1000 puzzling steps. > Bipartitions included in the quartet puzzling tree: > (bipartition with sequences in input order : number of times seen) > > ****... : 1000 > **..... : 1000 > **..*** : 1000 > > Congruent bipartitions occurred in 50% or less, not included in > the consensus tree: > (bipartition with sequences in input order : number of times seen) > > *****.. : 393 > > Incongruent bipartitions not included in the consensus tree: > (bipartition with sequences in input order : number of times seen) > > ****.*. : 380 > ****..* : 227 > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > > :--------------5 MYG_PHYCA > :-----8 > : :-------6 GLB5_PETMA > : : > : :-------------------7 LGB2_LUPLU > :------10 > : : :-3 HBA_HUMAN > : :---9 > : :-4 HBA_HORSE > : > :--2 HBB_HORSE > : > :-1 HBB_HUMAN > > > branch length S.E. branch length S.E. > HBB_HUMAN 1 0.04933 0.03409 8 0.50700 0.17281 > HBB_HORSE 2 0.12953 0.04093 9 0.23403 0.10586 > HBA_HUMAN 3 0.01995 0.02303 10 0.74732 0.14235 > HBA_HORSE 4 0.10548 0.03367 > MYG_PHYCA 5 1.68057 0.30228 > GLB5_PETMA 6 0.81182 0.18641 12 iterations until convergence > LGB2_LUPLU 7 2.33484 0.42478 log L: -1701.69 > > > Consensus tree with maximum likelihood branch lengths > (in CLUSTAL W notation): > > (HBB_HUMAN:0.04933,((MYG_PHYCA:1.68057,GLB5_PETMA:0.81182,LGB2_LUPLU:2.33484) > 100:0.50700,(HBA_HUMAN:0.01995,HBA_HORSE:0.10548)100:0.23403)100:0.74732, > HBB_HORSE:0.12953); > > > TIME STAMP > FAIL qp-jtt-rhet-prot.test (exit status: 1) FAIL: qp-jtt-rhet-clock-prot ============================ Testing: protein data, JTT, clock, rate heterogeneity, quartet puzzling (qp-jtt-rhet-clock-prot) ./qp-jtt-rhet-clock-prot.test: line 181: 18921 Segmentation fault ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 cat: qp-jtt-rhet-clock-prot.prot.puzzle: No such file or directory 0a1,357 > TREE-PUZZLE > > Input file name: qp-jtt-rhet-clock-prot.prot > Type of analysis: tree reconstruction > Parameter estimation: approximate (faster) > Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) > > Standard errors (S.E.) are obtained by the curvature method. > The upper and lower bounds of an approximate 95% confidence interval > for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. > > > SEQUENCE ALIGNMENT > > Input data: 7 sequences with 128 amino acid sites > Number of constant sites: 7 (= 5.5% of all sites) > Number of site patterns: 125 > Number of constant site patterns: 5 (= 4.0% of all site patterns) > > > SUBSTITUTION PROCESS > > Model of substitution: JTT (Jones et al. 1992) > Amino acid frequencies (estimated from data set): > > pi(A) = 12.2% > pi(R) = 2.3% > pi(N) = 3.0% > pi(D) = 4.9% > pi(C) = 0.7% > pi(Q) = 2.3% > pi(E) = 5.4% > pi(G) = 6.0% > pi(H) = 5.8% > pi(I) = 2.7% > pi(L) = 12.5% > pi(K) = 9.3% > pi(M) = 1.3% > pi(F) = 4.9% > pi(P) = 2.6% > pi(S) = 6.7% > pi(T) = 4.5% > pi(W) = 1.3% > pi(Y) = 2.2% > pi(V) = 9.4% > > > AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) > > gaps wildcards sum % sequence > HBB_HUMAN 0 0 0 0.00% > HBB_HORSE 0 0 0 0.00% > HBA_HUMAN 0 0 0 0.00% > HBA_HORSE 0 0 0 0.00% > MYG_PHYCA 0 0 0 0.00% > GLB5_PETMA 0 0 0 0.00% > LGB2_LUPLU 0 0 0 0.00% > ------------------------------------------------------- > Sum 0 0 0 0.00% > > > The table above shows the amount of gaps ('-') and other 'wildcard' > characters ('X', '?', etc.) and their percentage of the 128 columns > in the alignment. > Sequences with more than 50% ambiguous characters are marked with a '!' and > should be checked, whether they have sufficient overlap to other sequences. > Sequences with 100% ambiguous characters do not hold any phylogenetic > information and had to be discarded from the analysis. > > > > SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) > > 5% chi-square test p-value > HBB_HUMAN passed 92.31% > HBB_HORSE passed 79.58% > HBA_HUMAN passed 93.09% > HBA_HORSE passed 81.20% > MYG_PHYCA passed 33.23% > GLB5_PETMA passed 19.11% > LGB2_LUPLU passed 41.67% > > The chi-square tests compares the amino acid composition of each sequence > to the frequency distribution assumed in the maximum likelihood model. > > WARNING: Result of chi-square test may not be valid because of small > maximum likelihood frequencies and short sequence length! > > > IDENTICAL SEQUENCES > > The sequences in each of the following groups are all identical. To speed > up computation please remove all but one of each group from the data set. > > All sequences are unique. > > > MAXIMUM LIKELIHOOD DISTANCES > > Maximum likelihood distances are computed using the selected model of > substitution and rate heterogeneity. > > 7 > HBB_HUMAN 0.00000 0.17887 1.04805 1.08480 2.52050 2.10945 3.26098 > HBB_HORSE 0.17887 0.00000 1.09690 1.10752 2.49215 2.12870 3.34229 > HBA_HUMAN 1.04805 1.09690 0.00000 0.12538 2.35997 1.45565 3.24727 > HBA_HORSE 1.08480 1.10752 0.12538 0.00000 2.43814 1.57611 3.14845 > MYG_PHYCA 2.52050 2.49215 2.35997 2.43814 0.00000 2.54103 3.42222 > GLB5_PETMA 2.10945 2.12870 1.45565 1.57611 2.54103 0.00000 2.84131 > LGB2_LUPLU 3.26098 3.34229 3.24727 3.14845 3.42222 2.84131 0.00000 > > Average distance (over all possible pairs of sequences): 2.07265 > minimum : 0.12538, maximum : 3.42222 > variance : 1.03523, std.dev. : 1.01746 > > > RATE HETEROGENEITY > > Model of rate heterogeneity: Gamma distributed rates > Gamma distribution parameter alpha (estimated from data set): 2.85 (S.E. 1.58) > Number of Gamma rate categories: 8 > > Rates and their respective probabilities used in the likelihood function: > > Category Relative rate Probability > 1 0.2882 0.1250 > 2 0.4879 0.1250 > 3 0.6513 0.1250 > 4 0.8135 0.1250 > 5 0.9910 0.1250 > 6 1.2042 0.1250 > 7 1.4978 0.1250 > 8 2.0662 0.1250 > > Categories 1-8 approximate a continous Gamma-distribution with expectation 1 > and variance 0.35. > > Combination of categories that contributes the most to the likelihood > (computation done without clock assumption assuming quartet-puzzling tree): > > 8 1 1 8 3 2 6 4 8 1 8 2 4 1 8 4 1 8 8 8 6 6 1 8 3 3 1 4 1 6 > 2 8 5 8 1 8 1 4 4 7 1 8 8 1 4 2 1 6 6 1 4 4 2 2 8 1 2 7 3 1 > 8 8 2 5 8 8 2 4 8 4 8 3 7 6 8 8 7 1 4 8 1 1 7 8 1 2 8 1 7 6 > 1 1 8 1 1 6 4 2 5 7 4 1 6 8 1 2 4 8 7 4 1 5 8 6 2 8 6 6 8 3 > 6 6 7 2 6 4 3 1 > > > QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) > > > name | resolved | partly resolved | unresolved | sum > -------------------------------------------------------------------------- > HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 > HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 > HBA_HUMAN 19 [ 95.00%] 1 [ 5.00%] 0 [ 0.00%] 20 > HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 > MYG_PHYCA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 > GLB5_PETMA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 > LGB2_LUPLU 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 > -------------------------------------------------------------------------- > #quartets : 31 [ 88.57%] 1 [ 2.86%] 3 [ 8.57%] 35 > > The table shows the occurrences of fully resolved, partially, and > completely unresolved quartets for each sequence and their percentage > relative to the number of times the sequence occurs in the list of > quartets (i.e. 20 quartets out of 35 in total). > In fully resolved quartet one single topology is supported, while for > partially resolved quartets two and for completely unresolved quartets > none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. > Note: Because 4 sequences are involved in one quartet numbers add up > to a four-fold of the existing quartets. > > Hint: The overall numbers in the last row give information about the > phylogenetic content of the dataset. The higher the percentage of partially > and unresolved quartets, the lower the content of phylogenetic information. > This can be visualized in more detail by likelihood mapping analysis. > > > > TREE SEARCH > > Quartet puzzling is used to choose from the possible tree topologies > and to simultaneously infer support values for internal branches. > > Number of puzzling steps: 1000 > Analysed quartets: 35 > Fully resolved quartets: 31 (= 88.6%) > Partly resolved quartets: 1 (= 2.9%) > Unresolved quartets: 3 (= 8.6%) > > Quartet trees are based on approximate maximum likelihood values > using the selected model of substitution and rate heterogeneity. > > > QUARTET PUZZLING TREE > > Support for the internal branches of the unrooted quartet puzzling > tree topology is shown in percent. > > This quartet puzzling tree is not completely resolved! > > > :---MYG_PHYCA > : > :100:---GLB5_PETMA > : : > :100: :---LGB2_LUPLU > : : > : : :---HBA_HUMAN > : :100: > : :---HBA_HORSE > : > :-----------HBB_HORSE > : > :-----------HBB_HUMAN > > > Quartet puzzling tree (in CLUSTAL W notation): > > (HBB_HUMAN,((MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)100,(HBA_HUMAN, > HBA_HORSE)100)100,HBB_HORSE); > > > BIPARTITIONS > > The following bipartitions occured at least once in all intermediate > trees that have been generated in the 1000 puzzling steps. > Bipartitions included in the quartet puzzling tree: > (bipartition with sequences in input order : number of times seen) > > ****... : 1000 > **..... : 1000 > **..*** : 1000 > > Congruent bipartitions occurred in 50% or less, not included in > the consensus tree: > (bipartition with sequences in input order : number of times seen) > > *****.. : 393 > > Incongruent bipartitions not included in the consensus tree: > (bipartition with sequences in input order : number of times seen) > > ****.*. : 380 > ****..* : 227 > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > > :--------------5 MYG_PHYCA > :-----8 > : :-------6 GLB5_PETMA > : : > : :-------------------7 LGB2_LUPLU > :------10 > : : :-3 HBA_HUMAN > : :---9 > : :-4 HBA_HORSE > : > :--2 HBB_HORSE > : > :-1 HBB_HUMAN > > > branch length S.E. branch length S.E. > HBB_HUMAN 1 0.04933 0.03409 8 0.50700 0.17281 > HBB_HORSE 2 0.12953 0.04093 9 0.23403 0.10586 > HBA_HUMAN 3 0.01995 0.02303 10 0.74732 0.14235 > HBA_HORSE 4 0.10548 0.03367 > MYG_PHYCA 5 1.68057 0.30228 > GLB5_PETMA 6 0.81182 0.18641 12 iterations until convergence > LGB2_LUPLU 7 2.33484 0.42478 log L: -1701.69 > > > Consensus tree with maximum likelihood branch lengths > (in CLUSTAL W notation): > > (HBB_HUMAN:0.04933,((MYG_PHYCA:1.68057,GLB5_PETMA:0.81182,LGB2_LUPLU:2.33484) > 100:0.50700,(HBA_HUMAN:0.01995,HBA_HORSE:0.10548)100:0.23403)100:0.74732, > HBB_HORSE:0.12953); > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > Root located at branch: 7 "LGB2_LUPLU" (automatic search) > > If the automatic search misplaces the root please rerun the analysis > (rename "outtree" to "intree") and select location of root manually! > > > :----------5 MYG_PHYCA > :------8 > : :----------6 GLB5_PETMA > : : > : :------------------7 LGB2_LUPLU > :----10 > : : :-3 HBA_HUMAN > : :------9 > : :-4 HBA_HORSE > : > :-2 HBB_HORSE > : > :-1 HBB_HUMAN > > > Tree drawn as unrooted tree for better comparison with non-clock tree! > > branch length nc/c branch length nc/c (= non-clock/clock) > HBB_HUMAN 1 0.08775 0.562 8 0.58020 0.874 > HBB_HORSE 2 0.08775 1.476 9 0.51495 0.454 > HBA_HUMAN 3 0.06493 0.307 10 0.49213 1.519 > HBA_HORSE 4 0.06493 1.625 > MYG_PHYCA 5 1.16008 1.449 > GLB5_PETMA 6 1.16008 0.700 7 iterations until convergence > LGB2_LUPLU 7 2.28806 1.020 log L: -1708.27 > > height S.E. of node common to branches > 0.06493 0.01761 9 3 4 > 0.08775 0.02041 10 2 1 > 0.57988 0.07414 8 9 10 > 1.16008 0.11361 7 8 5 6 > 1.72407 0.21630 of root at branch 7 > > > Rooted consensus tree with clocklike maximum likelihood branch lengths > (in CLUSTAL W notation): > > (LGB2_LUPLU:1.72407,(((HBA_HUMAN:0.06493,HBA_HORSE:0.06493)100:0.51495 > ,(HBB_HORSE:0.08775,HBB_HUMAN:0.08775):0.49213):0.58020,MYG_PHYCA:1.16008, > GLB5_PETMA:1.16008):0.56399); > > > MOLECULAR CLOCK LIKELIHOOD RATIO TEST > > log L without clock: -1701.69 (independent branch parameters: 10) > log L with clock: -1708.27 (independent branch parameters: 5) > > Likelihood ratio test statistic delta: 13.15 > Degress of freedom of chi-square distribution: 5 > Critical significance level: 2.20% > > The simpler (clocklike) tree is rejected on a significance level > of 5%. The log-likelihood of the more complex (no clock) tree is > significantly increased. > > Please take care that the correct root is used! > > > TIME STAMP > FAIL qp-jtt-rhet-clock-prot.test (exit status: 1) FAIL: lm-pure-prot ================== Testing: protein data, default model, likelihood mapping (lm-pure-prot) ./lm-pure-prot.test: line 181: 18940 Segmentation fault ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 cat: lm-pure-prot.prot.puzzle: No such file or directory 0a1,175 > TREE-PUZZLE > > Input file name: lm-pure-prot.prot > Type of analysis: likelihood mapping > Parameter estimation: approximate (faster) > Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) > > Standard errors (S.E.) are obtained by the curvature method. > The upper and lower bounds of an approximate 95% confidence interval > for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. > > > SEQUENCE ALIGNMENT > > Input data: 7 sequences with 128 amino acid sites > Number of constant sites: 7 (= 5.5% of all sites) > Number of site patterns: 125 > Number of constant site patterns: 5 (= 4.0% of all site patterns) > > > SUBSTITUTION PROCESS > > Model of substitution: Dayhoff (Dayhoff et al. 1978) > Amino acid frequencies (estimated from data set): > > pi(A) = 12.2% > pi(R) = 2.3% > pi(N) = 3.0% > pi(D) = 4.9% > pi(C) = 0.7% > pi(Q) = 2.3% > pi(E) = 5.4% > pi(G) = 6.0% > pi(H) = 5.8% > pi(I) = 2.7% > pi(L) = 12.5% > pi(K) = 9.3% > pi(M) = 1.3% > pi(F) = 4.9% > pi(P) = 2.6% > pi(S) = 6.7% > pi(T) = 4.5% > pi(W) = 1.3% > pi(Y) = 2.2% > pi(V) = 9.4% > > > AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) > > gaps wildcards sum % sequence > HBB_HUMAN 0 0 0 0.00% > HBB_HORSE 0 0 0 0.00% > HBA_HUMAN 0 0 0 0.00% > HBA_HORSE 0 0 0 0.00% > MYG_PHYCA 0 0 0 0.00% > GLB5_PETMA 0 0 0 0.00% > LGB2_LUPLU 0 0 0 0.00% > ------------------------------------------------------- > Sum 0 0 0 0.00% > > > The table above shows the amount of gaps ('-') and other 'wildcard' > characters ('X', '?', etc.) and their percentage of the 128 columns > in the alignment. > Sequences with more than 50% ambiguous characters are marked with a '!' and > should be checked, whether they have sufficient overlap to other sequences. > Sequences with 100% ambiguous characters do not hold any phylogenetic > information and had to be discarded from the analysis. > > > > SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) > > 5% chi-square test p-value > HBB_HUMAN passed 92.31% > HBB_HORSE passed 79.58% > HBA_HUMAN passed 93.09% > HBA_HORSE passed 81.20% > MYG_PHYCA passed 33.23% > GLB5_PETMA passed 19.11% > LGB2_LUPLU passed 41.67% > > The chi-square tests compares the amino acid composition of each sequence > to the frequency distribution assumed in the maximum likelihood model. > > WARNING: Result of chi-square test may not be valid because of small > maximum likelihood frequencies and short sequence length! > > > IDENTICAL SEQUENCES > > The sequences in each of the following groups are all identical. To speed > up computation please remove all but one of each group from the data set. > > All sequences are unique. > > > MAXIMUM LIKELIHOOD DISTANCES > > Maximum likelihood distances are computed using the selected model of > substitution and rate heterogeneity. > > 7 > HBB_HUMAN 0.00000 0.17425 0.96068 0.99267 2.12932 1.77231 2.78644 > HBB_HORSE 0.17425 0.00000 1.01062 1.02118 2.09456 1.78465 2.86187 > HBA_HUMAN 0.96068 1.01062 0.00000 0.12147 1.93540 1.30123 2.54730 > HBA_HORSE 0.99267 1.02118 0.12147 0.00000 2.00515 1.39193 2.51172 > MYG_PHYCA 2.12932 2.09456 1.93540 2.00515 0.00000 2.12347 2.79386 > GLB5_PETMA 1.77231 1.78465 1.30123 1.39193 2.12347 0.00000 2.18272 > LGB2_LUPLU 2.78644 2.86187 2.54730 2.51172 2.79386 2.18272 0.00000 > > Average distance (over all possible pairs of sequences): 1.73823 > minimum : 0.12147, maximum : 2.86187 > variance : 0.65214, std.dev. : 0.80755 > > > RATE HETEROGENEITY > > Model of rate heterogeneity: uniform rate > > > LIKELIHOOD MAPPING ANALYSIS > > Number of quartets: 35 (all possible) > > Quartet trees are based on approximate maximum likelihood values > using the selected model of substitution and rate heterogeneity. > > > Sequences are not grouped in clusters. > > > LIKELIHOOD MAPPING STATISTICS > > Occupancies of the three areas 1, 2, 3: > > /\ > / \ > / \ > / 1 \ > / \ / \ > / \ / \ > / \/ \ > / 3 : 2 \ > / : \ > /__________________\ > > Number of quartets in region 1: 14 (= 40.0%) > Number of quartets in region 2: 11 (= 31.4%) > Number of quartets in region 3: 10 (= 28.6%) > > Occupancies of the seven areas 1, 2, 3, 4, 5, 6, 7: > > /\ > / \ > / 1 \ > / \ / \ > / /\ \ > / 6 / \ 4 \ > / / 7 \ \ > / \ /______\ / \ > / 3 : 5 : 2 \ > /__________________\ > > Number of quartets in region 1: 12 (= 34.3%) left: 3 right: 9 > Number of quartets in region 2: 11 (= 31.4%) bottom: 3 top: 8 > Number of quartets in region 3: 9 (= 25.7%) bottom: 4 top: 5 > Number of quartets in region 4: 0 (= 0.0%) bottom: 0 top: 0 > Number of quartets in region 5: 0 (= 0.0%) left: 0 right: 0 > Number of quartets in region 6: 0 (= 0.0%) bottom: 0 top: 0 > Number of quartets in region 7: 3 (= 8.6%) > > > TIME STAMP > FAIL lm-pure-prot.test (exit status: 1) FAIL: ut-pure-prot ================== Testing: protein data, default model, user tree evaluation (ut-pure-prot) ./ut-pure-prot.test: line 181: 18960 Segmentation fault ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INUTREE} < $PARAMS > ${INFILE}.out 2>&1 cat: ut-pure-prot.trees.puzzle: No such file or directory 0a1,309 > TREE-PUZZLE > > Input file name: ut-pure-prot.prot > User tree file name: ut-pure-prot.trees > Type of analysis: user tree evaluation > Parameter estimation: approximate (faster) > Parameter estimation uses: 1st user tree (for substitution process and rate variation) > > Standard errors (S.E.) are obtained by the curvature method. > The upper and lower bounds of an approximate 95% confidence interval > for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. > > > SEQUENCE ALIGNMENT > > Input data: 7 sequences with 128 amino acid sites > Number of constant sites: 7 (= 5.5% of all sites) > Number of site patterns: 125 > Number of constant site patterns: 5 (= 4.0% of all site patterns) > > > SUBSTITUTION PROCESS > > Model of substitution: Dayhoff (Dayhoff et al. 1978) > Amino acid frequencies (estimated from data set): > > pi(A) = 12.2% > pi(R) = 2.3% > pi(N) = 3.0% > pi(D) = 4.9% > pi(C) = 0.7% > pi(Q) = 2.3% > pi(E) = 5.4% > pi(G) = 6.0% > pi(H) = 5.8% > pi(I) = 2.7% > pi(L) = 12.5% > pi(K) = 9.3% > pi(M) = 1.3% > pi(F) = 4.9% > pi(P) = 2.6% > pi(S) = 6.7% > pi(T) = 4.5% > pi(W) = 1.3% > pi(Y) = 2.2% > pi(V) = 9.4% > > > AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) > > gaps wildcards sum % sequence > HBB_HUMAN 0 0 0 0.00% > HBB_HORSE 0 0 0 0.00% > HBA_HUMAN 0 0 0 0.00% > HBA_HORSE 0 0 0 0.00% > MYG_PHYCA 0 0 0 0.00% > GLB5_PETMA 0 0 0 0.00% > LGB2_LUPLU 0 0 0 0.00% > ------------------------------------------------------- > Sum 0 0 0 0.00% > > > The table above shows the amount of gaps ('-') and other 'wildcard' > characters ('X', '?', etc.) and their percentage of the 128 columns > in the alignment. > Sequences with more than 50% ambiguous characters are marked with a '!' and > should be checked, whether they have sufficient overlap to other sequences. > Sequences with 100% ambiguous characters do not hold any phylogenetic > information and had to be discarded from the analysis. > > > > SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) > > 5% chi-square test p-value > HBB_HUMAN passed 92.31% > HBB_HORSE passed 79.58% > HBA_HUMAN passed 93.09% > HBA_HORSE passed 81.20% > MYG_PHYCA passed 33.23% > GLB5_PETMA passed 19.11% > LGB2_LUPLU passed 41.67% > > The chi-square tests compares the amino acid composition of each sequence > to the frequency distribution assumed in the maximum likelihood model. > > WARNING: Result of chi-square test may not be valid because of small > maximum likelihood frequencies and short sequence length! > > > IDENTICAL SEQUENCES > > The sequences in each of the following groups are all identical. To speed > up computation please remove all but one of each group from the data set. > > All sequences are unique. > > > MAXIMUM LIKELIHOOD DISTANCES > > Maximum likelihood distances are computed using the selected model of > substitution and rate heterogeneity. > > 7 > HBB_HUMAN 0.00000 0.17425 0.96068 0.99267 2.12932 1.77231 2.78644 > HBB_HORSE 0.17425 0.00000 1.01062 1.02118 2.09456 1.78465 2.86187 > HBA_HUMAN 0.96068 1.01062 0.00000 0.12147 1.93540 1.30123 2.54730 > HBA_HORSE 0.99267 1.02118 0.12147 0.00000 2.00515 1.39193 2.51172 > MYG_PHYCA 2.12932 2.09456 1.93540 2.00515 0.00000 2.12347 2.79386 > GLB5_PETMA 1.77231 1.78465 1.30123 1.39193 2.12347 0.00000 2.18272 > LGB2_LUPLU 2.78644 2.86187 2.54730 2.51172 2.79386 2.18272 0.00000 > > Average distance (over all possible pairs of sequences): 1.73823 > minimum : 0.12147, maximum : 2.86187 > variance : 0.65214, std.dev. : 0.80755 > > > RATE HETEROGENEITY > > Model of rate heterogeneity: uniform rate > > > TREE SEARCH > > 4 tree topologies were specified by the user. > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 1 (NO CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > > :--2 HBB_HORSE > : > : :-3 HBA_HUMAN > : :----8 > : : :-4 HBA_HORSE > :------11 > : : :-------------5 MYG_PHYCA > : : :--9 > : : : :-------6 GLB5_PETMA > : :----10 > : :-----------------7 LGB2_LUPLU > : > :-1 HBB_HUMAN > > > branch length S.E. branch length S.E. > HBB_HUMAN 1 0.04834 0.03148 8 0.28039 0.08746 > HBB_HORSE 2 0.12686 0.03876 9 0.00001 0.00141 > HBA_HUMAN 3 0.02653 0.02208 10 0.40361 0.12824 > HBA_HORSE 4 0.09440 0.03145 11 0.60481 0.11282 > MYG_PHYCA 5 1.33106 0.21114 > GLB5_PETMA 6 0.70107 0.14140 9 iterations until convergence > LGB2_LUPLU 7 1.76830 0.28198 log L: -1699.50 > > WARNING --- at least one branch length is close to an internal boundary! > > > Unrooted user defined tree with maximum likelihood branch lengths > (in CLUSTAL W notation): > > (HBB_HUMAN:0.04834,HBB_HORSE:0.12686,((HBA_HUMAN:0.02653,HBA_HORSE:0.09440) > :0.28039,((MYG_PHYCA:1.33106,GLB5_PETMA:0.70107):0.00001,LGB2_LUPLU:1.76830) > :0.40361):0.60481); > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 2 (NO CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > > :--2 HBB_HORSE > : > : :-3 HBA_HUMAN > : :----8 > : : :-4 HBA_HORSE > :------11 > : : :-------------5 MYG_PHYCA > : :----10 > : : :------6 GLB5_PETMA > : :---9 > : :----------------7 LGB2_LUPLU > : > :-1 HBB_HUMAN > > > branch length S.E. branch length S.E. > HBB_HUMAN 1 0.04915 0.03158 8 0.28347 0.08778 > HBB_HORSE 2 0.12604 0.03871 9 0.18149 0.13088 > HBA_HUMAN 3 0.02555 0.02185 10 0.34695 0.12552 > HBA_HORSE 4 0.09541 0.03153 11 0.60238 0.11261 > MYG_PHYCA 5 1.33157 0.21115 > GLB5_PETMA 6 0.57473 0.13845 9 iterations until convergence > LGB2_LUPLU 7 1.71340 0.27647 log L: -1699.00 > > > Unrooted user defined tree with maximum likelihood branch lengths > (in CLUSTAL W notation): > > (HBB_HUMAN:0.04915,HBB_HORSE:0.12604,((HBA_HUMAN:0.02555,HBA_HORSE:0.09541) > :0.28347,(MYG_PHYCA:1.33157,(GLB5_PETMA:0.57473,LGB2_LUPLU:1.71340) > :0.18149):0.34695):0.60238); > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 3 (NO CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > > :--2 HBB_HORSE > : > : :-3 HBA_HUMAN > : :----8 > : : :-4 HBA_HORSE > :------11 > : : :------------5 MYG_PHYCA > : : :---9 > : : : :----------------7 LGB2_LUPLU > : :----10 > : :-------6 GLB5_PETMA > : > :-1 HBB_HUMAN > > > branch length S.E. branch length S.E. > HBB_HUMAN 1 0.04869 0.03153 8 0.27871 0.08717 > HBB_HORSE 2 0.12653 0.03874 9 0.12334 0.15661 > HBA_HUMAN 3 0.02634 0.02204 10 0.39110 0.12780 > HBA_HORSE 4 0.09459 0.03147 11 0.60627 0.11286 > MYG_PHYCA 5 1.22880 0.20960 > GLB5_PETMA 6 0.69972 0.14141 11 iterations until convergence > LGB2_LUPLU 7 1.68480 0.28106 log L: -1699.32 > > > Unrooted user defined tree with maximum likelihood branch lengths > (in CLUSTAL W notation): > > (HBB_HUMAN:0.04869,HBB_HORSE:0.12653,((HBA_HUMAN:0.02634,HBA_HORSE:0.09459) > :0.27871,((MYG_PHYCA:1.22880,LGB2_LUPLU:1.68480):0.12334,GLB5_PETMA:0.69972) > :0.39110):0.60627); > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 4 (NO CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > > :-------------5 MYG_PHYCA > :-----8 > : :-------6 GLB5_PETMA > : : > : :-----------------7 LGB2_LUPLU > :------10 > : : :-3 HBA_HUMAN > : :----9 > : :-4 HBA_HORSE > : > :--2 HBB_HORSE > : > :-1 HBB_HUMAN > > > branch length S.E. branch length S.E. > HBB_HUMAN 1 0.04834 0.03148 8 0.40364 0.12824 > HBB_HORSE 2 0.12685 0.03876 9 0.28040 0.08746 > HBA_HUMAN 3 0.02653 0.02208 10 0.60481 0.11281 > HBA_HORSE 4 0.09440 0.03145 > MYG_PHYCA 5 1.33095 0.21112 > GLB5_PETMA 6 0.70107 0.14140 10 iterations until convergence > LGB2_LUPLU 7 1.76831 0.28198 log L: -1699.50 > > > Unrooted user defined tree with maximum likelihood branch lengths > (in CLUSTAL W notation): > > (HBB_HUMAN:0.04834,((MYG_PHYCA:1.33095,GLB5_PETMA:0.70107,LGB2_LUPLU:1.76831) > :0.40364,(HBA_HUMAN:0.02653,HBA_HORSE:0.09440):0.28040):0.60481,HBB_HORSE:0.12685); > > > COMPARISON OF USER TREES (NO CLOCK) > > Tree log L difference S.E. p-1sKH p-SH c-ELW 2sKH > ------------------------------------------------------------------------------- > 1 -1699.50 0.49 1.0266 0.3020 + 0.4700 + 0.1881 + + > 2 -1699.00 0.00 <---- best 1.0000 + 1.0000 + 0.3650 + best > 3 -1699.32 0.32 1.3440 0.4030 + 0.4690 + 0.2588 + + > 4 -1699.50 0.49 1.0267 0.3070 + 0.4700 + 0.1881 + + > > The columns show the results and p-values of the following tests: > 1sKH - one sided KH test based on pairwise SH tests (Shimodaira-Hasegawa > 2000, Goldman et al., 2001, Kishino-Hasegawa 1989) > SH - Shimodaira-Hasegawa test (2000) > ELW - Expected Likelihood Weight (Strimmer-Rambaut 2002) > 2sKH - two sided Kishino-Hasegawa test (1989) > > Plus signs denote the confidence sets. Minus signs denote significant > exclusion. All tests used 5% significance level. 1sKH, SH, and ELW > performed 1000 resamplings using the RELL method. > 1sKH and 2sKH are correct to the 2nd position after the the decimal > point of the log-likelihoods. > > > TIME STAMP > FAIL ut-pure-prot.test (exit status: 1) FAIL: cons-pure-prot ==================== Testing: protein data, default model, consensus construction (cons-pure-prot) ./cons-pure-prot.test: line 181: 18980 Segmentation fault ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INCTREE} < $PARAMS > ${INFILE}.out 2>&1 cat: cons-pure-prot.ctrees.puzzle: No such file or directory 0a1,221 > TREE-PUZZLE > > Input file name: cons-pure-prot.prot > User tree file name: cons-pure-prot.ctrees > Type of analysis: consensus construction > Parameter estimation: approximate (faster) > Parameter estimation uses: 1st user tree (for substitution process and rate variation) > > Standard errors (S.E.) are obtained by the curvature method. > The upper and lower bounds of an approximate 95% confidence interval > for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. > > > SEQUENCE ALIGNMENT > > Input data: 7 sequences with 128 amino acid sites > Number of constant sites: 7 (= 5.5% of all sites) > Number of site patterns: 125 > Number of constant site patterns: 5 (= 4.0% of all site patterns) > > > SUBSTITUTION PROCESS > > Model of substitution: Dayhoff (Dayhoff et al. 1978) > Amino acid frequencies (estimated from data set): > > pi(A) = 12.2% > pi(R) = 2.3% > pi(N) = 3.0% > pi(D) = 4.9% > pi(C) = 0.7% > pi(Q) = 2.3% > pi(E) = 5.4% > pi(G) = 6.0% > pi(H) = 5.8% > pi(I) = 2.7% > pi(L) = 12.5% > pi(K) = 9.3% > pi(M) = 1.3% > pi(F) = 4.9% > pi(P) = 2.6% > pi(S) = 6.7% > pi(T) = 4.5% > pi(W) = 1.3% > pi(Y) = 2.2% > pi(V) = 9.4% > > > AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) > > gaps wildcards sum % sequence > HBB_HUMAN 0 0 0 0.00% > HBB_HORSE 0 0 0 0.00% > HBA_HUMAN 0 0 0 0.00% > HBA_HORSE 0 0 0 0.00% > MYG_PHYCA 0 0 0 0.00% > GLB5_PETMA 0 0 0 0.00% > LGB2_LUPLU 0 0 0 0.00% > ------------------------------------------------------- > Sum 0 0 0 0.00% > > > The table above shows the amount of gaps ('-') and other 'wildcard' > characters ('X', '?', etc.) and their percentage of the 128 columns > in the alignment. > Sequences with more than 50% ambiguous characters are marked with a '!' and > should be checked, whether they have sufficient overlap to other sequences. > Sequences with 100% ambiguous characters do not hold any phylogenetic > information and had to be discarded from the analysis. > > > > SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) > > 5% chi-square test p-value > HBB_HUMAN passed 92.31% > HBB_HORSE passed 79.58% > HBA_HUMAN passed 93.09% > HBA_HORSE passed 81.20% > MYG_PHYCA passed 33.23% > GLB5_PETMA passed 19.11% > LGB2_LUPLU passed 41.67% > > The chi-square tests compares the amino acid composition of each sequence > to the frequency distribution assumed in the maximum likelihood model. > > WARNING: Result of chi-square test may not be valid because of small > maximum likelihood frequencies and short sequence length! > > > IDENTICAL SEQUENCES > > The sequences in each of the following groups are all identical. To speed > up computation please remove all but one of each group from the data set. > > All sequences are unique. > > > MAXIMUM LIKELIHOOD DISTANCES > > Maximum likelihood distances are computed using the selected model of > substitution and rate heterogeneity. > > 7 > HBB_HUMAN 0.00000 0.17425 0.96068 0.99267 2.12932 1.77231 2.78644 > HBB_HORSE 0.17425 0.00000 1.01062 1.02118 2.09456 1.78465 2.86187 > HBA_HUMAN 0.96068 1.01062 0.00000 0.12147 1.93540 1.30123 2.54730 > HBA_HORSE 0.99267 1.02118 0.12147 0.00000 2.00515 1.39193 2.51172 > MYG_PHYCA 2.12932 2.09456 1.93540 2.00515 0.00000 2.12347 2.79386 > GLB5_PETMA 1.77231 1.78465 1.30123 1.39193 2.12347 0.00000 2.18272 > LGB2_LUPLU 2.78644 2.86187 2.54730 2.51172 2.79386 2.18272 0.00000 > > Average distance (over all possible pairs of sequences): 1.73823 > minimum : 0.12147, maximum : 2.86187 > variance : 0.65214, std.dev. : 0.80755 > > > RATE HETEROGENEITY > > Model of rate heterogeneity: uniform rate > > > TREE SEARCH > > 100 tree topologies were specified by the user. > > > CONSENSUS TREE > > Support for the internal branches of the unrooted consensus tree > topology is shown in percent. > > This consensus tree is not completely resolved! > > > :---HBA_HUMAN > :100: > : :---HBA_HORSE > :100: > : : :---MYG_PHYCA > : : : > : :100:---GLB5_PETMA > : : > : :---LGB2_LUPLU > : > :-----------HBB_HORSE > : > :-----------HBB_HUMAN > > > Consensus tree (in CLUSTAL W notation): > > (HBB_HUMAN,((HBA_HUMAN,HBA_HORSE)100,(MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)100)100, > HBB_HORSE); > > > BIPARTITIONS > > The following bipartitions occured at least once in the specified set > of 100 usertrees tree topologies. > Bipartitions included in the consensus tree: > (bipartition with sequences in input order : number of times seen) > > **..*** : 100 > ****... : 100 > **..... : 100 > > Congruent bipartitions occurred in 50% or less, not included in > the consensus tree: > (bipartition with sequences in input order : number of times seen) > > ****..* : 40 > > Incongruent bipartitions not included in the consensus tree: > (bipartition with sequences in input order : number of times seen) > > *****.. : 37 > ****.*. : 23 > > > MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) > > Branch lengths are computed using the selected model of > substitution and rate heterogeneity. > > > :-3 HBA_HUMAN > :----8 > : :-4 HBA_HORSE > :------10 > : : :-------------5 MYG_PHYCA > : :-----9 > : :-------6 GLB5_PETMA > : : > : :-----------------7 LGB2_LUPLU > : > :--2 HBB_HORSE > : > :-1 HBB_HUMAN > > > branch length S.E. branch length S.E. > HBB_HUMAN 1 0.04834 0.03148 8 0.28040 0.08746 > HBB_HORSE 2 0.12685 0.03876 9 0.40362 0.12823 > HBA_HUMAN 3 0.02653 0.02208 10 0.60481 0.11281 > HBA_HORSE 4 0.09440 0.03145 > MYG_PHYCA 5 1.33099 0.21112 > GLB5_PETMA 6 0.70102 0.14139 10 iterations until convergence > LGB2_LUPLU 7 1.76831 0.28198 log L: -1699.50 > > > Consensus tree with maximum likelihood branch lengths > (in CLUSTAL W notation): > > (HBB_HUMAN:0.04834,((HBA_HUMAN:0.02653,HBA_HORSE:0.09440)100:0.28040, > (MYG_PHYCA:1.33099,GLB5_PETMA:0.70102,LGB2_LUPLU:1.76831)100:0.40362) > 100:0.60481,HBB_HORSE:0.12685); > > > TIME STAMP > FAIL cons-pure-prot.test (exit status: 1) SKIP: build-remark ================== *** *** !!! Important remark !!! *** *** Please note that only the output file *.puzzle is checked *** for identity. The overall precision reached in the program *** is heavily dependent on the compiler as well as the optimization *** level (-O) used to compile the executable. *** Hence, even if tests are marked as failed this might just be *** due to differences in less significant digits caused by rounding *** errors from less acurate computations for the sake of faster *** running times. (If you want to be sure about this please refer *** to your compiler's manual!) *** *** Please check the output file differences which are printed during the tests. *** The template files which the results are checked against have been *** generated with TREE-PUZZLE 5.2 compiled with GCC version 3.3-20030226 *** and default compiler flags '-g -O2' and using the SPRNG random number *** generator. *** SKIP build-remark (exit status: 77) ============================================================================ Testsuite summary for ============================================================================ # TOTAL: 19 # PASS: 0 # SKIP: 2 # XFAIL: 0 # FAIL: 17 # XPASS: 0 # ERROR: 0 ============================================================================ See tests/test-suite.log ============================================================================ make[5]: *** [Makefile:564: test-suite.log] Error 1 make[5]: Leaving directory '/build/tree-puzzle-5.2/tests' make[4]: *** [Makefile:672: check-TESTS] Error 2 make[4]: Leaving directory '/build/tree-puzzle-5.2/tests' make[3]: *** [Makefile:752: check-am] Error 2 make[3]: Leaving directory '/build/tree-puzzle-5.2/tests' make[2]: *** [Makefile:380: check-recursive] Error 1 make[2]: Leaving directory '/build/tree-puzzle-5.2' dh_auto_test: make -j1 check VERBOSE=1 returned exit code 2 make[1]: Leaving directory '/build/tree-puzzle-5.2' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --no-parallel dh_testroot -O--no-parallel dh_prep -O--no-parallel dh_installdirs -O--no-parallel dh_auto_install -O--no-parallel make -j1 install DESTDIR=/build/tree-puzzle-5.2/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/tree-puzzle-5.2' Making install in src make[2]: Entering directory '/build/tree-puzzle-5.2/src' make[3]: Entering directory '/build/tree-puzzle-5.2/src' /bin/mkdir -p '/build/tree-puzzle-5.2/debian/tmp/usr/bin' /usr/bin/install -c puzzle ppuzzle '/build/tree-puzzle-5.2/debian/tmp/usr/bin' make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/tree-puzzle-5.2/src' make[2]: Leaving directory '/build/tree-puzzle-5.2/src' Making install in doc make[2]: Entering directory '/build/tree-puzzle-5.2/doc' make[3]: Entering directory '/build/tree-puzzle-5.2/doc' make[4]: Entering directory '/build/tree-puzzle-5.2/doc' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/tree-puzzle-5.2/doc' make[3]: Leaving directory '/build/tree-puzzle-5.2/doc' make[2]: Leaving directory '/build/tree-puzzle-5.2/doc' Making install in data make[2]: Entering directory '/build/tree-puzzle-5.2/data' make[3]: Entering directory '/build/tree-puzzle-5.2/data' 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/tree-puzzle-5.2/data' make[2]: Leaving directory '/build/tree-puzzle-5.2/data' Making install in tests make[2]: Entering directory '/build/tree-puzzle-5.2/tests' make[3]: Entering directory '/build/tree-puzzle-5.2/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/tree-puzzle-5.2/tests' make[2]: Leaving directory '/build/tree-puzzle-5.2/tests' make[2]: Entering directory '/build/tree-puzzle-5.2' make[3]: Entering directory '/build/tree-puzzle-5.2' 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/tree-puzzle-5.2' make[2]: Leaving directory '/build/tree-puzzle-5.2' make[1]: Leaving directory '/build/tree-puzzle-5.2' debian/rules override_dh_install-arch make[1]: Entering directory '/build/tree-puzzle-5.2' dh_install -a # The binary has to be renamed because of the generic name mv `pwd`/debian/tmp/usr/bin/puzzle `pwd`/debian/tree-puzzle/usr/bin/tree-puzzle mv `pwd`/debian/tmp/usr/bin/ppuzzle `pwd`/debian/tree-ppuzzle/usr/bin/tree-ppuzzle make[1]: Leaving directory '/build/tree-puzzle-5.2' dh_install -O--no-parallel -Ntree-puzzle -Ntree-ppuzzle dh_installdocs -O--no-parallel dh_installchangelogs -O--no-parallel dh_installexamples -O--no-parallel dh_installman -O--no-parallel dh_installinit -O--no-parallel dh_installmenu -O--no-parallel dh_perl -O--no-parallel dh_link -O--no-parallel dh_strip_nondeterminism -O--no-parallel debian/rules override_dh_compress make[1]: Entering directory '/build/tree-puzzle-5.2' dh_compress --exclude=.pdf --exclude .phy --exclude trees --exclude .b make[1]: Leaving directory '/build/tree-puzzle-5.2' dh_fixperms -O--no-parallel dh_missing -O--no-parallel dh_strip -O--no-parallel dh_makeshlibs -O--no-parallel dh_shlibdeps -O--no-parallel dh_installdeb -O--no-parallel dh_gencontrol -O--no-parallel dh_md5sums -O--no-parallel dh_builddeb -O--no-parallel dpkg-deb: building package 'tree-puzzle' in '../tree-puzzle_5.2-11_armhf.deb'. dpkg-deb: building package 'tree-ppuzzle' in '../tree-ppuzzle_5.2-11_armhf.deb'. dpkg-deb: building package 'tree-puzzle-doc' in '../tree-puzzle-doc_5.2-11_all.deb'. dpkg-deb: building package 'tree-puzzle-dbgsym' in '../tree-puzzle-dbgsym_5.2-11_armhf.deb'. dpkg-deb: building package 'tree-ppuzzle-dbgsym' in '../tree-ppuzzle-dbgsym_5.2-11_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../tree-puzzle_5.2-11_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) 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/16100 and its subdirectories I: Current time: Wed Jul 1 22:39:23 -12 2020 I: pbuilder-time-stamp: 1593686363 Thu Jul 2 10:39:44 UTC 2020 I: 1st build successful. Starting 2nd build on remote node p64b-armhf-rb.debian.net. Thu Jul 2 10:39:44 UTC 2020 I: Preparing to do remote build '2' on p64b-armhf-rb.debian.net. Thu Jul 2 10:52:24 UTC 2020 I: Deleting $TMPDIR on p64b-armhf-rb.debian.net. Thu Jul 2 10:52:26 UTC 2020 I: tree-puzzle_5.2-11_armhf.changes: Format: 1.8 Date: Tue, 16 Oct 2018 11:06:43 +0200 Source: tree-puzzle Binary: tree-ppuzzle tree-ppuzzle-dbgsym tree-puzzle tree-puzzle-dbgsym tree-puzzle-doc Architecture: armhf all Version: 5.2-11 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: tree-ppuzzle - Parallelized reconstruction of phylogenetic trees by maximum like tree-puzzle - Reconstruction of phylogenetic trees by maximum likelihood tree-puzzle-doc - Reconstruction of phylogenetic trees by maximum likelihood (doc) Changes: tree-puzzle (5.2-11) unstable; urgency=medium . * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 * Fix some spelling issues Checksums-Sha1: 517565b9408bb8aafbcf74d35de47a2bf0ed5e54 317560 tree-ppuzzle-dbgsym_5.2-11_armhf.deb 534a9705b456e32be94317af75eee72403e222ba 138912 tree-ppuzzle_5.2-11_armhf.deb 46ff7febe3bb9b8239e03564692f84ce943dd0f4 266848 tree-puzzle-dbgsym_5.2-11_armhf.deb 792a466abe60b2f86dfbb2b1e062a7c2910457ea 401004 tree-puzzle-doc_5.2-11_all.deb 014ce1d101ff21c71083fe140e3181ff03043513 6520 tree-puzzle_5.2-11_armhf.buildinfo 9aa3da0e231fcd9e07e71ad21067badc571cd04c 124060 tree-puzzle_5.2-11_armhf.deb Checksums-Sha256: 3cdb01bb2635ec31a7a6c25a2b3bee6e1bada5e4d47fdb24eca42185c5f2757c 317560 tree-ppuzzle-dbgsym_5.2-11_armhf.deb 5fab1614ae69236ca871d83c967152e6acd37c30ee456618d65b9369f4076cde 138912 tree-ppuzzle_5.2-11_armhf.deb 7f87aa128fbe4b203a2bc47eb4e7c5eb15d501833e4646121408429571342743 266848 tree-puzzle-dbgsym_5.2-11_armhf.deb f710451fea363461c027a6548d97a8c423cd96856f6282f59a571097d1c96184 401004 tree-puzzle-doc_5.2-11_all.deb 3ad9a4e4dee5fa55879b9c7a6c72b4142b6357f905e34d7e884bc3a45253dfd2 6520 tree-puzzle_5.2-11_armhf.buildinfo 00c80c1730b90970603ee775e2750fcca9136cccf8a9d0c2d0054671b5cdabfd 124060 tree-puzzle_5.2-11_armhf.deb Files: 0bbc582685a52ad93ad1132b4c0139d1 317560 debug optional tree-ppuzzle-dbgsym_5.2-11_armhf.deb ef2db46d2b53b75fba39b34c37b33bb3 138912 science optional tree-ppuzzle_5.2-11_armhf.deb 560e189ccde0809c4240e8868be1588e 266848 debug optional tree-puzzle-dbgsym_5.2-11_armhf.deb 7537aaf434b4f8be182dcb940c95fa92 401004 doc optional tree-puzzle-doc_5.2-11_all.deb 0ee60bfc8c531d215226bbc06dbe6d0c 6520 science optional tree-puzzle_5.2-11_armhf.buildinfo c62390c8e8a6cf972f66aa3bf88cf7f0 124060 science optional tree-puzzle_5.2-11_armhf.deb Thu Jul 2 10:52:27 UTC 2020 I: diffoscope 149 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.riEdOoUizN/tree-puzzle_5.2-11.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.riEdOoUizN/tree-puzzle_5.2-11.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.riEdOoUizN/tree-puzzle_5.2-11.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.riEdOoUizN/b1/tree-puzzle_5.2-11_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.riEdOoUizN/b2/tree-puzzle_5.2-11_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: 0.244s) 0.244s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.039s) 0.039s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Thu Jul 2 10:52:29 UTC 2020 I: diffoscope 149 found no differences in the changes files, and a .buildinfo file also exists. Thu Jul 2 10:52:29 UTC 2020 I: tree-puzzle from buster built successfully and reproducibly on armhf. Thu Jul 2 10:52:30 UTC 2020 I: Submitting .buildinfo files to external archives: Thu Jul 2 10:52:30 UTC 2020 I: Submitting 8.0K b1/tree-puzzle_5.2-11_armhf.buildinfo.asc Thu Jul 2 10:52:32 UTC 2020 I: Submitting 8.0K b2/tree-puzzle_5.2-11_armhf.buildinfo.asc Thu Jul 2 10:52:33 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Jul 2 10:52:33 UTC 2020 I: Done submitting .buildinfo files. Thu Jul 2 10:52:33 UTC 2020 I: Removing signed tree-puzzle_5.2-11_armhf.buildinfo.asc files: removed './b1/tree-puzzle_5.2-11_armhf.buildinfo.asc' removed './b2/tree-puzzle_5.2-11_armhf.buildinfo.asc'