https://launchpad.net/ubuntu/+source/tree-puzzle/5.2-10build1/+build/14874522 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos02-arm64-032 4.4.0-124-generic #148-Ubuntu SMP Wed May 2 13:04:12 UTC 2018 aarch64 Buildd toolchain package versions: launchpad-buildd_161 python-lpbuildd_161 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.3 dpkg-dev_1.18.4ubuntu1.4 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 13 May 15:09:29 ntpdate[1823]: adjust time server 10.211.37.1 offset 0.019907 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=cosmic --arch=armhf PACKAGEBUILD-14874522 /home/buildd/filecache-default/fc6c56f66744d62233b3c844f67cb7d83d839bbc Creating target for build PACKAGEBUILD-14874522 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=cosmic --arch=armhf PACKAGEBUILD-14874522 Starting target for build PACKAGEBUILD-14874522 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=cosmic --arch=armhf PACKAGEBUILD-14874522 'deb http://ftpmaster.internal/ubuntu cosmic main universe' 'deb http://ftpmaster.internal/ubuntu cosmic-security main universe' 'deb http://ftpmaster.internal/ubuntu cosmic-updates main universe' 'deb http://ftpmaster.internal/ubuntu cosmic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-14874522 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=cosmic --arch=armhf PACKAGEBUILD-14874522 Updating target for build PACKAGEBUILD-14874522 Get:1 http://ftpmaster.internal/ubuntu cosmic InRelease [242 kB] Get:2 http://ftpmaster.internal/ubuntu cosmic-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic-proposed InRelease [92.5 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main armhf Packages [966 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main Translation-en [516 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/universe armhf Packages [8311 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/universe Translation-en [4974 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf Packages [60.6 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic-proposed/main Translation-en [38.9 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic-proposed/universe armhf Packages [232 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic-proposed/universe Translation-en [136 kB] Fetched 15.7 MB in 7s (2394 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libncursesw5 Use 'sudo apt autoremove' to remove it. The following NEW packages will be installed: libncurses6 libncursesw6 libtinfo6 The following packages will be upgraded: apt base-files base-passwd bash binutils binutils-arm-linux-gnueabihf binutils-common bsdutils build-essential cpp cpp-7 dpkg dpkg-dev e2fslibs e2fsprogs fdisk g++ g++-7 gcc gcc-7 gcc-7-base gcc-8-base libapt-pkg5.0 libargon2-0 libasan4 libatomic1 libbinutils libblkid1 libcap-ng0 libcc1-0 libcilkrts5 libcom-err2 libcomerr2 libdpkg-perl libext2fs2 libfdisk1 libgcc-7-dev libgcc1 libgmp10 libgomp1 libgpg-error0 libmount1 libncurses5 libncursesw5 libp11-kit0 libperl5.26 libprocps6 libreadline7 libslang2 libsmartcols1 libsqlite3-0 libss2 libstdc++-7-dev libstdc++6 libtinfo5 libubsan0 libusb-0.1-4 libuuid1 linux-libc-dev mount ncurses-base ncurses-bin perl perl-base perl-modules-5.26 pinentry-curses procps readline-common tar tzdata util-linux 71 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 40.7 MB of archives. After this operation, 1054 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu cosmic/main armhf base-files armhf 10.1ubuntu4 [58.0 kB] Get:2 http://ftpmaster.internal/ubuntu cosmic/main armhf libtinfo6 armhf 6.1+20180210-2ubuntu2 [71.0 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic/main armhf bash armhf 4.4.18-2ubuntu2 [552 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf bsdutils armhf 1:2.31.1-0.4ubuntu4 [55.3 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf tar armhf 1.30+dfsg-1 [218 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main armhf dpkg armhf 1.19.0.5ubuntu3 [1096 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/main armhf libext2fs2 armhf 1.44.1-2 [145 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/main armhf e2fsprogs armhf 1.44.1-2 [369 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic/main armhf ncurses-bin armhf 6.1+20180210-2ubuntu2 [155 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf perl-modules-5.26 all 5.26.2-3 [2763 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libperl5.26 armhf 5.26.2-3 [2881 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf perl armhf 5.26.2-3 [201 kB] Get:13 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf perl-base armhf 5.26.2-3 [1290 kB] Get:14 http://ftpmaster.internal/ubuntu cosmic/main armhf libncursesw6 armhf 6.1+20180210-2ubuntu2 [104 kB] Get:15 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libuuid1 armhf 2.31.1-0.4ubuntu4 [19.2 kB] Get:16 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libblkid1 armhf 2.31.1-0.4ubuntu4 [112 kB] Get:17 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libfdisk1 armhf 2.31.1-0.4ubuntu4 [151 kB] Get:18 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libmount1 armhf 2.31.1-0.4ubuntu4 [122 kB] Get:19 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libsmartcols1 armhf 2.31.1-0.4ubuntu4 [74.3 kB] Get:20 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf fdisk armhf 2.31.1-0.4ubuntu4 [97.8 kB] Get:21 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf util-linux armhf 2.31.1-0.4ubuntu4 [845 kB] Get:22 http://ftpmaster.internal/ubuntu cosmic/main armhf base-passwd armhf 3.5.45 [46.0 kB] Get:23 http://ftpmaster.internal/ubuntu cosmic/main armhf ncurses-base all 6.1+20180210-2ubuntu2 [17.8 kB] Get:24 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libgomp1 armhf 8.1.0-3ubuntu1 [66.6 kB] Get:25 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf gcc-8-base armhf 8.1.0-3ubuntu1 [18.4 kB] Get:26 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libgcc1 armhf 1:8.1.0-3ubuntu1 [37.0 kB] Get:27 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libcc1-0 armhf 8.1.0-3ubuntu1 [32.7 kB] Get:28 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libatomic1 armhf 8.1.0-3ubuntu1 [7072 B] Get:29 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libstdc++6 armhf 8.1.0-3ubuntu1 [350 kB] Get:30 http://ftpmaster.internal/ubuntu cosmic/main armhf libapt-pkg5.0 armhf 1.7.0~alpha0ubuntu1 [729 kB] Get:31 http://ftpmaster.internal/ubuntu cosmic/main armhf apt armhf 1.7.0~alpha0ubuntu1 [1123 kB] Get:32 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf mount armhf 2.31.1-0.4ubuntu4 [99.8 kB] Get:33 http://ftpmaster.internal/ubuntu cosmic/main armhf libcap-ng0 armhf 0.7.9-1 [10.1 kB] Get:34 http://ftpmaster.internal/ubuntu cosmic/main armhf libcom-err2 armhf 1.44.1-2 [8612 B] Get:35 http://ftpmaster.internal/ubuntu cosmic/main armhf libgpg-error0 armhf 1.31-1 [48.5 kB] Get:36 http://ftpmaster.internal/ubuntu cosmic/main armhf libss2 armhf 1.44.1-2 [9388 B] Get:37 http://ftpmaster.internal/ubuntu cosmic/main armhf libncurses5 armhf 6.1+20180210-2ubuntu2 [74.8 kB] Get:38 http://ftpmaster.internal/ubuntu cosmic/main armhf libncursesw5 armhf 6.1+20180210-2ubuntu2 [95.3 kB] Get:39 http://ftpmaster.internal/ubuntu cosmic/main armhf libtinfo5 armhf 6.1+20180210-2ubuntu2 [67.4 kB] Get:40 http://ftpmaster.internal/ubuntu cosmic/main armhf libgmp10 armhf 2:6.1.2+dfsg-3 [182 kB] Get:41 http://ftpmaster.internal/ubuntu cosmic/main armhf libp11-kit0 armhf 0.23.10-2 [162 kB] Get:42 http://ftpmaster.internal/ubuntu cosmic/main armhf libprocps6 armhf 2:3.3.12-3ubuntu2 [28.5 kB] Get:43 http://ftpmaster.internal/ubuntu cosmic/main armhf libncurses6 armhf 6.1+20180210-2ubuntu2 [78.5 kB] Get:44 http://ftpmaster.internal/ubuntu cosmic/main armhf procps armhf 2:3.3.12-3ubuntu2 [213 kB] Get:45 http://ftpmaster.internal/ubuntu cosmic/main armhf libargon2-0 armhf 0~20161029-2 [20.5 kB] Get:46 http://ftpmaster.internal/ubuntu cosmic/main armhf readline-common all 7.0-5 [52.2 kB] Get:47 http://ftpmaster.internal/ubuntu cosmic/main armhf libreadline7 armhf 7.0-5 [102 kB] Get:48 http://ftpmaster.internal/ubuntu cosmic/main armhf libslang2 armhf 2.3.2-1ubuntu1 [383 kB] Get:49 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libsqlite3-0 armhf 3.23.1-1 [425 kB] Get:50 http://ftpmaster.internal/ubuntu cosmic/main armhf tzdata all 2018e-1 [188 kB] Get:51 http://ftpmaster.internal/ubuntu cosmic/main armhf libbinutils armhf 2.30-17ubuntu1 [309 kB] Get:52 http://ftpmaster.internal/ubuntu cosmic/main armhf binutils-common armhf 2.30-17ubuntu1 [193 kB] Get:53 http://ftpmaster.internal/ubuntu cosmic/main armhf binutils armhf 2.30-17ubuntu1 [3344 B] Get:54 http://ftpmaster.internal/ubuntu cosmic/main armhf binutils-arm-linux-gnueabihf armhf 2.30-17ubuntu1 [2175 kB] Get:55 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libasan4 armhf 7.3.0-19ubuntu1 [327 kB] Get:56 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libubsan0 armhf 7.3.0-19ubuntu1 [108 kB] Get:57 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libcilkrts5 armhf 7.3.0-19ubuntu1 [36.0 kB] Get:58 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf g++-7 armhf 7.3.0-19ubuntu1 [6047 kB] Get:59 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf gcc-7 armhf 7.3.0-19ubuntu1 [5945 kB] Get:60 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libstdc++-7-dev armhf 7.3.0-19ubuntu1 [1536 kB] Get:61 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libgcc-7-dev armhf 7.3.0-19ubuntu1 [709 kB] Get:62 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf cpp-7 armhf 7.3.0-19ubuntu1 [5296 kB] Get:63 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf gcc-7-base armhf 7.3.0-19ubuntu1 [18.9 kB] Get:64 http://ftpmaster.internal/ubuntu cosmic/main armhf cpp armhf 4:7.3.0-3ubuntu3 [27.6 kB] Get:65 http://ftpmaster.internal/ubuntu cosmic/main armhf gcc armhf 4:7.3.0-3ubuntu3 [5228 B] Get:66 http://ftpmaster.internal/ubuntu cosmic/main armhf g++ armhf 4:7.3.0-3ubuntu3 [1600 B] Get:67 http://ftpmaster.internal/ubuntu cosmic/main armhf dpkg-dev all 1.19.0.5ubuntu3 [608 kB] Get:68 http://ftpmaster.internal/ubuntu cosmic/main armhf libdpkg-perl all 1.19.0.5ubuntu3 [211 kB] Get:69 http://ftpmaster.internal/ubuntu cosmic/main armhf build-essential armhf 12.5ubuntu2 [4732 B] Get:70 http://ftpmaster.internal/ubuntu cosmic/main armhf e2fslibs armhf 1.44.1-2 [2704 B] Get:71 http://ftpmaster.internal/ubuntu cosmic/main armhf libcomerr2 armhf 1.44.1-2 [2692 B] Get:72 http://ftpmaster.internal/ubuntu cosmic/main armhf libusb-0.1-4 armhf 2:0.1.12-32 [15.6 kB] Get:73 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf linux-libc-dev armhf 4.15.0-21.22 [988 kB] Get:74 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf pinentry-curses armhf 1.1.0-1build1 [31.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 40.7 MB in 2s (24.4 MB/s) (Reading database ... 12378 files and directories currently installed.) Preparing to unpack .../base-files_10.1ubuntu4_armhf.deb ... Unpacking base-files (10.1ubuntu4) over (10.1ubuntu2) ... Setting up base-files (10.1ubuntu4) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Selecting previously unselected package libtinfo6:armhf. (Reading database ... 12378 files and directories currently installed.) Preparing to unpack .../libtinfo6_6.1+20180210-2ubuntu2_armhf.deb ... Unpacking libtinfo6:armhf (6.1+20180210-2ubuntu2) ... Setting up libtinfo6:armhf (6.1+20180210-2ubuntu2) ... (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../bash_4.4.18-2ubuntu2_armhf.deb ... Unpacking bash (4.4.18-2ubuntu2) over (4.4.18-2ubuntu1) ... Setting up bash (4.4.18-2ubuntu2) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.31.1-0.4ubuntu4_armhf.deb ... Unpacking bsdutils (1:2.31.1-0.4ubuntu4) over (1:2.31.1-0.4ubuntu3) ... Setting up bsdutils (1:2.31.1-0.4ubuntu4) ... (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../tar_1.30+dfsg-1_armhf.deb ... Unpacking tar (1.30+dfsg-1) over (1.29b-2) ... Setting up tar (1.30+dfsg-1) ... (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../dpkg_1.19.0.5ubuntu3_armhf.deb ... Unpacking dpkg (1.19.0.5ubuntu3) over (1.19.0.5ubuntu2) ... Setting up dpkg (1.19.0.5ubuntu3) ... (Reading database ... 12387 files and directories currently installed.) 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Setting up libblkid1:armhf (2.31.1-0.4ubuntu4) ... (Reading database ... 12396 files and directories currently installed.) Preparing to unpack .../libfdisk1_2.31.1-0.4ubuntu4_armhf.deb ... Unpacking libfdisk1:armhf (2.31.1-0.4ubuntu4) over (2.31.1-0.4ubuntu3) ... Setting up libfdisk1:armhf (2.31.1-0.4ubuntu4) ... (Reading database ... 12396 files and directories currently installed.) Preparing to unpack .../libmount1_2.31.1-0.4ubuntu4_armhf.deb ... Unpacking libmount1:armhf (2.31.1-0.4ubuntu4) over (2.31.1-0.4ubuntu3) ... Setting up libmount1:armhf (2.31.1-0.4ubuntu4) ... (Reading database ... 12396 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.31.1-0.4ubuntu4_armhf.deb ... Unpacking libsmartcols1:armhf (2.31.1-0.4ubuntu4) over (2.31.1-0.4ubuntu3) ... Setting up libsmartcols1:armhf (2.31.1-0.4ubuntu4) ... (Reading database ... 12396 files and directories currently installed.) Preparing to unpack .../fdisk_2.31.1-0.4ubuntu4_armhf.deb ... 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RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-14874522 armhf cosmic-proposed -c chroot:build-PACKAGEBUILD-14874522 --arch=armhf --dist=cosmic-proposed --nolog tree-puzzle_5.2-10build1.dsc Initiating build PACKAGEBUILD-14874522 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-124-generic #148-Ubuntu SMP Wed May 2 13:04:12 UTC 2018 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-032.buildd +==============================================================================+ | tree-puzzle 5.2-10build1 (armhf) 13 May 2018 15:10 | +==============================================================================+ Package: tree-puzzle Version: 5.2-10build1 Source Version: 5.2-10build1 Distribution: cosmic-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/tree-puzzle-_Gz_BD/tree-puzzle-5.2' with '<>' I: NOTICE: Log filtering will replace 'build/tree-puzzle-_Gz_BD' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-14874522/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- tree-puzzle_5.2-10build1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-HUdjSa/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-HUdjSa/apt_archive ./ InRelease Get:2 copy:/<>/resolver-HUdjSa/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-HUdjSa/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-HUdjSa/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-HUdjSa/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (120 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-HUdjSa/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12402 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 10), libopenmpi-dev, libsprng2-dev Filtered Build-Depends: debhelper (>= 10), libopenmpi-dev, libsprng2-dev dpkg-deb: building package 'sbuild-build-depends-tree-puzzle-dummy' in '/<>/resolver-A3hUrj/apt_archive/sbuild-build-depends-tree-puzzle-dummy.deb'. Ign:1 copy:/<>/resolver-A3hUrj/apt_archive ./ InRelease Get:2 copy:/<>/resolver-A3hUrj/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-A3hUrj/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-A3hUrj/apt_archive ./ Sources [231 B] Get:5 copy:/<>/resolver-A3hUrj/apt_archive ./ Packages [549 B] Fetched 2899 B in 0s (122 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install tree-puzzle build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base ibverbs-providers intltool-debian libarchive-zip-perl libbsd0 libcroco3 libedit2 libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6 libfile-stripnondeterminism-perl libglib2.0-0 libgmp-dev libgmpxx4ldbl libgssapi-krb5-2 libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu60 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libltdl-dev libltdl7 libmagic-mgc libmagic1 libnl-3-200 libnl-route-3-200 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libsigsegv2 libsprng2 libsprng2-dev libssl1.0.0 libtimedate-perl libtool libxml2 m4 man-db ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff gmp-doc libgmp10-doc libmpfr-dev krb5-doc krb5-user libhwloc-contrib-plugins libtool-doc openmpi-doc pciutils libsprng2-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser opencl-icd gfortran keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales xauth libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base ibverbs-providers intltool-debian libarchive-zip-perl libbsd0 libcroco3 libedit2 libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6 libfile-stripnondeterminism-perl libglib2.0-0 libgmp-dev libgmpxx4ldbl libgssapi-krb5-2 libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu60 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libltdl-dev libltdl7 libmagic-mgc libmagic1 libnl-3-200 libnl-route-3-200 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libsigsegv2 libsprng2 libsprng2-dev libssl1.0.0 libtimedate-perl libtool libxml2 m4 man-db ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf sbuild-build-depends-tree-puzzle-dummy 0 upgraded, 62 newly installed, 0 to remove and 0 not upgraded. Need to get 22.1 MB of archives. After this operation, 80.5 MB of additional disk space will be used. Get:1 copy:/<>/resolver-A3hUrj/apt_archive ./ sbuild-build-depends-tree-puzzle-dummy 0.invalid.0 [876 B] Get:2 http://ftpmaster.internal/ubuntu cosmic/main armhf libbsd0 armhf 0.8.7-1 [40.4 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic/main armhf bsdmainutils armhf 11.1.2ubuntu2 [176 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic/main armhf groff-base armhf 1.22.3-10 [1013 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main armhf libpipeline1 armhf 1.5.0-1 [21.1 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main armhf man-db armhf 2.8.3-2 [993 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/main armhf libmagic-mgc armhf 1:5.33-2 [193 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/main armhf libmagic1 armhf 1:5.33-2 [63.8 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic/main armhf file armhf 1:5.33-2 [22.1 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic/main armhf libglib2.0-0 armhf 2.56.1-2ubuntu1 [1014 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic/main armhf libicu60 armhf 60.2-3ubuntu3 [7797 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic/main armhf libxml2 armhf 2.9.4+dfsg1-6.1ubuntu1 [567 kB] Get:13 http://ftpmaster.internal/ubuntu cosmic/main armhf gettext-base armhf 0.19.8.1-6build1 [46.2 kB] Get:14 http://ftpmaster.internal/ubuntu cosmic/main armhf libedit2 armhf 3.1-20170329-1build1 [61.8 kB] Get:15 http://ftpmaster.internal/ubuntu cosmic/main armhf libkrb5support0 armhf 1.16-2build1 [27.5 kB] Get:16 http://ftpmaster.internal/ubuntu cosmic/main armhf libk5crypto3 armhf 1.16-2build1 [83.2 kB] Get:17 http://ftpmaster.internal/ubuntu cosmic/main armhf libkeyutils1 armhf 1.5.9-9.2ubuntu3 [7780 B] Get:18 http://ftpmaster.internal/ubuntu cosmic/main armhf libkrb5-3 armhf 1.16-2build1 [233 kB] Get:19 http://ftpmaster.internal/ubuntu cosmic/main armhf libgssapi-krb5-2 armhf 1.16-2build1 [101 kB] Get:20 http://ftpmaster.internal/ubuntu cosmic/main armhf libssl1.0.0 armhf 1.0.2n-1ubuntu5 [710 kB] Get:21 http://ftpmaster.internal/ubuntu cosmic/main armhf openssh-client armhf 1:7.7p1-2 [527 kB] Get:22 http://ftpmaster.internal/ubuntu cosmic/main armhf libsigsegv2 armhf 2.12-2 [13.1 kB] Get:23 http://ftpmaster.internal/ubuntu cosmic/main armhf m4 armhf 1.4.18-1 [181 kB] Get:24 http://ftpmaster.internal/ubuntu cosmic/main armhf autoconf all 2.69-11 [322 kB] Get:25 http://ftpmaster.internal/ubuntu cosmic/main armhf autotools-dev all 20180224.1 [39.6 kB] Get:26 http://ftpmaster.internal/ubuntu cosmic/main armhf automake all 1:1.15.1-3ubuntu2 [509 kB] Get:27 http://ftpmaster.internal/ubuntu cosmic/main armhf autopoint all 0.19.8.1-6build1 [412 kB] Get:28 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libtool all 2.4.6-2.1 [195 kB] Get:29 http://ftpmaster.internal/ubuntu cosmic/main armhf dh-autoreconf all 17 [15.8 kB] Get:30 http://ftpmaster.internal/ubuntu cosmic/main armhf libarchive-zip-perl all 1.60-1 [83.9 kB] Get:31 http://ftpmaster.internal/ubuntu cosmic/main armhf libfile-stripnondeterminism-perl all 0.041-1 [15.3 kB] Get:32 http://ftpmaster.internal/ubuntu cosmic/main armhf libtimedate-perl all 2.3000-2 [37.5 kB] Get:33 http://ftpmaster.internal/ubuntu cosmic/main armhf dh-strip-nondeterminism all 0.041-1 [5188 B] Get:34 http://ftpmaster.internal/ubuntu cosmic/main armhf libcroco3 armhf 0.6.12-2 [69.4 kB] Get:35 http://ftpmaster.internal/ubuntu cosmic/main armhf gettext armhf 0.19.8.1-6build1 [834 kB] Get:36 http://ftpmaster.internal/ubuntu cosmic/main armhf intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:37 http://ftpmaster.internal/ubuntu cosmic/main armhf po-debconf all 1.0.20 [232 kB] Get:38 http://ftpmaster.internal/ubuntu cosmic/main armhf debhelper all 11.2.1ubuntu1 [906 kB] Get:39 http://ftpmaster.internal/ubuntu cosmic/main armhf libnl-3-200 armhf 3.2.29-0ubuntu3 [45.8 kB] Get:40 http://ftpmaster.internal/ubuntu cosmic/main armhf libnl-route-3-200 armhf 3.2.29-0ubuntu3 [123 kB] Get:41 http://ftpmaster.internal/ubuntu cosmic/main armhf libibverbs1 armhf 17.1-2 [40.0 kB] Get:42 http://ftpmaster.internal/ubuntu cosmic/main armhf ibverbs-providers armhf 17.1-2 [18.5 kB] Get:43 http://ftpmaster.internal/ubuntu cosmic/main armhf libevent-2.1-6 armhf 2.1.8-stable-4build1 [115 kB] Get:44 http://ftpmaster.internal/ubuntu cosmic/main armhf libevent-core-2.1-6 armhf 2.1.8-stable-4build1 [75.0 kB] Get:45 http://ftpmaster.internal/ubuntu cosmic/main armhf libevent-pthreads-2.1-6 armhf 2.1.8-stable-4build1 [4904 B] Get:46 http://ftpmaster.internal/ubuntu cosmic/main armhf libgmpxx4ldbl armhf 2:6.1.2+dfsg-3 [8072 B] Get:47 http://ftpmaster.internal/ubuntu cosmic/main armhf libgmp-dev armhf 2:6.1.2+dfsg-3 [256 kB] Get:48 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libltdl7 armhf 2.4.6-2.1 [35.8 kB] Get:49 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libltdl-dev armhf 2.4.6-2.1 [159 kB] Get:50 http://ftpmaster.internal/ubuntu cosmic/universe armhf libhwloc5 armhf 1.11.10-1 [83.6 kB] Get:51 http://ftpmaster.internal/ubuntu cosmic/main armhf libpciaccess0 armhf 0.14-1 [15.5 kB] Get:52 http://ftpmaster.internal/ubuntu cosmic/main armhf ocl-icd-libopencl1 armhf 2.2.11-1ubuntu1 [28.7 kB] Get:53 http://ftpmaster.internal/ubuntu cosmic/universe armhf libhwloc-plugins armhf 1.11.10-1 [10.9 kB] Get:54 http://ftpmaster.internal/ubuntu cosmic/universe armhf libpmix2 armhf 2.1.1~rc1-4 [301 kB] Get:55 http://ftpmaster.internal/ubuntu cosmic-proposed/universe armhf libopenmpi3 armhf 3.0.1.real-4 [1781 kB] Get:56 http://ftpmaster.internal/ubuntu cosmic/universe armhf libsprng2 armhf 2.0a-11 [74.7 kB] Get:57 http://ftpmaster.internal/ubuntu cosmic/universe armhf libsprng2-dev armhf 2.0a-11 [76.3 kB] Get:58 http://ftpmaster.internal/ubuntu cosmic-proposed/universe armhf openmpi-common all 3.0.1.real-4 [143 kB] Get:59 http://ftpmaster.internal/ubuntu cosmic-proposed/universe armhf openmpi-bin armhf 3.0.1.real-4 [92.4 kB] Get:60 http://ftpmaster.internal/ubuntu cosmic/universe armhf libhwloc-dev armhf 1.11.10-1 [148 kB] Get:61 http://ftpmaster.internal/ubuntu cosmic/main armhf libibverbs-dev armhf 17.1-2 [88.7 kB] Get:62 http://ftpmaster.internal/ubuntu cosmic-proposed/universe armhf libopenmpi-dev armhf 3.0.1.real-4 [820 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 22.1 MB in 1s (17.5 MB/s) Selecting previously unselected package libbsd0:armhf. (Reading database ... 12402 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.8.7-1_armhf.deb ... Unpacking libbsd0:armhf (0.8.7-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2ubuntu2_armhf.deb ... Unpacking bsdmainutils (11.1.2ubuntu2) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.3-10_armhf.deb ... Unpacking groff-base (1.22.3-10) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../03-libpipeline1_1.5.0-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.0-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.8.3-2_armhf.deb ... Unpacking man-db (2.8.3-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.33-2_armhf.deb ... Unpacking libmagic-mgc (1:5.33-2) ... Selecting previously unselected package libmagic1:armhf. 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Setting up libarchive-zip-perl (1.60-1) ... Setting up libssl1.0.0:armhf (1.0.2n-1ubuntu5) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up libsprng2 (2.0a-11) ... Setting up groff-base (1.22.3-10) ... Setting up libglib2.0-0:armhf (2.56.1-2ubuntu1) ... No schema files found: doing nothing. Setting up gettext-base (0.19.8.1-6build1) ... Setting up libpipeline1:armhf (1.5.0-1) ... Setting up m4 (1.4.18-1) ... Setting up libbsd0:armhf (0.8.7-1) ... Setting up libkrb5support0:armhf (1.16-2build1) ... Setting up libxml2:armhf (2.9.4+dfsg1-6.1ubuntu1) ... Setting up libmagic-mgc (1:5.33-2) ... Setting up libmagic1:armhf (1:5.33-2) ... Setting up libcroco3:armhf (0.6.12-2) ... Setting up libevent-pthreads-2.1-6:armhf (2.1.8-stable-4build1) ... Setting up openmpi-common (3.0.1.real-4) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Setting up autotools-dev (20180224.1) ... Setting up libltdl7:armhf (2.4.6-2.1) ... Setting up libpciaccess0:armhf (0.14-1) ... Setting up ocl-icd-libopencl1:armhf (2.2.11-1ubuntu1) ... Setting up libkeyutils1:armhf (1.5.9-9.2ubuntu3) ... Setting up bsdmainutils (11.1.2ubuntu2) ... 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 libgmpxx4ldbl:armhf (2:6.1.2+dfsg-3) ... Setting up libnl-3-200:armhf (3.2.29-0ubuntu3) ... Setting up autopoint (0.19.8.1-6build1) ... Setting up libfile-stripnondeterminism-perl (0.041-1) ... Setting up libgmp-dev:armhf (2:6.1.2+dfsg-3) ... Setting up libk5crypto3:armhf (1.16-2build1) ... Setting up libltdl-dev:armhf (2.4.6-2.1) ... Setting up gettext (0.19.8.1-6build1) ... Setting up libnl-route-3-200:armhf (3.2.29-0ubuntu3) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.33-2) ... Setting up libhwloc5:armhf (1.11.10-1) ... Setting up libhwloc-plugins (1.11.10-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libsprng2-dev (2.0a-11) ... Setting up automake (1:1.15.1-3ubuntu2) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.3-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libkrb5-3:armhf (1.16-2build1) ... Setting up libtool (2.4.6-2.1) ... Setting up libibverbs1:armhf (17.1-2) ... Setting up po-debconf (1.0.20) ... Setting up libhwloc-dev:armhf (1.11.10-1) ... Setting up libpmix2:armhf (2.1.1~rc1-4) ... Setting up libgssapi-krb5-2:armhf (1.16-2build1) ... Setting up ibverbs-providers:armhf (17.1-2) ... Setting up openssh-client (1:7.7p1-2) ... Setting up libibverbs-dev:armhf (17.1-2) ... Setting up libopenmpi3:armhf (3.0.1.real-4) ... Setting up openmpi-bin (3.0.1.real-4) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: error: no alternatives for mpi update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:armhf (3.0.1.real-4) ... 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 dh-autoreconf (17) ... Setting up dh-strip-nondeterminism (0.041-1) ... Setting up debhelper (11.2.1ubuntu1) ... Setting up sbuild-build-depends-tree-puzzle-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-124-generic arm64 (armv7l) Toolchain package versions: binutils_2.30-17ubuntu1 dpkg-dev_1.19.0.5ubuntu3 g++-7_7.3.0-19ubuntu1 gcc-7_7.3.0-19ubuntu1 libc6-dev_2.27-3ubuntu1 libstdc++-7-dev_7.3.0-19ubuntu1 libstdc++6_8.1.0-3ubuntu1 linux-libc-dev_4.15.0-21.22 Package versions: adduser_3.116ubuntu1 advancecomp_2.1-1 apt_1.7.0~alpha0ubuntu1 autoconf_2.69-11 automake_1:1.15.1-3ubuntu2 autopoint_0.19.8.1-6build1 autotools-dev_20180224.1 base-files_10.1ubuntu4 base-passwd_3.5.45 bash_4.4.18-2ubuntu2 binutils_2.30-17ubuntu1 binutils-arm-linux-gnueabihf_2.30-17ubuntu1 binutils-common_2.30-17ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.31.1-0.4ubuntu4 build-essential_12.5ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20180409 coreutils_8.28-1ubuntu1 cpp_4:7.3.0-3ubuntu3 cpp-7_7.3.0-19ubuntu1 dash_0.5.8-2.10 debconf_1.5.66 debhelper_11.2.1ubuntu1 debianutils_4.8.4 dh-autoreconf_17 dh-strip-nondeterminism_0.041-1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu3 dpkg_1.19.0.5ubuntu3 dpkg-dev_1.19.0.5ubuntu3 e2fslibs_1.44.1-2 e2fsprogs_1.44.1-2 fakeroot_1.22-2ubuntu1 fdisk_2.31.1-0.4ubuntu4 file_1:5.33-2 findutils_4.6.0+git+20170828-2 g++_4:7.3.0-3ubuntu3 g++-7_7.3.0-19ubuntu1 gcc_4:7.3.0-3ubuntu3 gcc-7_7.3.0-19ubuntu1 gcc-7-base_7.3.0-19ubuntu1 gcc-8-base_8.1.0-3ubuntu1 gettext_0.19.8.1-6build1 gettext-base_0.19.8.1-6build1 gpg_2.2.4-1ubuntu1 gpg-agent_2.2.4-1ubuntu1 gpgconf_2.2.4-1ubuntu1 gpgv_2.2.4-1ubuntu1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5ubuntu1 hostname_3.20 ibverbs-providers_17.1-2 init_1.51 init-system-helpers_1.51 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu5 libapt-pkg5.0_1.7.0~alpha0ubuntu1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-2 libasan4_7.3.0-19ubuntu1 libassuan0_2.5.1-2 libatomic1_8.1.0-3ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.2-1ubuntu1 libaudit1_1:2.8.2-1ubuntu1 libbinutils_2.30-17ubuntu1 libblkid1_2.31.1-0.4ubuntu4 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3ubuntu1 libc-dev-bin_2.27-3ubuntu1 libc6_2.27-3ubuntu1 libc6-dev_2.27-3ubuntu1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.1.0-3ubuntu1 libcilkrts5_7.3.0-19ubuntu1 libcom-err2_1.44.1-2 libcomerr2_1.44.1-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1ubuntu1 libdb5.3_5.3.28-13.1ubuntu1 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu3 libdpkg-perl_1.19.0.5ubuntu3 libedit2_3.1-20170329-1build1 libevent-2.1-6_2.1.8-stable-4build1 libevent-core-2.1-6_2.1.8-stable-4build1 libevent-pthreads-2.1-6_2.1.8-stable-4build1 libext2fs2_1.44.1-2 libfakeroot_1.22-2ubuntu1 libfdisk1_2.31.1-0.4ubuntu4 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.041-1 libgcc-7-dev_7.3.0-19ubuntu1 libgcc1_1:8.1.0-3ubuntu1 libgcrypt20_1.8.1-4ubuntu1 libgdbm-compat4_1.14.1-6 libgdbm5_1.14.1-6 libglib2.0-0_2.56.1-2ubuntu1 libgmp-dev_2:6.1.2+dfsg-3 libgmp10_2:6.1.2+dfsg-3 libgmpxx4ldbl_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1ubuntu1 libgomp1_8.1.0-3ubuntu1 libgpg-error0_1.31-1 libgssapi-krb5-2_1.16-2build1 libhogweed4_3.4-1 libhwloc-dev_1.11.10-1 libhwloc-plugins_1.11.10-1 libhwloc5_1.11.10-1 libibverbs-dev_17.1-2 libibverbs1_17.1-2 libicu60_60.2-3ubuntu3 libidn11_1.33-2.1ubuntu1 libidn2-0_2.0.4-1.1build2 libip4tc0_1.6.1-2ubuntu2 libisl19_0.19-1 libjson-c3_0.12.1-1.3 libk5crypto3_1.16-2build1 libkeyutils1_1.5.9-9.2ubuntu3 libkmod2_24-1ubuntu3 libkrb5-3_1.16-2build1 libkrb5support0_1.16-2build1 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 libltdl-dev_2.4.6-2.1 libltdl7_2.4.6-2.1 liblz4-1_0.0~r131-2ubuntu3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.33-2 libmagic1_1:5.33-2 libmount1_2.31.1-0.4ubuntu4 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1+20180210-2ubuntu2 libncurses6_6.1+20180210-2ubuntu2 libncursesw5_6.1+20180210-2ubuntu2 libncursesw6_6.1+20180210-2ubuntu2 libnettle6_3.4-1 libnl-3-200_3.2.29-0ubuntu3 libnl-route-3-200_3.2.29-0ubuntu3 libnpth0_1.5-3 libopenmpi-dev_3.0.1.real-4 libopenmpi3_3.0.1.real-4 libp11-kit0_0.23.10-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpciaccess0_0.14-1 libpcre3_2:8.39-9 libperl5.26_5.26.2-3 libpipeline1_1.5.0-1 libpmix2_2.1.1~rc1-4 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-3ubuntu2 libreadline7_7.0-5 libseccomp2_2.3.1-2.1ubuntu4 libselinux1_2.7-2build2 libsemanage-common_2.7-2build2 libsemanage1_2.7-2build2 libsepol1_2.7-1 libsigsegv2_2.12-2 libslang2_2.3.2-1ubuntu1 libsmartcols1_2.31.1-0.4ubuntu4 libsprng2_2.0a-11 libsprng2-dev_2.0a-11 libsqlite3-0_3.23.1-1 libss2_1.44.1-2 libssl1.0.0_1.0.2n-1ubuntu5 libssl1.1_1.1.0g-2ubuntu4 libstdc++-7-dev_7.3.0-19ubuntu1 libstdc++6_8.1.0-3ubuntu1 libsystemd0_237-3ubuntu10 libtasn1-6_4.13-2 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180210-2ubuntu2 libtinfo6_6.1+20180210-2ubuntu2 libtool_2.4.6-2.1 libubsan0_7.3.0-19ubuntu1 libudev1_237-3ubuntu10 libunistring2_0.9.9-0ubuntu1 libusb-0.1-4_2:0.1.12-32 libuuid1_2.31.1-0.4ubuntu4 libxml2_2.9.4+dfsg1-6.1ubuntu1 libzstd1_1.3.3+dfsg-2ubuntu1 linux-libc-dev_4.15.0-21.22 lockfile-progs_0.1.17build1 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-1 make_4.1-9.1ubuntu1 man-db_2.8.3-2 mawk_1.3.3-17ubuntu3 mount_2.31.1-0.4ubuntu4 multiarch-support_2.27-3ubuntu1 ncurses-base_6.1+20180210-2ubuntu2 ncurses-bin_6.1+20180210-2ubuntu2 ocl-icd-libopencl1_2.2.11-1ubuntu1 openmpi-bin_3.0.1.real-4 openmpi-common_3.0.1.real-4 openssh-client_1:7.7p1-2 openssl_1.1.0g-2ubuntu4 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-2ubuntu1 perl_5.26.2-3 perl-base_5.26.2-3 perl-modules-5.26_5.26.2-3 pinentry-curses_1.1.0-1build1 pkgbinarymangler_138 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-3ubuntu2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-tree-puzzle-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_237-3ubuntu10 systemd-sysv_237-3ubuntu10 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tar_1.30+dfsg-1 tzdata_2018e-1 ubuntu-keyring_2018.02.28 util-linux_2.31.1-0.4ubuntu4 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sun May 13 15:06:53 2018 UTC gpgv: using RSA key D56571B88A8BBAF140BF63D6BD7EAA60778FA6F5 gpgv: issuer "doko@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./tree-puzzle_5.2-10build1.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_5.2-10build1.debian.tar.xz dpkg-source: info: applying 20_no_copy_of_sprng.patch dpkg-source: info: applying tests-need-bash.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-14874522 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-14874522 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-14874522 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package tree-puzzle dpkg-buildpackage: info: source version 5.2-10build1 dpkg-buildpackage: info: source distribution cosmic dpkg-source --before-build tree-puzzle-5.2 dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean --no-parallel dh_clean -O--no-parallel debian/rules build-arch dh build-arch --no-parallel dh_update_autotools_config -a -O--no-parallel dh_autoreconf -a -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 http://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: http://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 -a -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 --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 for style of include used by make... GNU 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 -a -O--no-parallel make -j1 make[1]: Entering directory '/<>' Making all in src make[2]: Entering directory '/<>/src' make all-am make[3]: Entering directory '/<>/src' gcc -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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); ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c ./treetest.c && mv treetest.o streetest.o gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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); ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/mpicc -DPARALLEL -DHAVE_CONFIG_H -I. -I.. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1818:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1818:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1818:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1818:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1818:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1818:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1818:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1818:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1818:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1818:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1818:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1818:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1818:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1818:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1818:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1818:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1818:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1201:20: 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:25:0: /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:1818:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ /usr/bin/mpicc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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 '/<>/src' make[2]: Leaving directory '/<>/src' Making all in doc make[2]: Entering directory '/<>/doc' make[3]: Entering directory '/<>/doc' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/<>/doc' make[2]: Leaving directory '/<>/doc' Making all in data make[2]: Entering directory '/<>/data' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/<>/data' Making all in tests make[2]: Entering directory '/<>/tests' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/<>/tests' make[2]: Entering directory '/<>' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' # 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 '/<>' Making check in src make[3]: Entering directory '/<>/src' make[3]: Leaving directory '/<>/src' Making check in doc make[3]: Entering directory '/<>/doc' make[4]: Entering directory '/<>/doc' make[4]: Nothing to be done for 'check-am'. make[4]: Leaving directory '/<>/doc' make[3]: Leaving directory '/<>/doc' Making check in data make[3]: Entering directory '/<>/data' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/data' Making check in tests make[3]: Entering directory '/<>/tests' make check-TESTS make[4]: Entering directory '/<>/tests' make[5]: Entering directory '/<>/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: 5472 Segmentation fault (core dumped) ../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: 5492 Segmentation fault (core dumped) ../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: 5512 Segmentation fault (core dumped) ../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: 5532 Segmentation fault (core dumped) ../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: 5552 Segmentation fault (core dumped) ../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: 5572 Segmentation fault (core dumped) ../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: 5592 Segmentation fault (core dumped) ../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: 5612 Segmentation fault (core dumped) ../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: 5632 Segmentation fault (core dumped) ../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: 5652 Segmentation fault (core dumped) ../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: 5672 Segmentation fault (core dumped) ../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: 5692 Segmentation fault (core dumped) ../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: 5712 Segmentation fault (core dumped) ../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: 5732 Segmentation fault (core dumped) ../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: 5752 Segmentation fault (core dumped) ../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: 5773 Segmentation fault (core dumped) ../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: 5794 Segmentation fault (core dumped) ../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 ============================================================================ Makefile:563: recipe for target 'test-suite.log' failed make[5]: *** [test-suite.log] Error 1 make[5]: Leaving directory '/<>/tests' Makefile:669: recipe for target 'check-TESTS' failed make[4]: *** [check-TESTS] Error 2 make[4]: Leaving directory '/<>/tests' Makefile:749: recipe for target 'check-am' failed make[3]: *** [check-am] Error 2 make[3]: Leaving directory '/<>/tests' Makefile:380: recipe for target 'check-recursive' failed make[2]: *** [check-recursive] Error 1 make[2]: Leaving directory '/<>' dh_auto_test: make -j1 check VERBOSE=1 returned exit code 2 make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --no-parallel dh_testroot -a -O--no-parallel dh_prep -a -O--no-parallel dh_installdirs -a -O--no-parallel dh_auto_install -a -O--no-parallel make -j1 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>' Making install in src make[2]: Entering directory '/<>/src' make[3]: Entering directory '/<>/src' /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c puzzle ppuzzle '/<>/debian/tmp/usr/bin' make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>/src' Making install in doc make[2]: Entering directory '/<>/doc' make[3]: Entering directory '/<>/doc' make[4]: Entering directory '/<>/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 '/<>/doc' make[3]: Leaving directory '/<>/doc' make[2]: Leaving directory '/<>/doc' Making install in data make[2]: Entering directory '/<>/data' make[3]: Entering directory '/<>/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 '/<>/data' make[2]: Leaving directory '/<>/data' Making install in tests make[2]: Entering directory '/<>/tests' make[3]: Entering directory '/<>/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 '/<>/tests' make[2]: Leaving directory '/<>/tests' make[2]: Entering directory '/<>' make[3]: Entering directory '/<>' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_install-arch make[1]: Entering directory '/<>' 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 '/<>' dh_installdocs -a -O--no-parallel dh_installchangelogs -a -O--no-parallel dh_installexamples -a -O--no-parallel dh_installman -a -O--no-parallel dh_installmenu -a -O--no-parallel dh_perl -a -O--no-parallel dh_link -a -O--no-parallel dh_strip_nondeterminism -a -O--no-parallel debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress --exclude=.pdf --exclude .phy --exclude trees --exclude .b make[1]: Leaving directory '/<>' dh_fixperms -a -O--no-parallel dh_missing -a -O--no-parallel dh_strip -a -O--no-parallel dh_makeshlibs -a -O--no-parallel dh_shlibdeps -a -O--no-parallel dh_installdeb -a -O--no-parallel dh_gencontrol -a -O--no-parallel dh_md5sums -a -O--no-parallel dh_builddeb -a -O--no-parallel INFO: pkgstriptranslations version 138 INFO: pkgstriptranslations version 138 INFO: pkgstriptranslations version 138 INFO: pkgstriptranslations version 138 pkgstriptranslations: processing tree-ppuzzle-dbgsym (in debian/.debhelper/tree-ppuzzle/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing tree-puzzle (in debian/tree-puzzle); do_strip: , oemstrip: pkgstriptranslations: processing tree-ppuzzle (in debian/tree-ppuzzle); do_strip: , oemstrip: pkgstriptranslations: processing tree-puzzle-dbgsym (in debian/.debhelper/tree-puzzle/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/tree-puzzle/DEBIAN/control, package tree-puzzle, directory debian/tree-puzzle pkgstripfiles: processing control file: debian/tree-ppuzzle/DEBIAN/control, package tree-ppuzzle, directory debian/tree-ppuzzle pkgstripfiles: processing control file: debian/.debhelper/tree-puzzle/dbgsym-root/DEBIAN/control, package tree-puzzle-dbgsym, directory debian/.debhelper/tree-puzzle/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package tree-puzzle-dbgsym ... pkgstripfiles: Truncating usr/share/doc/tree-puzzle/changelog.Debian.gz to topmost ten records pkgstripfiles: No PNG files. dpkg-deb: building package 'tree-puzzle-dbgsym' in 'debian/.debhelper/scratch-space/build-tree-puzzle/tree-puzzle-dbgsym_5.2-10build1_armhf.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package tree-puzzle ... pkgstripfiles: No PNG files. pkgstripfiles: Truncating usr/share/doc/tree-ppuzzle/changelog.Debian.gz to topmost ten records dpkg-deb: building package 'tree-puzzle' in '../tree-puzzle_5.2-10build1_armhf.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package tree-ppuzzle ... pkgstripfiles: No PNG files. dpkg-deb: building package 'tree-ppuzzle' in '../tree-ppuzzle_5.2-10build1_armhf.deb'. Renaming tree-puzzle-dbgsym_5.2-10build1_armhf.deb to tree-puzzle-dbgsym_5.2-10build1_armhf.ddeb pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/tree-ppuzzle/dbgsym-root/DEBIAN/control, package tree-ppuzzle-dbgsym, directory debian/.debhelper/tree-ppuzzle/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package tree-ppuzzle-dbgsym ... pkgstripfiles: No PNG files. dpkg-deb: building package 'tree-ppuzzle-dbgsym' in 'debian/.debhelper/scratch-space/build-tree-ppuzzle/tree-ppuzzle-dbgsym_5.2-10build1_armhf.deb'. Renaming tree-ppuzzle-dbgsym_5.2-10build1_armhf.deb to tree-ppuzzle-dbgsym_5.2-10build1_armhf.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../tree-puzzle_5.2-10build1_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build tree-puzzle-5.2 dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20180513-1511 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ tree-puzzle_5.2-10build1_armhf.changes: --------------------------------------- Format: 1.8 Date: Sun, 13 May 2018 15:06:08 +0000 Source: tree-puzzle Binary: tree-puzzle tree-ppuzzle tree-puzzle-doc Architecture: armhf Version: 5.2-10build1 Distribution: cosmic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Matthias Klose 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 (5.2-10build1) cosmic; urgency=medium . * No-change rebuild for dune openmpi soname change. Checksums-Sha1: e02b28d6be1950595d9f4cd8e9bdae6c636fccf5 241348 tree-ppuzzle-dbgsym_5.2-10build1_armhf.ddeb 507787c19be0628d8e46ca9c8e7fb6b2b56c9766 131852 tree-ppuzzle_5.2-10build1_armhf.deb ccb1e16e647354bfe9f5ef6bba4d6617e3f26803 199316 tree-puzzle-dbgsym_5.2-10build1_armhf.ddeb 01f51b9f6918aacd1938c7094b38156de07d0182 6792 tree-puzzle_5.2-10build1_armhf.buildinfo 83aa051166f937e4228fb9f9d100fb056efdca61 116212 tree-puzzle_5.2-10build1_armhf.deb Checksums-Sha256: 21b6278f1d99d5943a0288ce077c17bec8f5f53ecf77708616526e618534316a 241348 tree-ppuzzle-dbgsym_5.2-10build1_armhf.ddeb 4d0fa6cd78a778d3288c7d3a5727f4cbd3e604d1f9ec36a700caebf5823e5376 131852 tree-ppuzzle_5.2-10build1_armhf.deb 38b130d9468cb78fe34f0b41397fc13c3059b43e791d4d5b04868260b99adab3 199316 tree-puzzle-dbgsym_5.2-10build1_armhf.ddeb e35dfb140e66bc391c5fb040dab491b23e5594b822d3f6c9f792db23b177f6f7 6792 tree-puzzle_5.2-10build1_armhf.buildinfo 81fbe3bf8c467aacafe1d805b7c3872fb921fe46b0d69981a4444bfb685cf247 116212 tree-puzzle_5.2-10build1_armhf.deb Files: 5a873b509f4723926f5ea54d7e9d7527 241348 debug optional tree-ppuzzle-dbgsym_5.2-10build1_armhf.ddeb 98e036fa3e8057c1d7e8acea06fefc3a 131852 science optional tree-ppuzzle_5.2-10build1_armhf.deb ed6037a21b4d0b20db764942321ea2d9 199316 debug optional tree-puzzle-dbgsym_5.2-10build1_armhf.ddeb 2efb07db6ce30c986b0653235f7e2f8f 6792 science optional tree-puzzle_5.2-10build1_armhf.buildinfo 286f3813a56d5a141ec354e415d13f5a 116212 science optional tree-puzzle_5.2-10build1_armhf.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ tree-ppuzzle_5.2-10build1_armhf.deb ----------------------------------- new debian package, version 2.0. size 131852 bytes: control archive=1452 bytes. 1266 bytes, 26 lines control 621 bytes, 9 lines md5sums 199 bytes, 7 lines * postinst #!/bin/sh 174 bytes, 5 lines * postrm #!/bin/sh Package: tree-ppuzzle Source: tree-puzzle Version: 5.2-10build1 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 269 Depends: libc6 (>= 2.7), libopenmpi3, libsprng2, openmpi-bin Recommends: tree-puzzle-doc Suggests: phylip, treetool Section: science Priority: optional Homepage: http://www.tree-puzzle.de Description: Parallelized reconstruction of phylogenetic trees by maximum likelihood TREE-PUZZLE (the new name for PUZZLE) is an interactive console program that implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREE-PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can also be calculated under the clock-assumption. In addition, TREE-PUZZLE offers a novel method, likelihood mapping, to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment. . This is the parallelized version of tree-puzzle. drwxr-xr-x root/root 0 2018-05-13 15:06 ./ drwxr-xr-x root/root 0 2018-05-13 15:06 ./usr/ drwxr-xr-x root/root 0 2018-05-13 15:06 ./usr/bin/ -rwxr-xr-x root/root 247228 2018-05-13 15:06 ./usr/bin/tree-ppuzzle drwxr-xr-x root/root 0 2018-05-13 15:06 ./usr/share/ drwxr-xr-x root/root 0 2018-05-13 15:06 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-05-13 15:06 ./usr/share/doc/tree-ppuzzle/ -rw-r--r-- root/root 1063 2002-08-05 00:45 ./usr/share/doc/tree-ppuzzle/AUTHORS -rw-r--r-- root/root 1558 2004-07-01 02:39 ./usr/share/doc/tree-ppuzzle/README -rw-r--r-- root/root 411 2017-10-13 05:48 ./usr/share/doc/tree-ppuzzle/README.Debian -rw-r--r-- root/root 1664 2018-05-13 15:06 ./usr/share/doc/tree-ppuzzle/changelog.Debian.gz -rw-r--r-- root/root 1289 2017-10-13 05:48 ./usr/share/doc/tree-ppuzzle/copyright drwxr-xr-x root/root 0 2018-05-13 15:06 ./usr/share/man/ drwxr-xr-x root/root 0 2018-05-13 15:06 ./usr/share/man/man1/ -rw-r--r-- root/root 804 2018-05-13 15:06 ./usr/share/man/man1/tree-ppuzzle.1.gz drwxr-xr-x root/root 0 2018-05-13 15:06 ./usr/share/menu/ -rw-r--r-- root/root 276 2017-10-13 05:48 ./usr/share/menu/tree-ppuzzle drwxr-xr-x root/root 0 2018-05-13 15:06 ./usr/share/pixmaps/ -rw-r--r-- root/root 1292 2017-10-13 05:48 ./usr/share/pixmaps/tree-ppuzzle.xpm tree-puzzle_5.2-10build1_armhf.deb ---------------------------------- new debian package, version 2.0. size 116212 bytes: control archive=1404 bytes. 1153 bytes, 23 lines control 612 bytes, 9 lines md5sums 199 bytes, 7 lines * postinst #!/bin/sh 174 bytes, 5 lines * postrm #!/bin/sh Package: tree-puzzle Version: 5.2-10build1 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 241 Depends: libc6 (>= 2.7), libsprng2 Recommends: tree-puzzle-doc Suggests: phylip, treetool Section: science Priority: optional Homepage: http://www.tree-puzzle.de Description: Reconstruction of phylogenetic trees by maximum likelihood TREE-PUZZLE (the new name for PUZZLE) is an interactive console program that implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREE-PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can also be calculated under the clock-assumption. In addition, TREE-PUZZLE offers a novel method, likelihood mapping, to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment. drwxr-xr-x root/root 0 2018-05-13 15:06 ./ drwxr-xr-x root/root 0 2018-05-13 15:06 ./usr/ drwxr-xr-x root/root 0 2018-05-13 15:06 ./usr/bin/ -rwxr-xr-x root/root 218532 2018-05-13 15:06 ./usr/bin/tree-puzzle drwxr-xr-x root/root 0 2018-05-13 15:06 ./usr/share/ drwxr-xr-x root/root 0 2018-05-13 15:06 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-05-13 15:06 ./usr/share/doc/tree-puzzle/ -rw-r--r-- root/root 1063 2002-08-05 00:45 ./usr/share/doc/tree-puzzle/AUTHORS -rw-r--r-- root/root 1558 2004-07-01 02:39 ./usr/share/doc/tree-puzzle/README -rw-r--r-- root/root 411 2017-10-13 05:48 ./usr/share/doc/tree-puzzle/README.Debian -rw-r--r-- root/root 1664 2018-05-13 15:06 ./usr/share/doc/tree-puzzle/changelog.Debian.gz -rw-r--r-- root/root 1289 2017-10-13 05:48 ./usr/share/doc/tree-puzzle/copyright drwxr-xr-x root/root 0 2018-05-13 15:06 ./usr/share/man/ drwxr-xr-x root/root 0 2018-05-13 15:06 ./usr/share/man/man1/ -rw-r--r-- root/root 798 2018-05-13 15:06 ./usr/share/man/man1/tree-puzzle.1.gz drwxr-xr-x root/root 0 2018-05-13 15:06 ./usr/share/menu/ -rw-r--r-- root/root 245 2017-10-13 05:48 ./usr/share/menu/tree-puzzle drwxr-xr-x root/root 0 2018-05-13 15:06 ./usr/share/pixmaps/ -rw-r--r-- root/root 1286 2017-10-13 05:48 ./usr/share/pixmaps/tree-puzzle.xpm +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 11660 Build-Time: 81 Distribution: cosmic-proposed Host Architecture: armhf Install-Time: 22 Job: tree-puzzle_5.2-10build1.dsc Machine Architecture: arm64 Package: tree-puzzle Package-Time: 105 Source-Version: 5.2-10build1 Space: 11660 Status: successful Version: 5.2-10build1 -------------------------------------------------------------------------------- Finished at 20180513-1511 Build needed 00:01:45, 11660k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=cosmic --arch=armhf PACKAGEBUILD-14874522 Scanning for processes to kill in build PACKAGEBUILD-14874522 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=cosmic --arch=armhf PACKAGEBUILD-14874522 Stopping target for build PACKAGEBUILD-14874522 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=cosmic --arch=armhf PACKAGEBUILD-14874522 Removing build PACKAGEBUILD-14874522