https://launchpad.net/ubuntu/+source/paleomix/1.2.13.3-1/+build/15789404 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lcy01-amd64-009 4.4.0-140-generic #166-Ubuntu SMP Wed Nov 14 20:09:47 UTC 2018 x86_64 Buildd toolchain package versions: launchpad-buildd_165 python-lpbuildd_165 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_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.5 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 17 Dec 17:09:27 ntpdate[1809]: adjust time server 10.211.37.1 offset -0.030288 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15789404 /home/buildd/filecache-default/020b0022f770b890c357907d03d82568c584d50e Creating target for build PACKAGEBUILD-15789404 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15789404 Starting target for build PACKAGEBUILD-15789404 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15789404 'deb http://ftpmaster.internal/ubuntu disco main universe' 'deb http://ftpmaster.internal/ubuntu disco-security main universe' 'deb http://ftpmaster.internal/ubuntu disco-updates main universe' 'deb http://ftpmaster.internal/ubuntu disco-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-15789404 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15789404 Updating target for build PACKAGEBUILD-15789404 Get:1 http://ftpmaster.internal/ubuntu disco InRelease [243 kB] Get:2 http://ftpmaster.internal/ubuntu disco-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu disco-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed InRelease [93.2 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main amd64 Packages [1006 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main Translation-en [509 kB] Get:7 http://ftpmaster.internal/ubuntu disco/universe amd64 Packages [8975 kB] Get:8 http://ftpmaster.internal/ubuntu disco/universe Translation-en [5154 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 Packages [74.4 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main Translation-en [32.6 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/universe amd64 Packages [751 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/universe Translation-en [320 kB] Fetched 17.3 MB in 3s (6126 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: binutils binutils-common binutils-x86-64-linux-gnu cpp-8 dpkg dpkg-dev e2fslibs e2fsprogs g++-8 gcc-8 gcc-8-base libasan5 libassuan0 libatomic1 libbinutils libcc1-0 libcom-err2 libcomerr2 libdpkg-perl libext2fs2 libgcc-8-dev libgcc1 libgomp1 libgpg-error0 libitm1 liblsan0 libmpx2 libquadmath0 libsqlite3-0 libss2 libstdc++-8-dev libstdc++6 libtsan0 libubsan1 linux-libc-dev 35 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 35.6 MB of archives. After this operation, 87.0 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu disco/main amd64 dpkg amd64 1.19.2ubuntu2 [1101 kB] Get:2 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libext2fs2 amd64 1.44.5-1 [159 kB] Get:3 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 e2fsprogs amd64 1.44.5-1 [514 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libubsan1 amd64 8.2.0-12ubuntu2 [121 kB] Get:5 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libtsan0 amd64 8.2.0-12ubuntu2 [288 kB] Get:6 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 gcc-8-base amd64 8.2.0-12ubuntu2 [18.7 kB] Get:7 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libstdc++6 amd64 8.2.0-12ubuntu2 [398 kB] Get:8 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libgomp1 amd64 8.2.0-12ubuntu2 [76.5 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libitm1 amd64 8.2.0-12ubuntu2 [28.1 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libatomic1 amd64 8.2.0-12ubuntu2 [9088 B] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libasan5 amd64 8.2.0-12ubuntu2 [365 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 liblsan0 amd64 8.2.0-12ubuntu2 [132 kB] Get:13 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libmpx2 amd64 8.2.0-12ubuntu2 [11.7 kB] Get:14 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libquadmath0 amd64 8.2.0-12ubuntu2 [134 kB] Get:15 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 cpp-8 amd64 8.2.0-12ubuntu2 [7226 kB] Get:16 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libcc1-0 amd64 8.2.0-12ubuntu2 [39.4 kB] Get:17 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 g++-8 amd64 8.2.0-12ubuntu2 [8112 kB] Get:18 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 gcc-8 amd64 8.2.0-12ubuntu2 [7999 kB] Get:19 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libgcc-8-dev amd64 8.2.0-12ubuntu2 [2306 kB] Get:20 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libstdc++-8-dev amd64 8.2.0-12ubuntu2 [1539 kB] Get:21 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libgcc1 amd64 1:8.2.0-12ubuntu2 [40.7 kB] Get:22 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libbinutils amd64 2.31.1-11ubuntu1 [484 kB] Get:23 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 binutils-common amd64 2.31.1-11ubuntu1 [194 kB] Get:24 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 binutils amd64 2.31.1-11ubuntu1 [3396 B] Get:25 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 binutils-x86-64-linux-gnu amd64 2.31.1-11ubuntu1 [1829 kB] Get:26 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libgpg-error0 amd64 1.33-3 [57.4 kB] Get:27 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libcom-err2 amd64 1.44.5-1 [9372 B] Get:28 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libss2 amd64 1.44.5-1 [11.1 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main amd64 libsqlite3-0 amd64 3.26.0-3 [530 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main amd64 dpkg-dev all 1.19.2ubuntu2 [549 kB] Get:31 http://ftpmaster.internal/ubuntu disco/main amd64 libdpkg-perl all 1.19.2ubuntu2 [227 kB] Get:32 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 e2fslibs amd64 1.44.5-1 [2704 B] Get:33 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libassuan0 amd64 2.5.2-1 [35.1 kB] Get:34 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libcomerr2 amd64 1.44.5-1 [2700 B] Get:35 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 linux-libc-dev amd64 4.19.0-9.10 [1041 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 35.6 MB in 1s (58.1 MB/s) (Reading database ... 12665 files and directories currently installed.) Preparing to unpack .../dpkg_1.19.2ubuntu2_amd64.deb ... Unpacking dpkg (1.19.2ubuntu2) over (1.19.2ubuntu1) ... Setting up dpkg (1.19.2ubuntu2) ... (Reading database ... 12665 files and directories currently installed.) Preparing to unpack .../libext2fs2_1.44.5-1_amd64.deb ... Unpacking libext2fs2:amd64 (1.44.5-1) over (1.44.4-2ubuntu1) ... Setting up libext2fs2:amd64 (1.44.5-1) ... (Reading database ... 12664 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.44.5-1_amd64.deb ... Unpacking e2fsprogs (1.44.5-1) over (1.44.4-2ubuntu1) ... Preparing to unpack .../libubsan1_8.2.0-12ubuntu2_amd64.deb ... Unpacking libubsan1:amd64 (8.2.0-12ubuntu2) over (8.2.0-12ubuntu1) ... Preparing to unpack .../libtsan0_8.2.0-12ubuntu2_amd64.deb ... Unpacking libtsan0:amd64 (8.2.0-12ubuntu2) over (8.2.0-12ubuntu1) ... Preparing to unpack .../gcc-8-base_8.2.0-12ubuntu2_amd64.deb ... Unpacking gcc-8-base:amd64 (8.2.0-12ubuntu2) over (8.2.0-12ubuntu1) ... 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RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-15789404 amd64 disco-proposed -c chroot:build-PACKAGEBUILD-15789404 --arch=amd64 --dist=disco-proposed --nolog -A paleomix_1.2.13.3-1.dsc Initiating build PACKAGEBUILD-15789404 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-140-generic #166-Ubuntu SMP Wed Nov 14 20:09:47 UTC 2018 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-amd64-009.buildd +==============================================================================+ | paleomix 1.2.13.3-1 (amd64) 17 Dec 2018 17:09 | +==============================================================================+ Package: paleomix Version: 1.2.13.3-1 Source Version: 1.2.13.3-1 Distribution: disco-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/paleomix-UOaebR/paleomix-1.2.13.3' with '<>' I: NOTICE: Log filtering will replace 'build/paleomix-UOaebR' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15789404/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- paleomix_1.2.13.3-1.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-yvRDZw/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-yvRDZw/apt_archive ./ InRelease Get:2 copy:/<>/resolver-yvRDZw/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-yvRDZw/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-yvRDZw/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-yvRDZw/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (0 B/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 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-yvRDZw/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12667 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 11~), dh-python, python, python-setuptools, python-coverage, python-flexmock, python-nose, python-pysam, python-setproctitle, default-jre-headless, bowtie2, rsync Filtered Build-Depends: debhelper (>= 11~), dh-python, python, python-setuptools, python-coverage, python-flexmock, python-nose, python-pysam, python-setproctitle, default-jre-headless, bowtie2, rsync dpkg-deb: building package 'sbuild-build-depends-paleomix-dummy' in '/<>/resolver-C1SjKc/apt_archive/sbuild-build-depends-paleomix-dummy.deb'. Ign:1 copy:/<>/resolver-C1SjKc/apt_archive ./ InRelease Get:2 copy:/<>/resolver-C1SjKc/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-C1SjKc/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-C1SjKc/apt_archive ./ Sources [287 B] Get:5 copy:/<>/resolver-C1SjKc/apt_archive ./ Packages [610 B] Fetched 3016 B in 0s (298 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install paleomix 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 bowtie2 bsdmainutils ca-certificates-java debhelper default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism dwz file fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian java-common libarchive-zip-perl libasn1-8-heimdal libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libbsd0 libcroco3 libcups2 libcurl3-gnutls libdbus-1-3 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts2 libhx509-5-heimdal libicu63 libjpeg-turbo8 libjpeg8 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblcms2-2 libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libpipeline1 libpopt0 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libtbb2 libtool libwind0-heimdal libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxrender1 libxtst6 m4 man-db mime-support openjdk-11-jre-headless po-debconf python python-coverage python-flexmock python-minimal python-nose python-pkg-resources python-pysam python-setproctitle python-setuptools python2 python2-minimal python2.7 python2.7-minimal python3 python3-distutils python3-lib2to3 python3-minimal python3.7 python3.7-minimal rsync ucf x11-common Suggested packages: autoconf-archive gnu-standards autoconf-doc bowtie2-examples wamerican | wordlist whois vacation dh-make default-jre gettext-doc libasprintf-dev libgettextpo-dev groff libasound2-plugins alsa-utils cups-common krb5-doc krb5-user liblcms2-utils pcscd libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic libmail-box-perl python-doc python-tk python-coverage-doc python-nose-doc python-setuptools-doc python2-doc python2.7-doc binfmt-support python3-doc python3-tk python3-venv python3.7-venv python3.7-doc openssh-client openssh-server Recommended packages: curl | wget | lynx dbus libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl libjs-jquery-isonscreen libjs-jquery-tablesorter libjs-jquery-throttle-debounce libjs-jquery The following NEW packages will be installed: autoconf automake autopoint autotools-dev bowtie2 bsdmainutils ca-certificates-java debhelper default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism dwz file fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian java-common libarchive-zip-perl libasn1-8-heimdal libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libbsd0 libcroco3 libcups2 libcurl3-gnutls libdbus-1-3 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts2 libhx509-5-heimdal libicu63 libjpeg-turbo8 libjpeg8 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblcms2-2 libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libpipeline1 libpopt0 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libtbb2 libtool libwind0-heimdal libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxrender1 libxtst6 m4 man-db mime-support openjdk-11-jre-headless po-debconf python python-coverage python-flexmock python-minimal python-nose python-pkg-resources python-pysam python-setproctitle python-setuptools python2 python2-minimal python2.7 python2.7-minimal python3 python3-distutils python3-lib2to3 python3-minimal python3.7 python3.7-minimal rsync sbuild-build-depends-paleomix-dummy ucf x11-common 0 upgraded, 120 newly installed, 0 to remove and 0 not upgraded. Need to get 73.7 MB of archives. After this operation, 315 MB of additional disk space will be used. 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disco-proposed/main amd64 python-pkg-resources all 40.6.2-1 [129 kB] Get:113 http://ftpmaster.internal/ubuntu disco/universe amd64 python-coverage amd64 4.5.1+dfsg.1-1build1 [107 kB] Get:114 http://ftpmaster.internal/ubuntu disco/universe amd64 python-flexmock all 0.10.2-2 [15.5 kB] Get:115 http://ftpmaster.internal/ubuntu disco/universe amd64 python-nose all 1.3.7-4 [116 kB] Get:116 http://ftpmaster.internal/ubuntu disco-proposed/universe amd64 python-pysam amd64 0.15.1+ds-1 [1656 kB] Get:117 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 python-setuptools all 40.6.2-1 [327 kB] Get:118 http://ftpmaster.internal/ubuntu disco/universe amd64 libtbb2 amd64 2018~U6-4 [115 kB] Get:119 http://ftpmaster.internal/ubuntu disco/universe amd64 bowtie2 amd64 2.3.4.3-1 [1183 kB] Get:120 http://ftpmaster.internal/ubuntu disco/main amd64 python-setproctitle amd64 1.1.10-1build4 [14.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 73.7 MB in 1s (55.5 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Preparing to unpack .../86-libtbb2_2018~U6-4_amd64.deb ... Unpacking libtbb2:amd64 (2018~U6-4) ... Selecting previously unselected package bowtie2. Preparing to unpack .../87-bowtie2_2.3.4.3-1_amd64.deb ... Unpacking bowtie2 (2.3.4.3-1) ... Selecting previously unselected package python-setproctitle:amd64. Preparing to unpack .../88-python-setproctitle_1.1.10-1build4_amd64.deb ... Unpacking python-setproctitle:amd64 (1.1.10-1build4) ... Selecting previously unselected package sbuild-build-depends-paleomix-dummy. Preparing to unpack .../89-sbuild-build-depends-paleomix-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-paleomix-dummy (0.invalid.0) ... Setting up libpopt0:amd64 (1.16-11) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libnghttp2-14:amd64 (1.35.1-1) ... Setting up mime-support (3.60ubuntu1) ... Setting up libicu63:amd64 (63.1-5) ... Setting up liblcms2-2:amd64 (2.9-3) ... Setting up libpcsclite1:amd64 (1.8.24-1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up libldap-common (2.4.46+dfsg-5ubuntu3) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up libtbb2:amd64 (2018~U6-4) ... Setting up libelf1:amd64 (0.175-1) ... Setting up groff-base (1.22.3-10) ... Setting up libglib2.0-0:amd64 (2.58.1-2) ... No schema files found: doing nothing. Setting up libasound2-data (1.1.7-2ubuntu0.1) ... Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up java-common (0.70) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libjpeg-turbo8:amd64 (2.0.0-0ubuntu2) ... Setting up libpipeline1:amd64 (1.5.0-2) ... Setting up libroken18-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up m4 (1.4.18-2) ... Setting up libbsd0:amd64 (0.9.1-1) ... Setting up libkrb5support0:amd64 (1.16.1-1ubuntu1) ... Setting up libnspr4:amd64 (2:4.20-1ubuntu1) ... Setting up ucf (3.0038) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7ubuntu3) ... Setting up libfreetype6:amd64 (2.8.1-2ubuntu2) ... Setting up libmagic-mgc (1:5.34-2) ... Setting up libasound2:amd64 (1.1.7-2ubuntu0.1) ... Setting up libmagic1:amd64 (1:5.34-2) ... Setting up rsync (3.1.2-2.2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Created symlink /etc/systemd/system/multi-user.target.wants/rsync.service → /lib/systemd/system/rsync.service. Setting up libcroco3:amd64 (0.6.12-2) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up dwz (0.12-3) ... Setting up autotools-dev (20180224.1) ... Setting up libheimbase1-heimdal:amd64 (7.5.0+dfsg-2.1) ... Processing triggers for systemd (239-7ubuntu15) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libkeyutils1:amd64 (1.5.9-9.3) ... 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 x11-common (1:7.7+19ubuntu8) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Processing triggers for ca-certificates (20180409) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Setting up libx11-data (2:1.6.7-1) ... Setting up libpython2.7-stdlib:amd64 (2.7.15-5) ... Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up autopoint (0.19.8.1-9) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up libdbus-1-3:amd64 (1.12.10-1ubuntu2) ... Setting up libavahi-common-data:amd64 (0.7-4ubuntu4) ... Setting up libfile-stripnondeterminism-perl (1.0.0-1) ... Setting up libjpeg8:amd64 (8c-2ubuntu8) ... Setting up libk5crypto3:amd64 (1.16.1-1ubuntu1) ... Setting up libpython3.7-stdlib:amd64 (3.7.2~rc1-1) ... Setting up fontconfig-config (2.13.0-5ubuntu3) ... Setting up libwind0-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up gettext (0.19.8.1-9) ... Setting up libasn1-8-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up libhcrypto4-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up python2.7 (2.7.15-5) ... Setting up libnss3:amd64 (2:3.39-1ubuntu1) ... Setting up python3.7 (3.7.2~rc1-1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.34-2) ... Setting up libhx509-5-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.4-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython2-stdlib:amd64 (2.7.15-3) ... Setting up libkrb5-3:amd64 (1.16.1-1ubuntu1) ... Setting up libavahi-common3:amd64 (0.7-4ubuntu4) ... Setting up libkrb5-26-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up libxcb1:amd64 (1.13.1-2) ... Setting up libheimntlm0-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up libtool (2.4.6-6) ... Setting up libpython3-stdlib:amd64 (3.7.1-1ubuntu1) ... Setting up libfontconfig1:amd64 (2.13.0-5ubuntu3) ... Setting up po-debconf (1.0.21) ... Setting up python3 (3.7.1-1ubuntu1) ... Setting up libx11-6:amd64 (2:1.6.7-1) ... Setting up python2 (2.7.15-3) ... Setting up libgssapi-krb5-2:amd64 (1.16.1-1ubuntu1) ... Setting up libpython-stdlib:amd64 (2.7.15-3) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libavahi-client3:amd64 (0.7-4ubuntu4) ... Setting up libgssapi3-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up python3-lib2to3 (3.7.1-1ubuntu4) ... Setting up python3-distutils (3.7.1-1ubuntu4) ... Setting up python (2.7.15-3) ... Setting up python-setproctitle:amd64 (1.1.10-1build4) ... Setting up libcups2:amd64 (2.2.10-3) ... Setting up python-flexmock (0.10.2-2) ... Setting up libxext6:amd64 (2:1.3.3-1) ... Setting up python-pkg-resources (40.6.2-1) ... Setting up bowtie2 (2.3.4.3-1) ... Setting up libxtst6:amd64 (2:1.2.3-1) ... Setting up python-coverage (4.5.1+dfsg.1-1build1) ... Setting up libldap-2.4-2:amd64 (2.4.46+dfsg-5ubuntu3) ... Setting up dh-python (3.20180927ubuntu2) ... Setting up python-nose (1.3.7-4) ... Setting up libxi6:amd64 (2:1.7.9-1) ... Setting up python-setuptools (40.6.2-1) ... Setting up libcurl3-gnutls:amd64 (7.61.0-1ubuntu2.2) ... Setting up libhts2:amd64 (1.9-6) ... Setting up python-pysam (0.15.1+ds-1) ... Setting up dh-autoreconf (19) ... Setting up openjdk-11-jre-headless:amd64 (11.0.1+13-3ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up dh-strip-nondeterminism (1.0.0-1) ... Setting up default-jre-headless (2:1.11-70) ... Setting up debhelper (11.5.3ubuntu1) ... Setting up sbuild-build-depends-paleomix-dummy (0.invalid.0) ... Setting up ca-certificates-java (20180516ubuntu1) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:TÜRKTRUST_Elektronik_Sertifika_Hizmet_Sağlayıcısı_H5.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:ISRG_Root_X1.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:Certplus_Root_CA_G2.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:OpenTrust_Root_CA_G3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:Secure_Global_CA.pem Adding debian:Taiwan_GRCA.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Visa_eCommerce_Root.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:AddTrust_External_Root.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:EC-ACC.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:DST_Root_CA_X3.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:Izenpe.com.pem Adding debian:LuxTrust_Global_Root_2.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:SecureTrust_CA.pem Adding debian:OpenTrust_Root_CA_G2.pem Adding debian:Certinomis_-_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:AffirmTrust_Networking.pem Adding debian:Certplus_Root_CA_G1.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:AffirmTrust_Premium.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:SecureSign_RootCA11.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:ACCVRAIZ1.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:Certigna.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:OpenTrust_Root_CA_G1.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_Trusted_Root_G4.pem done. Processing triggers for libc-bin (2.28-0ubuntu1) ... Processing triggers for systemd (239-7ubuntu15) ... Processing triggers for ca-certificates (20180409) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-140-generic amd64 (x86_64) Toolchain package versions: binutils_2.31.1-11ubuntu1 dpkg-dev_1.19.2ubuntu2 g++-8_8.2.0-12ubuntu2 gcc-8_8.2.0-12ubuntu2 libc6-dev_2.28-0ubuntu1 libstdc++-8-dev_8.2.0-12ubuntu2 libstdc++6_8.2.0-12ubuntu2 linux-libc-dev_4.19.0-9.10 Package versions: adduser_3.117ubuntu1 advancecomp_2.1-1 apt_1.8.0~alpha2ubuntu1 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1ubuntu8 base-passwd_3.5.45 bash_4.4.18-2ubuntu3 binutils_2.31.1-11ubuntu1 binutils-common_2.31.1-11ubuntu1 binutils-x86-64-linux-gnu_2.31.1-11ubuntu1 bowtie2_2.3.4.3-1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.32-0.1ubuntu2 build-essential_12.5ubuntu2 bzip2_1.0.6-9 ca-certificates_20180409 ca-certificates-java_20180516ubuntu1 coreutils_8.28-1ubuntu2 cpp_4:8.2.0-2ubuntu2 cpp-8_8.2.0-12ubuntu2 dash_0.5.10.2-2 debconf_1.5.69 debhelper_11.5.3ubuntu1 debianutils_4.8.6 default-jre-headless_2:1.11-70 dh-autoreconf_19 dh-python_3.20180927ubuntu2 dh-strip-nondeterminism_1.0.0-1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu4 dpkg_1.19.2ubuntu2 dpkg-dev_1.19.2ubuntu2 dwz_0.12-3 e2fslibs_1.44.5-1 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.32-0.1ubuntu2 file_1:5.34-2 findutils_4.6.0+git+20181018-1 fontconfig-config_2.13.0-5ubuntu3 fonts-dejavu-core_2.37-1 g++_4:8.2.0-2ubuntu2 g++-8_8.2.0-12ubuntu2 gcc_4:8.2.0-2ubuntu2 gcc-8_8.2.0-12ubuntu2 gcc-8-base_8.2.0-12ubuntu2 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpg_2.2.8-3ubuntu1 gpg-agent_2.2.8-3ubuntu1 gpgconf_2.2.8-3ubuntu1 gpgv_2.2.8-3ubuntu1 grep_3.1-3 groff-base_1.22.3-10 gzip_1.6-5ubuntu2 hostname_3.21 init_1.56 init-system-helpers_1.56 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 java-common_0.70 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu10 libapt-pkg5.0_1.8.0~alpha2ubuntu1 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-12ubuntu2 libasn1-8-heimdal_7.5.0+dfsg-2.1 libasound2_1.1.7-2ubuntu0.1 libasound2-data_1.1.7-2ubuntu0.1 libassuan0_2.5.2-1 libatomic1_8.2.0-12ubuntu2 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.3-1ubuntu3 libaudit1_1:2.8.3-1ubuntu3 libavahi-client3_0.7-4ubuntu4 libavahi-common-data_0.7-4ubuntu4 libavahi-common3_0.7-4ubuntu4 libbinutils_2.31.1-11ubuntu1 libblkid1_2.32-0.1ubuntu2 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-0ubuntu1 libc-dev-bin_2.28-0ubuntu1 libc6_2.28-0ubuntu1 libc6-dev_2.28-0ubuntu1 libcap-ng0_0.7.9-1build1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-12ubuntu2 libcom-err2_1.44.5-1 libcomerr2_1.44.5-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2ubuntu2 libcups2_2.2.10-3 libcurl3-gnutls_7.61.0-1ubuntu2.2 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.10-1ubuntu2 libdebconfclient0_0.244ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu4 libdpkg-perl_1.19.2ubuntu2 libelf1_0.175-1 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.32-0.1ubuntu2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.0.0-1 libfontconfig1_2.13.0-5ubuntu3 libfreetype6_2.8.1-2ubuntu2 libgcc-8-dev_8.2.0-12ubuntu2 libgcc1_1:8.2.0-12ubuntu2 libgcrypt20_1.8.4-3ubuntu1 libgdbm-compat4_1.18.1-2 libgdbm6_1.18.1-2 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.4-2ubuntu2 libgomp1_8.2.0-12ubuntu2 libgpg-error0_1.33-3 libgssapi-krb5-2_1.16.1-1ubuntu1 libgssapi3-heimdal_7.5.0+dfsg-2.1 libhcrypto4-heimdal_7.5.0+dfsg-2.1 libheimbase1-heimdal_7.5.0+dfsg-2.1 libheimntlm0-heimdal_7.5.0+dfsg-2.1 libhogweed4_3.4.1~rc1-1 libhts2_1.9-6 libhx509-5-heimdal_7.5.0+dfsg-2.1 libicu63_63.1-5 libidn11_1.33-2.2ubuntu1 libidn2-0_2.0.5-1 libip4tc0_1.6.1-2ubuntu3 libisl19_0.20-2 libitm1_8.2.0-12ubuntu2 libjpeg-turbo8_2.0.0-0ubuntu2 libjpeg8_8c-2ubuntu8 libjson-c3_0.12.1-1.3 libk5crypto3_1.16.1-1ubuntu1 libkeyutils1_1.5.9-9.3 libkmod2_25-1ubuntu2 libkrb5-26-heimdal_7.5.0+dfsg-2.1 libkrb5-3_1.16.1-1ubuntu1 libkrb5support0_1.16.1-1ubuntu1 liblcms2-2_2.9-3 libldap-2.4-2_2.4.46+dfsg-5ubuntu3 libldap-common_2.4.46+dfsg-5ubuntu3 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblsan0_8.2.0-12ubuntu2 liblz4-1_1.8.2-1ubuntu1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32-0.1ubuntu2 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.1-2 libmpx2_8.2.0-12ubuntu2 libncurses6_6.1+20180210-4ubuntu1 libncursesw6_6.1+20180210-4ubuntu1 libnettle6_3.4.1~rc1-1 libnghttp2-14_1.35.1-1 libnpth0_1.6-1 libnspr4_2:4.20-1ubuntu1 libnss3_2:3.39-1ubuntu1 libp11-kit0_0.23.14-2 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 libpcre3_2:8.39-11 libpcsclite1_1.8.24-1 libperl5.28_5.28.1-3 libpipeline1_1.5.0-2 libpng16-16_1.6.34-2 libpopt0_1.16-11 libprocps7_2:3.3.15-2ubuntu1 libpsl5_0.20.2-2 libpython-stdlib_2.7.15-3 libpython2-stdlib_2.7.15-3 libpython2.7-minimal_2.7.15-5 libpython2.7-stdlib_2.7.15-5 libpython3-stdlib_3.7.1-1ubuntu1 libpython3.7-minimal_3.7.2~rc1-1 libpython3.7-stdlib_3.7.2~rc1-1 libquadmath0_8.2.0-12ubuntu2 libreadline7_7.0-5 libroken18-heimdal_7.5.0+dfsg-2.1 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu2 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu2 libseccomp2_2.3.3-3ubuntu2 libselinux1_2.8-1build2 libsemanage-common_2.8-1build2 libsemanage1_2.8-1build2 libsepol1_2.8-1 libsigsegv2_2.12-2 libslang2_2.3.2-1ubuntu1 libsmartcols1_2.32-0.1ubuntu2 libsqlite3-0_3.26.0-3 libss2_1.44.5-1 libssl1.1_1.1.1a-1ubuntu2 libstdc++-8-dev_8.2.0-12ubuntu2 libstdc++6_8.2.0-12ubuntu2 libsystemd0_239-7ubuntu15 libtasn1-6_4.13-3 libtbb2_2018~U6-4 libtinfo6_6.1+20180210-4ubuntu1 libtool_2.4.6-6 libtsan0_8.2.0-12ubuntu2 libubsan1_8.2.0-12ubuntu2 libudev1_239-7ubuntu15 libunistring2_0.9.10-1ubuntu1 libusb-0.1-4_2:0.1.12-32 libuuid1_2.32-0.1ubuntu2 libwind0-heimdal_7.5.0+dfsg-2.1 libx11-6_2:1.6.7-1 libx11-data_2:1.6.7-1 libxau6_1:1.0.8-1 libxcb1_1.13.1-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1 libxi6_2:1.7.9-1 libxml2_2.9.4+dfsg1-7ubuntu3 libxrender1_1:0.9.10-1 libxtst6_2:1.2.3-1 libzstd1_1.3.5+dfsg-1ubuntu1 linux-libc-dev_4.19.0-9.10 lockfile-progs_0.1.18 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.4-3 mawk_1.3.3-17ubuntu3 mime-support_3.60ubuntu1 mount_2.32-0.1ubuntu2 multiarch-support_2.28-0ubuntu1 ncurses-base_6.1+20180210-4ubuntu1 ncurses-bin_6.1+20180210-4ubuntu1 openjdk-11-jre-headless_11.0.1+13-3ubuntu1 openssl_1.1.1a-1ubuntu2 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1build2 pkgbinarymangler_143 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu1 python_2.7.15-3 python-coverage_4.5.1+dfsg.1-1build1 python-flexmock_0.10.2-2 python-minimal_2.7.15-3 python-nose_1.3.7-4 python-pkg-resources_40.6.2-1 python-pysam_0.15.1+ds-1 python-setproctitle_1.1.10-1build4 python-setuptools_40.6.2-1 python2_2.7.15-3 python2-minimal_2.7.15-3 python2.7_2.7.15-5 python2.7-minimal_2.7.15-5 python3_3.7.1-1ubuntu1 python3-distutils_3.7.1-1ubuntu4 python3-lib2to3_3.7.1-1ubuntu4 python3-minimal_3.7.1-1ubuntu1 python3.7_3.7.2~rc1-1 python3.7-minimal_3.7.2~rc1-1 readline-common_7.0-5 rsync_3.1.2-2.2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-paleomix-dummy_0.invalid.0 sed_4.5-2 sensible-utils_0.0.12 systemd_239-7ubuntu15 systemd-sysv_239-7ubuntu15 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu2 tar_1.30+dfsg-3 tzdata_2018g-1 ubuntu-keyring_2018.09.18.1 ucf_3.0038 util-linux_2.32-0.1ubuntu2 x11-common_1:7.7+19ubuntu8 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Mon Dec 17 12:47:04 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./paleomix_1.2.13.3-1.dsc dpkg-source: info: extracting paleomix in paleomix-1.2.13.3 dpkg-source: info: unpacking paleomix_1.2.13.3.orig.tar.gz dpkg-source: info: unpacking paleomix_1.2.13.3-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying avoid_downloading_prerequisites.patch dpkg-source: info: applying avoid_privacy_breach.patch dpkg-source: info: applying adapt_java_calling_test.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-15789404 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15789404 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15789404 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package paleomix dpkg-buildpackage: info: source version 1.2.13.3-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python2 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:217: python2.7 setup.py clean running clean removing '/<>/.pybuild/cpython2_2.7/build' (and everything under it) 'build/bdist.linux-amd64' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build dh build --with python2 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:217: python2.7 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python setup.py build running build running build_py creating /<>/.pybuild/cpython2_2.7/build/paleomix copying paleomix/pipeline.py -> /<>/.pybuild/cpython2_2.7/build/paleomix copying paleomix/nodegraph.py -> /<>/.pybuild/cpython2_2.7/build/paleomix copying paleomix/main.py -> /<>/.pybuild/cpython2_2.7/build/paleomix copying paleomix/config.py -> /<>/.pybuild/cpython2_2.7/build/paleomix copying paleomix/node.py -> /<>/.pybuild/cpython2_2.7/build/paleomix copying paleomix/ui.py -> /<>/.pybuild/cpython2_2.7/build/paleomix copying paleomix/logger.py -> /<>/.pybuild/cpython2_2.7/build/paleomix copying paleomix/__init__.py -> /<>/.pybuild/cpython2_2.7/build/paleomix creating /<>/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/coverage.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/gtf_to_bed.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/retable.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/dupcheck.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/duphist.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/genotype.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/vcf_to_fasta.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/ena.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/depths.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/cleanup.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/cat.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/sample_pileup.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/rmdup_collapsed.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/vcf_filter.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/factory.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/__init__.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources copying paleomix/resources/__init__.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources creating /<>/.pybuild/cpython2_2.7/build/paleomix/yaml copying paleomix/yaml/__init__.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/yaml creating /<>/.pybuild/cpython2_2.7/build/paleomix/atomiccmd copying paleomix/atomiccmd/command.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/atomiccmd copying paleomix/atomiccmd/builder.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/atomiccmd copying paleomix/atomiccmd/sets.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/atomiccmd copying paleomix/atomiccmd/pprint.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/atomiccmd copying paleomix/atomiccmd/__init__.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/atomiccmd creating /<>/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/fileutils.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/testing.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/bamfiles.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/signals.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/utilities.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/vcffilter.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/vcfwrap.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/sampling.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/text.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/versions.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/console.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/sequences.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/makefile.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/rtools.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/system.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/procs.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/bedtools.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/timer.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/__init__.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common creating /<>/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/phylip.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/formats.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/adapterremoval.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/validation.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/bowtie2.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/sequences.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/examl.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/mafft.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/gatk.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/newick.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/misc.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/raxml.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/commands.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/samtools.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/mapdamage.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/bwa.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/bedtools.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/picard.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/__init__.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/nodes creating /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_stats copying paleomix/tools/bam_stats/coverage.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_stats copying paleomix/tools/bam_stats/common.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_stats copying paleomix/tools/bam_stats/__init__.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_stats creating /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline copying paleomix/tools/bam_pipeline/pipeline.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline copying paleomix/tools/bam_pipeline/remap.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline copying paleomix/tools/bam_pipeline/makefile.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline copying paleomix/tools/bam_pipeline/mkfile.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline copying paleomix/tools/bam_pipeline/config.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline copying paleomix/tools/bam_pipeline/trim_pipeline.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline copying paleomix/tools/bam_pipeline/paths.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline copying paleomix/tools/bam_pipeline/nodes.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline copying paleomix/tools/bam_pipeline/__init__.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline creating /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline copying paleomix/tools/phylo_pipeline/pipeline.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline copying paleomix/tools/phylo_pipeline/makefile.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline copying paleomix/tools/phylo_pipeline/mkfile.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline copying paleomix/tools/phylo_pipeline/config.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline copying paleomix/tools/phylo_pipeline/__init__.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline creating /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey copying paleomix/tools/zonkey/pipeline.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey copying paleomix/tools/zonkey/build_mito.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey copying paleomix/tools/zonkey/common.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey copying paleomix/tools/zonkey/build_tped.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey copying paleomix/tools/zonkey/config.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey copying paleomix/tools/zonkey/database.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey copying paleomix/tools/zonkey/build_db.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey copying paleomix/tools/zonkey/__init__.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey creating /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts copying paleomix/tools/bam_pipeline/parts/library.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts copying paleomix/tools/bam_pipeline/parts/reads.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts copying paleomix/tools/bam_pipeline/parts/prefix.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts copying paleomix/tools/bam_pipeline/parts/statistics.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts copying paleomix/tools/bam_pipeline/parts/sample.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts copying paleomix/tools/bam_pipeline/parts/summary.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts copying paleomix/tools/bam_pipeline/parts/lane.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts copying paleomix/tools/bam_pipeline/parts/target.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts copying paleomix/tools/bam_pipeline/parts/__init__.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts creating /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts copying paleomix/tools/phylo_pipeline/parts/genotype.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts copying paleomix/tools/phylo_pipeline/parts/phylo.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts copying paleomix/tools/phylo_pipeline/parts/paml.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts copying paleomix/tools/phylo_pipeline/parts/msa.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts copying paleomix/tools/phylo_pipeline/parts/__init__.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts creating /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts copying paleomix/tools/zonkey/parts/nuclear.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts copying paleomix/tools/zonkey/parts/common.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts copying paleomix/tools/zonkey/parts/mitochondria.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts copying paleomix/tools/zonkey/parts/summary.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts copying paleomix/tools/zonkey/parts/report.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts copying paleomix/tools/zonkey/parts/__init__.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts copying paleomix/tools/zonkey/parts/admixture.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts creating /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/loader.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/tokens.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/serializer.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/error.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/dumper.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/resolver.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/representer.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/composer.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/events.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/emitter.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/nodes.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/parser.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/constructor.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/reader.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/__init__.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/scanner.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 creating /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats copying paleomix/common/formats/_common.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats copying paleomix/common/formats/phylip.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats copying paleomix/common/formats/fastq.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats copying paleomix/common/formats/newick.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats copying paleomix/common/formats/_graph.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats copying paleomix/common/formats/msa.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats copying paleomix/common/formats/__init__.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats copying paleomix/common/formats/fasta.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats running egg_info creating paleomix.egg-info writing requirements to paleomix.egg-info/requires.txt writing paleomix.egg-info/PKG-INFO writing top-level names to paleomix.egg-info/top_level.txt writing dependency_links to paleomix.egg-info/dependency_links.txt writing entry points to paleomix.egg-info/entry_points.txt writing manifest file 'paleomix.egg-info/SOURCES.txt' reading manifest file 'paleomix.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'paleomix.egg-info/SOURCES.txt' creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline copying paleomix/resources/examples/bam_pipeline/000_makefile.yaml -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data copying paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R1_01.fastq.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data copying paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R1_02.fastq.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data copying paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R1_03.fastq.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data copying paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R1_04.fastq.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data copying paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R2_01.fastq.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data copying paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R2_02.fastq.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data copying paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R2_03.fastq.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data copying paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R2_04.fastq.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data copying paleomix/resources/examples/bam_pipeline/000_data/GCTCTG_L1_R1_01.fastq.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data copying paleomix/resources/examples/bam_pipeline/000_data/GCTCTG_L1_R1_02.fastq.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data copying paleomix/resources/examples/bam_pipeline/000_data/GCTCTG_L1_R1_03.fastq.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data copying paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L1_R1_01.fastq.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data copying paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L1_R1_02.fastq.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data copying paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L1_R1_03.fastq.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data copying paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R1_01.fastq.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data copying paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R1_02.fastq.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data copying paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R1_03.fastq.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data copying paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R2_01.fastq.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data copying paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R2_02.fastq.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data copying paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R2_03.fastq.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2 copying paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2/reads.collapsed.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2 copying paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2/reads.collapsed.truncated.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2 copying paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2/reads.singleton.truncated.gz -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2 creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_prefixes copying paleomix/resources/examples/bam_pipeline/000_prefixes/rCRS.fasta -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_prefixes creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment copying paleomix/resources/examples/nature_protocols/alignment/000_makefile.yaml -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_prefixes copying paleomix/resources/examples/nature_protocols/alignment/000_prefixes/README -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_prefixes copying paleomix/resources/examples/nature_protocols/alignment/000_prefixes/setup.sh -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_prefixes creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads copying paleomix/resources/examples/nature_protocols/alignment/000_rawreads/setup.sh -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/06_3928A copying paleomix/resources/examples/nature_protocols/alignment/000_rawreads/06_3928A/000_ENA -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/06_3928A copying paleomix/resources/examples/nature_protocols/alignment/000_rawreads/06_3928A/000_README -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/06_3928A creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/DDR7602 copying paleomix/resources/examples/nature_protocols/alignment/000_rawreads/DDR7602/000_ENA -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/DDR7602 copying paleomix/resources/examples/nature_protocols/alignment/000_rawreads/DDR7602/000_README -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/DDR7602 creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/LBUS5 copying paleomix/resources/examples/nature_protocols/alignment/000_rawreads/LBUS5/000_ENA -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/LBUS5 copying paleomix/resources/examples/nature_protocols/alignment/000_rawreads/LBUS5/000_README -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/LBUS5 creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/M-0182896 copying paleomix/resources/examples/nature_protocols/alignment/000_rawreads/M-0182896/000_ENA -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/M-0182896 copying paleomix/resources/examples/nature_protocols/alignment/000_rawreads/M-0182896/000_README -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/M-0182896 creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/NL07434 copying paleomix/resources/examples/nature_protocols/alignment/000_rawreads/NL07434/000_ENA -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/NL07434 copying paleomix/resources/examples/nature_protocols/alignment/000_rawreads/NL07434/000_README -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/NL07434 creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13527 copying paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13527/000_ENA -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13527 copying paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13527/000_README -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13527 creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13626 copying paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13626/000_ENA -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13626 copying paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13626/000_README -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13626 creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P17777 copying paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P17777/000_ENA -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P17777 copying paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P17777/000_README -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P17777 creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1845A copying paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1845A/000_ENA -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1845A copying paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1845A/000_README -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1845A creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1889 copying paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1889/000_ENA -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1889 copying paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1889/000_README -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1889 creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment copying paleomix/resources/examples/nature_protocols/example_results/alignment/M-0182896.Pi_mito.coverage -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment copying paleomix/resources/examples/nature_protocols/example_results/alignment/M-0182896.Pi_mito.depths -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment copying paleomix/resources/examples/nature_protocols/example_results/alignment/M-0182896.Pi_nucl.coverage -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment copying paleomix/resources/examples/nature_protocols/example_results/alignment/M-0182896.Pi_nucl.depths -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment copying paleomix/resources/examples/nature_protocols/example_results/alignment/M-0182896.summary -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.coverage -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.depths -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.coverage -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.depths -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.summary -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.coverage -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.depths -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.coverage -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.depths -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.summary -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/3pGtoA_freq.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/5pCtoT_freq.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Fragmisincorporation_plot.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Length_plot.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Runtime_log.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_correct_prob.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_hist.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_iter_summ_stat.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_post_pred.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_trace.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/dnacomp.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/dnacomp_genome.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/lgdistribution.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/misincorporation.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/3pGtoA_freq.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/5pCtoT_freq.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Fragmisincorporation_plot.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Length_plot.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Runtime_log.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_correct_prob.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_hist.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_iter_summ_stat.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_post_pred.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_trace.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/dnacomp.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/dnacomp_genome.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/lgdistribution.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/misincorporation.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/3pGtoA_freq.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/5pCtoT_freq.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Fragmisincorporation_plot.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Length_plot.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Runtime_log.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_correct_prob.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_hist.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_iter_summ_stat.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_post_pred.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_trace.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/dnacomp.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/dnacomp_genome.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/lgdistribution.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/misincorporation.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/3pGtoA_freq.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/5pCtoT_freq.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Fragmisincorporation_plot.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Length_plot.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Runtime_log.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_correct_prob.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_hist.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_iter_summ_stat.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_post_pred.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_trace.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/dnacomp.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/dnacomp_genome.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/lgdistribution.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/misincorporation.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/3pGtoA_freq.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/5pCtoT_freq.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Fragmisincorporation_plot.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Length_plot.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Runtime_log.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_correct_prob.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_hist.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_iter_summ_stat.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_post_pred.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_trace.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/dnacomp.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/dnacomp_genome.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/lgdistribution.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/misincorporation.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/3pGtoA_freq.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/5pCtoT_freq.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Fragmisincorporation_plot.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Length_plot.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Runtime_log.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_correct_prob.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_hist.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_iter_summ_stat.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_post_pred.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_trace.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/dnacomp.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/dnacomp_genome.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/lgdistribution.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/misincorporation.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/3pGtoA_freq.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/5pCtoT_freq.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Fragmisincorporation_plot.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Length_plot.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Runtime_log.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_correct_prob.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_hist.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_iter_summ_stat.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_post_pred.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_trace.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/dnacomp.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/dnacomp_genome.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/lgdistribution.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/misincorporation.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/3pGtoA_freq.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/5pCtoT_freq.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Fragmisincorporation_plot.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Length_plot.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Runtime_log.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_correct_prob.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_hist.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_iter_summ_stat.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_post_pred.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_trace.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/dnacomp.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/dnacomp_genome.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/lgdistribution.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/misincorporation.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/3pGtoA_freq.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/5pCtoT_freq.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Fragmisincorporation_plot.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Length_plot.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Runtime_log.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_correct_prob.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_hist.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_iter_summ_stat.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_post_pred.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_trace.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/dnacomp.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/dnacomp_genome.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/lgdistribution.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/misincorporation.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/3pGtoA_freq.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/5pCtoT_freq.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Fragmisincorporation_plot.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Length_plot.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Runtime_log.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_correct_prob.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_hist.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_iter_summ_stat.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_post_pred.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_trace.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/dnacomp.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/dnacomp_genome.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/lgdistribution.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/misincorporation.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling copying paleomix/resources/examples/nature_protocols/example_results/profiling/M.0182896.NO.UDG.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling copying paleomix/resources/examples/nature_protocols/example_results/profiling/M.0182896.UDG.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling copying paleomix/resources/examples/nature_protocols/example_results/profiling/M.0182896.UDGa.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling copying paleomix/resources/examples/nature_protocols/example_results/profiling/M.0182896.UDGb.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling copying paleomix/resources/examples/nature_protocols/example_results/profiling/M.0182896.UDGc.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling copying paleomix/resources/examples/nature_protocols/example_results/profiling/Pi1845A.id.CGCTAT.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling copying paleomix/resources/examples/nature_protocols/example_results/profiling/Pi1889.id.CTTGTA.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling copying paleomix/resources/examples/nature_protocols/example_results/profiling/Pi1889.id.GGCTAC.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling copying paleomix/resources/examples/nature_protocols/example_results/profiling/Pi1889.id.TAGCTT.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Figure_Krona_M.0182896.all.html -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Figure_Krona_Pi1845A.all.html -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Figure_Krona_Pi1889.all.html -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Krona_M.0182896.all.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Krona_Pi1845A.all.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Krona_Pi1845A.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Krona_Pi1889.all.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying paleomix/resources/examples/nature_protocols/example_results/profiling/krona/M.0182896.all.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Pi1889.all.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying paleomix/resources/examples/nature_protocols/example_results/profiling/results/Barplot_class.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying paleomix/resources/examples/nature_protocols/example_results/profiling/results/Clustering_genus.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying paleomix/resources/examples/nature_protocols/example_results/profiling/results/Distances_genus.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying paleomix/resources/examples/nature_protocols/example_results/profiling/results/Diversity_genus.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying paleomix/resources/examples/nature_protocols/example_results/profiling/results/Heatmap_genus.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying paleomix/resources/examples/nature_protocols/example_results/profiling/results/PCA_genus.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying paleomix/resources/examples/nature_protocols/example_results/profiling/results/PCOA_genus.pdf -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying paleomix/resources/examples/nature_protocols/example_results/profiling/results/Potato_merged.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying paleomix/resources/examples/nature_protocols/example_results/profiling/results/Potato_merged_profiles.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying paleomix/resources/examples/nature_protocols/example_results/profiling/results/Relative_abundances_genus.csv -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying paleomix/resources/examples/nature_protocols/example_results/profiling/results/Taxon_count_genus.txt -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/phylogeny copying paleomix/resources/examples/nature_protocols/phylogeny/000_makefile.yaml -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/phylogeny copying paleomix/resources/examples/nature_protocols/phylogeny/select_highly_covered_genes.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/phylogeny copying paleomix/resources/examples/nature_protocols/phylogeny/summarize_heterozygosity.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/phylogeny creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/profiling copying paleomix/resources/examples/nature_protocols/profiling/build_all_profiles.sh -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/profiling copying paleomix/resources/examples/nature_protocols/profiling/build_profile.sh -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/profiling copying paleomix/resources/examples/nature_protocols/profiling/metagenomic_profile.R -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/profiling creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline copying paleomix/resources/examples/phylo_pipeline/setup.sh -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline copying paleomix/resources/examples/phylo_pipeline/synthesize_reads.py -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment copying paleomix/resources/examples/phylo_pipeline/alignment/000_makefile.yaml -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment copying paleomix/resources/examples/phylo_pipeline/alignment/setup.sh -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/bonobo.fasta -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/chimpanzee.fasta -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/gorilla.fasta -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/rCRS.fasta -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/rCRS.fasta.fai -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/sumatran_orangutan.fasta -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/white_handed_gibbon.fasta -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/phylogeny copying paleomix/resources/examples/phylo_pipeline/phylogeny/000_makefile.yaml -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/phylogeny creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.non_coding.bed -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.protein_coding.CDS.bed -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/reports creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/reports/zonkey copying paleomix/resources/reports/zonkey/report.css -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/reports/zonkey creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/common copying paleomix/resources/rscripts/common/requires.r -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/common creating /<>/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/admixture.r -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/coverage.r -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/pca.r -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/tinytree.r -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/treemix.r -> /<>/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/zonkey copying paleomix/yaml/CHANGES -> /<>/.pybuild/cpython2_2.7/build/paleomix/yaml copying paleomix/yaml/LICENSE -> /<>/.pybuild/cpython2_2.7/build/paleomix/yaml copying paleomix/yaml/PKG-INFO -> /<>/.pybuild/cpython2_2.7/build/paleomix/yaml copying paleomix/yaml/README -> /<>/.pybuild/cpython2_2.7/build/paleomix/yaml debian/rules override_dh_auto_test make[1]: Entering directory '/<>' # apply fix that seems to be needed due to improperly set # time zone in pbuilder sed -i~ 's/"MTime": "2005-07-07 08:50:00"/"MTime": "2005-07-07 06:50:00"/' tests/common_tests/makefile_test.py PATH=/<>/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games dh_auto_test I: pybuild base:217: cd /<>/.pybuild/cpython2_2.7/build; python2.7 -m nose -v --exclude='(test_requirementobj__version__command_not_executable)' atomiccmd_test.builder_test.test_builder__simple__call ... ok atomiccmd_test.builder_test.test_builder__simple__str ... ok atomiccmd_test.builder_test.test_builder__simple__iterable ... ok atomiccmd_test.builder_test.test_builder__complex ... ok atomiccmd_test.builder_test.test_builder__kwargs__empty ... ok atomiccmd_test.builder_test.test_builder__kwargs ... ok atomiccmd_test.builder_test.test_builder__kwargs__set_cwd ... ok atomiccmd_test.builder_test.test_builder__set_option ... ok atomiccmd_test.builder_test.test_builder__set_option__overwrite ... ok atomiccmd_test.builder_test.test_builder__set_option__overwrite_fixed ... ok atomiccmd_test.builder_test.test_builder__add_option ... ok atomiccmd_test.builder_test.test_builder__add_option__overwrite ... ok atomiccmd_test.builder_test.test_builder__add_or_set_option__without_value(,) ... ok atomiccmd_test.builder_test.test_builder__add_or_set_option__without_value(,) ... ok atomiccmd_test.builder_test.test_builder__add_or_set_option__with_sep(,) ... ok atomiccmd_test.builder_test.test_builder__add_or_set_option__with_sep(,) ... ok atomiccmd_test.builder_test.test_builder__add_or_set_option__with_non_str_value(,) ... ok atomiccmd_test.builder_test.test_builder__add_or_set_option__with_non_str_value(,) ... ok atomiccmd_test.builder_test.test_builder__add_or_set_option__add_and_set(, ) ... ok atomiccmd_test.builder_test.test_builder__add_or_set_option__add_and_set(, ) ... ok atomiccmd_test.builder_test.test_builder__add_or_set_option__with_non_str_key(,) ... ok atomiccmd_test.builder_test.test_builder__add_or_set_option__with_non_str_key(,) ... ok atomiccmd_test.builder_test.test_builder__add_or_set_option__after_finalize(,) ... ok atomiccmd_test.builder_test.test_builder__add_or_set_option__after_finalize(,) ... ok atomiccmd_test.builder_test.test_builder__add_or_set_option__empty_key(,) ... ok atomiccmd_test.builder_test.test_builder__add_or_set_option__empty_key(,) ... ok atomiccmd_test.builder_test.test_builder__pop_option(,) ... ok atomiccmd_test.builder_test.test_builder__pop_option(,) ... ok atomiccmd_test.builder_test.test_builder__pop_option__last_option ... ok atomiccmd_test.builder_test.test_builder__pop_option__different_options(,) ... ok atomiccmd_test.builder_test.test_builder__pop_option__different_options(,) ... ok atomiccmd_test.builder_test.test_builder__pop_option__is_fixed(,) ... ok atomiccmd_test.builder_test.test_builder__pop_option__is_fixed(,) ... ok atomiccmd_test.builder_test.test_builder__pop_option__empty ... ok atomiccmd_test.builder_test.test_builder__pop_option__missing_key ... ok atomiccmd_test.builder_test.test_builder__pop_option__with_non_str_key ... ok atomiccmd_test.builder_test.test_builder__pop_option__with_empty_key ... ok atomiccmd_test.builder_test.test_builder__add_value ... ok atomiccmd_test.builder_test.test_builder__add_value__two_values ... ok atomiccmd_test.builder_test.test_builder__set_kwargs__called_once ... ok atomiccmd_test.builder_test.test_builder__set_kwargs__called_twice ... ok atomiccmd_test.builder_test.test_builder__set_kwargs__atomiccmdbuilder ... ok atomiccmd_test.builder_test.test_builder__set_kwargs__after_finalize ... ok atomiccmd_test.builder_test.test_builder__set__kwargs__overwriting ... ok atomiccmd_test.builder_test.test_builder__finalized_call__simple_command ... ok atomiccmd_test.builder_test.test_builder__finalized_call__kwargs_are_instantiated ... ok atomiccmd_test.builder_test.test_builder__finalized_call__kwargs_are_instantiated__with_temp_dir ... ok atomiccmd_test.builder_test.test_builder__finalized_call__kwargs_are_instantiated__with_non_str_arg ... ok atomiccmd_test.builder_test.test_builder__finalize__returns_singleton ... ok atomiccmd_test.builder_test.test_builder__finalize__calls_atomiccmd ... ok atomiccmd_test.builder_test.test_builder__add_multiple_options ... ok atomiccmd_test.builder_test.test_builder__add_multiple_options_with_sep ... ok atomiccmd_test.builder_test.test_builder__add_multiple_options_with_template ... ok atomiccmd_test.builder_test.test_builder__add_multiple_options_multiple_times ... ok atomiccmd_test.builder_test.test_builder__add_multiple_values ... ok atomiccmd_test.builder_test.test_builder__add_multiple_values_with_template ... ok atomiccmd_test.builder_test.test_builder__add_multiple_values_multiple_times ... ok atomiccmd_test.builder_test.test_builder__add_multiple_kwargs ... ok atomiccmd_test.builder_test.test_builder__add_multiple_kwargs_with_template ... ok atomiccmd_test.builder_test.test_builder__add_multiple_kwargs_multiple_times ... ok atomiccmd_test.builder_test.test_java_builder__default__no_config ... ok atomiccmd_test.builder_test.test_java_builder__defaults__call ... ok atomiccmd_test.builder_test.test_java_builder__defaults__kwargs ... ok atomiccmd_test.builder_test.test_java_builder__multithreaded_gc ... ok atomiccmd_test.builder_test.test_java_builder__multithreaded_gc__zero_or_negative_threads ... ok atomiccmd_test.builder_test.test_java_builder__multithreaded_gc__non_int_threads ... ok atomiccmd_test.builder_test.test_java_builder__kwargs ... ok atomiccmd_test.builder_test.test_mpi_builder__defaults__str ... ok atomiccmd_test.builder_test.test_mpi_builder__multithreaded__str ... ok atomiccmd_test.builder_test.test_mpi_builder__defaults__complex_cmd ... ok atomiccmd_test.builder_test.test_mpi_builder__multithreaded__complex_cmd ... ok atomiccmd_test.builder_test.test_mpi_builder__kwargs ... ok atomiccmd_test.builder_test.test_mpi_builder__threads__zero_or_negative ... ok atomiccmd_test.builder_test.test_mpi_builder__threads__non_int ... ok atomiccmd_test.builder_test.test_custom_cli__single_named_arg ... ok atomiccmd_test.builder_test.test_custom_cli__adding_new_values ... ok atomiccmd_test.builder_test.test_custom_cli__multiple_named_args ... ok atomiccmd_test.builder_test.test_custom_cli__only_customize_is_valid_function_name ... ok atomiccmd_test.builder_test.test_apply_options__single_option__default_pred__set_when_pred_is_true ... ok atomiccmd_test.builder_test.test_apply_options__single_option__default_pred__ignore_false_pred ... ok atomiccmd_test.builder_test.test_apply_options__single_option__user_pred__set_when_pred_is_true ... ok atomiccmd_test.builder_test.test_apply_options__single_option__user_pred__ignore_when_pred_is_false ... ok atomiccmd_test.builder_test.test_apply_options__single_option__boolean__set_when_value_is_true ... ok atomiccmd_test.builder_test.test_apply_options__single_option__boolean__set_when_value_is_none ... ok atomiccmd_test.builder_test.test_apply_options__single_option__boolean__pop_when_value_is_false ... ok atomiccmd_test.builder_test.test_apply_options__single_option__boolean__pop_missing_throws ... ok atomiccmd_test.builder_test.test_apply_options__multiple_option ... ok atomiccmd_test.builder_test.test_apply_options__boolean_and_none_is_single_value_only ... ok atomiccmd_test.builder_test.test_apply_options__unexpected_types_in_values ... ok atomiccmd_test.builder_test.test_apply_options__non_string_types_in_keys ... ok atomiccmd_test.builder_test.test_apply_options__not_dict_like ... ok atomiccmd_test.command_test.test_file ... ok atomiccmd_test.command_test.test_atomiccmd__commit_before_join__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__commit_failure_cleanup__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__commit_missing_files__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__commit_simple__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__commit_temp_folder__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__commit_temp_only__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__commit_temp_out__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__commit_while_running__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__commit_with_pipes__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__commit_wrong_temp_folder__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__paths__key__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__paths_non_str__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__pipes_stdin__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__pipes_stdin__dev_null_explicit__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__pipes_stdin__dev_null_implicit_1__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__pipes_stdin__dev_null_implicit_2__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__pipes_stdin__temp_file__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__piping__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__piping_is_only_allowed_once__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__piping_temp__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__ready__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__run__already_running__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__run__exception_on_missing_command__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__run__exception_on_missing_command__no_wrap__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__run__invalid_temp__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__terminate_after_join__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__terminate_race_condition__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__terminate_sigkill__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__terminate_sigterm__wrapped_by_with_temp_folder ... ok atomiccmd_test.command_test.test_atomiccmd__command_str ... ok atomiccmd_test.command_test.test_atomiccmd__executables_empty_str ... ok atomiccmd_test.command_test.test_atomiccmd__command_tuple ... ok atomiccmd_test.command_test.test_atomiccmd__executables_empty_tuple ... ok atomiccmd_test.command_test.test_atomiccmd__executables_empty_str_in_tuple ... ok atomiccmd_test.command_test.test_atomiccmd__set_cwd(False,) ... ok atomiccmd_test.command_test.test_atomiccmd__set_cwd(True,) ... ok atomiccmd_test.command_test.test_atomiccmd__set_cwd__temp_in_out(True, {'TEMP_IN_FOO': 'test_file'}) ... ok atomiccmd_test.command_test.test_atomiccmd__set_cwd__temp_in_out(False, {'TEMP_IN_FOO': 'test_file'}) ... ok atomiccmd_test.command_test.test_atomiccmd__set_cwd__temp_in_out(True, {'TEMP_OUT_FOO': 'test_file'}) ... ok atomiccmd_test.command_test.test_atomiccmd__set_cwd__temp_in_out(False, {'TEMP_OUT_FOO': 'test_file'}) ... ok atomiccmd_test.command_test.test_atomiccmd__paths ... ok atomiccmd_test.command_test.test_atomiccmd__paths_optional ... ok atomiccmd_test.command_test.test_atomiccmd__pipes_out('pipe_bash_{0}.stdout', 'pipe_bash_{0}.stderr', {}) ... ok atomiccmd_test.command_test.test_atomiccmd__pipes_out('pipe_bash_{0}.stdout', 'stderr.txt', {'OUT_STDERR': 'stderr.txt'}) ... ok atomiccmd_test.command_test.test_atomiccmd__pipes_out('stdout.txt', 'pipe_bash_{0}.stderr', {'OUT_STDOUT': 'stdout.txt'}) ... ok atomiccmd_test.command_test.test_atomiccmd__pipes_out('stdout.txt', 'stderr.txt', {'OUT_STDERR': 'stderr.txt', 'OUT_STDOUT': 'stdout.txt'}) ... ok atomiccmd_test.command_test.test_atomiccmd__pipes_out(None, None, {'OUT_STDERR': , 'OUT_STDOUT': }) ... ok atomiccmd_test.command_test.test_atomiccmd__pipes_out(None, 'pipe_bash_{0}.stderr', {'OUT_STDOUT': }) ... ok atomiccmd_test.command_test.test_atomiccmd__pipes_out('pipe_bash_{0}.stdout', None, {'OUT_STDERR': }) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__malformed_keys({'IN': '/var/foo'},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__malformed_keys({'IN_': '/var/foo'},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__malformed_keys({'TEMP_OUT': '/var/foo'},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__malformed_keys({'TEMP_OUT_': '/var/foo'},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__malformed_keys({'TEMP_OUX_FOO': 'foo'},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__malformed_keys({'INS_BAR': 'foo'},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__invalid_values({'IN_FILE': 1},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__invalid_values({'TEMP_IN_FILE': set([])},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__invalid_values({'OUT_FILE': [1, 2, 3]},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__invalid_values({'TEMP_OUT_FILE': 1.0},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__invalid_values({'IN_STDIN': {}},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__invalid_values({'TEMP_IN_STDIN': frozenset([])},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__invalid_values({'OUT_STDOUT': 1.7},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__invalid_values({'TEMP_OUT_STDOUT': ()},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__invalid_values({'OUT_STDERR': xrange(3)},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__invalid_values({'TEMP_OUT_STDERR': -1},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__invalid_temp_paths({'TEMP_IN_FOO': 'sub/infile'},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__invalid_temp_paths({'TEMP_IN_STDIN': 'sub/stdin'},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__invalid_temp_paths({'TEMP_OUT_FOO': 'sub/outfile'},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__invalid_temp_paths({'TEMP_OUT_STDOUT': 'sub/stdout'},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__invalid_temp_paths({'TEMP_OUT_STDERR': 'sub/stderr'},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__invalid_temp_paths({'TEMP_IN_FOO': '/tmp/sub/infile'},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__invalid_temp_paths({'TEMP_IN_STDIN': '/dev/sub/stdin'},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__invalid_temp_paths({'TEMP_OUT_FOO': '/etc/sub/outfile'},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__invalid_temp_paths({'TEMP_OUT_STDOUT': '/var/sub/stdout'},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__invalid_temp_paths({'TEMP_OUT_STDERR': '/home/sub/stderr'},) ... ok atomiccmd_test.command_test.test_atomiccmd__paths__overlapping_output('OUT_FILE_1', '/foo/bar/outfile', 'OUT_FILE_2', '/var/outfile') ... ok atomiccmd_test.command_test.test_atomiccmd__paths__overlapping_output('TEMP_OUT_FILE_1', 'outfile', 'OUT_FILE_1', '/var/outfile') ... ok atomiccmd_test.command_test.test_atomiccmd__paths__overlapping_output('OUT_FILE_1', '/foo/bar/outfile', 'TEMP_OUT_FILE_1', 'outfile') ... ok atomiccmd_test.command_test.test_atomiccmd__paths__overlapping_output('TEMP_OUT_FILE_1', 'outfile', 'TEMP_OUT_FILE_2', 'outfile') ... ok atomiccmd_test.command_test.test_atomiccmd__paths__overlapping_output('OUT_FILE_1', '/foo/bar/outfile', 'OUT_STDOUT', '/var/outfile') ... ok atomiccmd_test.command_test.test_atomiccmd__paths__overlapping_output('TEMP_OUT_FILE_1', 'outfile', 'OUT_STDOUT', '/var/outfile') ... ok atomiccmd_test.command_test.test_atomiccmd__paths__overlapping_output('OUT_FILE_1', '/foo/bar/outfile', 'TEMP_OUT_STDOUT', 'outfile') ... ok atomiccmd_test.command_test.test_atomiccmd__paths__overlapping_output('TEMP_OUT_FILE_1', 'outfile', 'TEMP_OUT_STDOUT', 'outfile') ... ok atomiccmd_test.command_test.test_atomiccmd__paths__overlapping_output('OUT_FILE_1', '/foo/bar/outfile', 'OUT_STDERR', '/var/outfile') ... ok atomiccmd_test.command_test.test_atomiccmd__paths__overlapping_output('TEMP_OUT_FILE_1', 'outfile', 'OUT_STDERR', '/var/outfile') ... ok atomiccmd_test.command_test.test_atomiccmd__paths__overlapping_output('OUT_FILE_1', '/foo/bar/outfile', 'TEMP_OUT_STDERR', 'outfile') ... ok atomiccmd_test.command_test.test_atomiccmd__paths__overlapping_output('TEMP_OUT_FILE_1', 'outfile', 'TEMP_OUT_STDERR', 'outfile') ... ok atomiccmd_test.command_test.test_atomiccmd__pipes__duplicates('IN_STDIN',) ... ok atomiccmd_test.command_test.test_atomiccmd__pipes__duplicates('OUT_STDOUT',) ... ok atomiccmd_test.command_test.test_atomiccmd__pipes__duplicates('OUT_STDERR',) ... ok atomiccmd_test.command_test.test_atomicmcd__exec__reqobj ... ok atomiccmd_test.command_test.test_atomiccmd__checks__non_callable ... ok atomiccmd_test.command_test.test_atomiccmd__exec__invalid(,) ... ok atomiccmd_test.command_test.test_atomiccmd__exec__invalid({},) ... ok atomiccmd_test.command_test.test_atomiccmd__exec__invalid(1,) ... ok atomiccmd_test.command_test.test_atomiccmd__aux__invalid(,) ... ok atomiccmd_test.command_test.test_atomiccmd__aux__invalid({},) ... ok atomiccmd_test.command_test.test_atomiccmd__aux__invalid(1,) ... ok atomiccmd_test.command_test.test_atomiccmd__paths_missing ... ok atomiccmd_test.command_test.test_atomiccmd__paths_invalid ... ok atomiccmd_test.command_test.test_atomiccmd__piping__wrong_pipe('IN_STDIN',) ... ok atomiccmd_test.command_test.test_atomiccmd__piping__wrong_pipe('TEMP_IN_STDIN',) ... ok atomiccmd_test.command_test.test_atomiccmd__piping__wrong_pipe('OUT_STDERR',) ... ok atomiccmd_test.command_test.test_atomiccmd__piping__wrong_pipe('TEMP_OUT_STDERR',) ... ok atomiccmd_test.command_test.test_atomiccmd__join_wait(, 'true', [None], [0]) ... ok atomiccmd_test.command_test.test_atomiccmd__join_wait(, 'false', [None], [1]) ... ok atomiccmd_test.command_test.test_atomiccmd__join_wait(, 'true', None, 0) ... ok atomiccmd_test.command_test.test_atomiccmd__join_wait(, 'false', None, 1) ... ok atomiccmd_test.command_test.test_atomiccmd__terminate(False,) ... ok atomiccmd_test.command_test.test_atomiccmd__terminate(True,) ... ok atomiccmd_test.command_test.test_atomiccmd__commit_before_run ... ok atomiccmd_test.command_test.test_atomiccmd__str__ ... ok atomiccmd_test.command_test.test_atomiccmd__cleanup_proc(,) ... ok atomiccmd_test.command_test.test_atomiccmd__cleanup_proc( at 0x7f920a1bf1b8>,) ... ok atomiccmd_test.command_test.test_atomiccmd__cleanup_sigterm(0,) ... ok atomiccmd_test.command_test.test_atomiccmd__cleanup_sigterm(1,) ... ok atomiccmd_test.command_test.test_atomiccmd__cleanup_sigterm(2,) ... ok atomiccmd_test.command_test.test_atomiccmd__cleanup_sigterm__dead_weakrefs ... ok atomiccmd_test.pprint_test.test_pformat__simple ... ok atomiccmd_test.pprint_test.test_pformat__simple__done__wrapped_by_with_temp_folder ... ok atomiccmd_test.pprint_test.test_pformat__simple__done__before_join__wrapped_by_with_temp_folder ... ok atomiccmd_test.pprint_test.test_pformat__simple__done__set_cwd__wrapped_by_with_temp_folder ... ok atomiccmd_test.pprint_test.test_pformat__simple__killed_by_signal__wrapped_by_with_temp_folder ... ok atomiccmd_test.pprint_test.test_pformat__simple__running__wrapped_by_with_temp_folder ... ok atomiccmd_test.pprint_test.test_pformat__simple__running__set_cwd__wrapped_by_with_temp_folder ... ok atomiccmd_test.pprint_test.test_pformat__simple__temp_root_in_arguments__wrapped_by_with_temp_folder ... ok atomiccmd_test.pprint_test.test_pformat__simple__terminated_by_pipeline__wrapped_by_with_temp_folder ... ok atomiccmd_test.pprint_test.test_pformat__atomiccmd__simple_with_infile ... ok atomiccmd_test.pprint_test.test_pformat__atomiccmd__simple_with_infile__set_cwd ... ok atomiccmd_test.pprint_test.test_pformat__atomiccmd__simple_with_temp_infile ... ok atomiccmd_test.pprint_test.test_pformat__atomiccmd__simple_with_temp_infile__set_cwd ... ok atomiccmd_test.pprint_test.test_pformat__atomiccmd__simple_with_outfile ... ok atomiccmd_test.pprint_test.test_pformat__atomiccmd__simple_with_outfile__set_cwd ... ok atomiccmd_test.pprint_test.test_pformat__atomiccmd__simple_with_temp_outfile ... ok atomiccmd_test.pprint_test.test_pformat__atomiccmd__simple_with_temp_outfile__set_cwd ... ok atomiccmd_test.pprint_test.test_pformat__atomiccmd__simple_with_stdin ... ok atomiccmd_test.pprint_test.test_pformat__atomiccmd__simple_with_stdin__set_cwd ... ok atomiccmd_test.pprint_test.test_pformat__atomiccmd__simple_with_temp_stdin ... ok atomiccmd_test.pprint_test.test_pformat__atomiccmd__simple_with_temp_stdin__set_cwd ... ok atomiccmd_test.pprint_test.test_pformat__atomiccmd__simple_with_stdin__cmd ... ok atomiccmd_test.pprint_test.test_pformat__atomiccmd__simple_with_stdout ... ok atomiccmd_test.pprint_test.test_pformat__atomiccmd__simple_with_stdout__set_cwd ... ok atomiccmd_test.pprint_test.test_pformat__atomiccmd__simple_with_temp_stdout ... ok atomiccmd_test.pprint_test.test_pformat__atomiccmd__simple_with_temp_stdout__set_cwd ... ok atomiccmd_test.pprint_test.test_pformat__atomiccmd__simple_with_stdout_pipe ... ok atomiccmd_test.pprint_test.test_pformat__sets__simple(, 'Parallel processes') ... ok atomiccmd_test.pprint_test.test_pformat__sets__simple(, 'Sequential processes') ... ok atomiccmd_test.pprint_test.test_pformat__sets__nested ... ok atomiccmd_test.pprint_test.test_pformat__bad_input(1,) ... ok atomiccmd_test.pprint_test.test_pformat__bad_input({},) ... ok atomiccmd_test.pprint_test.test_pformat__bad_input('',) ... ok atomiccmd_test.pprint_test.test_pformat_list__empty ... ok atomiccmd_test.pprint_test.test_pformat_list__single ... ok atomiccmd_test.pprint_test.test_pformat_list__multiple ... ok atomiccmd_test.pprint_test.test_pformat_list__wrapped ... ok atomiccmd_test.pprint_test.test_pformat_list__escaped ... ok atomiccmd_test.sets_test.test_atomicsets__properties(,) ... ok atomiccmd_test.sets_test.test_atomicsets__properties(,) ... ok atomiccmd_test.sets_test.test_parallel_commands__join_after_run__wrapped_by_with_temp_folder ... ok atomiccmd_test.sets_test.test_parallel_commands__join_failure_1__wrapped_by_with_temp_folder ... ok atomiccmd_test.sets_test.test_parallel_commands__join_failure_2__wrapped_by_with_temp_folder ... ok atomiccmd_test.sets_test.test_parallel_commands__join_failure_3__wrapped_by_with_temp_folder ... ok atomiccmd_test.sets_test.test_sequential_commands__abort_on_error_1__wrapped_by_with_temp_folder ... ok atomiccmd_test.sets_test.test_sequential_commands__abort_on_error_2__wrapped_by_with_temp_folder ... ok atomiccmd_test.sets_test.test_sequential_commands__abort_on_error_3__wrapped_by_with_temp_folder ... ok atomiccmd_test.sets_test.test_atomicsets__no_clobbering(, {'OUT_A': '/foo/out.txt'}, {'OUT_B': '/bar/out.txt'}) ... ok atomiccmd_test.sets_test.test_atomicsets__no_clobbering(, {'OUT_A': '/foo/out.txt'}, {'TEMP_OUT_B': 'out.txt'}) ... ok atomiccmd_test.sets_test.test_atomicsets__no_clobbering(, {'OUT_A': '/foo/out.txt'}, {'OUT_STDOUT': '/bar/out.txt'}) ... ok atomiccmd_test.sets_test.test_atomicsets__no_clobbering(, {'OUT_A': '/foo/out.txt'}, {'TEMP_OUT_STDOUT': 'out.txt'}) ... ok atomiccmd_test.sets_test.test_atomicsets__no_clobbering(, {'OUT_A': '/foo/out.txt'}, {'OUT_STDERR': '/bar/out.txt'}) ... ok atomiccmd_test.sets_test.test_atomicsets__no_clobbering(, {'OUT_A': '/foo/out.txt'}, {'TEMP_OUT_STDERR': 'out.txt'}) ... ok atomiccmd_test.sets_test.test_atomicsets__no_clobbering(, {'OUT_A': '/foo/out.txt'}, {'OUT_B': '/bar/out.txt'}) ... ok atomiccmd_test.sets_test.test_atomicsets__no_clobbering(, {'OUT_A': '/foo/out.txt'}, {'TEMP_OUT_B': 'out.txt'}) ... ok atomiccmd_test.sets_test.test_atomicsets__no_clobbering(, {'OUT_A': '/foo/out.txt'}, {'OUT_STDOUT': '/bar/out.txt'}) ... ok atomiccmd_test.sets_test.test_atomicsets__no_clobbering(, {'OUT_A': '/foo/out.txt'}, {'TEMP_OUT_STDOUT': 'out.txt'}) ... ok atomiccmd_test.sets_test.test_atomicsets__no_clobbering(, {'OUT_A': '/foo/out.txt'}, {'OUT_STDERR': '/bar/out.txt'}) ... ok atomiccmd_test.sets_test.test_atomicsets__no_clobbering(, {'OUT_A': '/foo/out.txt'}, {'TEMP_OUT_STDERR': 'out.txt'}) ... ok atomiccmd_test.sets_test.test_atomicsets__commit(,) ... ok atomiccmd_test.sets_test.test_atomicsets__commit(,) ... ok atomiccmd_test.sets_test.test_atomicsets__stdout(,) ... ok atomiccmd_test.sets_test.test_atomicsets__stdout(,) ... ok atomiccmd_test.sets_test.test_atomicsets__terminate(,) ... ok atomiccmd_test.sets_test.test_atomicsets__terminate(,) ... ok atomiccmd_test.sets_test.test_atomicsets__str__(,) ... ok atomiccmd_test.sets_test.test_atomicsets__str__(,) ... ok atomiccmd_test.sets_test.test_atomicsets__duplicate_cmds(,) ... ok atomiccmd_test.sets_test.test_atomicsets__duplicate_cmds(,) ... ok atomiccmd_test.sets_test.test_parallel_commands__run ... ok atomiccmd_test.sets_test.test_parallel_commands__ready_single(True,) ... ok atomiccmd_test.sets_test.test_parallel_commands__ready_single(False,) ... ok atomiccmd_test.sets_test.test_parallel_commands__ready_two(True, True, True) ... ok atomiccmd_test.sets_test.test_parallel_commands__ready_two(False, True, False) ... ok atomiccmd_test.sets_test.test_parallel_commands__ready_two(True, False, False) ... ok atomiccmd_test.sets_test.test_parallel_commands__ready_two(False, False, False) ... ok atomiccmd_test.sets_test.test_parallel_commands__join_before_run ... ok atomiccmd_test.sets_test.test_parallel_commands__reject_sequential ... ok atomiccmd_test.sets_test.test_parallel_commands__accept_parallel ... ok atomiccmd_test.sets_test.test_parallel_commands__reject_noncommand ... ok atomiccmd_test.sets_test.test_parallel_commands__reject_empty_commandset ... ok atomiccmd_test.sets_test.test_sequential_commands__atomiccmds ... ok atomiccmd_test.sets_test.test_sequential_commands__accept_parallel ... ok atomiccmd_test.sets_test.test_sequential_commands__accept_sequential ... ok atomiccmd_test.sets_test.test_sequential_commands__reject_noncommand ... ok atomiccmd_test.sets_test.test_sequential_commands__reject_empty_commandset ... ok common_tests.bedtools_tests.test_bedrecord__constructor__defaults ... ok common_tests.bedtools_tests.test_bedrecord__constructor__empty_string ... ok common_tests.bedtools_tests.test_bedrecord__constructor__3_fields ... ok common_tests.bedtools_tests.test_bedrecord__constructor__6_fields ... ok common_tests.bedtools_tests.test_bedrecord__constructor__extra_fields ... ok common_tests.bedtools_tests.test_bedrecord__accessors__3_fields ... ok common_tests.bedtools_tests.test_bedrecord__accessors__6_fields ... ok common_tests.bedtools_tests.test_bedrecord__accessors__extra_fields ... ok common_tests.bedtools_tests.test_bedrecord__accessors__6_fields__getitem ... ok common_tests.bedtools_tests.test_bedrecord__setters__3_fields ... ok common_tests.bedtools_tests.test_bedrecord__setters__type_errors ... ok common_tests.bedtools_tests.test_bedrecord__setters__unset_fields__at_end ... ok common_tests.bedtools_tests.test_bedrecord__setters__unset_fields__after_end ... ok common_tests.bedtools_tests.test_bedrecord__cmp ... ok common_tests.bedtools_tests.test_bedrecord__copy ... ok common_tests.bedtools_tests.test_bedrecord__deepcopy ... ok common_tests.fileutils_test.test_copy_file__copy_to_different_folder__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_copy_file__copy_to_existing_folder__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_copy_file__copy_to_new_folder__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_copy_file__overwrite__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_copy_file__simple_copy__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_copy_file__simple_copy_in_cwd__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_create_temp_dir__create__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_create_temp_dir__creation_preempted__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_create_temp_dir__empty__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_create_temp_dir__permissions__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_make_dirs__create_dir__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_make_dirs__creation_preemted__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_make_dirs__permission_denied__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_make_dirs__permissions__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_make_dirs__return_values__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_make_dirs__sub_directories__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_make_dirs__subdirs_return_values__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_move_dirs__permission_denied__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_move_file__move_to_different_folder__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_move_file__move_to_existing_folder__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_move_file__move_to_new_folder__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_move_file__overwrite__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_move_file__simple_move__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_move_file__simple_move_in_cwd__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_try_remove__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_try_remove__missing__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_try_remove__non_file__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_try_rmdir__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_try_rmdir__missing__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_try_rmdir__non_file__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_try_rmtree__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_try_treedir__missing__wrapped_by_with_temp_folder ... ok common_tests.fileutils_test.test_dir ... ok common_tests.fileutils_test.test_file ... ok common_tests.fileutils_test.test_add_postfix__no_postfix ... ok common_tests.fileutils_test.test_add_postfix__dot_postfix ... ok common_tests.fileutils_test.test_add_postfix__underscore_postfix ... ok common_tests.fileutils_test.test_add_postfix__no_ext__no_postfix ... ok common_tests.fileutils_test.test_add_postfix__no_ext__dot_postfix ... ok common_tests.fileutils_test.test_add_postfix__no_ext__underscore_postfix ... ok common_tests.fileutils_test.test_swap_ext__has_ext_vs_empty_ext ... ok common_tests.fileutils_test.test_swap_ext__empty_ext_vs_empty_ext ... ok common_tests.fileutils_test.test_swap_ext__has_ext_vs_dot_ext ... ok common_tests.fileutils_test.test_swap_ext__dot_ext_vs_dot_ext ... ok common_tests.fileutils_test.test_swap_ext__multiple__has_ext_vs_empty_ext ... ok common_tests.fileutils_test.test_swap_ext__multiple__has_ext_vs_dot_ext ... ok common_tests.fileutils_test.test_swap_ext__multiple__dot_ext_vs_dot_ext ... ok common_tests.fileutils_test.test_swap_ext__has_ext_vs_new_ext ... ok common_tests.fileutils_test.test_swap_ext__has_ext_vs_new_dot_ext ... ok common_tests.fileutils_test.test_swap_ext__empty_ext_vs_new_ext ... ok common_tests.fileutils_test.test_swap_ext__dot_ext_vs_new_dot_ext ... ok common_tests.fileutils_test.test_reroot_path__empty_root ... ok common_tests.fileutils_test.test_reroot_path__empty_path ... ok common_tests.fileutils_test.test_reroot_path__abs_abs__wo_final_dash ... ok common_tests.fileutils_test.test_reroot_path__abs_abs__w_final_dash ... ok common_tests.fileutils_test.test_reroot_path__abs_rel__wo_final_dash ... ok common_tests.fileutils_test.test_reroot_path__abs_rel__w_final_dash ... ok common_tests.fileutils_test.test_reroot_path__rel_abs__wo_final_dash ... ok common_tests.fileutils_test.test_reroot_path__rel_abs__w_final_dash ... ok common_tests.fileutils_test.test_reroot_path__rel_rel__wo_final_dash ... ok common_tests.fileutils_test.test_reroot_path__rel_rel__w_final_dash ... ok common_tests.fileutils_test.test_create_temp_dir__permission_denied ... ok common_tests.fileutils_test.test_missing_files__file_exists ... ok common_tests.fileutils_test.test_missing_files__file_doesnt_exist ... ok common_tests.fileutils_test.test_missing_files__mixed_files ... ok common_tests.fileutils_test.test_modified_after__modified_after ... ok common_tests.fileutils_test.test_modified_after__not_modified_after ... ok common_tests.fileutils_test.test_modified_after__same_file ... ok common_tests.fileutils_test.test_is_executable__full_path__is_executable ... ok common_tests.fileutils_test.test_is_executable__full_path__is_non_executable ... ok common_tests.fileutils_test.test_is_executable__full_path__folder_is_non_executable ... ok common_tests.fileutils_test.test_is_executable__rel_path__is_executable ... ok common_tests.fileutils_test.test_is_executable__rel_path__is_non_executable ... ok common_tests.fileutils_test.test_which_executable__executable ... ok common_tests.fileutils_test.test_which_executable__non_executable ... ok common_tests.fileutils_test.test_which_executable__executable__but_no_path ... ok common_tests.fileutils_test.test_which_executable__executable__but_empty_path ... ok common_tests.fileutils_test.test_which_executable__executable__by_path_order_1 ... ok common_tests.fileutils_test.test_which_executable__executable__by_path_order_2 ... ok common_tests.fileutils_test.test_executable_exists__executable ... ok common_tests.fileutils_test.test_executable_exists__non_executable ... ok common_tests.fileutils_test.test_executable_exists__full_path__is_executable ... ok common_tests.fileutils_test.test_executable_exists__full_path__is_non_executable ... ok common_tests.fileutils_test.test_executable_exists__rel_path__is_executable ... ok common_tests.fileutils_test.test_executable_exists__rel_path__is_non_executable ... ok common_tests.fileutils_test.test_missing_executables__executable ... ok common_tests.fileutils_test.test_missing_executables__non_executable ... ok common_tests.fileutils_test.test_missing_executables__mixed ... ok common_tests.fileutils_test.test_make_dirs__empty_directory ... ok common_tests.fileutils_test.test_move_file__enoent_reraised_if_not_due_to_missing_folder ... ok common_tests.fileutils_test.test_copy_file__enoent_reraised_if_not_due_to_missing_folder ... ok common_tests.fileutils_test.test_open_ro__uncompressed ... ok common_tests.fileutils_test.test_open_ro__gz ... ok common_tests.fileutils_test.test_open_ro__bz2 ... ok common_tests.fileutils_test.test_open_ro__close_handle_on_error ... ok common_tests.fileutils_test.test_describe_files__no_files ... ok common_tests.fileutils_test.test_describe_files__single_file ... ok common_tests.fileutils_test.test_describe_files__same_path_abs__3_differences ... ok common_tests.fileutils_test.test_describe_files__same_path_abs__2_differences ... ok common_tests.fileutils_test.test_describe_files__same_path_abs__1_differences ... ok common_tests.fileutils_test.test_describe_files__different_paths_abs ... ok common_tests.fileutils_test.test_describe_files__same_path_rel ... ok common_tests.fileutils_test.test_describe_files__different_paths_rel ... ok common_tests.fileutils_test.test_describe_files__iterable ... ok common_tests.fileutils_test.test_describe_files__none_files ... ok common_tests.fileutils_test.test_describe_paired_files__single_file ... ok common_tests.fileutils_test.test_describe_paired_files__identical_files ... ok common_tests.fileutils_test.test_describe_paired_files__same_path__similar_files ... ok common_tests.fileutils_test.test_describe_paired_files__same_path__similar_files__different_prefixes ... ok common_tests.fileutils_test.test_describe_paired_files__same_path__similar_files__too_different ... ok common_tests.fileutils_test.test_describe_paired_files__same_path__different_files ... ok common_tests.fileutils_test.test_describe_paired_files__same_path__different_file_lens ... ok common_tests.fileutils_test.test_describe_paired_files__different_path_and_files ... ok common_tests.fileutils_test.test_describe_paired_files__files_1_longer ... ok common_tests.fileutils_test.test_describe_paired_files__files_2_longer ... ok common_tests.fileutils_test.test_describe_paired_files__none_files ... ok common_tests.fileutils_test.test_describe_paired_files__none_files_1 ... ok common_tests.fileutils_test.test_describe_paired_files__none_files_2 ... ok common_tests.formats_tests.fasta_test.test_dir ... ok common_tests.formats_tests.fasta_test.test_file ... ok common_tests.formats_tests.fasta_test.test_fasta__constructor__name ... ok common_tests.formats_tests.fasta_test.test_fasta__constructor__meta ... ok common_tests.formats_tests.fasta_test.test_fasta__constructor__sequence ... ok common_tests.formats_tests.fasta_test.test_fasta__constructor__name_must_be_non_empty ... ok common_tests.formats_tests.fasta_test.test_fasta__constructor__name_must_be_string_type ... ok common_tests.formats_tests.fasta_test.test_fasta__constructor__name_must_be_string_type_or_none ... ok common_tests.formats_tests.fasta_test.test_fasta__constructor__sequence_must_be_string_type ... ok common_tests.formats_tests.fasta_test.test_fasta__repr__partial_line_test ... ok common_tests.formats_tests.fasta_test.test_fasta__repr__complete_line_test ... ok common_tests.formats_tests.fasta_test.test_fasta__repr__multiple_lines ... ok common_tests.formats_tests.fasta_test.test_fasta__repr__partial_line_test_with_meta_information ... ok common_tests.formats_tests.fasta_test.test_fasta__write__partial_line ... ok common_tests.formats_tests.fasta_test.test_fasta__write__complete_line_test ... ok common_tests.formats_tests.fasta_test.test_fasta__write__multiple_lines ... ok common_tests.formats_tests.fasta_test.test_fasta__from_lines__no_records ... ok common_tests.formats_tests.fasta_test.test_fasta__from_lines_single_record ... ok common_tests.formats_tests.fasta_test.test_fasta__from_lines__multiple_records ... ok common_tests.formats_tests.fasta_test.test_fasta__from_lines__empty_record_name_only__nothing_else ... ok common_tests.formats_tests.fasta_test.test_fasta__from_lines__empty_record_name_only__first ... ok common_tests.formats_tests.fasta_test.test_fasta__from_lines__empty_record__middle ... ok common_tests.formats_tests.fasta_test.test_fasta__from_lines__empty_record_last ... ok common_tests.formats_tests.fasta_test.test_fasta__from_lines__missing_name__alone ... ok common_tests.formats_tests.fasta_test.test_fasta__from_lines__missing_name__with_others ... ok common_tests.formats_tests.fasta_test.test_fasta__from_lines__empty_name__alone ... ok common_tests.formats_tests.fasta_test.test_fasta__from_lines__empty_name__with_others ... ok common_tests.formats_tests.fasta_test.test_fasta__from_file__uncompressed ... ok common_tests.formats_tests.fasta_test.test_fasta__from_file__compressed_gz ... ok common_tests.formats_tests.fasta_test.test_fasta__from_file__compressed_bz2 ... ok common_tests.formats_tests.fasta_test.test_fasta__equality ... ok common_tests.formats_tests.fasta_test.test_fasta__inequality ... ok common_tests.formats_tests.fasta_test.test_fasta__sorting_less_equal ... ok common_tests.formats_tests.fasta_test.test_fasta__sorting_greater_equal ... ok common_tests.formats_tests.fasta_test.test_fasta__hash ... ok common_tests.formats_tests.fasta_test.test_fasta__unimplemented_comparison ... ok common_tests.formats_tests.msa_test.test_dir ... ok common_tests.formats_tests.msa_test.test_file ... ok common_tests.formats_tests.msa_test.test_msa_constructor__calls_validate ... ok common_tests.formats_tests.msa_test.test_msa_constructor__duplicate_names ... ok common_tests.formats_tests.msa_test.test_msa_constructor__empty_msa ... ok common_tests.formats_tests.msa_test.test_msa__len__corresponds_to_sequence_number_of_records ... ok common_tests.formats_tests.msa_test.test_msa__seqlen__corresponds_to_sequence_lengths ... ok common_tests.formats_tests.msa_test.test_msa_exclude__remove_one ... ok common_tests.formats_tests.msa_test.test_msa_exclude__missing_keys ... ok common_tests.formats_tests.msa_test.test_msa_exclude__no_keys ... ok common_tests.formats_tests.msa_test.test_msa_select__remove_one ... ok common_tests.formats_tests.msa_test.test_msa_select__missing_keys ... ok common_tests.formats_tests.msa_test.test_msa_select__no_keys ... ok common_tests.formats_tests.msa_test.test_msa_reduce__no_empty_columns__no_columns_are_removed ... ok common_tests.formats_tests.msa_test.test_msa_reduce__one_empty_column__column_are_removed ... ok common_tests.formats_tests.msa_test.test_msa_reduce__multiple_empty_column__all_empty_column_are_removed ... ok common_tests.formats_tests.msa_test.test_msa_reduce__only_empty_column__none_is_returned ... ok common_tests.formats_tests.msa_test.test_msa_filter_singletons__filter_by_second ... ok common_tests.formats_tests.msa_test.test_msa_filter_singletons__filter_by_third ... ok common_tests.formats_tests.msa_test.test_msa_filter_singletons__filter_by_both ... ok common_tests.formats_tests.msa_test.test_msa_filter_singletons__filter_by_itself ... ok common_tests.formats_tests.msa_test.test_msa_filter_singletons__filter_by_nothing ... ok common_tests.formats_tests.msa_test.test_msa_join__single_msa ... ok common_tests.formats_tests.msa_test.test_msa_join__two_msa ... ok common_tests.formats_tests.msa_test.test_msa_join__three_msa ... ok common_tests.formats_tests.msa_test.test_msa_join__missing_arguments ... ok common_tests.formats_tests.msa_test.test_msa_from_lines__single_entry ... ok common_tests.formats_tests.msa_test.test_msa_from_lines__single_entry_with_meta ... ok common_tests.formats_tests.msa_test.test_msa_from_lines__two_entries ... ok common_tests.formats_tests.msa_test.test_msa_from_lines__two_entries_with_meta ... ok common_tests.formats_tests.msa_test.test_msa_from_lines__duplicate_names ... ok common_tests.formats_tests.msa_test.test_msa_from_lines__mismatched_lengths ... ok common_tests.formats_tests.msa_test.test_msa_from_lines__empty_name ... ok common_tests.formats_tests.msa_test.test_msa_from_file__uncompressed ... ok common_tests.formats_tests.msa_test.test_msa_from_file__compressed_gz ... ok common_tests.formats_tests.msa_test.test_msa_from_file__compressed_bz2 ... ok common_tests.formats_tests.msa_test.test_msa_split_msa__single_group ... ok common_tests.formats_tests.msa_test.test_msa_split_msa__two_groups ... ok common_tests.formats_tests.msa_test.test_msa_split__three_groups ... ok common_tests.formats_tests.msa_test.test_msa_split__empty_group ... ok common_tests.formats_tests.msa_test.test_msa_split__partial_group ... ok common_tests.formats_tests.msa_test.test_msa_split_msa__no_split_by ... ok common_tests.formats_tests.msa_test.test_msa_to_file__complete_line_test ... ok common_tests.formats_tests.msa_test.test_msa_validate__missing_names_first ... ok common_tests.formats_tests.msa_test.test_msa_validate__missing_names_second ... ok common_tests.formats_tests.msa_test.test_msa_names ... ok common_tests.formats_tests.msa_test.test_msa_repr ... ok common_tests.formats_tests.msa_test.test_msa_repr__same_as_str ... ok common_tests.formats_tests.newick_tests.test_newick__constructor__name ... ok common_tests.formats_tests.newick_tests.test_newick__constructor__children_set_in_internal_nodes ... ok common_tests.formats_tests.newick_tests.test_newick__constructor__children_not_set_in_leaf_nodes ... ok common_tests.formats_tests.newick_tests.test_newick__constructor__is_leaf_true_for_leaf_nodes ... ok common_tests.formats_tests.newick_tests.test_newick__constructor__is_leaf_false_for_internal_nodes ... ok common_tests.formats_tests.newick_tests.test_newick__constuctor__leaf_nodes_must_have_name_or_length ... ok common_tests.formats_tests.newick_tests.test_newick__constructor__internal_nodes_must_have_children ... ok common_tests.formats_tests.newick_tests.test_newick__constructor__children_must_be_newick ... ok common_tests.formats_tests.newick_tests.test_newick__get_leaf_nodes__leaf_returns_self ... ok common_tests.formats_tests.newick_tests.test_newick__get_leaf_nodes__internal_node_returns_leaf_nodes ... ok common_tests.formats_tests.newick_tests.test_newick__get_leaf_nodes__complex_case ... ok common_tests.formats_tests.newick_tests.test_newick__get_leaf_names__leaf_returns_self ... ok common_tests.formats_tests.newick_tests.test_newick__get_leaf_names__internal_node_returns_leaf_nodes ... ok common_tests.formats_tests.newick_tests.test_newick__get_leaf_names__complex_case ... ok common_tests.formats_tests.newick_tests.test_newick__reroot_on_taxa__single_taxa ... ok common_tests.formats_tests.newick_tests.test_newick__reroot_on_taxa__single_taxa_with_branch_lengths ... ok common_tests.formats_tests.newick_tests.test_newick__reroot_on_taxa__multiple_taxa__clade ... ok common_tests.formats_tests.newick_tests.test_newick__reroot_on_taxa__multiple_taxa__paraphylogeny ... ok common_tests.formats_tests.newick_tests.test_newick__reroot_on_taxa__no_taxa ... ok common_tests.formats_tests.newick_tests.test_newick__reroot_on_taxa__unknown_taxa ... ok common_tests.formats_tests.newick_tests.test_newick__reroot_on_taxa__no_non_root_taxa ... ok common_tests.formats_tests.newick_tests.test_newick__reroot_on_midpoint__single_node ... ok common_tests.formats_tests.newick_tests.test_newick__reroot_on_midpoint__two_nodes ... ok common_tests.formats_tests.newick_tests.test_newick__reroot_on_midpoint__two_clades ... ok common_tests.formats_tests.newick_tests.test_newick__reroot_on_midpoint__nested_clades ... ok common_tests.formats_tests.newick_tests.test_newick__reroot_on_midpoint__reroot_on_internal_node ... ok common_tests.formats_tests.newick_tests.test_newick__reroot_on_midpoint__invalid_branch_lengths('(A,B);',) ... ok common_tests.formats_tests.newick_tests.test_newick__reroot_on_midpoint__invalid_branch_lengths('(A:7,B);',) ... ok common_tests.formats_tests.newick_tests.test_newick__reroot_on_midpoint__invalid_branch_lengths('(A:7,(B:3));',) ... ok common_tests.formats_tests.newick_tests.test_newick__reroot_on_midpoint__invalid_branch_lengths('(A:7,(B:3):-1);',) ... ok common_tests.formats_tests.newick_tests.test_newick__reroot_on_midpoint__invalid_branch_lengths('(A:7,B:-1);',) ... ok common_tests.formats_tests.newick_tests.test_newick__add_support__no_trees ... ok common_tests.formats_tests.newick_tests.test_newick__add_support__single_identical_tree ... ok common_tests.formats_tests.newick_tests.test_newick__add_support__single_identical_tree__different_rooting ... ok common_tests.formats_tests.newick_tests.test_newick__add_support__multiple_trees__different_topologies ... ok common_tests.formats_tests.newick_tests.test_newick__add_support__multiple_trees__partially_different_topologies ... ok common_tests.formats_tests.newick_tests.test_newick__add_support__multiple_trees__two_cladees ... ok common_tests.formats_tests.newick_tests.test_newick__add_support__differing_leaf_names ... ok common_tests.formats_tests.newick_tests.test_newick__add_support__formatting('{Support}', '(((A,B)1,C)3,D);') ... ok common_tests.formats_tests.newick_tests.test_newick__add_support__formatting('{Percentage:.0f}', '(((A,B)33,C)100,D);') ... ok common_tests.formats_tests.newick_tests.test_newick__add_support__formatting('{Fraction:.2f}', '(((A,B)0.33,C)1.00,D);') ... ok common_tests.formats_tests.newick_tests.test_newick__add_support__unique_names_required ... ok common_tests.formats_tests.newick_tests.test_newick__parse__minimal_newick__name_only ... ok common_tests.formats_tests.newick_tests.test_newick__parse__single_taxa ... ok common_tests.formats_tests.newick_tests.test_newick__parse__two_taxa ... ok common_tests.formats_tests.newick_tests.test_newick__parse__three_taxa ... ok common_tests.formats_tests.newick_tests.test_newick__parse__ignore_whitespace ... ok common_tests.formats_tests.newick_tests.test_newick__parse__missing_semicolon ... ok common_tests.formats_tests.newick_tests.test_newick__parse__subnode__single_taxa ... ok common_tests.formats_tests.newick_tests.test_newick__parse__subnode__two_taxa ... ok common_tests.formats_tests.newick_tests.test_newick__cmp__identical ... ok common_tests.formats_tests.newick_tests.test_newick__cmp__identical_for_empty_string_length ... ok common_tests.formats_tests.newick_tests.test_newick__cmp__identical_for_empty_string_name ... ok common_tests.formats_tests.newick_tests.test_newick__cmp__not_identical((B)B:13;,) ... ok common_tests.formats_tests.newick_tests.test_newick__cmp__not_identical((B)A:14;,) ... ok common_tests.formats_tests.newick_tests.test_newick__cmp__not_identical(A:13;,) ... ok common_tests.formats_tests.newick_tests.test_newick__cmp__not_identical((C)A:13;,) ... ok common_tests.formats_tests.newick_tests.test_newick__cmp__not_identical((C)B:14;,) ... ok common_tests.formats_tests.newick_tests.test_newick__hash__identical ... ok common_tests.formats_tests.newick_tests.test_newick__hash__not_identical((B)B:13;,) ... ok common_tests.formats_tests.newick_tests.test_newick__hash__not_identical((B)A:14;,) ... ok common_tests.formats_tests.newick_tests.test_newick__hash__not_identical(A:13;,) ... ok common_tests.formats_tests.newick_tests.test_newick__hash__not_identical((C)A:13;,) ... ok common_tests.formats_tests.newick_tests.test_newick__hash__not_identical((C)B:14;,) ... ok common_tests.formats_tests.newick_tests.test_newick__hash__hashable ... ok common_tests.formats_tests.newick_tests.test_newick__malformed__unbalanced_parantheses ... ok common_tests.formats_tests.newick_tests.test_newick__malformed__mismatched_parantheses ... ok common_tests.formats_tests.newick_tests.test_newick__malformed__missing_parantheses ... ok common_tests.formats_tests.newick_tests.test_newick__malformed__missing_length ... ok common_tests.formats_tests.newick_tests.test_newick__malformed__multiple_lengths ... ok common_tests.formats_tests.newick_tests.test_newick__parse__first_taxa_unnamed ... ok common_tests.formats_tests.newick_tests.test_newick__parse__second_taxa_unnamed ... ok common_tests.formats_tests.newick_tests.test_newick__parse__two_taxa_unnamed ... ok common_tests.formats_tests.newick_tests.test_newick__parse__three_taxa_unnamed ... ok common_tests.formats_tests.newick_tests.test_newick__parse__minimal_newick__implicit_nodes ... ok common_tests.formats_tests.newick_tests.test_newick__parse__subnode__empty ... ok common_tests.formats_tests.newick_tests.test_newick__wikipedia_example_1 ... ok common_tests.formats_tests.newick_tests.test_newick__wikipedia_example_2 ... ok common_tests.formats_tests.newick_tests.test_newick__wikipedia_example_3 ... ok common_tests.formats_tests.newick_tests.test_newick__wikipedia_example_4 ... ok common_tests.formats_tests.newick_tests.test_newick__wikipedia_example_5 ... ok common_tests.formats_tests.newick_tests.test_newick__wikipedia_example_6 ... ok common_tests.formats_tests.newick_tests.test_newick__wikipedia_example_7 ... ok common_tests.formats_tests.newick_tests.test_newick__wikipedia_example_8 ... ok common_tests.formats_tests.newick_tests.test_newick__str__non_string_name ... ok common_tests.formats_tests.newick_tests.test_newick__str__non_string_length ... ok common_tests.formats_tests.newick_tests.test_newick__str__repr_equal_to_str ... ok common_tests.formats_tests.newick_tests.test_newick__str__single_leaf_should_not_be_followed_by_comma ... ok common_tests.formats_tests.newick_tests.test_newick__wikipedia_examples__str_equality('(A,B,(C,D));',) ... ok common_tests.formats_tests.newick_tests.test_newick__wikipedia_examples__str_equality('(A,B,(C,D)E)F;',) ... ok common_tests.formats_tests.newick_tests.test_newick__wikipedia_examples__str_equality('(:0.1,:0.2,(:0.3,:0.4):0.5);',) ... ok common_tests.formats_tests.newick_tests.test_newick__wikipedia_examples__str_equality('(:0.1,:0.2,(:0.3,:0.4):0.5):0.0;',) ... ok common_tests.formats_tests.newick_tests.test_newick__wikipedia_examples__str_equality('(A:0.1,B:0.2,(C:0.3,D:0.4):0.5);',) ... ok common_tests.formats_tests.newick_tests.test_newick__wikipedia_examples__str_equality('(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;',) ... ok common_tests.formats_tests.newick_tests.test_newick__properties_are_immutable('name', 'foo') ... ok common_tests.formats_tests.newick_tests.test_newick__properties_are_immutable('length', '13') ... ok common_tests.formats_tests.newick_tests.test_newick__properties_are_immutable('children', []) ... ok common_tests.formats_tests.newick_tests.test_newick__properties_are_immutable('foobar', True) ... ok common_tests.formats_tests.newick_tests.test_newick__properties_cannot_be_deleted('name',) ... ok common_tests.formats_tests.newick_tests.test_newick__properties_cannot_be_deleted('length',) ... ok common_tests.formats_tests.newick_tests.test_newick__properties_cannot_be_deleted('children',) ... ok common_tests.formats_tests.newick_tests.test_newick__properties_cannot_be_deleted('foobar',) ... ok common_tests.formats_tests.phylip_test.test_sequential_phy__short_sequences ... ok common_tests.formats_tests.phylip_test.test_sequential_phy__multi_line_sequences ... ok common_tests.formats_tests.phylip_test.test_sequential_phy__with_flag ... ok common_tests.formats_tests.phylip_test.test_sequentual_phy__long_names ... ok common_tests.formats_tests.phylip_test.test_sequential_phy__different_lengths ... ok common_tests.formats_tests.phylip_test.test_interleaved_phy__short_sequences ... ok common_tests.formats_tests.phylip_test.test_interleaved_phy__multi_line_sequences ... ok common_tests.formats_tests.phylip_test.test_interleaved_phy__with_flag ... ok common_tests.formats_tests.phylip_test.test_interleaved_phy__medium_names ... ok common_tests.formats_tests.phylip_test.test_interleaved_phy__long_names ... ok common_tests.formats_tests.phylip_test.test_sequentual_phy__different_length_names_1 ... ok common_tests.formats_tests.phylip_test.test_sequentual_phy__different_length_names_2 ... ok common_tests.formats_tests.phylip_test.test_interleaved_phy__different_lengths ... ok common_tests.makefile_test.test_dir ... ok common_tests.makefile_test.test_file ... ok common_tests.makefile_test.test_makefilespec__description_is_set ... ok common_tests.makefile_test.test_makefilespec__meets_spec_must_be_implemented ... ok common_tests.makefile_test.test_is_int__accepts_integers ... ok common_tests.makefile_test.test_is_int__accepts_longs ... ok common_tests.makefile_test.test_is_int__rejects_not_int(None,) ... ok common_tests.makefile_test.test_is_int__rejects_not_int(False,) ... ok common_tests.makefile_test.test_is_int__rejects_not_int([],) ... ok common_tests.makefile_test.test_is_int__rejects_not_int((),) ... ok common_tests.makefile_test.test_is_int__rejects_not_int({},) ... ok common_tests.makefile_test.test_is_int__rejects_not_int([],) ... ok common_tests.makefile_test.test_is_int__rejects_not_int((,),) ... ok common_tests.makefile_test.test_is_int__rejects_not_int({None: },) ... ok common_tests.makefile_test.test_is_int__rejects_not_int(,) ... ok common_tests.makefile_test.test_is_int__rejects_not_int(,) ... ok common_tests.makefile_test.test_is_int__default_description ... ok common_tests.makefile_test.test_is_int__custom_description ... ok common_tests.makefile_test.test_is_int__default_not_set ... ok common_tests.makefile_test.test_is_int__default_set__valid_value ... ok common_tests.makefile_test.test_is_int__default_set__must_meet_spec ... ok common_tests.makefile_test.test_is_unsigned_int__accepts_non_negative_integers ... ok common_tests.makefile_test.test_is_unsigned_int__accepts_longs ... ok common_tests.makefile_test.test_is_unsigned_int__rejects_not_unsigned_int(-1,) ... ok common_tests.makefile_test.test_is_unsigned_int__rejects_not_unsigned_int(-1L,) ... ok common_tests.makefile_test.test_is_unsigned_int__rejects_not_unsigned_int(None,) ... ok common_tests.makefile_test.test_is_unsigned_int__rejects_not_unsigned_int(False,) ... ok common_tests.makefile_test.test_is_unsigned_int__rejects_not_unsigned_int([],) ... ok common_tests.makefile_test.test_is_unsigned_int__rejects_not_unsigned_int((),) ... ok common_tests.makefile_test.test_is_unsigned_int__rejects_not_unsigned_int({},) ... ok common_tests.makefile_test.test_is_unsigned_int__rejects_not_unsigned_int([],) ... ok common_tests.makefile_test.test_is_unsigned_int__rejects_not_unsigned_int((,),) ... ok common_tests.makefile_test.test_is_unsigned_int__rejects_not_unsigned_int({None: },) ... ok common_tests.makefile_test.test_is_unsigned_int__rejects_not_unsigned_int(,) ... ok common_tests.makefile_test.test_is_unsigned_int__rejects_not_unsigned_int(,) ... ok common_tests.makefile_test.test_is_unsigned_int__default_description ... ok common_tests.makefile_test.test_is_unsigned_int__custom_description ... ok common_tests.makefile_test.test_is_unsigned_int__default_not_set ... ok common_tests.makefile_test.test_is_unsigned_int__default_set__valid_value ... ok common_tests.makefile_test.test_is_unsigned_int__default_set__must_meet_spec ... ok common_tests.makefile_test.test_is_float__accepts_float ... ok common_tests.makefile_test.test_is_float__rejects_not_float(0,) ... ok common_tests.makefile_test.test_is_float__rejects_not_float(None,) ... ok common_tests.makefile_test.test_is_float__rejects_not_float(False,) ... ok common_tests.makefile_test.test_is_float__rejects_not_float([],) ... ok common_tests.makefile_test.test_is_float__rejects_not_float((),) ... ok common_tests.makefile_test.test_is_float__rejects_not_float({},) ... ok common_tests.makefile_test.test_is_float__rejects_not_float([],) ... ok common_tests.makefile_test.test_is_float__rejects_not_float((,),) ... ok common_tests.makefile_test.test_is_float__rejects_not_float({None: },) ... ok common_tests.makefile_test.test_is_float__rejects_not_float(,) ... ok common_tests.makefile_test.test_is_float__rejects_not_float(,) ... ok common_tests.makefile_test.test_is_float__default_description ... ok common_tests.makefile_test.test_is_float__custom_description ... ok common_tests.makefile_test.test_is_float__default_not_set ... ok common_tests.makefile_test.test_is_float__default_set__valid_value ... ok common_tests.makefile_test.test_is_float__default_set__must_meet_spec ... ok common_tests.makefile_test.test_is_boolean__accepts_boolean ... ok common_tests.makefile_test.test_is_boolean__rejects_not_boolean(0,) ... ok common_tests.makefile_test.test_is_boolean__rejects_not_boolean(None,) ... ok common_tests.makefile_test.test_is_boolean__rejects_not_boolean([],) ... ok common_tests.makefile_test.test_is_boolean__rejects_not_boolean((),) ... ok common_tests.makefile_test.test_is_boolean__rejects_not_boolean({},) ... ok common_tests.makefile_test.test_is_boolean__rejects_not_boolean([],) ... ok common_tests.makefile_test.test_is_boolean__rejects_not_boolean((,),) ... ok common_tests.makefile_test.test_is_boolean__rejects_not_boolean({None: },) ... ok common_tests.makefile_test.test_is_boolean__rejects_not_boolean(,) ... ok common_tests.makefile_test.test_is_boolean__rejects_not_boolean(,) ... ok common_tests.makefile_test.test_is_boolean__default_description ... ok common_tests.makefile_test.test_is_boolean__custom_description ... ok common_tests.makefile_test.test_is_boolean__default_not_set ... ok common_tests.makefile_test.test_is_boolean__default_set__valid_value ... ok common_tests.makefile_test.test_is_boolean__default_set__must_meet_spec ... ok common_tests.makefile_test.test_is_str__accepts_standard_str ... ok common_tests.makefile_test.test_is_str__accepts_unicode_str ... ok common_tests.makefile_test.test_is_str__rejects_empty_str ... ok common_tests.makefile_test.test_is_str__rejects_not_str(1,) ... ok common_tests.makefile_test.test_is_str__rejects_not_str(None,) ... ok common_tests.makefile_test.test_is_str__rejects_not_str(False,) ... ok common_tests.makefile_test.test_is_str__rejects_not_str([],) ... ok common_tests.makefile_test.test_is_str__rejects_not_str((),) ... ok common_tests.makefile_test.test_is_str__rejects_not_str({},) ... ok common_tests.makefile_test.test_is_str__rejects_not_str([],) ... ok common_tests.makefile_test.test_is_str__rejects_not_str((,),) ... ok common_tests.makefile_test.test_is_str__rejects_not_str({None: },) ... ok common_tests.makefile_test.test_is_str__rejects_not_str(,) ... ok common_tests.makefile_test.test_is_str__rejects_not_str(,) ... ok common_tests.makefile_test.test_is_str__default_description ... ok common_tests.makefile_test.test_is_str__custom_description ... ok common_tests.makefile_test.test_is_str__default_not_set ... ok common_tests.makefile_test.test_is_str__default_set__valid_value ... ok common_tests.makefile_test.test_is_str__default_set__must_meet_spec ... ok common_tests.makefile_test.test_is_none__accepts_none ... ok common_tests.makefile_test.test_is_none__rejects_not_none('',) ... ok common_tests.makefile_test.test_is_none__rejects_not_none(0,) ... ok common_tests.makefile_test.test_is_none__rejects_not_none(False,) ... ok common_tests.makefile_test.test_is_none__rejects_not_none([],) ... ok common_tests.makefile_test.test_is_none__rejects_not_none((),) ... ok common_tests.makefile_test.test_is_none__rejects_not_none({},) ... ok common_tests.makefile_test.test_is_none__rejects_not_none([],) ... ok common_tests.makefile_test.test_is_none__rejects_not_none((,),) ... ok common_tests.makefile_test.test_is_none__rejects_not_none({None: },) ... ok common_tests.makefile_test.test_is_none__rejects_not_none(,) ... ok common_tests.makefile_test.test_is_none__rejects_not_none(,) ... ok common_tests.makefile_test.test_is_none__default_description ... ok common_tests.makefile_test.test_is_none__custom_description ... ok common_tests.makefile_test.test_is_none__default_not_set ... ok common_tests.makefile_test.test_is_none__default_not_implemented_for_is_none ... ok common_tests.makefile_test.test_value_lt__accepts_value_lt ... ok common_tests.makefile_test.test_value_lt__rejects_value_eq ... ok common_tests.makefile_test.test_value_lt__rejects_value_gt ... ok common_tests.makefile_test.test_value_lt__accepts_value_lt__with_key ... ok common_tests.makefile_test.test_value_lt__rejects_value_eq__with_key ... ok common_tests.makefile_test.test_value_lt__rejects_value_gt__with_key ... ok common_tests.makefile_test.test_value_lt__default_description ... ok common_tests.makefile_test.test_value_lt__custom_description ... ok common_tests.makefile_test.test_is_value_lt__default_not_set ... ok common_tests.makefile_test.test_is_value_lt__default_set__valid_value ... ok common_tests.makefile_test.test_is_value_lt__default_set__must_meet_spec ... ok common_tests.makefile_test.test_is_value_lt__handles_not_number('foo',) ... ok common_tests.makefile_test.test_is_value_lt__handles_not_number(None,) ... ok common_tests.makefile_test.test_is_value_lt__handles_not_number(False,) ... ok common_tests.makefile_test.test_is_value_lt__handles_not_number([],) ... ok common_tests.makefile_test.test_is_value_lt__handles_not_number((),) ... ok common_tests.makefile_test.test_is_value_lt__handles_not_number({},) ... ok common_tests.makefile_test.test_is_value_lt__handles_not_number([],) ... ok common_tests.makefile_test.test_is_value_lt__handles_not_number((,),) ... ok common_tests.makefile_test.test_is_value_lt__handles_not_number({None: },) ... ok common_tests.makefile_test.test_is_value_lt__handles_not_number(,) ... ok common_tests.makefile_test.test_is_value_lt__handles_not_number(,) ... ok common_tests.makefile_test.test_value_le__accepts_value_lt ... ok common_tests.makefile_test.test_value_le__accepts_value_eq ... ok common_tests.makefile_test.test_value_le__rejects_value_gt ... ok common_tests.makefile_test.test_value_le__accepts_value_lt__with_key ... ok common_tests.makefile_test.test_value_le__accepts_value_eq__with_key ... ok common_tests.makefile_test.test_value_le__rejects_value_gt__with_key ... ok common_tests.makefile_test.test_value_le__default_description ... ok common_tests.makefile_test.test_value_le__custom_description ... ok common_tests.makefile_test.test_is_value_le__default_not_set ... ok common_tests.makefile_test.test_is_value_le__default_set__valid_value ... ok common_tests.makefile_test.test_is_value_le__default_set__must_meet_spec ... ok common_tests.makefile_test.test_is_value_le__handles_not_number('foo',) ... ok common_tests.makefile_test.test_is_value_le__handles_not_number(None,) ... ok common_tests.makefile_test.test_is_value_le__handles_not_number(False,) ... ok common_tests.makefile_test.test_is_value_le__handles_not_number([],) ... ok common_tests.makefile_test.test_is_value_le__handles_not_number((),) ... ok common_tests.makefile_test.test_is_value_le__handles_not_number({},) ... ok common_tests.makefile_test.test_is_value_le__handles_not_number([],) ... ok common_tests.makefile_test.test_is_value_le__handles_not_number((,),) ... ok common_tests.makefile_test.test_is_value_le__handles_not_number({None: },) ... ok common_tests.makefile_test.test_is_value_le__handles_not_number(,) ... ok common_tests.makefile_test.test_is_value_le__handles_not_number(,) ... ok common_tests.makefile_test.test_value_ge__rejects_value_lt ... ok common_tests.makefile_test.test_value_ge__accepts_value_eq ... ok common_tests.makefile_test.test_value_ge__accepts_value_gt ... ok common_tests.makefile_test.test_value_ge__accepts_value_lt__with_key ... ok common_tests.makefile_test.test_value_ge__accepts_value_eq__with_key ... ok common_tests.makefile_test.test_value_ge__accepts_value_gt__with_key ... ok common_tests.makefile_test.test_value_ge__default_description ... ok common_tests.makefile_test.test_value_ge__custom_description ... ok common_tests.makefile_test.test_is_value_ge__default_not_set ... ok common_tests.makefile_test.test_is_value_ge__default_set__valid_value ... ok common_tests.makefile_test.test_is_value_ge__default_set__must_meet_spec ... ok common_tests.makefile_test.test_is_value_ge__handles_not_number('foo',) ... ok common_tests.makefile_test.test_is_value_ge__handles_not_number(None,) ... ok common_tests.makefile_test.test_is_value_ge__handles_not_number(False,) ... ok common_tests.makefile_test.test_is_value_ge__handles_not_number([],) ... ok common_tests.makefile_test.test_is_value_ge__handles_not_number((),) ... ok common_tests.makefile_test.test_is_value_ge__handles_not_number({},) ... ok common_tests.makefile_test.test_is_value_ge__handles_not_number([],) ... ok common_tests.makefile_test.test_is_value_ge__handles_not_number((,),) ... ok common_tests.makefile_test.test_is_value_ge__handles_not_number({None: },) ... ok common_tests.makefile_test.test_is_value_ge__handles_not_number(,) ... ok common_tests.makefile_test.test_is_value_ge__handles_not_number(,) ... ok common_tests.makefile_test.test_value_gt__rejects_value_lt ... ok common_tests.makefile_test.test_value_gt__rejects_value_eq ... ok common_tests.makefile_test.test_value_gt__accepts_value_gt ... ok common_tests.makefile_test.test_value_gt__accepts_value_lt__with_key ... ok common_tests.makefile_test.test_value_gt__accepts_value_eq__with_key ... ok common_tests.makefile_test.test_value_gt__accepts_value_gt__with_key ... ok common_tests.makefile_test.test_value_gt__default_description ... ok common_tests.makefile_test.test_value_gt__custom_description ... ok common_tests.makefile_test.test_is_value_gt__default_not_set ... ok common_tests.makefile_test.test_is_value_gt__default_set__valid_value ... ok common_tests.makefile_test.test_is_value_gt__default_set__must_meet_spec ... ok common_tests.makefile_test.test_is_value_gt__handles_not_number('foo',) ... ok common_tests.makefile_test.test_is_value_gt__handles_not_number(None,) ... ok common_tests.makefile_test.test_is_value_gt__handles_not_number(False,) ... ok common_tests.makefile_test.test_is_value_gt__handles_not_number([],) ... ok common_tests.makefile_test.test_is_value_gt__handles_not_number((),) ... ok common_tests.makefile_test.test_is_value_gt__handles_not_number({},) ... ok common_tests.makefile_test.test_is_value_gt__handles_not_number([],) ... ok common_tests.makefile_test.test_is_value_gt__handles_not_number((,),) ... ok common_tests.makefile_test.test_is_value_gt__handles_not_number({None: },) ... ok common_tests.makefile_test.test_is_value_gt__handles_not_number(,) ... ok common_tests.makefile_test.test_is_value_gt__handles_not_number(,) ... ok common_tests.makefile_test.test_value_in__single_value_in_set ... ok common_tests.makefile_test.test_value_in__single_value_not_in_set ... ok common_tests.makefile_test.test_value_in__single_value_in_set__with_key ... ok common_tests.makefile_test.test_value_in__single_value_not_in_set__with_key ... ok common_tests.makefile_test.test_value_in__case_sensitive__value_in_set ... ok common_tests.makefile_test.test_value_in__case_sensitive__value_in_not_set ... ok common_tests.makefile_test.test_value_in__default_description ... ok common_tests.makefile_test.test_value_in__custom_description ... ok common_tests.makefile_test.test_is_value_in__default_not_set ... ok common_tests.makefile_test.test_is_value_in__default_set__valid_value ... ok common_tests.makefile_test.test_is_value_in__default_set__must_meet_spec ... ok common_tests.makefile_test.test_is_value_in__handles_types('foo',) ... ok common_tests.makefile_test.test_is_value_in__handles_types(None,) ... ok common_tests.makefile_test.test_is_value_in__handles_types(False,) ... ok common_tests.makefile_test.test_is_value_in__handles_types([],) ... ok common_tests.makefile_test.test_is_value_in__handles_types((),) ... ok common_tests.makefile_test.test_is_value_in__handles_types({},) ... ok common_tests.makefile_test.test_is_value_in__handles_types([],) ... ok common_tests.makefile_test.test_is_value_in__handles_types((,),) ... ok common_tests.makefile_test.test_is_value_in__handles_types({None: },) ... ok common_tests.makefile_test.test_is_value_in__handles_types(,) ... ok common_tests.makefile_test.test_is_value_in__handles_types(,) ... ok common_tests.makefile_test.test_intersects__single_value_in_set ... ok common_tests.makefile_test.test_intersects__multiple_values_in_set ... ok common_tests.makefile_test.test_intersects__single_value_not_in_set ... ok common_tests.makefile_test.test_intersects__some_values_in_set ... ok common_tests.makefile_test.test_intersects__empty_set ... ok common_tests.makefile_test.test_intersects__case_sensitive__value_in_set ... ok common_tests.makefile_test.test_intersects__case_sensitive__value_in_not_set ... ok common_tests.makefile_test.test_intersects__chars__case_sensitive ... ok common_tests.makefile_test.test_intersects__chars__case_sensitive__rejects_differences_in_case ... ok common_tests.makefile_test.test_intersects__rejects_dictionary ... ok common_tests.makefile_test.test_intersects__default_not_set ... ok common_tests.makefile_test.test_intersects__default_set__valid_value ... ok common_tests.makefile_test.test_intersects__default_set__must_meet_spec ... ok common_tests.makefile_test.test_intersects__handles_types('foo',) ... ok common_tests.makefile_test.test_intersects__handles_types(None,) ... ok common_tests.makefile_test.test_intersects__handles_types(False,) ... ok common_tests.makefile_test.test_intersects__handles_types([],) ... ok common_tests.makefile_test.test_intersects__handles_types((),) ... ok common_tests.makefile_test.test_intersects__handles_types({},) ... ok common_tests.makefile_test.test_intersects__handles_types([],) ... ok common_tests.makefile_test.test_intersects__handles_types((,),) ... ok common_tests.makefile_test.test_intersects__handles_types({None: },) ... ok common_tests.makefile_test.test_intersects__handles_types(,) ... ok common_tests.makefile_test.test_intersects__handles_types(,) ... ok common_tests.makefile_test.test_subset_of__single_value_in_set ... ok common_tests.makefile_test.test_subset_of__multiple_values_in_set ... ok common_tests.makefile_test.test_subset_of__empty_set_is_subset ... ok common_tests.makefile_test.test_subset_of__single_value_not_in_set ... ok common_tests.makefile_test.test_subset_of__multiple_values_not_in_set ... ok common_tests.makefile_test.test_subset_of__empty_set ... ok common_tests.makefile_test.test_subset_of__case_sensitive__value_in_set ... ok common_tests.makefile_test.test_subset_of__case_sensitive__value_in_not_set ... ok common_tests.makefile_test.test_subset_of__chars__case_sensitive ... ok common_tests.makefile_test.test_subset_of__chars__case_sensitive__rejects_differences_in_case ... ok common_tests.makefile_test.test_subset_of__rejects_dictionary ... ok common_tests.makefile_test.test_subset_of__default_not_set ... ok common_tests.makefile_test.test_subset_of__default_set__valid_value ... ok common_tests.makefile_test.test_subset_of__default_set__must_meet_spec ... ok common_tests.makefile_test.test_subset_of__handles_types('foo',) ... ok common_tests.makefile_test.test_subset_of__handles_types(None,) ... ok common_tests.makefile_test.test_subset_of__handles_types(False,) ... ok common_tests.makefile_test.test_subset_of__handles_types((),) ... ok common_tests.makefile_test.test_subset_of__handles_types({},) ... ok common_tests.makefile_test.test_subset_of__handles_types([],) ... ok common_tests.makefile_test.test_subset_of__handles_types((,),) ... ok common_tests.makefile_test.test_subset_of__handles_types({None: },) ... ok common_tests.makefile_test.test_subset_of__handles_types(,) ... ok common_tests.makefile_test.test_subset_of__handles_types(,) ... ok common_tests.makefile_test.test_and__accepts_when_all_true ... ok common_tests.makefile_test.test_and__rejects_when_first_is_false ... ok common_tests.makefile_test.test_and__rejects_when_second_is_false ... ok common_tests.makefile_test.test_and__rejects_when_both_is_false ... ok common_tests.makefile_test.test_and__rejects_no_tests ... ok common_tests.makefile_test.test_and__rejects_non_spec_tests ... ok common_tests.makefile_test.test_and__default_not_set ... ok common_tests.makefile_test.test_and__default_set__valid_value ... ok common_tests.makefile_test.test_and__default_set__must_meet_spec ... ok common_tests.makefile_test.test_and__defaults_not_set_in_specs ... ok common_tests.makefile_test.test_or__accepts_first_test ... ok common_tests.makefile_test.test_or__accepts_second_test ... ok common_tests.makefile_test.test_or__rejects_if_both_specs_fail ... ok common_tests.makefile_test.test_or__rejects_no_tests ... ok common_tests.makefile_test.test_or__rejects_non_spec_tests ... ok common_tests.makefile_test.test_or__default_not_set ... ok common_tests.makefile_test.test_or__default_set__valid_value ... ok common_tests.makefile_test.test_or__default_set__must_meet_spec ... ok common_tests.makefile_test.test_or__defaults_not_set_in_specs ... ok common_tests.makefile_test.test_xor__rejects_when_all_true ... ok common_tests.makefile_test.test_xor__accepts_when_first_is_false ... ok common_tests.makefile_test.test_xor__accepts_when_second_is_false ... ok common_tests.makefile_test.test_xor__rejects_when_both_is_false ... ok common_tests.makefile_test.test_xor__rejects_no_tests ... ok common_tests.makefile_test.test_xor__rejects_one_test ... ok common_tests.makefile_test.test_xor__rejects_three_tests ... ok common_tests.makefile_test.test_xor__rejects_non_spec_tests ... ok common_tests.makefile_test.test_xor__default_not_set ... ok common_tests.makefile_test.test_xor__default_set__valid_value ... ok common_tests.makefile_test.test_xor__default_set__must_meet_spec ... ok common_tests.makefile_test.test_xor__defaults_not_set_in_specs ... ok common_tests.makefile_test.test_not__accepts_when_test_is_false ... ok common_tests.makefile_test.test_not__rejects_when_test_is_true ... ok common_tests.makefile_test.test_not__defaults_not_set_in_specs ... ok common_tests.makefile_test.test_string_in__case_sensitive__value_in_set ... ok common_tests.makefile_test.test_string_in__case_insensitive__value_in_set ... ok common_tests.makefile_test.test_string_in__case_insensitive__value_not_set ... ok common_tests.makefile_test.test_string_in__case_insensitive__mixed_string__non_string_found ... ok common_tests.makefile_test.test_string_in__case_insensitive__mixed_string__string_found ... ok common_tests.makefile_test.test_string_in__default_not_set ... ok common_tests.makefile_test.test_string_in__default_set__valid_value ... ok common_tests.makefile_test.test_string_in__default_set__must_meet_spec ... ok common_tests.makefile_test.test_string_in__handles_types('foo',) ... ok common_tests.makefile_test.test_string_in__handles_types(None,) ... ok common_tests.makefile_test.test_string_in__handles_types(False,) ... ok common_tests.makefile_test.test_string_in__handles_types([],) ... ok common_tests.makefile_test.test_string_in__handles_types((),) ... ok common_tests.makefile_test.test_string_in__handles_types({},) ... ok common_tests.makefile_test.test_string_in__handles_types([],) ... ok common_tests.makefile_test.test_string_in__handles_types((,),) ... ok common_tests.makefile_test.test_string_in__handles_types({None: },) ... ok common_tests.makefile_test.test_string_in__handles_types(,) ... ok common_tests.makefile_test.test_string_in__handles_types(,) ... ok common_tests.makefile_test.test_strings_intersect__case_insensitive__value_in_set ... ok common_tests.makefile_test.test_strings_intersect__chars__case_insensitive__accepts_differt_in_case ... ok common_tests.makefile_test.test_strings_intersect__case_insensitive__mixed_string__non_string_found ... ok common_tests.makefile_test.test_strings_intersect__case_insensitive__mixed_string_string_found ... ok common_tests.makefile_test.test_strings_intersect__rejects_dictionary ... ok common_tests.makefile_test.test_strings_intersect__default_not_set ... ok common_tests.makefile_test.test_strings_intersect__default_set__valid_value ... ok common_tests.makefile_test.test_strings_intersect__default_set__must_meet_spec ... ok common_tests.makefile_test.test_string_intersects__handles_types('xyz',) ... ok common_tests.makefile_test.test_string_intersects__handles_types(None,) ... ok common_tests.makefile_test.test_string_intersects__handles_types(False,) ... ok common_tests.makefile_test.test_string_intersects__handles_types([],) ... ok common_tests.makefile_test.test_string_intersects__handles_types((),) ... ok common_tests.makefile_test.test_string_intersects__handles_types({},) ... ok common_tests.makefile_test.test_string_intersects__handles_types([],) ... ok common_tests.makefile_test.test_string_intersects__handles_types((,),) ... ok common_tests.makefile_test.test_string_intersects__handles_types({None: },) ... ok common_tests.makefile_test.test_string_intersects__handles_types(,) ... ok common_tests.makefile_test.test_string_intersects__handles_types(,) ... ok common_tests.makefile_test.test_subset_of__case_insensitive__value_in_set ... ok common_tests.makefile_test.test_subset_of__case_insensitive__empty_set_is_subset ... ok common_tests.makefile_test.test_subset_of__chars__case_insensitive__accepts_differences_in_case ... ok common_tests.makefile_test.test_subset_of__case_insensitive__mixed_string__non_string_found ... ok common_tests.makefile_test.test_subset_of__case_insensitive__mixed_string_string_found ... ok common_tests.makefile_test.test_strings_subset_of__rejects_dictionary ... ok common_tests.makefile_test.test_strings_subset_of__default_not_set ... ok common_tests.makefile_test.test_strings_subset_of__default_set__valid_value ... ok common_tests.makefile_test.test_string_subset_of__default_set__must_meet_spec ... ok common_tests.makefile_test.test_string_subset_of__handles_types('foo',) ... ok common_tests.makefile_test.test_string_subset_of__handles_types(None,) ... ok common_tests.makefile_test.test_string_subset_of__handles_types(False,) ... ok common_tests.makefile_test.test_string_subset_of__handles_types((),) ... ok common_tests.makefile_test.test_string_subset_of__handles_types({},) ... ok common_tests.makefile_test.test_string_subset_of__handles_types([],) ... ok common_tests.makefile_test.test_string_subset_of__handles_types((,),) ... ok common_tests.makefile_test.test_string_subset_of__handles_types({None: },) ... ok common_tests.makefile_test.test_string_subset_of__handles_types(,) ... ok common_tests.makefile_test.test_string_subset_of__handles_types(,) ... ok common_tests.makefile_test.test_string_is_uppercase__accepts_standard_str ... ok common_tests.makefile_test.test_string_is_uppercase__accepts_unicode_str ... ok common_tests.makefile_test.test_string_is_uppercase__rejects_empty_string ... ok common_tests.makefile_test.test_string_is_uppercase__rejects_not_uppercase_str('AcEf',) ... ok common_tests.makefile_test.test_string_is_uppercase__rejects_not_uppercase_str(1,) ... ok common_tests.makefile_test.test_string_is_uppercase__rejects_not_uppercase_str(None,) ... ok common_tests.makefile_test.test_string_is_uppercase__rejects_not_uppercase_str(False,) ... ok common_tests.makefile_test.test_string_is_uppercase__rejects_not_uppercase_str([],) ... ok common_tests.makefile_test.test_string_is_uppercase__rejects_not_uppercase_str((),) ... ok common_tests.makefile_test.test_string_is_uppercase__rejects_not_uppercase_str({},) ... ok common_tests.makefile_test.test_string_is_uppercase__rejects_not_uppercase_str([],) ... ok common_tests.makefile_test.test_string_is_uppercase__rejects_not_uppercase_str((,),) ... ok common_tests.makefile_test.test_string_is_uppercase__rejects_not_uppercase_str({None: },) ... ok common_tests.makefile_test.test_string_is_uppercase__rejects_not_uppercase_str(,) ... ok common_tests.makefile_test.test_string_is_uppercase__rejects_not_uppercase_str(,) ... ok common_tests.makefile_test.test_string_is_uppercase__default_not_set ... ok common_tests.makefile_test.test_string_is_uppercase__default_set__valid_value ... ok common_tests.makefile_test.test_string_is_uppercase__default_set__must_meet_spec ... ok common_tests.makefile_test.test_string_starts_with__accepts_standard_str ... ok common_tests.makefile_test.test_string_starts_with__accepts_unicode_str ... ok common_tests.makefile_test.test_string_starts_with__rejects_string_without_prefix ... ok common_tests.makefile_test.test_string_starts_with__rejects_not_uppercase_str(1,) ... ok common_tests.makefile_test.test_string_starts_with__rejects_not_uppercase_str(None,) ... ok common_tests.makefile_test.test_string_starts_with__rejects_not_uppercase_str(False,) ... ok common_tests.makefile_test.test_string_starts_with__rejects_not_uppercase_str([],) ... ok common_tests.makefile_test.test_string_starts_with__rejects_not_uppercase_str((),) ... ok common_tests.makefile_test.test_string_starts_with__rejects_not_uppercase_str({},) ... ok common_tests.makefile_test.test_string_starts_with__rejects_not_uppercase_str([],) ... ok common_tests.makefile_test.test_string_starts_with__rejects_not_uppercase_str((,),) ... ok common_tests.makefile_test.test_string_starts_with__rejects_not_uppercase_str({None: },) ... ok common_tests.makefile_test.test_string_starts_with__rejects_not_uppercase_str(,) ... ok common_tests.makefile_test.test_string_starts_with__rejects_not_uppercase_str(,) ... ok common_tests.makefile_test.test_string_starts_with__default_not_set ... ok common_tests.makefile_test.test_string_starts_with__default_set__valid_value ... ok common_tests.makefile_test.test_string_starts_with__default_set__must_meet_spec ... ok common_tests.makefile_test.test_string_ends_with__accepts_standard_str ... ok common_tests.makefile_test.test_string_ends_with__accepts_unicode_str ... ok common_tests.makefile_test.test_string_ends_with__rejects_string_without_prefix ... ok common_tests.makefile_test.test_string_ends_with__rejects_not_uppercase_str(1,) ... ok common_tests.makefile_test.test_string_ends_with__rejects_not_uppercase_str(None,) ... ok common_tests.makefile_test.test_string_ends_with__rejects_not_uppercase_str(False,) ... ok common_tests.makefile_test.test_string_ends_with__rejects_not_uppercase_str([],) ... ok common_tests.makefile_test.test_string_ends_with__rejects_not_uppercase_str((),) ... ok common_tests.makefile_test.test_string_ends_with__rejects_not_uppercase_str({},) ... ok common_tests.makefile_test.test_string_ends_with__rejects_not_uppercase_str([],) ... ok common_tests.makefile_test.test_string_ends_with__rejects_not_uppercase_str((,),) ... ok common_tests.makefile_test.test_string_ends_with__rejects_not_uppercase_str({None: },) ... ok common_tests.makefile_test.test_string_ends_with__rejects_not_uppercase_str(,) ... ok common_tests.makefile_test.test_string_ends_with__rejects_not_uppercase_str(,) ... ok common_tests.makefile_test.test_string_ends_with__default_not_set ... ok common_tests.makefile_test.test_string_ends_with__default_set__valid_value ... ok common_tests.makefile_test.test_string_ends_with__default_set__must_meet_spec ... ok common_tests.makefile_test.test_is_list_of__empty_list_always_ok ... ok common_tests.makefile_test.test_is_list_of__list_of_ints_accepted ... ok common_tests.makefile_test.test_is_list_of__list_of_non_ints_rejected ... ok common_tests.makefile_test.test_is_list_of__mixed_list_rejected ... ok common_tests.makefile_test.test_is_list_of__default_description ... ok common_tests.makefile_test.test_is_list_of__non_list_rejected ... ok common_tests.makefile_test.test_is_list_of__default_not_set ... ok common_tests.makefile_test.test_is_list_of__default_set__valid_value ... ok common_tests.makefile_test.test_is_list_of__default_set__must_meet_spec ... ok common_tests.makefile_test.test_is_list_of__defaults_not_set_in_specs ... ok common_tests.makefile_test.test_is_dict_of__empty_dict_always_ok ... ok common_tests.makefile_test.test_is_dict_of__correct_key_and_value_accepted ... ok common_tests.makefile_test.test_is_dict_of__wrong_key_and_correct_value_rejected ... ok common_tests.makefile_test.test_is_dict_of__correct_key_and_wrong_value_rejected ... ok common_tests.makefile_test.test_is_dict_of__mixed_rejected ... ok common_tests.makefile_test.test_is_dict_of__default_description ... ok common_tests.makefile_test.test_is_dict_of__rejects_non_dict ... ok common_tests.makefile_test.test_is_dict_of__default_not_set ... ok common_tests.makefile_test.test_is_dict_of__default_set__valid_value ... ok common_tests.makefile_test.test_is_dict_of__default_set__must_meet_spec ... ok common_tests.makefile_test.test_is_dict_of__defaults_not_set_in_key_specs ... ok common_tests.makefile_test.test_is_dict_of__defaults_not_set_in_value_specs ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, 'foo') ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, -1) ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, 'abc') ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, 1) ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, 1) ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, 1) ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, 1) ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, 1) ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, -1) ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, -1) ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, 2) ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, [2]) ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, [2]) ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, True) ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, 1) ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, 1) ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, True) ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, 1) ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, 1) ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, [1]) ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, [1]) ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, 1) ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, 1) ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, 1) ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, 'foo') ... ok common_tests.makefile_test.test_specs__path_is_displayed_in_exception(, 1) ... ok common_tests.makefile_test.test_process_makefile__dict_keys_found({'B': 7}, {'A': , 'B': }) ... ok common_tests.makefile_test.test_process_makefile__dict_keys_found({1: 'Abc'}, {: , : }) ... ok common_tests.makefile_test.test_process_makefile__dict_keys_found({1: 'Abc'}, {: , : }) ... ok common_tests.makefile_test.test_process_makefile__dict_keys_found({3: 14}, {: , 'A': }) ... ok common_tests.makefile_test.test_process_makefile__dict_keys_found({'A': 23}, {: , 'A': }) ... ok common_tests.makefile_test.test_process_makefile__dict_keys_not_found({'C': 7}, {'A': , 'B': }) ... ok common_tests.makefile_test.test_process_makefile__dict_keys_not_found({1.3: 'Abc'}, {: , : }) ... ok common_tests.makefile_test.test_process_makefile__dict_keys_not_found({1.3: 'Abc'}, {: , : }) ... ok common_tests.makefile_test.test_process_makefile__dict_keys_not_found({'C': 14}, {: , 'A': }) ... ok common_tests.makefile_test.test_process_makefile__dict_keys_not_found({'A': 23}, {}) ... ok common_tests.makefile_test.test_validate_makefile__unexpected_type_in_reference ... ok common_tests.makefile_test.test_validate_makefile__unexpected_type_in_current ... ok common_tests.makefile_test.test_process_makefile__sets_missing_keys ... ok common_tests.makefile_test.test_process_makefile__mixed_keys ... ok common_tests.makefile_test.test_process_makefile__sets_missing_recursive ... ok common_tests.makefile_test.test_process_makefile__sets_missing_recursive__with_missing_substructure ... ok common_tests.makefile_test.test_process_makefile__shared_subtrees_with_defaults ... ok common_tests.makefile_test.test_process_makefile__shared_subtrees_with_defaults__defaults_disabled ... ok common_tests.makefile_test.test_process_makefile__accept_when_required_value_is_set ... ok common_tests.makefile_test.test_process_makefile__fails_when_required_value_not_set ... ok common_tests.makefile_test.test_process_makefile__fails_required_value_not_set_in_dynamic_subtree ... ok common_tests.makefile_test.test_process_makefile__accept_missing_value_if_in_implicit_subtree ... ok common_tests.makefile_test.test_process_makefile__path_shown_in_exception_for_list ... ok common_tests.makefile_test.test_process_makefile__path_shown_in_exception_for_dict ... ok common_tests.makefile_test.test_process_makefile__implicit_subdict_is_allowed ... ok common_tests.makefile_test.test_process_makefile__list_types_accepted ... ok common_tests.makefile_test.test_process_makefile__wrong_list_types ... ok common_tests.makefile_test.test_process_makefile__missing_list_defaults_to_empty ... ok common_tests.makefile_test.test_process_makefile__missing_list_default_value ... ok common_tests.makefile_test.test_process_makefile__key_specified_but_no_entries ... ok common_tests.makefile_test.test_process_makefile__list_spec_must_contain_specs ... ok common_tests.makefile_test.test_process_makefile__list_spec_must_contain_only_specs ... ok common_tests.makefile_test.test_read_makefile__missing_file ... ok common_tests.makefile_test.test_read_makefile__not_a_yaml_file ... ok common_tests.makefile_test.test_read_makefile__simple_file ... ok common_tests.makefile_test.test__preprocess_makefile__missing_value ... ok common_tests.makefile_test.test__preprocess_makefile__expected_value ... ok common_tests.makefile_test.test__preprocess_makefile__processed_value ... ok common_tests.makefile_test.test__preprocess_makefile__invalid_value ... ok common_tests.makefile_test.test__preprocess_makefile__invalid_string ... ok common_tests.makefile_test.test__preprocess_makefile__with_default__missing_value ... ok common_tests.makefile_test.test__preprocess_makefile__with_default__expected_value ... ok common_tests.sampling_tests.test_weighted_sampling__select_by_weight(0.0, 'a') ... ok common_tests.sampling_tests.test_weighted_sampling__select_by_weight(0.16666, 'a') ... ok common_tests.sampling_tests.test_weighted_sampling__select_by_weight(0.16666666666666666, 'b') ... ok common_tests.sampling_tests.test_weighted_sampling__select_by_weight(0.49999, 'b') ... ok common_tests.sampling_tests.test_weighted_sampling__select_by_weight(0.5, 'c') ... ok common_tests.sampling_tests.test_weighted_sampling__select_by_weight(0.99999, 'c') ... ok common_tests.sampling_tests.test_weighted_sampling__empty_input_raises_value_error_for_lists([], []) ... ok common_tests.sampling_tests.test_weighted_sampling__empty_input_raises_value_error_for_lists([], [1, 2]) ... ok common_tests.sampling_tests.test_weighted_sampling__empty_input_raises_value_error_for_lists([1, 2], []) ... ok common_tests.sampling_tests.test_weighted_sampling__different_length_input_raises_value_error([0, 1], [1, 2, 3]) ... ok common_tests.sampling_tests.test_weighted_sampling__different_length_input_raises_value_error([0, 1, 2], [1, 2]) ... ok common_tests.sampling_tests.test_weighted_sampling__different_length_input_raises_value_error(, [1, 2, 3]) ... ok common_tests.sampling_tests.test_weighted_sampling__different_length_input_raises_value_error([0, 1], ) ... ok common_tests.sampling_tests.test_weighted_sampling__different_length_input_raises_value_error(, ) ... ok common_tests.sampling_tests.test_weighted_sampling__negative_weight_value_error ... ok common_tests.sampling_tests.test_weighted_sampling__zero_weight_raises_value_error ... ok common_tests.sampling_tests.test_weighted_sampling__non_numerical_weight_raises_type_error ... ok common_tests.sampling_tests.test_reservoir_sampling__select_first_item ... ok common_tests.sampling_tests.test_reservoir_sampling__select_second_item ... ok common_tests.sampling_tests.test_reservoir_sampling__upsample_equals_input ... ok common_tests.sampling_tests.test_reservoir_sampling__downsample_to_zero ... ok common_tests.sampling_tests.test_reservoir_sampling__downsample_to_negative_raises_value_error ... ok common_tests.sampling_tests.test_reservoir_sampling__downsample_to_float_raises_type_error ... ok common_tests.sampling_tests.test_reservoir_sampling__downsample_to_non_number_raises_type_error ... ok common_tests.sequences_test.test_complement__single_nt('A', 'T') ... ok common_tests.sequences_test.test_complement__single_nt('a', 't') ... ok common_tests.sequences_test.test_complement__single_nt('C', 'G') ... ok common_tests.sequences_test.test_complement__single_nt('c', 'g') ... ok common_tests.sequences_test.test_complement__single_nt('G', 'C') ... ok common_tests.sequences_test.test_complement__single_nt('g', 'c') ... ok common_tests.sequences_test.test_complement__single_nt('T', 'A') ... ok common_tests.sequences_test.test_complement__single_nt('t', 'a') ... ok common_tests.sequences_test.test_complement__single_nt('M', 'K') ... ok common_tests.sequences_test.test_complement__single_nt('m', 'k') ... ok common_tests.sequences_test.test_complement__single_nt('R', 'Y') ... ok common_tests.sequences_test.test_complement__single_nt('r', 'y') ... ok common_tests.sequences_test.test_complement__single_nt('W', 'W') ... ok common_tests.sequences_test.test_complement__single_nt('w', 'w') ... ok common_tests.sequences_test.test_complement__single_nt('S', 'S') ... ok common_tests.sequences_test.test_complement__single_nt('s', 's') ... ok common_tests.sequences_test.test_complement__single_nt('Y', 'R') ... ok common_tests.sequences_test.test_complement__single_nt('y', 'r') ... ok common_tests.sequences_test.test_complement__single_nt('K', 'M') ... ok common_tests.sequences_test.test_complement__single_nt('k', 'm') ... ok common_tests.sequences_test.test_complement__single_nt('V', 'B') ... ok common_tests.sequences_test.test_complement__single_nt('v', 'b') ... ok common_tests.sequences_test.test_complement__single_nt('H', 'D') ... ok common_tests.sequences_test.test_complement__single_nt('h', 'd') ... ok common_tests.sequences_test.test_complement__single_nt('D', 'H') ... ok common_tests.sequences_test.test_complement__single_nt('d', 'h') ... ok common_tests.sequences_test.test_complement__single_nt('B', 'V') ... ok common_tests.sequences_test.test_complement__single_nt('b', 'v') ... ok common_tests.sequences_test.test_complement__single_nt('N', 'N') ... ok common_tests.sequences_test.test_complement__single_nt('n', 'n') ... ok common_tests.sequences_test.test_complement__single_nt('X', 'X') ... ok common_tests.sequences_test.test_complement__single_nt('x', 'x') ... ok common_tests.sequences_test.test_complement__multiple_nts_upper ... ok common_tests.sequences_test.test_complement__multiple_nts_lower ... ok common_tests.sequences_test.test_complement__multiple_nts_mixed_case ... ok common_tests.sequences_test.test_reverse_complement ... ok common_tests.sequences_test.test_genotype__permutations('A', 'A') ... ok common_tests.sequences_test.test_genotype__permutations('C', 'C') ... ok common_tests.sequences_test.test_genotype__permutations('G', 'G') ... ok common_tests.sequences_test.test_genotype__permutations('T', 'T') ... ok common_tests.sequences_test.test_genotype__permutations('AC', 'M') ... ok common_tests.sequences_test.test_genotype__permutations('CA', 'M') ... ok common_tests.sequences_test.test_genotype__permutations('AG', 'R') ... ok common_tests.sequences_test.test_genotype__permutations('GA', 'R') ... ok common_tests.sequences_test.test_genotype__permutations('AT', 'W') ... ok common_tests.sequences_test.test_genotype__permutations('TA', 'W') ... ok common_tests.sequences_test.test_genotype__permutations('CG', 'S') ... ok common_tests.sequences_test.test_genotype__permutations('GC', 'S') ... ok common_tests.sequences_test.test_genotype__permutations('CT', 'Y') ... ok common_tests.sequences_test.test_genotype__permutations('TC', 'Y') ... ok common_tests.sequences_test.test_genotype__permutations('GT', 'K') ... ok common_tests.sequences_test.test_genotype__permutations('TG', 'K') ... ok common_tests.sequences_test.test_genotype__permutations('ACG', 'V') ... ok common_tests.sequences_test.test_genotype__permutations('AGC', 'V') ... ok common_tests.sequences_test.test_genotype__permutations('CAG', 'V') ... ok common_tests.sequences_test.test_genotype__permutations('CGA', 'V') ... ok common_tests.sequences_test.test_genotype__permutations('GAC', 'V') ... ok common_tests.sequences_test.test_genotype__permutations('GCA', 'V') ... ok common_tests.sequences_test.test_genotype__permutations('ACT', 'H') ... ok common_tests.sequences_test.test_genotype__permutations('ATC', 'H') ... ok common_tests.sequences_test.test_genotype__permutations('CAT', 'H') ... ok common_tests.sequences_test.test_genotype__permutations('CTA', 'H') ... ok common_tests.sequences_test.test_genotype__permutations('TAC', 'H') ... ok common_tests.sequences_test.test_genotype__permutations('TCA', 'H') ... ok common_tests.sequences_test.test_genotype__permutations('AGT', 'D') ... ok common_tests.sequences_test.test_genotype__permutations('ATG', 'D') ... ok common_tests.sequences_test.test_genotype__permutations('GAT', 'D') ... ok common_tests.sequences_test.test_genotype__permutations('GTA', 'D') ... ok common_tests.sequences_test.test_genotype__permutations('TAG', 'D') ... ok common_tests.sequences_test.test_genotype__permutations('TGA', 'D') ... ok common_tests.sequences_test.test_genotype__permutations('CGT', 'B') ... ok common_tests.sequences_test.test_genotype__permutations('CTG', 'B') ... ok common_tests.sequences_test.test_genotype__permutations('GCT', 'B') ... ok common_tests.sequences_test.test_genotype__permutations('GTC', 'B') ... ok common_tests.sequences_test.test_genotype__permutations('TCG', 'B') ... ok common_tests.sequences_test.test_genotype__permutations('TGC', 'B') ... ok common_tests.sequences_test.test_genotype__bad_input__lowercase ... ok common_tests.sequences_test.test_genotype__bad_input__mixedcase ... ok common_tests.sequences_test.test_genotype__bad_input__unknown_nucleotide ... ok common_tests.sequences_test.test_genotype__bad_input__non_nucleotide ... ok common_tests.sequences_test.test_comma_or_not('CT',) ... ok common_tests.sequences_test.test_comma_or_not('C,T',) ... ok common_tests.sequences_test.test_comma_or_not(',C,T',) ... ok common_tests.sequences_test.test_comma_or_not('C,T,',) ... ok common_tests.sequences_test.test_comma_or_not(',C,T,',) ... ok common_tests.sequences_test.test_count_nts__empty_str ... ok common_tests.sequences_test.test_count_nts__simple ... ok common_tests.sequences_test.test_count_nts__simple_mixed_case ... ok common_tests.sequences_test.test_count_nts__complex ... ok common_tests.sequences_test.test_count_nts__complex_mixed_case ... ok common_tests.sequences_test.test_count_nts__bad_nt ... ok common_tests.sequences_test.test_count_nts__bad_nt_lowercase ... ok common_tests.sequences_test.test_count_gc_diploid__empty_string ... ok common_tests.sequences_test.test_count_gc_diploid__simple ... ok common_tests.sequences_test.test_count_gc_diploid__simple_mixed_case ... ok common_tests.sequences_test.test_count_gc_diploid__complex ... ok common_tests.sequences_test.test_count_gc_diploid__complex_mixed_case ... ok common_tests.sequences_test.test_count_gc_dipoid__ambigious ... ok common_tests.sequences_test.test_count_gc_diploid__ambigous_mixed_case ... ok common_tests.sequences_test.test_count_gc_diploid__triploid ... ok common_tests.sequences_test.test_split__empty_sequence ... ok common_tests.sequences_test.test_split__no_split_by ... ok common_tests.sequences_test.test_split__single_group ... ok common_tests.sequences_test.test_split__two_groups ... ok common_tests.sequences_test.test_split__three_groups ... ok common_tests.sequences_test.test_split__empty_group ... ok common_tests.sequences_test.test_split__partial_group ... ok common_tests.signals_test.test_signal__sigterm_to_str ... ok common_tests.signals_test.test_signal__str_to_sigterm ... ok common_tests.signals_test.test_signal__to_str__unknown_signal ... ok common_tests.signals_test.test_signal__from_str__unknown_signal ... ok common_tests.signals_test.test_signal__to_str__wrong_type ... ok common_tests.signals_test.test_signal__from_str__wrong_type ... ok common_tests.text_tests.test_padded_table__empty ... ok common_tests.text_tests.test_padded_table__single_line ... ok common_tests.text_tests.test_padded_table__two_lines ... ok common_tests.text_tests.test_padded_table__three_lines ... ok common_tests.text_tests.test_padded_table__with_text(['# An insightful comment goes here', (1, 20, 3000), (3000, 20, 1)], ['# An insightful comment goes here', '1 20 3000', '3000 20 1']) ... ok common_tests.text_tests.test_padded_table__with_text([(1, 20, 3000), '# An insightful comment goes here', (3000, 20, 1)], ['1 20 3000', '# An insightful comment goes here', '3000 20 1']) ... ok common_tests.text_tests.test_padded_table__with_text([(1, 20, 3000), (3000, 20, 1), '# An insightful comment goes here'], ['1 20 3000', '3000 20 1', '# An insightful comment goes here']) ... ok common_tests.text_tests.test_parse_padded_table__empty ... ok common_tests.text_tests.test_parse_padded_table__header_only ... ok common_tests.text_tests.test_parse_padded_table__single_row ... ok common_tests.text_tests.test_parse_padded_table__two_rows ... ok common_tests.text_tests.test_parse_padded_table__single_row__with_whitespace ... ok common_tests.text_tests.test_parse_padded_table__single_row__with_tabs ... ok common_tests.text_tests.test_padded_table__comments_and_empty_lines(['# comment', 'A B C', '3000 20 1'],) ... ok common_tests.text_tests.test_padded_table__comments_and_empty_lines(['A B C', ' # comment', '3000 20 1'],) ... ok common_tests.text_tests.test_padded_table__comments_and_empty_lines(['A B C', '3000 20 1', ' # comment'],) ... ok common_tests.text_tests.test_padded_table__comments_and_empty_lines(['', 'A B C', '3000 20 1'],) ... ok common_tests.text_tests.test_padded_table__comments_and_empty_lines(['A B C', ' ', '3000 20 1'],) ... ok common_tests.text_tests.test_padded_table__comments_and_empty_lines(['A B C', '3000 20 1', ' '],) ... ok common_tests.text_tests.test_padded_table__newlines('\r',) ... ok common_tests.text_tests.test_padded_table__newlines('\n',) ... ok common_tests.text_tests.test_padded_table__newlines('\r\n',) ... ok common_tests.text_tests.test_padded_table__padding__comments__whitespace ... ok common_tests.text_tests.test_parse_padded_table__malformed_table_0 ... ok common_tests.text_tests.test_parse_padded_table__malformed_table_1 ... ok common_tests.text_tests.test_parse_lines__empty_file ... ok common_tests.text_tests.test_parse_lines__single ... ok common_tests.text_tests.test_parse_lines__comments_and_empty_lines(['# comment\n', 'abc line1 \n', 'def line2 \n'],) ... ok common_tests.text_tests.test_parse_lines__comments_and_empty_lines(['abc line1 \n', ' # comment\n', 'def line2 \n'],) ... ok common_tests.text_tests.test_parse_lines__comments_and_empty_lines(['abc line1 \n', 'def line2 \n', ' # comment\n'],) ... ok common_tests.text_tests.test_parse_lines__comments_and_empty_lines(['\n', 'abc line1 \n', 'def line2 \n'],) ... ok common_tests.text_tests.test_parse_lines__comments_and_empty_lines(['abc line1 \n', ' \n', 'def line2 \n'],) ... ok common_tests.text_tests.test_parse_lines__comments_and_empty_lines(['abc line1 \n', 'def line2 \n', ' \n'],) ... ok common_tests.text_tests.test_parse_lines__padding__newlines('\r',) ... ok common_tests.text_tests.test_parse_lines__padding__newlines('\n',) ... ok common_tests.text_tests.test_parse_lines__padding__newlines('\r\n',) ... ok common_tests.text_tests.test_parse_lines__uncallable ... ok common_tests.text_tests.test_parse_lines_by_contig__single_contig ... ok common_tests.text_tests.test_parse_lines__two_contigs ... ok common_tests.utilities_test.test_safe_coerce_to_tuple__str ... ok common_tests.utilities_test.test_safe_coerce_to_tuple__unicode ... ok common_tests.utilities_test.test_safe_coerce_to_tuple__int ... ok common_tests.utilities_test.test_safe_coerce_to_tuple__list ... ok common_tests.utilities_test.test_safe_coerce_to_tuple__tuple ... ok common_tests.utilities_test.test_safe_coerce_to_tuple__iterable ... ok common_tests.utilities_test.test_safe_coerce_to_tuple__dict ... ok common_tests.utilities_test.test_safe_coerce_to_frozenset__str ... ok common_tests.utilities_test.test_safe_coerce_to_frozenset__unicode ... ok common_tests.utilities_test.test_safe_coerce_to_frozenset__int ... ok common_tests.utilities_test.test_safe_coerce_to_frozenset__list ... ok common_tests.utilities_test.test_safe_coerce_to_frozenset__tuple ... ok common_tests.utilities_test.test_safe_coerce_to_frozenset__iterable ... ok common_tests.utilities_test.test_safe_coerce_to_frozenset__dict ... ok common_tests.utilities_test.test_try_cast__int_to_int ... ok common_tests.utilities_test.test_try_cast__float_to_int ... ok common_tests.utilities_test.test_try_cast__good_str_to_int ... ok common_tests.utilities_test.test_try_cast__bad_str_to_int ... ok common_tests.utilities_test.test_try_cast__list_to_int ... ok common_tests.utilities_test.test_crc32_is_unsigned ... ok common_tests.utilities_test.test_set_in__single_kw_in_empty_dictionary ... ok common_tests.utilities_test.test_set_in__two_kws_in_empty_dictionary ... ok common_tests.utilities_test.test_set_in__three_kws_in_empty_dictionary ... ok common_tests.utilities_test.test_set_in__three_kws_in_partial_dictionary ... ok common_tests.utilities_test.test_set_in__update_value_one_kw ... ok common_tests.utilities_test.test_set_in__update_value_two_kw ... ok common_tests.utilities_test.test_set_in__fail_on_no_kws ... ok common_tests.utilities_test.test_set_in__fail_on_invalid_sub_dictionary_first_level ... ok common_tests.utilities_test.test_set_in__fail_on_invalid_sub_dictionary_second_level ... ok common_tests.utilities_test.test_set_in__fail_on_invalid_sub_dictionary_third_level ... ok common_tests.utilities_test.test_set_in__iteratable_keywords ... ok common_tests.utilities_test.test_get_in__get_value_one_keyword ... ok common_tests.utilities_test.test_get_in__get_value_two_keywords ... ok common_tests.utilities_test.test_get_in__get_value_three_keywords ... ok common_tests.utilities_test.test_get_in__get_default_one_keyword ... ok common_tests.utilities_test.test_get_in__get_default_one_keyword_with_default ... ok common_tests.utilities_test.test_get_in__get_default_three_keywords_fail_at_first ... ok common_tests.utilities_test.test_get_in__get_default_three_keywords_fail_at_first_with_default ... ok common_tests.utilities_test.test_get_in__get_default_three_keywords_fail_at_second ... ok common_tests.utilities_test.test_get_in__get_default_three_keywords_fail_at_second_with_default ... ok common_tests.utilities_test.test_get_in__get_default_three_keywords_fail_at_third ... ok common_tests.utilities_test.test_get_in__get_default_three_keywords_fail_at_third_with_default ... ok common_tests.utilities_test.test_get_in__iterator_keywords ... ok common_tests.utilities_test.test_split_before__split_empty_list ... ok common_tests.utilities_test.test_split_before__split_list_with_no_true_pred ... ok common_tests.utilities_test.test_split_before__split_list_true_pred_at_first_position ... ok common_tests.utilities_test.test_split_before__split_list_true_pred_at_second_position ... ok common_tests.utilities_test.test_split_before__split_consequtive_true_pred ... ok common_tests.utilities_test.test_split_before__no_hits ... ok common_tests.utilities_test.test_is_strictly_increasing__increasing_sequence ... ok common_tests.utilities_test.test_is_strictly_increasing__non_increasing_sequence ... ok common_tests.utilities_test.test_grouper__empty_list ... ok common_tests.utilities_test.test_grouper__non_empty_list ... ok common_tests.utilities_test.test_grouper__non_empty_list_with_trailing ... ok common_tests.utilities_test.test_grouper__non_empty_list_with_trailing_fill_value ... ok common_tests.utilities_test.test_group_by_pred__empty_list ... ok common_tests.utilities_test.test_group_by_pred__always_false ... ok common_tests.utilities_test.test_group_by_pred__always_true ... ok common_tests.utilities_test.test_group_by_pred__is_even ... ok common_tests.utilities_test.test_group_by_pred__iterable ... ok common_tests.utilities_test.test_fragment__empty ... ok common_tests.utilities_test.test_fragment__partial_fragment ... ok common_tests.utilities_test.test_fragment__single_fragment ... ok common_tests.utilities_test.test_fragment__multiple_fragments ... ok common_tests.utilities_test.test_fragment__multiple_fragments_partial ... ok common_tests.utilities_test.test_fragment__iterable ... ok common_tests.utilities_test.test_fragment__set ... ok common_tests.utilities_test.test_cumsum__empty ... ok common_tests.utilities_test.test_cumsum__integers ... ok common_tests.utilities_test.test_cumsum__float ... ok common_tests.utilities_test.test_cumsum__initial ... ok common_tests.utilities_test.test_fast_pickle_test__picklable ... ok common_tests.utilities_test.test_fast_pickle_test__unpicklable_1 ... ok common_tests.utilities_test.test_fast_pickle_test__unpicklable_2 ... ok common_tests.utilities_test.test_fill_dict__empty_dicts ... ok common_tests.utilities_test.test_fill_dict__filling_empty_dict ... ok common_tests.utilities_test.test_fill_dict__filling_full_dict ... ok common_tests.utilities_test.test_fill_dict__destination_not_modified ... ok common_tests.utilities_test.test_fill_dict__source_not_modified ... ok common_tests.utilities_test.test_fill_dict__destination_must_be_dict ... ok common_tests.utilities_test.test_fill_dict__source_must_be_dict ... ok common_tests.utilities_test.test_chain_sorted__no_sequences ... ok common_tests.utilities_test.test_chain_sorted__single_sequence ... ok common_tests.utilities_test.test_chain_sorted__sequential_contents((1, 2, 3), (4, 5, 6)) ... ok common_tests.utilities_test.test_chain_sorted__sequential_contents((4, 5, 6), (1, 2, 3)) ... ok common_tests.utilities_test.test_chain_sorted__mixed_contents ... ok common_tests.utilities_test.test_chain_sorted__mixed_length_contents ... ok common_tests.utilities_test.test_chain_sorted__mixed_contents__key ... ok common_tests.utilities_test.test_chain_sorted__identical_objects_are_preserved ... ok common_tests.utilities_test.test_chain_sorted__stable_sort ... ok common_tests.utilities_test.test_chain_sorted__runs_of_values ... ok common_tests.utilities_test.test_chain_sorted__invalid_keywords ... ok common_tests.utilities_test.test_immutable__properties_set ... ok common_tests.utilities_test.test_immutable__properties_immutable('value', 13) ... ok common_tests.utilities_test.test_immutable__properties_immutable('new_value', 'foo') ... ok common_tests.utilities_test.test_immutable__properties_del ... ok common_tests.utilities_test.test_totally_ordered__lt_vs_lt ... ok common_tests.utilities_test.test_totally_ordered__lt_vs_gt ... ok common_tests.utilities_test.test_totally_ordered__lt_vs_wrong_type ... ok common_tests.utilities_test.test_totally_ordered__le_vs_le ... ok common_tests.utilities_test.test_totally_ordered__le_vs_gt ... ok common_tests.utilities_test.test_totally_ordered__le_vs_wrong_type ... ok common_tests.utilities_test.test_totally_ordered__ge_vs_ge ... ok common_tests.utilities_test.test_totally_ordered__ge_vs_lt ... ok common_tests.utilities_test.test_totally_ordered__ge_vs_wrong_type ... ok common_tests.utilities_test.test_totally_ordered__gt_vs_gt ... ok common_tests.utilities_test.test_totally_ordered__gt_vs_eq ... ok common_tests.utilities_test.test_totally_ordered__gt_vs_wrong_type ... ok common_tests.utilities_test.test_totally_ordered__eq_vs_eq ... ok common_tests.utilities_test.test_totally_ordered__eq_vs_ne ... ok common_tests.utilities_test.test_totally_ordered__eq_vs_wrong_type ... ok common_tests.utilities_test.test_totally_ordered__ne_vs_ne ... ok common_tests.utilities_test.test_totally_ordered__ne_vs_eq ... ok common_tests.utilities_test.test_totally_ordered__ne_vs_wrong_type ... ok common_tests.utilities_test.test_totally_ordered__missing_implementation ... ok common_tests.versions_tests.test_check__func_must_be_callable ... ok common_tests.versions_tests.test_check_str ... ok common_tests.versions_tests.test_check__eq_same_func_desc_and_version ... ok common_tests.versions_tests.test_check__not_eq_for_diff_func_same_desc_and_version ... ok common_tests.versions_tests.test_check__not_eq_for_diff_desc_same_func_and_version ... ok common_tests.versions_tests.test_check__not_eq_for_same_func_desc_diff_version ... ok common_tests.versions_tests.test_eq__str__one_value ... ok common_tests.versions_tests.test_eq__str__two_values ... ok common_tests.versions_tests.test_eq__check_values__equal ... ok common_tests.versions_tests.test_eq__check_values__not_equal ... ok common_tests.versions_tests.test_eq__check_values__equal_truncated ... ok common_tests.versions_tests.test_eq__check_values__equal_too_few_values ... ok common_tests.versions_tests.test_eq__check_values__not_equal_too_few_values ... ok common_tests.versions_tests.test_ge__str__one_value ... ok common_tests.versions_tests.test_ge__str__two_values ... ok common_tests.versions_tests.test_ge__check_values__greater_than_or_equal ... ok common_tests.versions_tests.test_ge__check_values__not_greater_than_or_equal ... ok common_tests.versions_tests.test_ge__check_values__greater_than_or_equal_truncated ... ok common_tests.versions_tests.test_ge__check_values__equal_too_few_values ... ok common_tests.versions_tests.test_ge__check_values__not_equal_too_few_values ... ok common_tests.versions_tests.test_lt__str__one_value ... ok common_tests.versions_tests.test_lt__str__two_values ... ok common_tests.versions_tests.test_lt__check_values__less_than ... ok common_tests.versions_tests.test_lt__check_values__not_less_than ... ok common_tests.versions_tests.test_lt__check_values__less_than_truncated ... ok common_tests.versions_tests.test_lt__check_values__less_than_too_few_values ... ok common_tests.versions_tests.test_lt__check_values__not_less_than_too_few_values ... ok common_tests.versions_tests.test_any__str ... ok common_tests.versions_tests.test_lt__check_values__always_true ... ok common_tests.versions_tests.test_and__init__non_check_value ... ok common_tests.versions_tests.test_and__str__single_item ... ok common_tests.versions_tests.test_and__str__two_items ... ok common_tests.versions_tests.test_and__str__two_items__first_is_operator ... ok common_tests.versions_tests.test_and__str__two_items__second_is_operator ... ok common_tests.versions_tests.test_and__check_version__both_true ... ok common_tests.versions_tests.test_and__check_version__first_true ... ok common_tests.versions_tests.test_and__check_version__second_true ... ok common_tests.versions_tests.test_and__check_version__neither_true ... ok common_tests.versions_tests.test_and__check_version__truncated(, ) ... ok common_tests.versions_tests.test_and__check_version__truncated(, ) ... ok common_tests.versions_tests.test_and__check_version__truncated(, ) ... ok common_tests.versions_tests.test_and__check_version__insufficient_number_of_values(, ) ... ok common_tests.versions_tests.test_and__check_version__insufficient_number_of_values(, ) ... ok common_tests.versions_tests.test_and__check_version__insufficient_number_of_values(, ) ... ok common_tests.versions_tests.test_or__init__non_check_value ... ok common_tests.versions_tests.test_or__str__single_item ... ok common_tests.versions_tests.test_or__str__two_items ... ok common_tests.versions_tests.test_or__str__two_items__first_is_operator ... ok common_tests.versions_tests.test_or__str__two_items__second_is_operator ... ok common_tests.versions_tests.test_or__check_version__both_true ... ok common_tests.versions_tests.test_or__check_version__first_true ... ok common_tests.versions_tests.test_or__check_version__second_true ... ok common_tests.versions_tests.test_or__check_version__neither_true ... ok common_tests.versions_tests.test_or__check_version__truncated(, ) ... ok common_tests.versions_tests.test_or__check_version__truncated(, ) ... ok common_tests.versions_tests.test_or__check_version__truncated(, ) ... ok common_tests.versions_tests.test_or__check_version__insufficient_number_of_values(, ) ... ok common_tests.versions_tests.test_or__check_version__insufficient_number_of_values(, ) ... ok common_tests.versions_tests.test_or__check_version__insufficient_number_of_values__is_lazy ... ok common_tests.versions_tests.test_requirementobj__init__defaults ... ok common_tests.versions_tests.test_requirementobj__init__non_defaults ... ok common_tests.versions_tests.test_requirementobj__version__call('stderr', 'v(\\d+)', (3,)) ... ok common_tests.versions_tests.test_requirementobj__version__call('stderr', 'v(\\d+)\\.(\\d+)', (3, 5)) ... ok common_tests.versions_tests.test_requirementobj__version__call('stderr', 'v(\\d+)\\.(\\d+)\\.(\\d+)', (3, 5, 2)) ... ok common_tests.versions_tests.test_requirementobj__version__call('stdout', 'v(\\d+)', (3,)) ... ok common_tests.versions_tests.test_requirementobj__version__call('stdout', 'v(\\d+)\\.(\\d+)', (3, 5)) ... ok common_tests.versions_tests.test_requirementobj__version__call('stdout', 'v(\\d+)\\.(\\d+)\\.(\\d+)', (3, 5, 2)) ... ok common_tests.versions_tests.test_requirementobj__version__version_str_not_found ... ok common_tests.versions_tests.test_requirementobj__version__command_not_found ... ok common_tests.versions_tests.test_requirementobj__version__return_code_is_ignored ... ok common_tests.versions_tests.test_requirementobj__version__func_call ... ok common_tests.versions_tests.test_requirementobj__version__func_call_with_arguments ... ok common_tests.versions_tests.test_requirementobj__version__outdated_jre__with_or_without_version_str('UnsupportedClassVersionError',) ... ok common_tests.versions_tests.test_requirementobj__version__outdated_jre__with_or_without_version_str('UnsupportedClassVersionError v1.2.3',) ... ok common_tests.versions_tests.test_requirementobj__executable__no_cli_args ... ok common_tests.versions_tests.test_requirementobj__executable__with_cli_arguments ... ok common_tests.versions_tests.test_requirementobj__executable__function ... ok common_tests.versions_tests.test_requirementobj__call__result_is_cached ... ok common_tests.versions_tests.test_requirementobj__call__result_is_cached_unless_forced ... ok common_tests.versions_tests.test_requirementobj__call__check_fails__function ... ok common_tests.versions_tests.test_requirementobj__call__check_fails ... ok common_tests.versions_tests.test_requirementobj__call__check_fails__jre_outdated ... ok common_tests.versions_tests.test_check__can_pickle(,) ... ok common_tests.versions_tests.test_check__can_pickle(,) ... ok common_tests.versions_tests.test_check__can_pickle(,) ... ok common_tests.versions_tests.test_check__can_pickle(,) ... ok common_tests.versions_tests.test_check__can_pickle(,) ... ok common_tests.versions_tests.test_check__can_pickle(,) ... ok common_tests.versions_tests.test_requirement__obj_is_cached_for_same_values ... ok common_tests.versions_tests.test_requirement__new_obj_if_call_differ ... ok common_tests.versions_tests.test_requirement__new_obj_if_search_differ ... ok common_tests.versions_tests.test_requirement__new_obj_if_checks_differ ... ok common_tests.versions_tests.test_requirement__same_obj_if_name_differ ... ok common_tests.versions_tests.test_requirement_highest_priority_overrides ... ok common_tests.versions_tests.test_requirement_highest_priority_retained ... ok node_test._test_commandnode_teardown__missing_files_in_dest__wrapped_by_with_temp_folder ... ok node_test.test_commandnode_teardown__wrapped_by_with_temp_folder ... ok node_test.test_commandnode_teardown__commit__wrapped_by_with_temp_folder ... ok node_test.test_commandnode_teardown__extra_files_in_temp__wrapped_by_with_temp_folder ... ok node_test.test_commandnode_teardown__missing_files_in_temp__wrapped_by_with_temp_folder ... ok node_test.test_commandnode_teardown__missing_optional_files__wrapped_by_with_temp_folder ... ok node_test.test_dir ... ok node_test.test_file ... ok node_test.test_constructor('input_files', '/<>/.pybuild/cpython2_2.7/build/tests/data/empty_file_1') ... ok node_test.test_constructor('output_files', '/<>/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_2') ... ok node_test.test_constructor('executables', 'ls') ... ok node_test.test_constructor('auxiliary_files', '/<>/.pybuild/cpython2_2.7/build/tests/data/rCRS.fasta.fai') ... ok node_test.test_constructor('input_files', ['/<>/.pybuild/cpython2_2.7/build/tests/data/empty_file_2']) ... ok node_test.test_constructor('output_files', ['/<>/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_2']) ... ok node_test.test_constructor('executables', ['ls']) ... ok node_test.test_constructor('auxiliary_files', ['/<>/.pybuild/cpython2_2.7/build/tests/data/rCRS.fasta']) ... ok node_test.test_constructor('input_files', frozenset(['/<>/.pybuild/cpython2_2.7/build/tests/data/empty_file_1', '/<>/.pybuild/cpython2_2.7/build/tests/data/empty_file_2'])) ... ok node_test.test_constructor('output_files', frozenset(['/<>/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_1', '/<>/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_2'])) ... ok node_test.test_constructor('executables', frozenset(['sh', 'ls'])) ... ok node_test.test_constructor('auxiliary_files', frozenset(['/<>/.pybuild/cpython2_2.7/build/tests/data/rCRS.fasta.fai', '/<>/.pybuild/cpython2_2.7/build/tests/data/rCRS.fasta'])) ... ok node_test.test_constructor__invalid_values('input_files', []) ... ok node_test.test_constructor__invalid_values('output_files', [-1]) ... ok node_test.test_constructor__invalid_values('executables', [{}]) ... ok node_test.test_constructor__invalid_values('auxiliary_files', [1.3]) ... ok node_test.test_constructor__requirements ... ok node_test.test_constructor__requirements__wrong_type(17,) ... ok node_test.test_constructor__requirements__wrong_type({},) ... ok node_test.test_constructor__requirements__wrong_type('867-5309',) ... ok node_test.test_constructor__nodes_is_none ... ok node_test.test_constructor__single_node ... ok node_test.test_constructor__iterable ... ok node_test.test_constructor__not_a_node ... ok node_test.test_constructor__description(,) ... ok node_test.test_constructor__description(,) ... ok node_test.test_constructor__description__default(,) ... ok node_test.test_constructor__description__default(,) ... ok node_test.test_constructor__description__non_string(, 1) ... ok node_test.test_constructor__description__non_string(, {}) ... ok node_test.test_constructor__description__non_string(, 1) ... ok node_test.test_constructor__description__non_string(, {}) ... ok node_test.test_constructor__threads(, 1L) ... ok node_test.test_constructor__threads(, 3) ... ok node_test.test_constructor__threads(, 1L) ... ok node_test.test_constructor__threads(, 3) ... ok node_test.test_constructor__threads_invalid_range(, -1) ... ok node_test.test_constructor__threads_invalid_range(, 0) ... ok node_test.test_constructor__threads_invalid_range(, -1) ... ok node_test.test_constructor__threads_invalid_range(, 0) ... ok node_test.test_constructor__threads_invalid_type(, '1') ... ok node_test.test_constructor__threads_invalid_type(, {}) ... ok node_test.test_constructor__threads_invalid_type(, 2.7) ... ok node_test.test_constructor__threads_invalid_type(, '1') ... ok node_test.test_constructor__threads_invalid_type(, {}) ... ok node_test.test_constructor__threads_invalid_type(, 2.7) ... ok node_test.test_run__order ... ok node_test.test_run__exceptions ... ok node_test.test_run__exceptions ... ok node_test.test_run__exceptions ... ok node_test.test_run__exceptions ... ok node_test.test_run__exceptions ... ok node_test.test_run__exceptions ... ok node_test.test_run__exception__create_temp_dir ... ok node_test.test_run__exception__remove_temp_dir ... ok node_test.test_run__error_log__node_error(NodeError('ARGH!',),) ... ok node_test.test_run__error_log__node_error(OSError('ARGH!',),) ... ok node_test.test__setup__input_files({'executables': ('ls', 'sh')},) ... ok node_test.test__setup__input_files({'input_files': frozenset(['/<>/.pybuild/cpython2_2.7/build/tests/data/empty_file_1', '/<>/.pybuild/cpython2_2.7/build/tests/data/empty_file_2'])},) ... ok node_test.test__setup__input_files({'auxiliary_files': frozenset(['/<>/.pybuild/cpython2_2.7/build/tests/data/empty_file_1', '/<>/.pybuild/cpython2_2.7/build/tests/data/empty_file_2'])},) ... ok node_test.test__setup__input_files_missing({'executables': ('ls', 'shxxxx')},) ... ok node_test.test__setup__input_files_missing({'input_files': frozenset(['/<>/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_1', '/<>/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_2'])},) ... ok node_test.test__setup__input_files_missing({'auxiliary_files': frozenset(['/<>/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_1', '/<>/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_2'])},) ... ok node_test.test__teardown__output_files ... ok node_test.test__teardown__output_files_missing ... ok node_test.test_commandnode_constructor__input_files ... ok node_test.test_commandnode_constructor__output_files ... ok node_test.test_commandnode_constructor__auxiliary_files ... ok node_test.test_commandnode_constructor__executables ... ok node_test.test_commandnode_constructor__requirements ... ok node_test.test_commandnode_constructor__dependencies ... ok node_test.test_commandnode_constructor__dependencies__default ... ok node_test.test_command_node__run ... ok node_test.test_commandnode_setup__files_exist({'executables': ('ls', 'sh')},) ... ok node_test.test_commandnode_setup__files_exist({'input_files': frozenset(['/<>/.pybuild/cpython2_2.7/build/tests/data/empty_file_1', '/<>/.pybuild/cpython2_2.7/build/tests/data/empty_file_2'])},) ... ok node_test.test_commandnode_setup__files_exist({'auxiliary_files': frozenset(['/<>/.pybuild/cpython2_2.7/build/tests/data/empty_file_1', '/<>/.pybuild/cpython2_2.7/build/tests/data/empty_file_2'])},) ... ok node_test.test_commandnode_setup__files_missing({'executables': ('ls', 'shxxxxxxxxxxx')},) ... ok node_test.test_commandnode_setup__files_missing({'input_files': frozenset(['/<>/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_1', '/<>/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_2'])},) ... ok node_test.test_commandnode_setup__files_missing({'auxiliary_files': frozenset(['/<>/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_1', '/<>/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_2'])},) ... ok node_test.test_commandnode_run__call_order ... ok node_test.test_commandnode_run__exception_on_error ... ok nodegraph_test.test_dir ... ok nodegraph_test.test_file ... ok nodegraph_test.test_nodegraph_is_done__output_changes__wrapped_by_with_temp_folder ... ok nodegraph_test.test_nodegraph_is_done__subnode_not_considered__wrapped_by_with_temp_folder ... ok nodegraph_test.test_nodegraph_is_done__no_output ... ok nodegraph_test.test_nodegraph_is_outdated__no_output ... ok nodegraph_test.test_nodegraph_is_outdated__input_but_no_output ... ok nodegraph_test.test_nodegraph_is_outdated__output_but_no_input ... ok nodegraph_test.test_nodegraph_is_outdated__not_outdated ... ok nodegraph_test.test_nodegraph_is_outdated__outdated ... ok nodegraph_test.test_nodegraph_is_outdated__updates ... ok factory_test.test_paleomix_command ... ok factory_test.test_factory__commands('bam_pipeline', 'Usage: paleomix bam_pipeline [options] [makefiles]') ... ok factory_test.test_factory__commands('trim_pipeline', 'Usage: paleomix trim_pipeline [options] [makefiles]') ... ok factory_test.test_factory__commands('phylo_pipeline', 'Usage: paleomix phylo_pipeline [options] [makefiles]') ... ok factory_test.test_factory__commands('cleanup', 'usage: paleomix cleanup --temp-prefix prefix --fasta reference.fasta < in.sam') ... ok factory_test.test_factory__commands('coverage', 'usage: paleomix coverage [options] sorted.bam [out.coverage]') ... ok factory_test.test_factory__commands('depths', 'usage: paleomix depths [options] sorted.bam [out.depths]') ... ok factory_test.test_factory__commands('duphist', 'usage: paleomix duphist sorted.bam > out.histogram') ... ok factory_test.test_factory__commands('rmdup_collapsed', 'usage: paleomix rmdup_collapsed [options] < sorted.bam > out.bam') ... ok factory_test.test_factory__commands('genotype', 'usage: paleomix genotype [options] sorted.bam out.vcf.bgz') ... ok factory_test.test_factory__commands('gtf_to_bed', 'usage: paleomix gtf_to_bed [options] in.gtf out_prefix [in.scaffolds]') ... ok factory_test.test_factory__commands('sample_pileup', 'usage: paleomix sample_pileup [options] --genotype in.vcf --intervals in.bed > out.fasta') ... ok factory_test.test_factory__commands('vcf_filter', 'Usage: paleomix vcf_filter [options] [in1.vcf, ...]') ... ok factory_test.test_factory__commands('vcf_to_fasta', 'usage: paleomix vcf_to_fasta [options] --genotype in.vcf --intervals in.bed') ... ok factory_test.test_factory__commands('cat', 'usage: paleomix cat [-h] [--output OUTPUT] file [file ...]') ... ok factory_test.test_factory__command_alias('bam_pipeline', 'bam_pipeline') ... ok factory_test.test_factory__command_alias('bam_rmdup_collapsed', 'rmdup_collapsed') ... ok factory_test.test_factory__command_alias('conv_gtf_to_bed', 'gtf_to_bed') ... ok factory_test.test_factory__command_alias('phylo_pipeline', 'phylo_pipeline') ... ok factory_test.test_factory__command_alias('trim_pipeline', 'trim_pipeline') ... ok ---------------------------------------------------------------------- Ran 1634 tests in 4.152s OK mv tests/common_tests/makefile_test.py~ tests/common_tests/makefile_test.py make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python2 --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_installdirs -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python setup.py install --root /<>/debian/paleomix running install running build running build_py running egg_info writing requirements to paleomix.egg-info/requires.txt writing paleomix.egg-info/PKG-INFO writing top-level names to paleomix.egg-info/top_level.txt writing dependency_links to paleomix.egg-info/dependency_links.txt writing entry points to paleomix.egg-info/entry_points.txt reading manifest file 'paleomix.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'paleomix.egg-info/SOURCES.txt' running install_lib creating /<>/debian/paleomix/usr creating /<>/debian/paleomix/usr/lib creating /<>/debian/paleomix/usr/lib/python2.7 creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /<>/.pybuild/cpython2_2.7/build/paleomix/pipeline.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/coverage.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/genotype.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/gtf_to_bed.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/__init__.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/retable.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/dupcheck.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/duphist.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/sample_pileup.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/cleanup.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/genotype.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/vcf_to_fasta.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_stats copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_stats/coverage.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_stats copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_stats/__init__.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_stats copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_stats/common.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_stats copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_stats/common.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_stats copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_stats/coverage.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_stats copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_stats/__init__.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_stats copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/vcf_to_fasta.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/pipeline.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/mkfile.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/__init__.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/nodes.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/remap.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/library.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/__init__.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/reads.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/target.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/lane.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/prefix.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/statistics.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/sample.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/library.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/summary.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/summary.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/prefix.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/statistics.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/lane.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/target.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/sample.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/reads.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/__init__.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/makefile.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/mkfile.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/trim_pipeline.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/config.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/config.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/trim_pipeline.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/paths.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/nodes.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/makefile.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/paths.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/pipeline.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/__init__.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/rmdup_collapsed.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/depths.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/ena.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/cat.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/factory.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/pipeline.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/mkfile.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/__init__.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts/genotype.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts/__init__.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts/paml.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts/genotype.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts/msa.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts/phylo.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts/paml.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts/phylo.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts/msa.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts/__init__.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/makefile.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/mkfile.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/config.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/config.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/makefile.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/pipeline.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/__init__.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/vcf_filter.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/duphist.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/depths.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/cleanup.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/pipeline.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/build_mito.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/__init__.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/common.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/build_tped.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts/__init__.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts/nuclear.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts/common.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts/mitochondria.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts/summary.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts/report.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts/__init__.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts/admixture.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/config.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/database.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/build_db.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/__init__.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/coverage.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/cat.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/sample_pileup.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/rmdup_collapsed.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/vcf_filter.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/factory.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/__init__.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/tools/gtf_to_bed.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /<>/.pybuild/cpython2_2.7/build/paleomix/__init__.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodegraph.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/__init__.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/reports creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/reports/zonkey copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/reports/zonkey/report.css -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/reports/zonkey creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R1_03.fastq.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R2_03.fastq.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R1_02.fastq.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/GCTCTG_L1_R1_03.fastq.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/GCTCTG_L1_R1_01.fastq.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R1_01.fastq.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R1_02.fastq.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R2_02.fastq.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R2_01.fastq.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R1_01.fastq.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/GCTCTG_L1_R1_02.fastq.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R2_01.fastq.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L1_R1_03.fastq.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L1_R1_01.fastq.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2/reads.singleton.truncated.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2/reads.collapsed.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2/reads.collapsed.truncated.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R1_04.fastq.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L1_R1_02.fastq.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R1_03.fastq.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R2_03.fastq.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R2_04.fastq.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R2_02.fastq.gz -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_prefixes copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_prefixes/rCRS.fasta -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_prefixes copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_makefile.yaml -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_prefixes copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_prefixes/README -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_prefixes copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_prefixes/setup.sh -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_prefixes creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P17777 copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P17777/000_README -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P17777 copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P17777/000_ENA -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P17777 creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1889 copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1889/000_README -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1889 copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1889/000_ENA -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1889 copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/setup.sh -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/M-0182896 copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/M-0182896/000_README -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/M-0182896 copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/M-0182896/000_ENA -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/M-0182896 creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/06_3928A copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/06_3928A/000_README -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/06_3928A copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/06_3928A/000_ENA -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/06_3928A creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13626 copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13626/000_README -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13626 copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13626/000_ENA -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13626 creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1845A copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1845A/000_README -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1845A copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1845A/000_ENA -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1845A creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/LBUS5 copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/LBUS5/000_README -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/LBUS5 copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/LBUS5/000_ENA -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/LBUS5 creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/NL07434 copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/NL07434/000_README -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/NL07434 copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/NL07434/000_ENA -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/NL07434 creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13527 copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13527/000_README -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13527 copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13527/000_ENA -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13527 creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/DDR7602 copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/DDR7602/000_README -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/DDR7602 copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/DDR7602/000_ENA -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/DDR7602 copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_makefile.yaml -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/phylogeny copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/phylogeny/select_highly_covered_genes.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/phylogeny copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/phylogeny/summarize_heterozygosity.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/phylogeny copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/phylogeny/000_makefile.yaml -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/phylogeny creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/profiling copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/profiling/build_all_profiles.sh -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/profiling copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/profiling/metagenomic_profile.R -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/profiling copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/profiling/build_profile.sh -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/profiling creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.depths -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.coverage -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.summary -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.depths -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/M-0182896.Pi_nucl.coverage -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/M-0182896.Pi_mito.coverage -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/M-0182896.Pi_nucl.depths -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.coverage -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.depths -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_iter_summ_stat.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_hist.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Length_plot.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/dnacomp.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_post_pred.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/lgdistribution.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/dnacomp_genome.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/misincorporation.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_trace.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Fragmisincorporation_plot.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/3pGtoA_freq.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Runtime_log.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_correct_prob.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/5pCtoT_freq.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_iter_summ_stat.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_hist.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Length_plot.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/dnacomp.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_post_pred.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/lgdistribution.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/dnacomp_genome.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/misincorporation.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_trace.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Fragmisincorporation_plot.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/3pGtoA_freq.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Runtime_log.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_correct_prob.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/5pCtoT_freq.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_iter_summ_stat.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_hist.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Length_plot.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/dnacomp.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_post_pred.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/lgdistribution.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/dnacomp_genome.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/misincorporation.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_trace.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Fragmisincorporation_plot.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/3pGtoA_freq.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Runtime_log.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_correct_prob.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/5pCtoT_freq.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_iter_summ_stat.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_hist.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Length_plot.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/dnacomp.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_post_pred.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/lgdistribution.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/dnacomp_genome.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/misincorporation.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_trace.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Fragmisincorporation_plot.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/3pGtoA_freq.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Runtime_log.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_correct_prob.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/5pCtoT_freq.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_iter_summ_stat.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_hist.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Length_plot.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/dnacomp.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_post_pred.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/lgdistribution.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/dnacomp_genome.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/misincorporation.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_trace.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Fragmisincorporation_plot.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/3pGtoA_freq.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Runtime_log.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_correct_prob.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/5pCtoT_freq.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/M-0182896.Pi_mito.depths -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.coverage -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/M-0182896.summary -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.depths -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_iter_summ_stat.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_hist.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Length_plot.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/dnacomp.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_post_pred.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/lgdistribution.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/dnacomp_genome.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/misincorporation.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_trace.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Fragmisincorporation_plot.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/3pGtoA_freq.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Runtime_log.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Stats_out_MCMC_correct_prob.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/5pCtoT_freq.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_iter_summ_stat.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_hist.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Length_plot.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/dnacomp.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_post_pred.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/lgdistribution.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/dnacomp_genome.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/misincorporation.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_trace.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Fragmisincorporation_plot.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/3pGtoA_freq.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Runtime_log.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Stats_out_MCMC_correct_prob.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/5pCtoT_freq.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.coverage -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.summary -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_iter_summ_stat.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_hist.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Length_plot.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/dnacomp.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_post_pred.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/lgdistribution.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/dnacomp_genome.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/misincorporation.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_trace.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Fragmisincorporation_plot.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/3pGtoA_freq.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Runtime_log.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Stats_out_MCMC_correct_prob.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/5pCtoT_freq.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_iter_summ_stat.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_hist.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Length_plot.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/dnacomp.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_post_pred.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/lgdistribution.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/dnacomp_genome.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/misincorporation.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_trace.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Fragmisincorporation_plot.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/3pGtoA_freq.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Runtime_log.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Stats_out_MCMC_correct_prob.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/5pCtoT_freq.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_iter_summ_stat.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_hist.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Length_plot.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/dnacomp.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_post_pred.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/lgdistribution.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/dnacomp_genome.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/misincorporation.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_trace.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Fragmisincorporation_plot.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/3pGtoA_freq.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Runtime_log.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Stats_out_MCMC_correct_prob.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/5pCtoT_freq.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/M.0182896.UDGc.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/Pi1845A.id.CGCTAT.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/Pi1889.id.GGCTAC.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/M.0182896.UDG.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/Pi1889.id.TAGCTT.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results/Relative_abundances_genus.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results/Taxon_count_genus.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results/Potato_merged_profiles.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results/Potato_merged.csv -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results/Diversity_genus.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results/PCA_genus.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results/Heatmap_genus.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results/Distances_genus.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results/PCOA_genus.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results/Barplot_class.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results/Clustering_genus.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/Pi1889.id.CTTGTA.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/M.0182896.UDGb.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/M.0182896.UDGa.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Krona_Pi1845A.all.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Figure_Krona_M.0182896.all.html -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Krona_Pi1845A.pdf -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Pi1889.all.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Krona_Pi1889.all.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Figure_Krona_Pi1889.all.html -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/M.0182896.all.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Figure_Krona_Pi1845A.all.html -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Krona_M.0182896.all.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/M.0182896.NO.UDG.txt -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/white_handed_gibbon.fasta -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/gorilla.fasta -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/sumatran_orangutan.fasta -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/chimpanzee.fasta -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/rCRS.fasta -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/bonobo.fasta -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/rCRS.fasta.fai -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/setup.sh -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_makefile.yaml -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.protein_coding.CDS.bed -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.non_coding.bed -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/phylogeny/000_makefile.yaml -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/setup.sh -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/synthesize_reads.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/rscripts creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/rscripts/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/common/requires.r -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/rscripts/common creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/rscripts/zonkey copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/zonkey/coverage.r -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/rscripts/zonkey copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/zonkey/tinytree.r -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/rscripts/zonkey copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/zonkey/pca.r -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/rscripts/zonkey copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/zonkey/treemix.r -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/rscripts/zonkey copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/zonkey/admixture.r -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/rscripts/zonkey copying /<>/.pybuild/cpython2_2.7/build/paleomix/resources/__init__.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/__init__.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/README -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/LICENSE -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/CHANGES -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/PKG-INFO -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/loader.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/__init__.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/serializer.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/loader.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/representer.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/nodes.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/resolver.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/tokens.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/serializer.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/error.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/scanner.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/parser.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/dumper.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/resolver.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/composer.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/representer.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/constructor.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/emitter.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/composer.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/reader.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/events.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/emitter.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/dumper.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/nodes.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/parser.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/events.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/tokens.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/constructor.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/reader.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/__init__.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/error.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/scanner.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /<>/.pybuild/cpython2_2.7/build/paleomix/yaml/__init__.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd copying /<>/.pybuild/cpython2_2.7/build/paleomix/atomiccmd/__init__.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd copying /<>/.pybuild/cpython2_2.7/build/paleomix/atomiccmd/pprint.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd copying /<>/.pybuild/cpython2_2.7/build/paleomix/atomiccmd/command.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd copying /<>/.pybuild/cpython2_2.7/build/paleomix/atomiccmd/builder.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd copying /<>/.pybuild/cpython2_2.7/build/paleomix/atomiccmd/sets.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd copying /<>/.pybuild/cpython2_2.7/build/paleomix/atomiccmd/sets.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd copying /<>/.pybuild/cpython2_2.7/build/paleomix/atomiccmd/pprint.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd copying /<>/.pybuild/cpython2_2.7/build/paleomix/atomiccmd/builder.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd copying /<>/.pybuild/cpython2_2.7/build/paleomix/atomiccmd/__init__.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd copying /<>/.pybuild/cpython2_2.7/build/paleomix/atomiccmd/command.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd copying /<>/.pybuild/cpython2_2.7/build/paleomix/ui.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/fileutils.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/system.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/testing.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/bamfiles.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/timer.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/signals.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/__init__.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/bedtools.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/fileutils.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/utilities.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/vcffilter.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/text.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats/_common.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats/phylip.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats/__init__.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats/fastq.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats/msa.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats/_common.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats/phylip.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats/fasta.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats/fastq.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats/newick.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats/_graph.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats/newick.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats/_graph.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats/msa.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats/__init__.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/formats/fasta.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/vcfwrap.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/sequences.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/sampling.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/text.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/versions.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/console.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/testing.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/utilities.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/sequences.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/vcfwrap.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/sampling.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/rtools.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/makefile.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/procs.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/rtools.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/bamfiles.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/vcffilter.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/versions.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/console.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/system.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/makefile.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/procs.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/bedtools.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/signals.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/timer.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/common/__init__.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /<>/.pybuild/cpython2_2.7/build/paleomix/main.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /<>/.pybuild/cpython2_2.7/build/paleomix/config.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /<>/.pybuild/cpython2_2.7/build/paleomix/config.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /<>/.pybuild/cpython2_2.7/build/paleomix/logger.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /<>/.pybuild/cpython2_2.7/build/paleomix/node.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodegraph.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /<>/.pybuild/cpython2_2.7/build/paleomix/main.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /<>/.pybuild/cpython2_2.7/build/paleomix/ui.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /<>/.pybuild/cpython2_2.7/build/paleomix/logger.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /<>/.pybuild/cpython2_2.7/build/paleomix/node.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix creating /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/adapterremoval.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/phylip.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/__init__.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/formats.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/bedtools.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/picard.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/mapdamage.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/adapterremoval.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/validation.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/sequences.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/bowtie2.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/sequences.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/examl.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/phylip.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/mafft.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/mafft.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/gatk.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/newick.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/misc.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/raxml.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/commands.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/newick.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/samtools.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/validation.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/mapdamage.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/examl.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/raxml.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/bwa.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/gatk.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/formats.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/samtools.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/bowtie2.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/commands.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/bedtools.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/picard.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/__init__.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/nodes/bwa.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /<>/.pybuild/cpython2_2.7/build/paleomix/pipeline.pyc -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /<>/.pybuild/cpython2_2.7/build/paleomix/__init__.py -> /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/pipeline.py to pipeline.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/coverage.py to coverage.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/gtf_to_bed.py to gtf_to_bed.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/retable.py to retable.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/dupcheck.py to dupcheck.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/duphist.py to duphist.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/genotype.py to genotype.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_stats/coverage.py to coverage.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_stats/common.py to common.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_stats/__init__.py to __init__.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/vcf_to_fasta.py to vcf_to_fasta.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/pipeline.py to pipeline.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/remap.py to remap.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts/library.py to library.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts/reads.py to reads.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts/prefix.py to prefix.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts/statistics.py to statistics.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts/sample.py to sample.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts/summary.py to summary.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts/lane.py to lane.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts/target.py to target.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts/__init__.py to __init__.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/makefile.py to makefile.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/mkfile.py to mkfile.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/config.py to config.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/trim_pipeline.py to trim_pipeline.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/paths.py to paths.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/nodes.py to nodes.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/__init__.py to __init__.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/ena.py to ena.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/pipeline.py to pipeline.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts/genotype.py to genotype.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts/phylo.py to phylo.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts/paml.py to paml.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts/msa.py to msa.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts/__init__.py to __init__.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/makefile.py to makefile.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/mkfile.py to mkfile.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/config.py to config.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/__init__.py to __init__.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/depths.py to depths.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/cleanup.py to cleanup.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/pipeline.py to pipeline.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/build_mito.py to build_mito.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/common.py to common.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/build_tped.py to build_tped.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts/nuclear.py to nuclear.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts/common.py to common.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts/mitochondria.py to mitochondria.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts/summary.py to summary.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts/report.py to report.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts/__init__.py to __init__.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts/admixture.py to admixture.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/config.py to config.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/database.py to database.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/build_db.py to build_db.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/__init__.py to __init__.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/cat.py to cat.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/sample_pileup.py to sample_pileup.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/rmdup_collapsed.py to rmdup_collapsed.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/vcf_filter.py to vcf_filter.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/factory.py to factory.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/__init__.py to __init__.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodegraph.py to nodegraph.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/phylogeny/select_highly_covered_genes.py to select_highly_covered_genes.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/phylogeny/summarize_heterozygosity.py to summarize_heterozygosity.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/synthesize_reads.py to synthesize_reads.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/__init__.py to __init__.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/loader.py to loader.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/tokens.py to tokens.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/serializer.py to serializer.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/error.py to error.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/dumper.py to dumper.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/resolver.py to resolver.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/representer.py to representer.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/composer.py to composer.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/events.py to events.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/emitter.py to emitter.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/nodes.py to nodes.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/parser.py to parser.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/constructor.py to constructor.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/reader.py to reader.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/__init__.py to __init__.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/scanner.py to scanner.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/__init__.py to __init__.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd/command.py to command.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd/builder.py to builder.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd/sets.py to sets.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd/pprint.py to pprint.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd/__init__.py to __init__.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/fileutils.py to fileutils.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/testing.py to testing.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/bamfiles.py to bamfiles.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/signals.py to signals.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/utilities.py to utilities.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/vcffilter.py to vcffilter.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats/_common.py to _common.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats/phylip.py to phylip.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats/fastq.py to fastq.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats/newick.py to newick.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats/_graph.py to _graph.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats/msa.py to msa.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats/__init__.py to __init__.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats/fasta.py to fasta.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/vcfwrap.py to vcfwrap.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/sampling.py to sampling.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/text.py to text.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/versions.py to versions.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/console.py to console.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/sequences.py to sequences.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/makefile.py to makefile.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/rtools.py to rtools.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/system.py to system.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/procs.py to procs.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/bedtools.py to bedtools.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/timer.py to timer.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/__init__.py to __init__.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/main.py to main.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/config.py to config.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/node.py to node.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/ui.py to ui.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/logger.py to logger.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/phylip.py to phylip.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/formats.py to formats.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/adapterremoval.py to adapterremoval.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/validation.py to validation.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/bowtie2.py to bowtie2.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/sequences.py to sequences.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/examl.py to examl.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/mafft.py to mafft.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/gatk.py to gatk.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/newick.py to newick.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/misc.py to misc.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/raxml.py to raxml.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/commands.py to commands.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/samtools.py to samtools.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/mapdamage.py to mapdamage.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/bwa.py to bwa.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/bedtools.py to bedtools.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/picard.py to picard.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/__init__.py to __init__.pyc byte-compiling /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/__init__.py to __init__.pyc running install_egg_info Copying paleomix.egg-info to /<>/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix-1.2.13.3.egg-info Skipping SOURCES.txt running install_scripts Installing trim_pipeline script to /<>/debian/paleomix/usr/bin Installing bam_rmdup_collapsed script to /<>/debian/paleomix/usr/bin Installing bam_pipeline script to /<>/debian/paleomix/usr/bin Installing paleomix script to /<>/debian/paleomix/usr/bin Installing conv_gtf_to_bed script to /<>/debian/paleomix/usr/bin Installing phylo_pipeline script to /<>/debian/paleomix/usr/bin debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install find debian -name LICENSE -delete make[1]: Leaving directory '/<>' debian/rules override_dh_installdocs make[1]: Entering directory '/<>' dh_installdocs # since tests dir contains empty files which are used afterwards for # testing and dh_installdocs is ignoring empty files we need to make # sure all files are really copied rsync -a -v tests debian/paleomix/usr/share/doc/paleomix sending incremental file list tests/atomiccmd_test/ tests/bwa/testcases/case_01a/ tests/bwa/testcases/case_01b/ tests/bwa/testcases/case_02/ tests/bwa/testcases/case_03/ tests/bwa/testcases/case_04/ tests/common_tests/ tests/common_tests/formats_tests/ tests/data/ tests/data/empty_file_1 tests/data/empty_file_2 tests/data/empty_file_3 tests/data/timestamp_a_older tests/data/timestamp_a_younger tests/data/timestamp_b_older tests/data/timestamp_b_younger tests/data/alignments/ tests/data/raw_reads/ tests/data/sim_reads/ sent 2,277 bytes received 205 bytes 4,964.00 bytes/sec total size is 605,728 speedup is 244.05 # test runner is seeking for paleomix modules in source - we use inside the installed package ### sed -i 's:(find paleomix -mindepth 1:(find /usr/lib/python2.7/dist-packages/paleomix -mindepth 1:' debian/*/usr/share/doc/*/tests/run #echo "====== Also empty files belong to the docs ======" #find debian -name "empty_file*" #find debian -name "timestamp_*" #echo "====== Hope something was printed between these lines ====" # # This test tries to execute setup.sh which does not work outside source directory find debian/paleomix/usr/share/doc/ -name fileutils_test.py -delete find debian/paleomix/usr/share/doc/ -name setup.h -delete make[1]: Leaving directory '/<>' dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_installcatalogs -O--buildsystem=pybuild dh_installcron -O--buildsystem=pybuild dh_installdebconf -O--buildsystem=pybuild dh_installemacsen -O--buildsystem=pybuild dh_installifupdown -O--buildsystem=pybuild dh_installinfo -O--buildsystem=pybuild dh_python2 -O--buildsystem=pybuild I: dh_python2 tools:113: replacing shebang in debian/paleomix/usr/bin/bam_rmdup_collapsed I: dh_python2 tools:113: replacing shebang in debian/paleomix/usr/bin/conv_gtf_to_bed I: dh_python2 tools:113: replacing shebang in debian/paleomix/usr/bin/bam_pipeline I: dh_python2 tools:113: replacing shebang in debian/paleomix/usr/bin/phylo_pipeline I: dh_python2 tools:113: replacing shebang in debian/paleomix/usr/bin/trim_pipeline I: dh_python2 tools:113: replacing shebang in debian/paleomix/usr/bin/paleomix dh_installinit -O--buildsystem=pybuild dh_installsystemd -O--buildsystem=pybuild dh_installmenu -O--buildsystem=pybuild dh_installmime -O--buildsystem=pybuild dh_installmodules -O--buildsystem=pybuild dh_installlogcheck -O--buildsystem=pybuild dh_installlogrotate -O--buildsystem=pybuild dh_installpam -O--buildsystem=pybuild dh_installppp -O--buildsystem=pybuild dh_installudev -O--buildsystem=pybuild dh_installgsettings -O--buildsystem=pybuild dh_bugfiles -O--buildsystem=pybuild dh_ucf -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_gconf -O--buildsystem=pybuild dh_gconf: Please migrate to dh_installgsettings; gconf + dh_gconf is scheduled for removal. dh_icons -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_usrlocal -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_installwm -O--buildsystem=pybuild dh_installxfonts -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild debian/rules override_dh_fixperms make[1]: Entering directory '/<>' dh_fixperms for rs in `find debian -iname "*.r"` ; do \ if head -n 1 $rs | grep -q '^#!/usr/bin/.*Rscript' ; then \ chmod +x $rs ; \ else \ chmod -x $rs ; \ fi ; \ done make[1]: Leaving directory '/<>' dh_missing -O--buildsystem=pybuild dh_strip -O--buildsystem=pybuild dh_makeshlibs -O--buildsystem=pybuild dh_shlibdeps -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package paleomix: substitution variable ${python:Versions} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild INFO: pkgstriptranslations version 143 pkgstriptranslations: processing paleomix (in debian/paleomix); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/paleomix/DEBIAN/control, package paleomix, directory debian/paleomix pkgstripfiles: Running PNG optimization (using 4 cpus) for package paleomix ... pkgstripfiles: No PNG files. dpkg-deb: building package 'paleomix' in '../paleomix_1.2.13.3-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../paleomix_1.2.13.3-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20181217-1710 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ paleomix_1.2.13.3-1_amd64.changes: ---------------------------------- Format: 1.8 Date: Mon, 17 Dec 2018 13:35:27 +0100 Source: paleomix Binary: paleomix Architecture: amd64 Version: 1.2.13.3-1 Distribution: disco-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: paleomix - pipelines and tools for the processing of ancient and modern HTS Changes: paleomix (1.2.13.3-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.2.1 * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target * Do not use tox to run full test suite in autopkgtest since it relies on full source dir Checksums-Sha1: 1ab582c0a6c77a491f5ce71002fecc76a9a4c152 8027 paleomix_1.2.13.3-1_amd64.buildinfo c4adc129a3b9495a907c6e75e019a5420543a5e5 4668144 paleomix_1.2.13.3-1_amd64.deb Checksums-Sha256: 7dcb2495d19638c77e09b169680f3b4becf70396d826609b54ca3c6c047d3935 8027 paleomix_1.2.13.3-1_amd64.buildinfo a437d317a7722402d216d057786d3144f563b22e499d708a9f814ab93bdcf17f 4668144 paleomix_1.2.13.3-1_amd64.deb Files: f44da70874a5ce8cb00847a8d2538f6a 8027 science optional paleomix_1.2.13.3-1_amd64.buildinfo b29df4a63fabc25a782f7dae5441be5a 4668144 science optional paleomix_1.2.13.3-1_amd64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ paleomix_1.2.13.3-1_amd64.deb ----------------------------- new debian package, version 2.0. size 4668144 bytes: control archive=13568 bytes. 1658 bytes, 27 lines control 68718 bytes, 500 lines md5sums 158 bytes, 9 lines * postinst #!/bin/sh 255 bytes, 14 lines * prerm #!/bin/sh Package: paleomix Version: 1.2.13.3-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 7898 Depends: python-pysam, python-setproctitle, python:any (<< 2.8), python:any (>= 2.7~), adapterremoval, bedtools, bowtie2, bwa, bcftools, examl, mafft, mapdamage, phylip, picard-tools, r-base-core, radiant, raxml, samtools, python-coverage, python-flexmock Section: science Priority: optional Homepage: http://geogenetics.ku.dk/publications/paleomix Description: pipelines and tools for the processing of ancient and modern HTS data The PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data: The BAM pipeline processes de-multiplexed reads from one or more samples, through sequence processing and alignment, to generate BAM alignment files useful in downstream analyses; the Phylogenetic pipeline carries out genotyping and phylogenetic inference on BAM alignment files, either produced using the BAM pipeline or generated elsewhere; and the Zonkey pipeline carries out a suite of analyses on low coverage equine alignments, in order to detect the presence of F1-hybrids in archaeological assemblages. In addition, PALEOMIX aids in metagenomic analysis of the extracts. . 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+------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 33592 Build-Time: 17 Distribution: disco-proposed Host Architecture: amd64 Install-Time: 23 Job: paleomix_1.2.13.3-1.dsc Machine Architecture: amd64 Package: paleomix Package-Time: 41 Source-Version: 1.2.13.3-1 Space: 33592 Status: successful Version: 1.2.13.3-1 -------------------------------------------------------------------------------- Finished at 20181217-1710 Build needed 00:00:41, 33592k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15789404 Scanning for processes to kill in build PACKAGEBUILD-15789404