I: pbuilder: network access will be disabled during build I: Current time: Mon Jan 10 16:41:30 +14 2022 I: pbuilder-time-stamp: 1641782490 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [paleomix_1.2.13.3-1.dsc] I: copying [./paleomix_1.2.13.3.orig.tar.gz] I: copying [./paleomix_1.2.13.3-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Tue Dec 18 02:47:04 2018 +14 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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/46733/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/46733/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/46733/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=f5ed27c514fa49049e18daa537848938 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=46733 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.kglvkoChTP/pbuilderrc_Oi41 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.kglvkoChTP/b2 --logfile b2/build.log paleomix_1.2.13.3-1.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 5.9.0-0.bpo.2-amd64 #1 SMP Debian 5.9.6-1~bpo10+1 (2020-11-19) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash -rwxr-xr-x 1 root root 109408 Mar 1 2019 date -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd -rwxr-xr-x 1 root root 93744 Mar 1 2019 df -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 35424 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln -rwxr-xr-x 1 root root 56760 Jul 27 2018 login -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 10 2019 more -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jan 10 16:41 sh -> bash lrwxrwxrwx 1 root root 4 Jan 10 04:46 sh.distrib -> dash -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty -rwsr-xr-x 1 root root 63568 Jan 10 2019 su -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch -rwxr-xr-x 1 root root 35424 Mar 1 2019 true -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/46733/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 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 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python; however: Package python is not installed. pbuilder-satisfydepends-dummy depends on python-setuptools; however: Package python-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python-coverage; however: Package python-coverage is not installed. pbuilder-satisfydepends-dummy depends on python-flexmock; however: Package python-flexmock is not installed. pbuilder-satisfydepends-dummy depends on python-nose; however: Package python-nose is not installed. pbuilder-satisfydepends-dummy depends on python-pysam; however: Package python-pysam is not installed. pbuilder-satisfydepends-dummy depends on python-setproctitle; however: Package python-setproctitle is not installed. pbuilder-satisfydepends-dummy depends on default-jre-headless; however: Package default-jre-headless is not installed. pbuilder-satisfydepends-dummy depends on bowtie2; however: Package bowtie2 is not installed. pbuilder-satisfydepends-dummy depends on rsync; however: Package rsync is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bowtie2{a} bsdmainutils{a} ca-certificates{a} ca-certificates-java{a} debhelper{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} java-common{a} libarchive-zip-perl{a} libasound2{a} libasound2-data{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbsd0{a} libcroco3{a} libcups2{a} libcurl3-gnutls{a} libdbus-1-3{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libglib2.0-0{a} libgssapi-krb5-2{a} libhts2{a} libicu63{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} libldap-2.4-2{a} libldap-common{a} libmagic-mgc{a} libmagic1{a} libmpdec2{a} libncurses6{a} libnghttp2-14{a} libnspr4{a} libnss3{a} libpcsclite1{a} libpipeline1{a} libpng16-16{a} libpopt0{a} libpsl5{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libpython3-stdlib{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.1{a} libtbb2{a} libtool{a} libuchardet0{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxrender1{a} libxtst6{a} lsb-base{a} m4{a} man-db{a} mime-support{a} openjdk-11-jre-headless{a} openssl{a} po-debconf{a} python{a} python-coverage{a} python-flexmock{a} python-minimal{a} python-nose{a} python-pkg-resources{a} python-pysam{a} python-setproctitle{a} python-setuptools{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.7{a} python3.7-minimal{a} readline-common{a} rsync{a} sensible-utils{a} ucf{a} x11-common{a} The following packages are RECOMMENDED but will NOT be installed: curl dbus krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libjs-jquery libjs-jquery-isonscreen libjs-jquery-tablesorter libjs-jquery-throttle-debounce libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 121 newly installed, 0 to remove and 0 not upgraded. Need to get 82.2 MB of archives. After unpacking 330 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u3 [1538 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u2 [589 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u2 [1731 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u2 [1732 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u2 [330 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u1 [242 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u1 [117 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u1 [66.4 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libtbb2 amd64 2018~U6-4 [147 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 bowtie2 amd64 2.3.4.3-1 [1188 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1d-0+deb10u3 [844 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20190110 [157 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 java-common all 0.71 [14.4 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 libavahi-common-data amd64 0.7-4+b1 [122 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 libavahi-common3 amd64 0.7-4+b1 [54.6 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libdbus-1-3 amd64 1.12.20-0+deb10u1 [215 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libavahi-client3 amd64 0.7-4+b1 [58.1 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u1 [65.8 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u1 [122 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u1 [369 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u1 [158 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 libcups2 amd64 2.2.10-6+deb10u4 [324 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u2 [380 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libnspr4 amd64 2:4.20-1 [112 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libnss3 amd64 2:3.42.1-1+deb10u3 [1159 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libasound2-data all 1.1.8-1 [59.6 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 libasound2 amd64 1.1.8-1 [361 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 libpcsclite1 amd64 1.8.24-1 [58.5 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 libx11-data all 2:1.6.7-1+deb10u1 [294 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 libx11-6 amd64 2:1.6.7-1+deb10u1 [757 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 libxi6 amd64 2:1.7.9-1 [82.6 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 x11-common all 1:7.7+19 [251 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 libxtst6 amd64 2:1.2.3-1 [27.8 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 openjdk-11-jre-headless amd64 11.0.9.1+1-1~deb10u2 [37.7 MB] Get: 81 http://deb.debian.org/debian buster/main amd64 default-jre-headless amd64 2:1.11-71 [10.9 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 ca-certificates-java all 20190405 [15.7 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u2 [1258 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u1 [689 kB] Get: 93 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 95 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 96 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 98 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 99 http://deb.debian.org/debian buster/main amd64 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 100 http://deb.debian.org/debian buster/main amd64 python3-distutils all 3.7.3-1 [142 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 dh-python all 3.20190308 [99.3 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 104 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u4 [89.8 kB] Get: 105 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u4 [224 kB] Get: 106 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 107 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 108 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 109 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 110 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u1 [330 kB] Get: 111 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get: 112 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-11 [305 kB] Get: 113 http://deb.debian.org/debian buster/main amd64 libpopt0 amd64 1.16-12 [49.4 kB] Get: 114 http://deb.debian.org/debian buster/main amd64 python-pkg-resources all 40.8.0-1 [182 kB] Get: 115 http://deb.debian.org/debian buster/main amd64 python-coverage amd64 4.5.2+dfsg.1-1 [144 kB] Get: 116 http://deb.debian.org/debian buster/main amd64 python-flexmock all 0.10.3-1 [19.0 kB] Get: 117 http://deb.debian.org/debian buster/main amd64 python-nose all 1.3.7-4 [132 kB] Get: 118 http://deb.debian.org/debian buster/main amd64 python-pysam amd64 0.15.2+ds-2 [1629 kB] Get: 119 http://deb.debian.org/debian buster/main amd64 python-setproctitle amd64 1.1.10-1+b2 [15.4 kB] Get: 120 http://deb.debian.org/debian buster/main amd64 python-setuptools all 40.8.0-1 [382 kB] Get: 121 http://deb.debian.org/debian buster/main amd64 rsync amd64 3.1.3-6 [397 kB] Fetched 82.2 MB in 1s (60.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_amd64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libpython2.7-minimal:amd64. Preparing to unpack .../06-libpython2.7-minimal_2.7.16-2+deb10u1_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../07-python2.7-minimal_2.7.16-2+deb10u1_amd64.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u1) ... Selecting previously unselected package python2-minimal. Preparing to unpack .../08-python2-minimal_2.7.16-1_amd64.deb ... Unpacking python2-minimal (2.7.16-1) ... Selecting previously unselected package python-minimal. Preparing to unpack .../09-python-minimal_2.7.16-1_amd64.deb ... Unpacking python-minimal (2.7.16-1) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../10-libssl1.1_1.1.1d-0+deb10u3_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1d-0+deb10u3) ... Selecting previously unselected package mime-support. Preparing to unpack .../11-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../12-libexpat1_2.2.6-2+deb10u1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-2+deb10u1) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:amd64. Preparing to unpack .../14-libreadline7_7.0-5_amd64.deb ... Unpacking libreadline7:amd64 (7.0-5) ... Selecting previously unselected package libpython2.7-stdlib:amd64. Preparing to unpack .../15-libpython2.7-stdlib_2.7.16-2+deb10u1_amd64.deb ... Unpacking libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7. Preparing to unpack .../16-python2.7_2.7.16-2+deb10u1_amd64.deb ... Unpacking python2.7 (2.7.16-2+deb10u1) ... Selecting previously unselected package libpython2-stdlib:amd64. Preparing to unpack .../17-libpython2-stdlib_2.7.16-1_amd64.deb ... Unpacking libpython2-stdlib:amd64 (2.7.16-1) ... Selecting previously unselected package libpython-stdlib:amd64. Preparing to unpack .../18-libpython-stdlib_2.7.16-1_amd64.deb ... Unpacking libpython-stdlib:amd64 (2.7.16-1) ... Setting up libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20658 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_amd64.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20691 files and directories currently installed.) Preparing to unpack .../python_2.7.16-1_amd64.deb ... Unpacking python (2.7.16-1) ... Selecting previously unselected package libpython3.7-minimal:amd64. Preparing to unpack .../libpython3.7-minimal_3.7.3-2+deb10u2_amd64.deb ... Unpacking libpython3.7-minimal:amd64 (3.7.3-2+deb10u2) ... Selecting previously unselected package python3.7-minimal. Preparing to unpack .../python3.7-minimal_3.7.3-2+deb10u2_amd64.deb ... Unpacking python3.7-minimal (3.7.3-2+deb10u2) ... Setting up libssl1.1:amd64 (1.1.1d-0+deb10u3) ... Setting up libpython3.7-minimal:amd64 (3.7.3-2+deb10u2) ... Setting up libexpat1:amd64 (2.2.6-2+deb10u1) ... Setting up python3.7-minimal (3.7.3-2+deb10u2) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20945 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.7.3-1_amd64.deb ... Unpacking python3-minimal (3.7.3-1) ... Selecting previously unselected package libmpdec2:amd64. Preparing to unpack .../libmpdec2_2.4.2-2_amd64.deb ... Unpacking libmpdec2:amd64 (2.4.2-2) ... Selecting previously unselected package libpython3.7-stdlib:amd64. Preparing to unpack .../libpython3.7-stdlib_3.7.3-2+deb10u2_amd64.deb ... Unpacking libpython3.7-stdlib:amd64 (3.7.3-2+deb10u2) ... Selecting previously unselected package python3.7. Preparing to unpack .../python3.7_3.7.3-2+deb10u2_amd64.deb ... Unpacking python3.7 (3.7.3-2+deb10u2) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../libpython3-stdlib_3.7.3-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.7.3-1) ... Setting up python3-minimal (3.7.3-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21357 files and directories currently installed.) Preparing to unpack .../00-python3_3.7.3-1_amd64.deb ... Unpacking python3 (3.7.3-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.35-4+deb10u1_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../03-libmagic1_1%3a5.35-4+deb10u1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.35-4+deb10u1_amd64.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package ucf. Preparing to unpack .../06-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../07-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../08-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../09-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../10-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../11-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../12-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtbb2:amd64. Preparing to unpack .../13-libtbb2_2018~U6-4_amd64.deb ... Unpacking libtbb2:amd64 (2018~U6-4) ... Selecting previously unselected package bowtie2. Preparing to unpack .../14-bowtie2_2.3.4.3-1_amd64.deb ... Unpacking bowtie2 (2.3.4.3-1) ... Selecting previously unselected package openssl. Preparing to unpack .../15-openssl_1.1.1d-0+deb10u3_amd64.deb ... Unpacking openssl (1.1.1d-0+deb10u3) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../16-ca-certificates_20190110_all.deb ... Unpacking ca-certificates (20190110) ... Selecting previously unselected package java-common. Preparing to unpack .../17-java-common_0.71_all.deb ... Unpacking java-common (0.71) ... Selecting previously unselected package libavahi-common-data:amd64. Preparing to unpack .../18-libavahi-common-data_0.7-4+b1_amd64.deb ... Unpacking libavahi-common-data:amd64 (0.7-4+b1) ... Selecting previously unselected package libavahi-common3:amd64. Preparing to unpack .../19-libavahi-common3_0.7-4+b1_amd64.deb ... Unpacking libavahi-common3:amd64 (0.7-4+b1) ... Selecting previously unselected package libdbus-1-3:amd64. Preparing to unpack .../20-libdbus-1-3_1.12.20-0+deb10u1_amd64.deb ... Unpacking libdbus-1-3:amd64 (1.12.20-0+deb10u1) ... Selecting previously unselected package libavahi-client3:amd64. Preparing to unpack .../21-libavahi-client3_0.7-4+b1_amd64.deb ... Unpacking libavahi-client3:amd64 (0.7-4+b1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../22-libkeyutils1_1.6-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6-6) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../23-libkrb5support0_1.17-3+deb10u1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.17-3+deb10u1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../24-libk5crypto3_1.17-3+deb10u1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.17-3+deb10u1) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../25-libkrb5-3_1.17-3+deb10u1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.17-3+deb10u1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../26-libgssapi-krb5-2_1.17-3+deb10u1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.17-3+deb10u1) ... Selecting previously unselected package libcups2:amd64. Preparing to unpack .../27-libcups2_2.2.10-6+deb10u4_amd64.deb ... Unpacking libcups2:amd64 (2.2.10-6+deb10u4) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../28-liblcms2-2_2.9-3_amd64.deb ... Unpacking liblcms2-2:amd64 (2.9-3) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../29-libjpeg62-turbo_1%3a1.5.2-2+deb10u1_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../30-libpng16-16_1.6.36-6_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.36-6) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../31-libfreetype6_2.9.1-3+deb10u2_amd64.deb ... Unpacking libfreetype6:amd64 (2.9.1-3+deb10u2) ... 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No schema files found: doing nothing. Setting up libtbb2:amd64 (2018~U6-4) ... Setting up x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up libmagic1:amd64 (1:5.35-4+deb10u1) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u4) ... Setting up libicu63:amd64 (63.1-6+deb10u1) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u1) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up libasound2-data (1.1.8-1) ... Setting up autotools-dev (20180224.1) ... Setting up libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Setting up libx11-data (2:1.6.7-1+deb10u1) ... Setting up libnspr4:amd64 (2:4.20-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libavahi-common-data:amd64 (0.7-4+b1) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libdbus-1-3:amd64 (1.12.20-0+deb10u1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up libpng16-16:amd64 (1.6.36-6) ... Setting up autopoint (0.19.8.1-9) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libpcsclite1:amd64 (1.8.24-1) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u1) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libasound2:amd64 (1.1.8-1) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u1) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up openssl (1.1.1d-0+deb10u3) ... Setting up libbsd0:amd64 (0.9.1-2) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u1) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libpopt0:amd64 (1.16-12) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libpython3.7-stdlib:amd64 (3.7.3-2+deb10u2) ... Setting up libxcb1:amd64 (1.13.1-2) ... Setting up libtool (2.4.6-9) ... Setting up libavahi-common3:amd64 (0.7-4+b1) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u4) ... Setting up m4 (1.4.18-2) ... Setting up libnss3:amd64 (2:3.42.1-1+deb10u3) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Setting up ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 128 added, 0 removed; done. Setting up libfreetype6:amd64 (2.9.1-3+deb10u2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u1) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up ucf (3.0038+nmu1) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libx11-6:amd64 (2:1.6.7-1+deb10u1) ... Setting up libavahi-client3:amd64 (0.7-4+b1) ... Setting up rsync (3.1.3-6) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of restart. Setting up libpython3-stdlib:amd64 (3.7.3-1) ... 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 python3.7 (3.7.3-2+deb10u2) ... Setting up gettext (0.19.8.1-9) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libpython2-stdlib:amd64 (2.7.16-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u1) ... Setting up python3 (3.7.3-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python2 (2.7.16-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython-stdlib:amd64 (2.7.16-1) ... Setting up libcups2:amd64 (2.2.10-6+deb10u4) ... Setting up libfontconfig1:amd64 (2.13.1-2) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python (2.7.16-1) ... Setting up python3-distutils (3.7.3-1) ... Setting up dh-python (3.20190308) ... Setting up libxi6:amd64 (2:1.7.9-1) ... Setting up libhts2:amd64 (1.9-11) ... Setting up python-pkg-resources (40.8.0-1) ... Setting up libxtst6:amd64 (2:1.2.3-1) ... Setting up po-debconf (1.0.21) ... Setting up bowtie2 (2.3.4.3-1) ... Setting up python-coverage (4.5.2+dfsg.1-1) ... Setting up python-flexmock (0.10.3-1) ... Setting up python-setuptools (40.8.0-1) ... Setting up python-setproctitle:amd64 (1.1.10-1+b2) ... Setting up python-pysam (0.15.2+ds-2) ... Setting up python-nose (1.3.7-4) ... Setting up dh-autoreconf (19) ... Setting up default-jre-headless (2:1.11-71) ... Setting up openjdk-11-jre-headless:amd64 (11.0.9.1+1-1~deb10u2) ... 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/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) 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/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up debhelper (12.1.1) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up ca-certificates-java (20190405) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Taiwan_GRCA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Secure_Global_CA.pem Adding debian:SecureTrust_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:LuxTrust_Global_Root_2.pem Adding debian:Izenpe.com.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:ISRG_Root_X1.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:EC-ACC.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:DST_Root_CA_X3.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:Certinomis_-_Root_CA.pem Adding debian:Certigna.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AddTrust_External_Root.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:ACCVRAIZ1.pem done. Processing triggers for libc-bin (2.28-10) ... Processing triggers for ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/paleomix-1.2.13.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package paleomix dpkg-buildpackage: info: source version 1.2.13.3-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille 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 '/build/paleomix-1.2.13.3/.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 /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix copying paleomix/ui.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix copying paleomix/pipeline.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix copying paleomix/nodegraph.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix copying paleomix/node.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix copying paleomix/main.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix copying paleomix/logger.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix copying paleomix/config.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix copying paleomix/__init__.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml copying paleomix/yaml/__init__.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/vcf_to_fasta.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/vcf_filter.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/sample_pileup.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/rmdup_collapsed.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/retable.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/gtf_to_bed.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/genotype.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/factory.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/ena.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/duphist.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/dupcheck.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/depths.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/coverage.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/cleanup.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/cat.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools copying paleomix/tools/__init__.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources copying paleomix/resources/__init__.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/validation.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/sequences.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/samtools.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/raxml.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/picard.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/phylip.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/newick.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/misc.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/mapdamage.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/mafft.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/gatk.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/formats.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/examl.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/commands.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/bwa.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/bowtie2.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/bedtools.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/adapterremoval.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes copying paleomix/nodes/__init__.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/versions.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/vcfwrap.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/vcffilter.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/utilities.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/timer.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/text.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/testing.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/system.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/signals.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/sequences.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/sampling.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/rtools.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/procs.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/makefile.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/fileutils.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/console.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/bedtools.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/bamfiles.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common copying paleomix/common/__init__.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/atomiccmd copying paleomix/atomiccmd/sets.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/atomiccmd copying paleomix/atomiccmd/pprint.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/atomiccmd copying paleomix/atomiccmd/command.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/atomiccmd copying paleomix/atomiccmd/builder.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/atomiccmd copying paleomix/atomiccmd/__init__.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/atomiccmd creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/tokens.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/serializer.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/scanner.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/resolver.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/representer.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/reader.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/parser.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/nodes.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/loader.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/events.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/error.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/emitter.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/dumper.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/constructor.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/composer.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 copying paleomix/yaml/lib2/__init__.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2 creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey copying paleomix/tools/zonkey/pipeline.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey copying paleomix/tools/zonkey/database.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey copying paleomix/tools/zonkey/config.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey copying paleomix/tools/zonkey/common.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey copying paleomix/tools/zonkey/build_tped.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey copying paleomix/tools/zonkey/build_mito.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey copying paleomix/tools/zonkey/build_db.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey copying paleomix/tools/zonkey/__init__.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline copying paleomix/tools/phylo_pipeline/pipeline.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline copying paleomix/tools/phylo_pipeline/mkfile.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline copying paleomix/tools/phylo_pipeline/makefile.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline copying paleomix/tools/phylo_pipeline/config.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline copying paleomix/tools/phylo_pipeline/__init__.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_stats copying paleomix/tools/bam_stats/coverage.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_stats copying paleomix/tools/bam_stats/common.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_stats copying paleomix/tools/bam_stats/__init__.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_stats creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline copying paleomix/tools/bam_pipeline/trim_pipeline.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline copying paleomix/tools/bam_pipeline/remap.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline copying paleomix/tools/bam_pipeline/pipeline.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline copying paleomix/tools/bam_pipeline/paths.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline copying paleomix/tools/bam_pipeline/nodes.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline copying paleomix/tools/bam_pipeline/mkfile.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline copying paleomix/tools/bam_pipeline/makefile.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline copying paleomix/tools/bam_pipeline/config.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline copying paleomix/tools/bam_pipeline/__init__.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts copying paleomix/tools/zonkey/parts/summary.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts copying paleomix/tools/zonkey/parts/report.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts copying paleomix/tools/zonkey/parts/nuclear.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts copying paleomix/tools/zonkey/parts/mitochondria.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts copying paleomix/tools/zonkey/parts/common.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts copying paleomix/tools/zonkey/parts/admixture.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts copying paleomix/tools/zonkey/parts/__init__.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts copying paleomix/tools/phylo_pipeline/parts/phylo.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts copying paleomix/tools/phylo_pipeline/parts/paml.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts copying paleomix/tools/phylo_pipeline/parts/msa.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts copying paleomix/tools/phylo_pipeline/parts/genotype.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts copying paleomix/tools/phylo_pipeline/parts/__init__.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts copying paleomix/tools/bam_pipeline/parts/target.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts copying paleomix/tools/bam_pipeline/parts/summary.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts copying paleomix/tools/bam_pipeline/parts/statistics.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts copying paleomix/tools/bam_pipeline/parts/sample.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts copying paleomix/tools/bam_pipeline/parts/reads.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts copying paleomix/tools/bam_pipeline/parts/prefix.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts copying paleomix/tools/bam_pipeline/parts/library.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts copying paleomix/tools/bam_pipeline/parts/lane.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts copying paleomix/tools/bam_pipeline/parts/__init__.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats copying paleomix/common/formats/phylip.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats copying paleomix/common/formats/newick.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats copying paleomix/common/formats/msa.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats copying paleomix/common/formats/fastq.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats copying paleomix/common/formats/fasta.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats copying paleomix/common/formats/_graph.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats copying paleomix/common/formats/_common.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats copying paleomix/common/formats/__init__.py -> /build/paleomix-1.2.13.3/.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' copying paleomix/yaml/CHANGES -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml copying paleomix/yaml/LICENSE -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml copying paleomix/yaml/PKG-INFO -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml copying paleomix/yaml/README -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline copying paleomix/resources/examples/bam_pipeline/000_makefile.yaml -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2 creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_prefixes copying paleomix/resources/examples/bam_pipeline/000_prefixes/rCRS.fasta -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_prefixes creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment copying paleomix/resources/examples/nature_protocols/alignment/000_makefile.yaml -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_prefixes copying paleomix/resources/examples/nature_protocols/alignment/000_prefixes/README -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_prefixes copying paleomix/resources/examples/nature_protocols/alignment/000_prefixes/setup.sh -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_prefixes creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads copying paleomix/resources/examples/nature_protocols/alignment/000_rawreads/setup.sh -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/06_3928A creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/DDR7602 creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/LBUS5 creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/M-0182896 creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/NL07434 creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13527 creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13626 creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P17777 creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1845A creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1889 creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.summary -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment copying paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.summary -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/phylogeny copying paleomix/resources/examples/nature_protocols/phylogeny/000_makefile.yaml -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/phylogeny copying paleomix/resources/examples/nature_protocols/phylogeny/select_highly_covered_genes.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/phylogeny copying paleomix/resources/examples/nature_protocols/phylogeny/summarize_heterozygosity.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/phylogeny creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/profiling copying paleomix/resources/examples/nature_protocols/profiling/build_all_profiles.sh -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/profiling copying paleomix/resources/examples/nature_protocols/profiling/build_profile.sh -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/profiling copying paleomix/resources/examples/nature_protocols/profiling/metagenomic_profile.R -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/profiling creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline copying paleomix/resources/examples/phylo_pipeline/setup.sh -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline copying paleomix/resources/examples/phylo_pipeline/synthesize_reads.py -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment copying paleomix/resources/examples/phylo_pipeline/alignment/000_makefile.yaml -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment copying paleomix/resources/examples/phylo_pipeline/alignment/setup.sh -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/bonobo.fasta -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/chimpanzee.fasta -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/gorilla.fasta -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/rCRS.fasta -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/phylogeny copying paleomix/resources/examples/phylo_pipeline/phylogeny/000_makefile.yaml -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/phylogeny creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data creating /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/reports creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/reports/zonkey copying paleomix/resources/reports/zonkey/report.css -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/reports/zonkey creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/common copying paleomix/resources/rscripts/common/requires.r -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/common creating /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/admixture.r -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/coverage.r -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/pca.r -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/tinytree.r -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/treemix.r -> /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/zonkey debian/rules override_dh_auto_test make[1]: Entering directory '/build/paleomix-1.2.13.3' # 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=/build/paleomix-1.2.13.3/bin/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path dh_auto_test I: pybuild base:217: cd /build/paleomix-1.2.13.3/.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 0x7f2e832f6668>,) ... 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', '/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/empty_file_2') ... ok node_test.test_constructor('output_files', '/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_2') ... ok node_test.test_constructor('executables', 'sh') ... ok node_test.test_constructor('auxiliary_files', '/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/rCRS.fasta') ... ok node_test.test_constructor('input_files', ['/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/empty_file_2']) ... ok node_test.test_constructor('output_files', ['/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_2']) ... ok node_test.test_constructor('executables', ['sh']) ... ok node_test.test_constructor('auxiliary_files', ['/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/rCRS.fasta.fai']) ... ok node_test.test_constructor('input_files', frozenset(['/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/empty_file_2', '/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/empty_file_1'])) ... ok node_test.test_constructor('output_files', frozenset(['/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_2', '/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_1'])) ... ok node_test.test_constructor('executables', frozenset(['sh', 'ls'])) ... ok node_test.test_constructor('auxiliary_files', frozenset(['/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/rCRS.fasta.fai', '/build/paleomix-1.2.13.3/.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(['/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/empty_file_2', '/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/empty_file_1'])},) ... ok node_test.test__setup__input_files({'auxiliary_files': frozenset(['/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/empty_file_2', '/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/empty_file_1'])},) ... ok node_test.test__setup__input_files_missing({'executables': ('ls', 'shxxxx')},) ... ok node_test.test__setup__input_files_missing({'input_files': frozenset(['/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_2', '/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_1'])},) ... ok node_test.test__setup__input_files_missing({'auxiliary_files': frozenset(['/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_2', '/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_1'])},) ... 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(['/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/empty_file_2', '/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/empty_file_1'])},) ... ok node_test.test_commandnode_setup__files_exist({'auxiliary_files': frozenset(['/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/empty_file_2', '/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/empty_file_1'])},) ... ok node_test.test_commandnode_setup__files_missing({'executables': ('ls', 'shxxxxxxxxxxx')},) ... ok node_test.test_commandnode_setup__files_missing({'input_files': frozenset(['/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_2', '/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_1'])},) ... ok node_test.test_commandnode_setup__files_missing({'auxiliary_files': frozenset(['/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_2', '/build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/tests/data/missing_out_file_1'])},) ... 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 6.766s OK mv tests/common_tests/makefile_test.py~ tests/common_tests/makefile_test.py make[1]: Leaving directory '/build/paleomix-1.2.13.3' 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_auto_install -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python setup.py install --root /build/paleomix-1.2.13.3/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 /build/paleomix-1.2.13.3/debian/paleomix/usr creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7 creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/config.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/pipeline.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/logger.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodegraph.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/ui.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/main.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/node.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/__init__.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/atomiccmd/sets.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/atomiccmd/pprint.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/atomiccmd/command.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/atomiccmd/builder.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/atomiccmd/__init__.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/atomiccmd/__init__.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/atomiccmd/builder.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/atomiccmd/command.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/atomiccmd/pprint.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/atomiccmd/sets.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/vcfwrap.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/vcffilter.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/bamfiles.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/timer.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/bedtools.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/console.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/text.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/rtools.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/system.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/sampling.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/sequences.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/versions.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/signals.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/procs.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/makefile.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/utilities.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/fileutils.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/testing.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/__init__.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats/phylip.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats/_graph.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats/newick.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats/msa.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats/fasta.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats/fastq.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats/_common.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats/__init__.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats/__init__.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats/_common.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats/_graph.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats/fasta.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats/fastq.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats/msa.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats/newick.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/formats/phylip.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/__init__.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/bamfiles.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/bedtools.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/console.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/fileutils.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/makefile.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/procs.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/rtools.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/sampling.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/sequences.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/signals.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/system.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/testing.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/text.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/timer.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/utilities.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/vcffilter.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/vcfwrap.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/common/versions.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/newick.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/examl.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/phylip.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/raxml.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/formats.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/mafft.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/sequences.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/bedtools.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/gatk.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/commands.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/mapdamage.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/picard.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/bowtie2.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/samtools.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/bwa.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/validation.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/adapterremoval.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/__init__.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/__init__.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/adapterremoval.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/bedtools.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/bowtie2.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/bwa.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/commands.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/examl.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/formats.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/gatk.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/mafft.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/mapdamage.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/misc.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/newick.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/phylip.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/picard.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/raxml.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/samtools.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/sequences.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodes/validation.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/__init__.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/rscripts creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/rscripts/zonkey copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/zonkey/treemix.r -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/rscripts/zonkey copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/zonkey/tinytree.r -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/rscripts/zonkey copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/zonkey/pca.r -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/rscripts/zonkey copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/zonkey/coverage.r -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/rscripts/zonkey copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/zonkey/admixture.r -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/rscripts/zonkey creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/rscripts/common copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/rscripts/common/requires.r -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/rscripts/common creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/reports creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/reports/zonkey copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/reports/zonkey/report.css -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/reports/zonkey creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.protein_coding.CDS.bed -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.non_coding.bed -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/phylogeny/000_makefile.yaml -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/white_handed_gibbon.fasta -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/sumatran_orangutan.fasta -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/rCRS.fasta.fai -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/rCRS.fasta -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/gorilla.fasta -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/chimpanzee.fasta -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes/bonobo.fasta -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/000_prefixes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/setup.sh -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/alignment/000_makefile.yaml -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/synthesize_reads.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/phylo_pipeline/setup.sh -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/profiling copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/profiling/metagenomic_profile.R -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/profiling copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/profiling/build_profile.sh -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/profiling copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/profiling/build_all_profiles.sh -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/profiling creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/phylogeny copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/phylogeny/summarize_heterozygosity.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/phylogeny copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/phylogeny/select_highly_covered_genes.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/phylogeny copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/phylogeny/000_makefile.yaml -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/phylogeny creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results/Taxon_count_genus.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results/Relative_abundances_genus.csv -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results/Potato_merged_profiles.csv -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results/Potato_merged.csv -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results/PCOA_genus.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results/PCA_genus.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results/Heatmap_genus.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results/Diversity_genus.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results/Distances_genus.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results/Clustering_genus.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/results/Barplot_class.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/results creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Pi1889.all.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/M.0182896.all.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Krona_Pi1889.all.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Krona_Pi1845A.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Krona_Pi1845A.all.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Krona_M.0182896.all.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Figure_Krona_Pi1889.all.html -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Figure_Krona_Pi1845A.all.html -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Figure_Krona_M.0182896.all.html -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling/krona copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/Pi1889.id.TAGCTT.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/Pi1889.id.GGCTAC.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/Pi1889.id.CTTGTA.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/Pi1845A.id.CGCTAT.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/M.0182896.UDGc.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/M.0182896.UDGb.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/M.0182896.UDGa.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/M.0182896.UDG.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/profiling/M.0182896.NO.UDG.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/profiling creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/misincorporation.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/lgdistribution.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/dnacomp_genome.csv -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/dnacomp.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Runtime_log.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Length_plot.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/Fragmisincorporation_plot.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/5pCtoT_freq.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT/3pGtoA_freq.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_TAGCTT creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/misincorporation.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/lgdistribution.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/dnacomp_genome.csv -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/dnacomp.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Runtime_log.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Length_plot.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/Fragmisincorporation_plot.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/5pCtoT_freq.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC/3pGtoA_freq.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_GGCTAC creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/misincorporation.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/lgdistribution.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/dnacomp_genome.csv -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/dnacomp.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Runtime_log.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Length_plot.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/Fragmisincorporation_plot.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/5pCtoT_freq.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA/3pGtoA_freq.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.mapDamage/Pi1889_id_CTTGTA creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/misincorporation.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/lgdistribution.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/dnacomp_genome.csv -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/dnacomp.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Runtime_log.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Length_plot.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/Fragmisincorporation_plot.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/5pCtoT_freq.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT/3pGtoA_freq.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_TAGCTT creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/misincorporation.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/lgdistribution.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/dnacomp_genome.csv -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/dnacomp.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Runtime_log.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Length_plot.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/Fragmisincorporation_plot.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/5pCtoT_freq.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC/3pGtoA_freq.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_GGCTAC creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/misincorporation.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/lgdistribution.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/dnacomp_genome.csv -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/dnacomp.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Runtime_log.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Length_plot.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/Fragmisincorporation_plot.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/5pCtoT_freq.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA/3pGtoA_freq.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.mapDamage/Pi1889_id_CTTGTA creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/misincorporation.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/lgdistribution.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/dnacomp_genome.csv -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/dnacomp.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Runtime_log.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Length_plot.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/Fragmisincorporation_plot.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/5pCtoT_freq.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT/3pGtoA_freq.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CGCTAT creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/misincorporation.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/lgdistribution.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/dnacomp_genome.csv -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/dnacomp.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Runtime_log.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Length_plot.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/Fragmisincorporation_plot.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/5pCtoT_freq.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA/3pGtoA_freq.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.mapDamage/Pi1845A_id_CATAGA creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/misincorporation.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/lgdistribution.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/dnacomp_genome.csv -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/dnacomp.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Runtime_log.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Length_plot.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/Fragmisincorporation_plot.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/5pCtoT_freq.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT/3pGtoA_freq.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CGCTAT creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/misincorporation.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/lgdistribution.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/dnacomp_genome.csv -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/dnacomp.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.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 -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Runtime_log.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Length_plot.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/Fragmisincorporation_plot.pdf -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/5pCtoT_freq.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA/3pGtoA_freq.txt -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.mapDamage/Pi1845A_id_CATAGA copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.summary -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.depths -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_nucl.coverage -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.depths -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1889.Pi_mito.coverage -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.summary -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.depths -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_nucl.coverage -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.depths -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/Pi1845A.Pi_mito.coverage -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/M-0182896.summary -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/M-0182896.Pi_nucl.depths -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/M-0182896.Pi_nucl.coverage -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/M-0182896.Pi_mito.depths -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/example_results/alignment/M-0182896.Pi_mito.coverage -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/example_results/alignment creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1889 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1889/000_README -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1889 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1889/000_ENA -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1889 creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1845A copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1845A/000_README -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1845A copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1845A/000_ENA -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/Pi1845A creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P17777 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P17777/000_README -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P17777 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P17777/000_ENA -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P17777 creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13626 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13626/000_README -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13626 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13626/000_ENA -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13626 creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13527 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13527/000_README -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13527 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13527/000_ENA -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/P13527 creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/NL07434 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/NL07434/000_README -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/NL07434 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/NL07434/000_ENA -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/NL07434 creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/M-0182896 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/M-0182896/000_README -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/M-0182896 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/M-0182896/000_ENA -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/M-0182896 creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/LBUS5 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/LBUS5/000_README -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/LBUS5 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/LBUS5/000_ENA -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/LBUS5 creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/DDR7602 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/DDR7602/000_README -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/DDR7602 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/DDR7602/000_ENA -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/DDR7602 creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/06_3928A copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/06_3928A/000_README -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/06_3928A copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/06_3928A/000_ENA -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/06_3928A copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_rawreads/setup.sh -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_rawreads creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_prefixes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_prefixes/setup.sh -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_prefixes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_prefixes/README -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment/000_prefixes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/nature_protocols/alignment/000_makefile.yaml -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/alignment creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_prefixes copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_prefixes/rCRS.fasta -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_prefixes creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2/reads.singleton.truncated.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2/reads.collapsed.truncated.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2/reads.collapsed.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R2_03.fastq.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R2_02.fastq.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R2_01.fastq.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R1_03.fastq.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R1_02.fastq.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L2_R1_01.fastq.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L1_R1_03.fastq.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L1_R1_02.fastq.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/TGCTCA_L1_R1_01.fastq.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/GCTCTG_L1_R1_03.fastq.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/GCTCTG_L1_R1_02.fastq.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/GCTCTG_L1_R1_01.fastq.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R2_04.fastq.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R2_03.fastq.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R2_02.fastq.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R2_01.fastq.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R1_04.fastq.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R1_03.fastq.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R1_02.fastq.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_data/ACGATA_L1_R1_01.fastq.gz -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline/000_data copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/examples/bam_pipeline/000_makefile.yaml -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/bam_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/resources/__init__.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/cat.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/vcf_to_fasta.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/vcf_filter.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/sample_pileup.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/gtf_to_bed.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/genotype.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/rmdup_collapsed.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/duphist.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/depths.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/coverage.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/cleanup.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/factory.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/__init__.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/trim_pipeline.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/mkfile.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/config.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/makefile.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/pipeline.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/nodes.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/paths.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/__init__.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/summary.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/statistics.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/target.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/prefix.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/sample.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/library.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/lane.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/reads.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/__init__.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/__init__.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/lane.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/library.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/prefix.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/reads.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/sample.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/statistics.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/summary.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/parts/target.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/__init__.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/config.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/makefile.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/mkfile.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/nodes.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/paths.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/pipeline.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/remap.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_pipeline/trim_pipeline.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_stats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_stats/common.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_stats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_stats/coverage.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_stats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_stats/__init__.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_stats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_stats/__init__.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_stats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_stats/common.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_stats copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/bam_stats/coverage.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_stats creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/config.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/makefile.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/mkfile.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/pipeline.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/__init__.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts/phylo.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts/paml.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts/msa.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts/genotype.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts/__init__.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts/__init__.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts/genotype.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts/msa.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts/paml.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/parts/phylo.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/__init__.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/config.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/makefile.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/mkfile.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/phylo_pipeline/pipeline.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/__init__.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts/__init__.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts/__init__.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts/admixture.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts/common.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts/mitochondria.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts/nuclear.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts/report.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/parts/summary.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/__init__.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/build_db.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/build_mito.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/build_tped.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/common.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/config.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/database.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/zonkey/pipeline.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/__init__.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/cat.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/cleanup.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/coverage.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/depths.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/dupcheck.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/duphist.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/ena.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/factory.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/genotype.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/gtf_to_bed.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/retable.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/rmdup_collapsed.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/sample_pileup.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/vcf_filter.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/tools/vcf_to_fasta.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/__init__.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/README -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/PKG-INFO -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/LICENSE -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/CHANGES -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml creating /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/representer.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/serializer.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/emitter.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/dumper.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/resolver.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/constructor.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/composer.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/parser.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/scanner.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/reader.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/loader.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/nodes.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/events.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/tokens.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/error.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/__init__.pyc -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/__init__.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/composer.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/constructor.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/dumper.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/emitter.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/error.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/events.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/loader.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/nodes.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/parser.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/reader.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/representer.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/resolver.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/scanner.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/serializer.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/lib2/tokens.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2 copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/yaml/__init__.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/__init__.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/config.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/logger.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/main.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/node.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/nodegraph.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/pipeline.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix copying /build/paleomix-1.2.13.3/.pybuild/cpython2_2.7/build/paleomix/ui.py -> /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd/__init__.py to __init__.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd/builder.py to builder.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd/command.py to command.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd/pprint.py to pprint.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/atomiccmd/sets.py to sets.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats/__init__.py to __init__.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats/_common.py to _common.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats/_graph.py to _graph.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats/fasta.py to fasta.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats/fastq.py to fastq.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats/msa.py to msa.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats/newick.py to newick.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/formats/phylip.py to phylip.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/__init__.py to __init__.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/bamfiles.py to bamfiles.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/bedtools.py to bedtools.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/console.py to console.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/fileutils.py to fileutils.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/makefile.py to makefile.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/procs.py to procs.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/rtools.py to rtools.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/sampling.py to sampling.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/sequences.py to sequences.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/signals.py to signals.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/system.py to system.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/testing.py to testing.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/text.py to text.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/timer.py to timer.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/utilities.py to utilities.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/vcffilter.py to vcffilter.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/vcfwrap.py to vcfwrap.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/common/versions.py to versions.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/__init__.py to __init__.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/adapterremoval.py to adapterremoval.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/bedtools.py to bedtools.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/bowtie2.py to bowtie2.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/bwa.py to bwa.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/commands.py to commands.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/examl.py to examl.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/formats.py to formats.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/gatk.py to gatk.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/mafft.py to mafft.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/mapdamage.py to mapdamage.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/misc.py to misc.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/newick.py to newick.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/phylip.py to phylip.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/picard.py to picard.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/raxml.py to raxml.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/samtools.py to samtools.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/sequences.py to sequences.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodes/validation.py to validation.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/phylo_pipeline/synthesize_reads.py to synthesize_reads.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/examples/nature_protocols/phylogeny/summarize_heterozygosity.py to summarize_heterozygosity.pyc byte-compiling /build/paleomix-1.2.13.3/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 /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/resources/__init__.py to __init__.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts/__init__.py to __init__.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts/lane.py to lane.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts/library.py to library.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts/prefix.py to prefix.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts/reads.py to reads.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts/sample.py to sample.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts/statistics.py to statistics.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts/summary.py to summary.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/parts/target.py to target.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/__init__.py to __init__.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/config.py to config.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/makefile.py to makefile.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/mkfile.py to mkfile.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/nodes.py to nodes.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/paths.py to paths.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/pipeline.py to pipeline.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/remap.py to remap.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_pipeline/trim_pipeline.py to trim_pipeline.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_stats/__init__.py to __init__.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_stats/common.py to common.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/bam_stats/coverage.py to coverage.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts/__init__.py to __init__.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts/genotype.py to genotype.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts/msa.py to msa.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts/paml.py to paml.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/parts/phylo.py to phylo.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/__init__.py to __init__.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/config.py to config.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/makefile.py to makefile.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/mkfile.py to mkfile.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/phylo_pipeline/pipeline.py to pipeline.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts/__init__.py to __init__.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts/admixture.py to admixture.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts/common.py to common.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts/mitochondria.py to mitochondria.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts/nuclear.py to nuclear.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts/report.py to report.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/parts/summary.py to summary.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/__init__.py to __init__.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/build_db.py to build_db.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/build_mito.py to build_mito.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/build_tped.py to build_tped.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/common.py to common.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/config.py to config.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/database.py to database.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/zonkey/pipeline.py to pipeline.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/__init__.py to __init__.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/cat.py to cat.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/cleanup.py to cleanup.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/coverage.py to coverage.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/depths.py to depths.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/dupcheck.py to dupcheck.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/duphist.py to duphist.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/ena.py to ena.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/factory.py to factory.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/genotype.py to genotype.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/gtf_to_bed.py to gtf_to_bed.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/retable.py to retable.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/rmdup_collapsed.py to rmdup_collapsed.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/sample_pileup.py to sample_pileup.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/vcf_filter.py to vcf_filter.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/tools/vcf_to_fasta.py to vcf_to_fasta.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/__init__.py to __init__.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/composer.py to composer.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/constructor.py to constructor.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/dumper.py to dumper.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/emitter.py to emitter.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/error.py to error.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/events.py to events.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/loader.py to loader.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/nodes.py to nodes.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/parser.py to parser.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/reader.py to reader.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/representer.py to representer.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/resolver.py to resolver.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/scanner.py to scanner.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/serializer.py to serializer.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/lib2/tokens.py to tokens.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/yaml/__init__.py to __init__.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/__init__.py to __init__.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/config.py to config.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/logger.py to logger.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/main.py to main.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/node.py to node.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/nodegraph.py to nodegraph.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/pipeline.py to pipeline.pyc byte-compiling /build/paleomix-1.2.13.3/debian/paleomix/usr/lib/python2.7/dist-packages/paleomix/ui.py to ui.pyc running install_egg_info Copying paleomix.egg-info to /build/paleomix-1.2.13.3/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 /build/paleomix-1.2.13.3/debian/paleomix/usr/bin Installing bam_rmdup_collapsed script to /build/paleomix-1.2.13.3/debian/paleomix/usr/bin Installing bam_pipeline script to /build/paleomix-1.2.13.3/debian/paleomix/usr/bin Installing paleomix script to /build/paleomix-1.2.13.3/debian/paleomix/usr/bin Installing conv_gtf_to_bed script to /build/paleomix-1.2.13.3/debian/paleomix/usr/bin Installing phylo_pipeline script to /build/paleomix-1.2.13.3/debian/paleomix/usr/bin debian/rules override_dh_install make[1]: Entering directory '/build/paleomix-1.2.13.3' dh_install find debian -name LICENSE -delete make[1]: Leaving directory '/build/paleomix-1.2.13.3' debian/rules override_dh_installdocs make[1]: Entering directory '/build/paleomix-1.2.13.3' 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/ tests/atomiccmd_test/ tests/bwa/ tests/bwa/testcases/ 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/ tests/tools_test/ sent 2,310 bytes received 424 bytes 5,468.00 bytes/sec total size is 605,728 speedup is 221.55 # 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 '/build/paleomix-1.2.13.3' dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python2 -O--buildsystem=pybuild I: dh_python2 tools:114: replacing shebang in debian/paleomix/usr/bin/phylo_pipeline I: dh_python2 tools:114: replacing shebang in debian/paleomix/usr/bin/conv_gtf_to_bed I: dh_python2 tools:114: replacing shebang in debian/paleomix/usr/bin/paleomix I: dh_python2 tools:114: replacing shebang in debian/paleomix/usr/bin/bam_pipeline I: dh_python2 tools:114: replacing shebang in debian/paleomix/usr/bin/bam_rmdup_collapsed I: dh_python2 tools:114: replacing shebang in debian/paleomix/usr/bin/trim_pipeline dh_installinit -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild debian/rules override_dh_fixperms make[1]: Entering directory '/build/paleomix-1.2.13.3' 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 '/build/paleomix-1.2.13.3' 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 dpkg-deb: building package 'paleomix' in '../paleomix_1.2.13.3-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../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) I: copying local configuration I: user script /srv/workspace/pbuilder/46733/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/46733/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/46733 and its subdirectories I: Current time: Mon Jan 10 16:42:44 +14 2022 I: pbuilder-time-stamp: 1641782564