RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux kissel 3.2.0-58-generic #88-Ubuntu SMP Tue Dec 3 17:37:58 UTC 2013 x86_64 Buildd toolchain package versions: launchpad-buildd_125 python-lpbuildd_125 bzr_2.5.1-0ubuntu2 dpkg-dev_1.16.1.2ubuntu7.5. Syncing the system clock with the buildd NTP service... 26 Oct 01:00:10 ntpdate[34646]: adjust time server 10.211.37.1 offset -0.000037 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-6503219', '/home/buildd/filecache-default/a665269cbd0fd566602516993cd02903b7df1cae'] Unpacking chroot for build PACKAGEBUILD-6503219 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-6503219'] Mounting chroot for build PACKAGEBUILD-6503219 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-6503219', 'deb http://ftpmaster.internal/ubuntu vivid main universe', 'deb http://ftpmaster.internal/ubuntu vivid-security main universe', 'deb http://ftpmaster.internal/ubuntu vivid-updates main universe', 'deb http://ftpmaster.internal/ubuntu vivid-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-6503219 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-6503219', 'amd64'] Updating debian chroot for build PACKAGEBUILD-6503219 Ign http://archive-team.internal vivid InRelease Ign http://ftpmaster.internal vivid InRelease Ign http://archive-team.internal vivid Release.gpg Ign http://ftpmaster.internal vivid-security InRelease Get:1 http://archive-team.internal vivid Release [728 B] Ign http://ftpmaster.internal vivid-updates InRelease Ign http://ftpmaster.internal vivid-proposed InRelease Get:2 http://ftpmaster.internal vivid Release.gpg [933 B] Get:3 http://ftpmaster.internal vivid-security Release.gpg [933 B] Get:4 http://ftpmaster.internal vivid-updates Release.gpg [933 B] Get:5 http://ftpmaster.internal vivid-proposed Release.gpg [933 B] Get:6 http://archive-team.internal vivid/main amd64 Packages Get:7 http://ftpmaster.internal vivid Release [112 kB] Ign http://archive-team.internal vivid/main Translation-en Get:8 http://ftpmaster.internal vivid-security Release [59.7 kB] Get:9 http://ftpmaster.internal vivid-updates Release [59.7 kB] Get:10 http://ftpmaster.internal vivid-proposed Release [59.7 kB] Get:11 http://ftpmaster.internal vivid/main amd64 Packages [1332 kB] Get:12 http://ftpmaster.internal vivid/universe amd64 Packages [6204 kB] Get:13 http://ftpmaster.internal vivid/main Translation-en [770 kB] Get:14 http://ftpmaster.internal vivid/universe Translation-en [4299 kB] Get:15 http://ftpmaster.internal vivid-security/main amd64 Packages [14 B] Get:16 http://ftpmaster.internal vivid-security/universe amd64 Packages [14 B] Get:17 http://ftpmaster.internal vivid-security/main Translation-en [14 B] Get:18 http://ftpmaster.internal vivid-security/universe Translation-en [14 B] Get:19 http://ftpmaster.internal vivid-updates/main amd64 Packages [14 B] Get:20 http://ftpmaster.internal vivid-updates/universe amd64 Packages [14 B] Get:21 http://ftpmaster.internal vivid-updates/main Translation-en [14 B] Get:22 http://ftpmaster.internal vivid-updates/universe Translation-en [14 B] Get:23 http://ftpmaster.internal vivid-proposed/main amd64 Packages [44.3 kB] Get:24 http://ftpmaster.internal vivid-proposed/universe amd64 Packages [326 kB] Get:25 http://ftpmaster.internal vivid-proposed/main Translation-en [44.4 kB] Get:26 http://ftpmaster.internal vivid-proposed/universe Translation-en [314 kB] Fetched 13.6 MB in 5s (2678 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: base-files binutils ca-certificates cpp-4.9 g++-4.9 gcc-4.9 gcc-4.9-base grep libacl1 libasan1 libatomic1 libcilkrts5 libdb5.3 libdrm2 libgcc-4.9-dev libgcc1 libgmp10 libgomp1 libgpg-error0 libgssapi-krb5-2 libitm1 libk5crypto3 libkrb5-3 libkrb5support0 liblsan0 libp11-kit0 libplymouth4 libquadmath0 libsasl2-2 libsasl2-modules-db libselinux1 libsqlite3-0 libstdc++-4.9-dev libstdc++6 libsystemd-journal0 libtasn1-6 libtsan0 libubsan0 libudev1 libusb-0.1-4 patch perl perl-base perl-modules plymouth tzdata udev 47 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 45.0 MB of archives. After this operation, 356 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ vivid/main base-files amd64 7.2ubuntu8 [63.5 kB] Get:2 http://ftpmaster.internal/ubuntu/ vivid/main grep amd64 2.20-4 [146 kB] Get:3 http://ftpmaster.internal/ubuntu/ vivid-proposed/main perl amd64 5.20.1-2 [2632 kB] Get:4 http://ftpmaster.internal/ubuntu/ vivid-proposed/main perl-base amd64 5.20.1-2 [1207 kB] Get:5 http://ftpmaster.internal/ubuntu/ vivid-proposed/main perl-modules all 5.20.1-2 [2531 kB] Get:6 http://ftpmaster.internal/ubuntu/ vivid/main libdb5.3 amd64 5.3.28-6 [671 kB] Get:7 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libubsan0 amd64 4.9.1-19ubuntu1 [83.7 kB] Get:8 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libtsan0 amd64 4.9.1-19ubuntu1 [216 kB] Get:9 http://ftpmaster.internal/ubuntu/ vivid-proposed/main gcc-4.9-base amd64 4.9.1-19ubuntu1 [15.6 kB] Get:10 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libstdc++6 amd64 4.9.1-19ubuntu1 [277 kB] Get:11 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libgomp1 amd64 4.9.1-19ubuntu1 [38.4 kB] Get:12 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libitm1 amd64 4.9.1-19ubuntu1 [30.1 kB] Get:13 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libatomic1 amd64 4.9.1-19ubuntu1 [9266 B] Get:14 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libasan1 amd64 4.9.1-19ubuntu1 [198 kB] Get:15 http://ftpmaster.internal/ubuntu/ vivid-proposed/main liblsan0 amd64 4.9.1-19ubuntu1 [94.0 kB] Get:16 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libcilkrts5 amd64 4.9.1-19ubuntu1 [40.5 kB] Get:17 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libquadmath0 amd64 4.9.1-19ubuntu1 [130 kB] Get:18 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libgcc-4.9-dev amd64 4.9.1-19ubuntu1 [2084 kB] Get:19 http://ftpmaster.internal/ubuntu/ vivid-proposed/main cpp-4.9 amd64 4.9.1-19ubuntu1 [5019 kB] Get:20 http://ftpmaster.internal/ubuntu/ vivid-proposed/main binutils amd64 2.24.90.20141023-1ubuntu1 [2198 kB] Get:21 http://ftpmaster.internal/ubuntu/ vivid-proposed/main gcc-4.9 amd64 4.9.1-19ubuntu1 [5638 kB] Get:22 http://ftpmaster.internal/ubuntu/ vivid-proposed/main g++-4.9 amd64 4.9.1-19ubuntu1 [17.5 MB] Get:23 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libstdc++-4.9-dev amd64 4.9.1-19ubuntu1 [1123 kB] Get:24 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libgcc1 amd64 1:4.9.1-19ubuntu1 [39.6 kB] Get:25 http://ftpmaster.internal/ubuntu/ vivid/main libgmp10 amd64 2:6.0.0+dfsg-6 [240 kB] Get:26 http://ftpmaster.internal/ubuntu/ vivid/main libusb-0.1-4 amd64 2:0.1.12-25 [16.6 kB] Get:27 http://ftpmaster.internal/ubuntu/ vivid/main libacl1 amd64 2.2.52-2 [16.3 kB] Get:28 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libgpg-error0 amd64 1.17-2 [32.2 kB] Get:29 http://ftpmaster.internal/ubuntu/ vivid/main libselinux1 amd64 2.3-2 [59.8 kB] Get:30 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libsystemd-journal0 amd64 215-5ubuntu1 [52.2 kB] Get:31 http://ftpmaster.internal/ubuntu/ vivid/main libp11-kit0 amd64 0.20.7-1 [77.1 kB] Get:32 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libsqlite3-0 amd64 3.8.7-1 [371 kB] Get:33 http://ftpmaster.internal/ubuntu/ vivid/main libtasn1-6 amd64 4.2-2 [42.1 kB] Get:34 http://ftpmaster.internal/ubuntu/ vivid/main libdrm2 amd64 2.4.58-2 [23.3 kB] Get:35 http://ftpmaster.internal/ubuntu/ vivid/main plymouth amd64 0.9.0-0ubuntu8 [103 kB] Get:36 http://ftpmaster.internal/ubuntu/ vivid-proposed/main udev amd64 215-5ubuntu1 [852 kB] Get:37 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libudev1 amd64 215-5ubuntu1 [33.9 kB] Get:38 http://ftpmaster.internal/ubuntu/ vivid/main libplymouth4 amd64 0.9.0-0ubuntu8 [85.9 kB] Get:39 http://ftpmaster.internal/ubuntu/ vivid/main libgssapi-krb5-2 amd64 1.12.1+dfsg-11 [119 kB] Get:40 http://ftpmaster.internal/ubuntu/ vivid/main libkrb5-3 amd64 1.12.1+dfsg-11 [270 kB] Get:41 http://ftpmaster.internal/ubuntu/ vivid/main libkrb5support0 amd64 1.12.1+dfsg-11 [30.7 kB] Get:42 http://ftpmaster.internal/ubuntu/ vivid/main libk5crypto3 amd64 1.12.1+dfsg-11 [82.4 kB] Get:43 http://ftpmaster.internal/ubuntu/ vivid/main libsasl2-modules-db amd64 2.1.26.dfsg1-12 [14.6 kB] Get:44 http://ftpmaster.internal/ubuntu/ vivid/main libsasl2-2 amd64 2.1.26.dfsg1-12 [49.5 kB] Get:45 http://ftpmaster.internal/ubuntu/ vivid/main tzdata all 2014i-1 [182 kB] Get:46 http://ftpmaster.internal/ubuntu/ vivid/main ca-certificates all 20141019 [192 kB] Get:47 http://ftpmaster.internal/ubuntu/ vivid/main patch amd64 2.7.1-6 [84.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 45.0 MB in 1s (31.4 MB/s) (Reading database ... 11482 files and directories currently installed.) Preparing to unpack .../base-files_7.2ubuntu8_amd64.deb ... Unpacking base-files (7.2ubuntu8) over (7.2ubuntu7) ... Setting up base-files (7.2ubuntu8) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Installing new version of config file /etc/os-release ... (Reading database ... 11482 files and directories currently installed.) Preparing to unpack .../archives/grep_2.20-4_amd64.deb ... Unpacking grep (2.20-4) over (2.20-3) ... Setting up grep (2.20-4) ... (Reading database ... 11482 files and directories currently installed.) Preparing to unpack .../perl_5.20.1-2_amd64.deb ... Unpacking perl (5.20.1-2) over (5.20.1-1) ... Preparing to unpack .../perl-base_5.20.1-2_amd64.deb ... Unpacking perl-base (5.20.1-2) over (5.20.1-1) ... Setting up perl-base (5.20.1-2) ... (Reading database ... 11482 files and directories currently installed.) 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Unpacking libplymouth4:amd64 (0.9.0-0ubuntu8) over (0.9.0-0ubuntu7) ... Preparing to unpack .../libgssapi-krb5-2_1.12.1+dfsg-11_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.12.1+dfsg-11) over (1.12.1+dfsg-10) ... Preparing to unpack .../libkrb5-3_1.12.1+dfsg-11_amd64.deb ... Unpacking libkrb5-3:amd64 (1.12.1+dfsg-11) over (1.12.1+dfsg-10) ... Preparing to unpack .../libkrb5support0_1.12.1+dfsg-11_amd64.deb ... Unpacking libkrb5support0:amd64 (1.12.1+dfsg-11) over (1.12.1+dfsg-10) ... Preparing to unpack .../libk5crypto3_1.12.1+dfsg-11_amd64.deb ... Unpacking libk5crypto3:amd64 (1.12.1+dfsg-11) over (1.12.1+dfsg-10) ... Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-12_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.26.dfsg1-12) over (2.1.26.dfsg1-11) ... Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-12_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.26.dfsg1-12) over (2.1.26.dfsg1-11) ... Preparing to unpack .../tzdata_2014i-1_all.deb ... Unpacking tzdata (2014i-1) over (2014h-2) ... Setting up tzdata (2014i-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Oct 26 01:01:47 UTC 2014. Universal Time is now: Sun Oct 26 01:01:47 UTC 2014. Run 'dpkg-reconfigure tzdata' if you wish to change it. (Reading database ... 11492 files and directories currently installed.) Preparing to unpack .../ca-certificates_20141019_all.deb ... Unpacking ca-certificates (20141019) over (20140325) ... Preparing to unpack .../patch_2.7.1-6_amd64.deb ... Unpacking patch (2.7.1-6) over (2.7.1-5) ... Setting up libubsan0:amd64 (4.9.1-19ubuntu1) ... Setting up libtsan0:amd64 (4.9.1-19ubuntu1) ... Setting up libgomp1:amd64 (4.9.1-19ubuntu1) ... Setting up libitm1:amd64 (4.9.1-19ubuntu1) ... Setting up libatomic1:amd64 (4.9.1-19ubuntu1) ... Setting up libasan1:amd64 (4.9.1-19ubuntu1) ... Setting up liblsan0:amd64 (4.9.1-19ubuntu1) ... Setting up libcilkrts5:amd64 (4.9.1-19ubuntu1) ... Setting up libquadmath0:amd64 (4.9.1-19ubuntu1) ... Setting up libgcc-4.9-dev:amd64 (4.9.1-19ubuntu1) ... Setting up libgmp10:amd64 (2:6.0.0+dfsg-6) ... Setting up cpp-4.9 (4.9.1-19ubuntu1) ... Setting up binutils (2.24.90.20141023-1ubuntu1) ... Setting up gcc-4.9 (4.9.1-19ubuntu1) ... Setting up libstdc++-4.9-dev:amd64 (4.9.1-19ubuntu1) ... Setting up g++-4.9 (4.9.1-19ubuntu1) ... Setting up libp11-kit0:amd64 (0.20.7-1) ... Setting up libsqlite3-0:amd64 (3.8.7-1) ... Setting up libtasn1-6:amd64 (4.2-2) ... Setting up libdrm2:amd64 (2.4.58-2) ... Setting up libudev1:amd64 (215-5ubuntu1) ... Setting up libplymouth4:amd64 (0.9.0-0ubuntu8) ... Setting up udev (215-5ubuntu1) ... Installing new version of config file /etc/init.d/udev-finish ... A chroot environment has been detected, udev not started. update-initramfs: deferring update (trigger activated) Removing obsolete conffile /etc/udev/rules.d/README ... Setting up plymouth (0.9.0-0ubuntu8) ... update-initramfs: deferring update (trigger activated) Setting up libkrb5support0:amd64 (1.12.1+dfsg-11) ... Setting up libk5crypto3:amd64 (1.12.1+dfsg-11) ... Setting up libkrb5-3:amd64 (1.12.1+dfsg-11) ... Setting up libgssapi-krb5-2:amd64 (1.12.1+dfsg-11) ... Setting up libsasl2-modules-db:amd64 (2.1.26.dfsg1-12) ... Setting up libsasl2-2:amd64 (2.1.26.dfsg1-12) ... Setting up ca-certificates (20141019) ... Setting up patch (2.7.1-6) ... Setting up perl-modules (5.20.1-2) ... Setting up perl (5.20.1-2) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... Processing triggers for initramfs-tools (0.103ubuntu8) ... Processing triggers for ca-certificates (20141019) ... Updating certificates in /etc/ssl/certs... 10 added, 5 removed; done. Running hooks in /etc/ca-certificates/update.d....done. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-6503219', 'amd64', 'vivid-proposed', '--nolog', '--batch', '--archive=ubuntu', '--dist=vivid-proposed', '-A', '--purpose=PRIMARY', '--architecture=amd64', '--comp=universe', 'fastaq_1.5.0-1.dsc'] Initiating build PACKAGEBUILD-6503219 with 12 jobs across 12 processor cores. Kernel reported to sbuild: 3.2.0-58-generic #88-Ubuntu SMP Tue Dec 3 17:37:58 UTC 2013 x86_64 Automatic build of fastaq_1.5.0-1 on kissel by sbuild/amd64 1.170.5 Build started at 20141026-0102 ****************************************************************************** fastaq_1.5.0-1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 9), python3, python3-setuptools, python3-numpy, python3-nose, samtools, help2man Checking for already installed source dependencies... debhelper: missing python3: missing python3-setuptools: missing python3-numpy: missing python3-nose: missing samtools: missing help2man: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper python3 python3-setuptools python3-numpy python3-nose samtools help2man Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils dh-apparmor dh-python file gettext gettext-base groff-base intltool-debian libasprintf0c2 libblas3 libcroco3 libexpat1 libgfortran3 libglib2.0-0 liblapack3 liblocale-gettext-perl libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.4-minimal libpython3.4-stdlib libunistring0 libxml2 man-db mime-support po-debconf python3-minimal python3-pkg-resources python3.4 python3.4-minimal Suggested packages: wamerican wordlist whois vacation dh-make apparmor-easyprof gettext-doc groff less www-browser libmail-box-perl python3-doc python3-tk python3-venv python-nose-doc gfortran python-numpy-doc python3-dev python3-numpy-dbg python3.4-venv python3.4-doc binfmt-support python Recommended packages: curl wget lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xdg-user-dirs xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper dh-apparmor dh-python file gettext gettext-base groff-base help2man intltool-debian libasprintf0c2 libblas3 libcroco3 libexpat1 libgfortran3 libglib2.0-0 liblapack3 liblocale-gettext-perl libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.4-minimal libpython3.4-stdlib libunistring0 libxml2 man-db mime-support po-debconf python3 python3-minimal python3-nose python3-numpy python3-pkg-resources python3-setuptools python3.4 python3.4-minimal samtools 0 upgraded, 38 newly installed, 0 to remove and 0 not upgraded. Need to get 15.8 MB of archives. After this operation, 62.8 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ vivid/main libexpat1 amd64 2.1.0-6ubuntu1 [70.6 kB] Get:2 http://ftpmaster.internal/ubuntu/ vivid/main liblocale-gettext-perl amd64 1.05-8build1 [17.9 kB] Get:3 http://ftpmaster.internal/ubuntu/ vivid/main libmagic1 amd64 1:5.19-1ubuntu1.1 [201 kB] Get:4 http://ftpmaster.internal/ubuntu/ vivid/main libmpdec2 amd64 2.4.1-1 [82.7 kB] Get:5 http://ftpmaster.internal/ubuntu/ vivid/main libpython3.4-minimal amd64 3.4.2-1 [460 kB] Get:6 http://ftpmaster.internal/ubuntu/ vivid/main mime-support all 3.55ubuntu1 [31.1 kB] Get:7 http://ftpmaster.internal/ubuntu/ vivid/main libpython3.4-stdlib amd64 3.4.2-1 [2086 kB] Get:8 http://ftpmaster.internal/ubuntu/ vivid/main python3.4-minimal amd64 3.4.2-1 [1613 kB] Get:9 http://ftpmaster.internal/ubuntu/ vivid/main libasprintf0c2 amd64 0.19.2-2ubuntu1 [6296 B] Get:10 http://ftpmaster.internal/ubuntu/ vivid/main libglib2.0-0 amd64 2.42.0-2 [1088 kB] Get:11 http://ftpmaster.internal/ubuntu/ vivid/main libpipeline1 amd64 1.3.1-1 [24.4 kB] Get:12 http://ftpmaster.internal/ubuntu/ vivid/main libxml2 amd64 2.9.1+dfsg1-4ubuntu1 [580 kB] Get:13 http://ftpmaster.internal/ubuntu/ vivid/main groff-base amd64 1.22.2-8 [1165 kB] Get:14 http://ftpmaster.internal/ubuntu/ vivid/main bsdmainutils amd64 9.0.5ubuntu1 [203 kB] Get:15 http://ftpmaster.internal/ubuntu/ vivid/main man-db amd64 2.7.0.2-2 [863 kB] Get:16 http://ftpmaster.internal/ubuntu/ vivid/main libcroco3 amd64 0.6.8-3 [83.2 kB] Get:17 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libgfortran3 amd64 4.9.1-19ubuntu1 [259 kB] Get:18 http://ftpmaster.internal/ubuntu/ vivid/main libunistring0 amd64 0.9.3-5ubuntu3 [271 kB] Get:19 http://ftpmaster.internal/ubuntu/ vivid/main python3.4 amd64 3.4.2-1 [173 kB] Get:20 http://ftpmaster.internal/ubuntu/ vivid/main python3-minimal amd64 3.4.2-1 [23.4 kB] Get:21 http://ftpmaster.internal/ubuntu/ vivid/main libpython3-stdlib amd64 3.4.2-1 [7090 B] Get:22 http://ftpmaster.internal/ubuntu/ vivid/main python3 amd64 3.4.2-1 [8786 B] Get:23 http://ftpmaster.internal/ubuntu/ vivid/main dh-python all 1.20140511-1 [52.2 kB] Get:24 http://ftpmaster.internal/ubuntu/ vivid/main file amd64 1:5.19-1ubuntu1.1 [20.1 kB] Get:25 http://ftpmaster.internal/ubuntu/ vivid/main gettext-base amd64 0.19.2-2ubuntu1 [48.3 kB] Get:26 http://ftpmaster.internal/ubuntu/ vivid/main gettext amd64 0.19.2-2ubuntu1 [851 kB] Get:27 http://ftpmaster.internal/ubuntu/ vivid/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:28 http://ftpmaster.internal/ubuntu/ vivid/main po-debconf all 1.0.16+nmu3 [207 kB] Get:29 http://ftpmaster.internal/ubuntu/ vivid/main dh-apparmor all 2.8.98-0ubuntu2 [11.0 kB] Get:30 http://ftpmaster.internal/ubuntu/ vivid/main debhelper all 9.20141003ubuntu1 [726 kB] Get:31 http://ftpmaster.internal/ubuntu/ vivid/main help2man amd64 1.46.4 [98.9 kB] Get:32 http://ftpmaster.internal/ubuntu/ vivid/main libblas3 amd64 1.2.20110419-7ubuntu1 [161 kB] Get:33 http://ftpmaster.internal/ubuntu/ vivid/main liblapack3 amd64 3.5.0-4 [1844 kB] Get:34 http://ftpmaster.internal/ubuntu/ vivid/main python3-pkg-resources all 5.5.1-1 [31.6 kB] Get:35 http://ftpmaster.internal/ubuntu/ vivid/main python3-nose all 1.3.4-1 [116 kB] Get:36 http://ftpmaster.internal/ubuntu/ vivid/main python3-numpy amd64 1:1.8.2-1ubuntu1 [1614 kB] Get:37 http://ftpmaster.internal/ubuntu/ vivid/main python3-setuptools all 5.5.1-1 [130 kB] Get:38 http://ftpmaster.internal/ubuntu/ vivid/universe samtools amd64 0.1.19-1ubuntu1 [562 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 15.8 MB in 1s (13.5 MB/s) Selecting previously unselected package libexpat1:amd64. (Reading database ... 11497 files and directories currently installed.) Preparing to unpack .../libexpat1_2.1.0-6ubuntu1_amd64.deb ... Unpacking libexpat1:amd64 (2.1.0-6ubuntu1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../liblocale-gettext-perl_1.05-8build1_amd64.deb ... Unpacking liblocale-gettext-perl (1.05-8build1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../libmagic1_1%3a5.19-1ubuntu1.1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.19-1ubuntu1.1) ... Selecting previously unselected package libmpdec2:amd64. Preparing to unpack .../libmpdec2_2.4.1-1_amd64.deb ... Unpacking libmpdec2:amd64 (2.4.1-1) ... Selecting previously unselected package libpython3.4-minimal:amd64. Preparing to unpack .../libpython3.4-minimal_3.4.2-1_amd64.deb ... Unpacking libpython3.4-minimal:amd64 (3.4.2-1) ... Selecting previously unselected package mime-support. 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Setting up libxml2:amd64 (2.9.1+dfsg1-4ubuntu1) ... Setting up groff-base (1.22.2-8) ... Setting up bsdmainutils (9.0.5ubuntu1) ... 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 man-db (2.7.0.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcroco3:amd64 (0.6.8-3) ... Setting up libgfortran3:amd64 (4.9.1-19ubuntu1) ... Setting up libunistring0:amd64 (0.9.3-5ubuntu3) ... Setting up python3.4 (3.4.2-1) ... Setting up python3-minimal (3.4.2-1) ... Setting up libpython3-stdlib:amd64 (3.4.2-1) ... Setting up file (1:5.19-1ubuntu1.1) ... Setting up gettext-base (0.19.2-2ubuntu1) ... Setting up gettext (0.19.2-2ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu3) ... Setting up dh-apparmor (2.8.98-0ubuntu2) ... Setting up debhelper (9.20141003ubuntu1) ... Setting up help2man (1.46.4) ... Setting up libblas3 (1.2.20110419-7ubuntu1) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up liblapack3 (3.5.0-4) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up samtools (0.1.19-1ubuntu1) ... Setting up python3 (3.4.2-1) ... running python rtupdate hooks for python3.4... running python post-rtupdate hooks for python3.4... Setting up dh-python (1.20140511-1) ... Setting up python3-pkg-resources (5.5.1-1) ... Setting up python3-nose (1.3.4-1) ... Setting up python3-numpy (1:1.8.2-1ubuntu1) ... Setting up python3-setuptools (5.5.1-1) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.19-10ubuntu2 make_4.0-8 dpkg-dev_1.17.13ubuntu1 gcc-4.9_4.9.1-19ubuntu1 g++-4.9_4.9.1-19ubuntu1 binutils_2.24.90.20141023-1ubuntu1 libstdc++-4.9-dev_4.9.1-19ubuntu1 libstdc++6_4.9.1-19ubuntu1 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::Quilt gpgv: Signature made Thu Oct 23 18:30:49 2014 UTC using RSA key ID D1C646D1 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./fastaq_1.5.0-1.dsc dpkg-source: info: extracting fastaq in fastaq-1.5.0 dpkg-source: info: unpacking fastaq_1.5.0.orig.tar.gz dpkg-source: info: unpacking fastaq_1.5.0-1.debian.tar.xz dpkg-source: info: applying delay-import-statements-for-manpage-creation.patch dpkg-buildpackage: source package fastaq dpkg-buildpackage: source version 1.5.0-1 dpkg-buildpackage: source distribution unstable dpkg-source --before-build fastaq-1.5.0 dpkg-buildpackage: host architecture amd64 /usr/bin/fakeroot debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_testdir -O--buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/buildd/fastaq-1.5.0' rm -rf build .pybuild rm -rf /build/buildd/fastaq-1.5.0/debian/man make[1]: Leaving directory '/build/buildd/fastaq-1.5.0' dh_clean -O--buildsystem=pybuild rm -f debian/fastaq.substvars rm -f debian/fastaq.*.debhelper rm -rf debian/fastaq/ rm -f debian/*.debhelper.log rm -f debian/files find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) rm -f *-stamp debian/rules build dh build --with python3 --buildsystem=pybuild dh_testdir -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild pybuild --configure -i python{version} -p 3.4 --dir . I: pybuild base:170: python3.4 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/buildd/fastaq-1.5.0' dh_python3 D: dh_python3 dh_python3:149: version: 1.20140511-1 D: dh_python3 dh_python3:150: argv: ['/usr/bin/dh_python3'] D: dh_python3 dh_python3:151: options: {'clean_dbg_pkg': True, 'skip_private': False, 'recommends': None, 'depends': None, 'requires': None, 'regexpr': None, 'guess_deps': True, 'no_shebang_rewrite': False, 'ignore_shebangs': False, 'compile_all': False, 'verbose': False, 'O': None, 'no_ext_rename': False, 'shebang': None, 'suggests': None, 'vrange': None, 'package': None, 'arch': None, 'no_package': None} D: dh_python3 dh_python3:152: args: [] D: dh_python3 dh_python3:154: supported Python versions: 3.4 (default=3.4) D: dh_python3 debhelper:98: source=fastaq, binary packages=['fastaq'] D: dh_python3 dh_python3:171: processing package fastaq... D: dh_python3 fs:219: package fastaq details = {'shebangs': set(), 'nsp.txt': set(), 'requires.txt': set(), 'ext_vers': set(), 'compile': False, 'ext_no_version': set(), 'private_dirs': {}, 'public_vers': set()} D: dh_python3 depends:107: generating dependencies for package fastaq D: dh_python3 depends:236: D=set(); R=[]; S=[]; E=[], B=[]; RT=[] dh_auto_build pybuild --build -i python{version} -p 3.4 --dir . I: pybuild base:170: /usr/bin/python3 setup.py build running build running build_py creating /build/buildd/fastaq-1.5.0/.pybuild/pythonX.Y_3.4/build/fastaq copying fastaq/sequences.py -> /build/buildd/fastaq-1.5.0/.pybuild/pythonX.Y_3.4/build/fastaq copying fastaq/tasks.py -> /build/buildd/fastaq-1.5.0/.pybuild/pythonX.Y_3.4/build/fastaq copying fastaq/__init__.py -> /build/buildd/fastaq-1.5.0/.pybuild/pythonX.Y_3.4/build/fastaq copying fastaq/intervals.py -> /build/buildd/fastaq-1.5.0/.pybuild/pythonX.Y_3.4/build/fastaq copying fastaq/utils.py -> /build/buildd/fastaq-1.5.0/.pybuild/pythonX.Y_3.4/build/fastaq running build_scripts creating build creating build/scripts-3.4 copying and adjusting scripts/fastaq_strip_illumina_suffix -> build/scripts-3.4 copying and adjusting scripts/fastaq_count_sequences -> build/scripts-3.4 copying and adjusting scripts/fastaq_to_orfs_gff -> build/scripts-3.4 copying and adjusting scripts/fastaq_fasta_to_fastq -> build/scripts-3.4 copying and adjusting scripts/fastaq_to_unique_by_id -> build/scripts-3.4 copying and adjusting scripts/fastaq_enumerate_names -> build/scripts-3.4 copying and adjusting scripts/fastaq_trim_ends -> build/scripts-3.4 copying and adjusting scripts/fastaq_search_for_seq -> build/scripts-3.4 copying and adjusting scripts/fastaq_split_by_base_count -> build/scripts-3.4 copying and adjusting scripts/fastaq_to_fasta -> build/scripts-3.4 copying and adjusting scripts/fastaq_capillary_to_pairs -> build/scripts-3.4 copying and adjusting scripts/fastaq_deinterleave -> build/scripts-3.4 copying and adjusting scripts/fastaq_to_quasr_primers_file -> build/scripts-3.4 copying and adjusting scripts/fastaq_reverse_complement -> build/scripts-3.4 copying and adjusting scripts/fastaq_insert_or_delete_bases -> build/scripts-3.4 copying and adjusting scripts/fastaq_to_tiling_bam -> build/scripts-3.4 copying and adjusting scripts/fastaq_replace_bases -> build/scripts-3.4 copying and adjusting scripts/fastaq_expand_nucleotides -> build/scripts-3.4 copying and adjusting scripts/fastaq_merge -> build/scripts-3.4 copying and adjusting scripts/fastaq_scaffolds_to_contigs -> build/scripts-3.4 copying and adjusting scripts/fastaq_chunker -> build/scripts-3.4 copying and adjusting scripts/fastaq_get_ids -> build/scripts-3.4 copying and adjusting scripts/fastaq_to_random_subset -> build/scripts-3.4 copying and adjusting scripts/fastaq_filter -> build/scripts-3.4 copying and adjusting scripts/fastaq_to_mira_xml -> build/scripts-3.4 copying and adjusting scripts/fastaq_interleave -> build/scripts-3.4 copying and adjusting scripts/fastaq_translate -> build/scripts-3.4 copying and adjusting scripts/fastaq_make_random_contigs -> build/scripts-3.4 copying and adjusting scripts/fastaq_get_seq_flanking_gaps -> build/scripts-3.4 copying and adjusting scripts/fastaq_trim_Ns_at_end -> build/scripts-3.4 copying and adjusting scripts/fastaq_to_perfect_reads -> build/scripts-3.4 copying and adjusting scripts/fastaq_to_fake_qual -> build/scripts-3.4 copying and adjusting scripts/fastaq_sequence_trim -> build/scripts-3.4 copying and adjusting scripts/fastaq_extend_gaps -> build/scripts-3.4 copying and adjusting scripts/fastaq_long_read_simulate -> build/scripts-3.4 changing mode of build/scripts-3.4/fastaq_strip_illumina_suffix from 664 to 775 changing mode of build/scripts-3.4/fastaq_count_sequences from 664 to 775 changing mode of build/scripts-3.4/fastaq_to_orfs_gff from 664 to 775 changing mode of build/scripts-3.4/fastaq_fasta_to_fastq from 664 to 775 changing mode of build/scripts-3.4/fastaq_to_unique_by_id from 664 to 775 changing mode of build/scripts-3.4/fastaq_enumerate_names from 664 to 775 changing mode of build/scripts-3.4/fastaq_trim_ends from 664 to 775 changing mode of build/scripts-3.4/fastaq_search_for_seq from 664 to 775 changing mode of build/scripts-3.4/fastaq_split_by_base_count from 664 to 775 changing mode of build/scripts-3.4/fastaq_to_fasta from 664 to 775 changing mode of build/scripts-3.4/fastaq_capillary_to_pairs from 664 to 775 changing mode of build/scripts-3.4/fastaq_deinterleave from 664 to 775 changing mode of build/scripts-3.4/fastaq_to_quasr_primers_file from 664 to 775 changing mode of build/scripts-3.4/fastaq_reverse_complement from 664 to 775 changing mode of build/scripts-3.4/fastaq_insert_or_delete_bases from 664 to 775 changing mode of build/scripts-3.4/fastaq_to_tiling_bam from 664 to 775 changing mode of build/scripts-3.4/fastaq_replace_bases from 664 to 775 changing mode of build/scripts-3.4/fastaq_expand_nucleotides from 664 to 775 changing mode of build/scripts-3.4/fastaq_merge from 664 to 775 changing mode of build/scripts-3.4/fastaq_scaffolds_to_contigs from 664 to 775 changing mode of build/scripts-3.4/fastaq_chunker from 664 to 775 changing mode of build/scripts-3.4/fastaq_get_ids from 664 to 775 changing mode of build/scripts-3.4/fastaq_to_random_subset from 664 to 775 changing mode of build/scripts-3.4/fastaq_filter from 664 to 775 changing mode of build/scripts-3.4/fastaq_to_mira_xml from 664 to 775 changing mode of build/scripts-3.4/fastaq_interleave from 664 to 775 changing mode of build/scripts-3.4/fastaq_translate from 664 to 775 changing mode of build/scripts-3.4/fastaq_make_random_contigs from 664 to 775 changing mode of build/scripts-3.4/fastaq_get_seq_flanking_gaps from 664 to 775 changing mode of build/scripts-3.4/fastaq_trim_Ns_at_end from 664 to 775 changing mode of build/scripts-3.4/fastaq_to_perfect_reads from 664 to 775 changing mode of build/scripts-3.4/fastaq_to_fake_qual from 664 to 775 changing mode of build/scripts-3.4/fastaq_sequence_trim from 664 to 775 changing mode of build/scripts-3.4/fastaq_extend_gaps from 664 to 775 changing mode of build/scripts-3.4/fastaq_long_read_simulate from 664 to 775 mkdir /build/buildd/fastaq-1.5.0/doc cd /build/buildd/fastaq-1.5.0/doc make[1]: Leaving directory '/build/buildd/fastaq-1.5.0' dh_auto_test -O--buildsystem=pybuild pybuild --test -i python{version} -p 3.4 --dir . I: pybuild base:170: python3.4 setup.py test running test running egg_info creating Fastaq.egg-info writing top-level names to Fastaq.egg-info/top_level.txt writing requirements to Fastaq.egg-info/requires.txt writing Fastaq.egg-info/PKG-INFO writing dependency_links to Fastaq.egg-info/dependency_links.txt writing manifest file 'Fastaq.egg-info/SOURCES.txt' reading manifest file 'Fastaq.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.sh' under directory 'fastaq/tests' writing manifest file 'Fastaq.egg-info/SOURCES.txt' running build_ext test_comparisons (intervals_test.TestIntervals) <, <=, == should work as expected ... ok test_contains (intervals_test.TestIntervals) Check that contains() works as expected ... ok test_init (intervals_test.TestIntervals) Throw error if try to construct genome_interval from a non-int, or end amino acid conversion works on Fasta ... ok test_trim_Ns (sequences_test.TestFasta) trim_Ns() should do the right trimming of a sequence ... ok test_get_next_from_file (sequences_test.TestFastq) get_next_from_file() should read seqs from OK, and raise error at badly formatted file ... ok test_init (sequences_test.TestFastq) __init__ should get the ID, sequence and quality correctly ... ok test_init_length_mismatch (sequences_test.TestFastq) __init__ should raise an error when length of seq and quality not the same ... ok test_revcomp (sequences_test.TestFastq) revcomp() should correctly reverse complement a sequence ... ok test_to_Fasta_and_qual (sequences_test.TestFastq) Check to_Fasta_and_qual converts quality scores correctly ... ok test_translate (sequences_test.TestFastq) Test nucleatide -> amino acid conversion works on Fasta ... ok test_trim (sequences_test.TestFastq) trim() should trim the right number of bases off start and end ... ok test_trim_Ns (sequences_test.TestFastq) trim_Ns() should do the right trimming of a fastq sequence ... ok test_file_reader_bad_format (sequences_test.TestFileReader) file_reader should die properly when not given fasta or fastq file ... ok test_file_reader_embl (sequences_test.TestFileReader) Test read embl file ... ok test_file_reader_fasta (sequences_test.TestFileReader) file_reader should iterate through a fasta file correctly ... ok test_file_reader_fastq (sequences_test.TestFileReader) file_reader should iterate through a fastq file correctly ... ok test_file_reader_gff (sequences_test.TestFileReader) Test read gff file ... ok test_file_reader_phylip (sequences_test.TestFileReader) Test read phylip file ... ok test_orfs_from_aa_seq (sequences_test.TestOther) Test _orfs_from_aa_seq() ... ok test_capillary_to_pairs (tasks_test.TestCapillaryToPairs) Check that capillary reads file converted to paired and unpaired ... ok test_count_sequences (tasks_test.TestCountSequences) Check that count_sequences does as expected ... ok test_deinterleave (tasks_test.TestDeinterleave) deinterleave should deal with an interleaved file correctly ... ok test_enumerate_names (tasks_test.TestEnumerateNames) Test enomereate_names works with all options ... ok test_expand_nucleoties (tasks_test.TestExpandNucleotides) Test expand_nucleotides ... /build/buildd/fastaq-1.5.0/fastaq/tests/tasks_test.py:81: ResourceWarning: unclosed file <_io.TextIOWrapper name='tmp.expanded' mode='w' encoding='ANSI_X3.4-1968'> tasks.expand_nucleotides(fq_in, tmp) /build/buildd/fastaq-1.5.0/fastaq/tests/tasks_test.py:84: ResourceWarning: unclosed file <_io.TextIOWrapper name='tmp.expanded' mode='w' encoding='ANSI_X3.4-1968'> tasks.expand_nucleotides(fa_in, tmp) ok test_extend_gaps (tasks_test.TestExtendGaps) Test that gap extension works ... ok test_fasta_to_fake_qual (tasks_test.TestFastaToFakeQual) Test fasta_to_fake_qual ... ok test_fasta_to_fastq (tasks_test.TestFastaToFastq) Check fasta_to_fastq converts files as expected ... ok test_fastaq_to_orfs_gff (tasks_test.TestFastaqToOrfsGFF) Test fastaq_to_orfs_gff ... ok test_fastaq_to_mira_xml (tasks_test.TestFastqToMiraXml) check that fastaq_to_mira_xml makes the correct xml file from a fastq file ... ok test_file_to_dict (tasks_test.TestFileToDict) check file_to_dict fills dictionary correctly ... ok test_ids_from_file_filter (tasks_test.TestFilter) Test that can extract reads from a file of read names ... ok test_invert_filter (tasks_test.TestFilter) Test that inverting filtering works ... ok test_length_filter (tasks_test.TestFilter) Check that filtering by length works as expected ... ok test_regex_filter (tasks_test.TestFilter) Check that filtering by name regex works as expected ... ok test_get_ids (tasks_test.TestGetIds) Check that IDs extracted correctly from fasta/q file ... ok test_get_seqs_flanking_gaps (tasks_test.TestGetSeqsFlankingGaps) ... ok test_interleave (tasks_test.TestInterleave) Check that interleave works as expected ... ok test_lengths_from_fai (tasks_test.TestLengthsFromFai) Check lengths_from_fai gets the length of each seq OK ... ok test_tiling_reads (tasks_test.TestMakeLongReads) ... ok test_make_random_contigs (tasks_test.TestMakeRandomContigs) Test make_random_contigs() ... ok test_merge_to_one_seq_fa (tasks_test.TestMergeToOneSeq) Test merge_to_one_seq with fasta ... ok test_merge_to_one_seq_fq (tasks_test.TestMergeToOneSeq) Test merge_to_one_seq with fastq ... ok test_sequences_replace_bases (tasks_test.TestReplaceBases) Check that fasta file gets all bases replaced OK ... ok test_reverse_complement (tasks_test.TestReverseComplement) reverse_complement should correctly reverse complement each seq in a file ... ok test_scaffolds_to_contigs (tasks_test.TestScaffoldsToContigs) Test scaffolds_to_contigs ... ok test_scaffolds_to_contigs_number_contigs (tasks_test.TestScaffoldsToContigs) Test scaffolds_to_contigs with contig numbering ... ok test_search_for_seq (tasks_test.TestSearchForSeq) Test that sequence search finds all hits ... ok test_sequence_trim (tasks_test.TestSequenceTrim) Test sequence_trim ... ok test_split_by_base_count (tasks_test.TestSplit) Check that fasta/q files get split by base count correctly ... ok test_split_by_fixed_size (tasks_test.TestSplit) Test fasta/q file split by fixed size ... /build/buildd/fastaq-1.5.0/fastaq/tests/tasks_test.py:391: ResourceWarning: unclosed file <_io.TextIOWrapper name='tmp.sequences_test_split.coords' mode='w' encoding='ANSI_X3.4-1968'> tasks.split_by_fixed_size(infile, outprefix, 4, 1) ok test_split_by_fixed_size_exclude_Ns (tasks_test.TestSplit) ... /build/buildd/fastaq-1.5.0/fastaq/tests/tasks_test.py:406: ResourceWarning: unclosed file <_io.TextIOWrapper name='tmp.sequences_test_split.coords' mode='w' encoding='ANSI_X3.4-1968'> tasks.split_by_fixed_size(infile, outprefix, 4, 1, skip_if_all_Ns=True) ok test_strip_illumina_suffix (tasks_test.TestStripIlluminaSuffix) Check illumina suffixes stripped correctly off read names ... ok test_to_fasta (tasks_test.TestToFasta) Test to_fasta ... ok test_to_fasta_union (tasks_test.TestToFastaUnion) Test to_fasta_union ... ok test_to_quasr_primers (tasks_test.TestToQuasrPrimers) Check that fasta file gets converted to QUASR sequence file ... ok test_to_unique_by_id (tasks_test.TestToUniqueByID) Test to_unique_by_id() ... ok test_translate (tasks_test.TestTranslate) Test translate works in each frame ... ok test_trim (tasks_test.TestTrim) trim should correctly trim each seq in a file ... ok test_trim_Ns_at_end (tasks_test.TestTrim) Test Ns at ends of sequences trimmed OK ... ok test_file_transpose (utils_test.TestUtils) Test that file_transpose() does what it should ... ok test_raise_exception (utils_test.TestUtils) open_file_write() and open_file_read() should raise an exception when can't do the opening ... gzip: this_file_is_not_here_so_throw_error.gz: No such file or directory gzip: /build/buildd/fastaq-1.5.0/fastaq/tests/data/utils_test_not_really_zipped.gz: not in gzip format ok test_system_call (utils_test.TestUtils) Test that system call appears to work and die as it should ... /bin/sh: 1: thisisveryunlikelytoebarealcommandandshouldthrowerror: not found ok test_write_and_read (utils_test.TestUtils) open_file_write() and open_file_read() should do the right thing depending gzipped or not ... ok ---------------------------------------------------------------------- Ran 98 tests in 0.594s OK /usr/bin/fakeroot debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild rm -f debian/fastaq.substvars rm -f debian/fastaq.*.debhelper rm -rf debian/fastaq/ dh_auto_install -O--buildsystem=pybuild install -d debian/fastaq pybuild --install -i python{version} -p 3.4 --dir . --dest-dir /build/buildd/fastaq-1.5.0/debian/fastaq I: pybuild base:170: /usr/bin/python3 setup.py install --root /build/buildd/fastaq-1.5.0/debian/fastaq running install running build running build_py running build_scripts running install_lib creating /build/buildd/fastaq-1.5.0/debian/fastaq/usr creating /build/buildd/fastaq-1.5.0/debian/fastaq/usr/lib creating /build/buildd/fastaq-1.5.0/debian/fastaq/usr/lib/python3.4 creating /build/buildd/fastaq-1.5.0/debian/fastaq/usr/lib/python3.4/dist-packages creating /build/buildd/fastaq-1.5.0/debian/fastaq/usr/lib/python3.4/dist-packages/fastaq copying /build/buildd/fastaq-1.5.0/.pybuild/pythonX.Y_3.4/build/fastaq/sequences.py -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/lib/python3.4/dist-packages/fastaq copying /build/buildd/fastaq-1.5.0/.pybuild/pythonX.Y_3.4/build/fastaq/tasks.py -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/lib/python3.4/dist-packages/fastaq copying /build/buildd/fastaq-1.5.0/.pybuild/pythonX.Y_3.4/build/fastaq/__init__.py -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/lib/python3.4/dist-packages/fastaq copying /build/buildd/fastaq-1.5.0/.pybuild/pythonX.Y_3.4/build/fastaq/intervals.py -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/lib/python3.4/dist-packages/fastaq copying /build/buildd/fastaq-1.5.0/.pybuild/pythonX.Y_3.4/build/fastaq/utils.py -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/lib/python3.4/dist-packages/fastaq byte-compiling /build/buildd/fastaq-1.5.0/debian/fastaq/usr/lib/python3.4/dist-packages/fastaq/sequences.py to sequences.cpython-34.pyc byte-compiling /build/buildd/fastaq-1.5.0/debian/fastaq/usr/lib/python3.4/dist-packages/fastaq/tasks.py to tasks.cpython-34.pyc byte-compiling /build/buildd/fastaq-1.5.0/debian/fastaq/usr/lib/python3.4/dist-packages/fastaq/__init__.py to __init__.cpython-34.pyc byte-compiling /build/buildd/fastaq-1.5.0/debian/fastaq/usr/lib/python3.4/dist-packages/fastaq/intervals.py to intervals.cpython-34.pyc byte-compiling /build/buildd/fastaq-1.5.0/debian/fastaq/usr/lib/python3.4/dist-packages/fastaq/utils.py to utils.cpython-34.pyc running install_egg_info running egg_info writing Fastaq.egg-info/PKG-INFO writing dependency_links to Fastaq.egg-info/dependency_links.txt writing top-level names to Fastaq.egg-info/top_level.txt writing requirements to Fastaq.egg-info/requires.txt reading manifest file 'Fastaq.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.sh' under directory 'fastaq/tests' writing manifest file 'Fastaq.egg-info/SOURCES.txt' Copying Fastaq.egg-info to /build/buildd/fastaq-1.5.0/debian/fastaq/usr/lib/python3.4/dist-packages/Fastaq-1.5.0.egg-info running install_scripts creating /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_strip_illumina_suffix -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_count_sequences -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_to_orfs_gff -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_fasta_to_fastq -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_to_unique_by_id -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_enumerate_names -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_trim_ends -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_search_for_seq -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_split_by_base_count -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_to_fasta -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_capillary_to_pairs -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_deinterleave -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_to_quasr_primers_file -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_reverse_complement -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_insert_or_delete_bases -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_to_tiling_bam -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_replace_bases -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_expand_nucleotides -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_merge -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_scaffolds_to_contigs -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_chunker -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_get_ids -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_to_random_subset -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_filter -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_to_mira_xml -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_interleave -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_translate -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_make_random_contigs -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_get_seq_flanking_gaps -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_trim_Ns_at_end -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_to_perfect_reads -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_to_fake_qual -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_sequence_trim -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_extend_gaps -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin copying build/scripts-3.4/fastaq_long_read_simulate -> /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_strip_illumina_suffix to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_count_sequences to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_to_orfs_gff to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_fasta_to_fastq to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_to_unique_by_id to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_enumerate_names to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_trim_ends to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_search_for_seq to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_split_by_base_count to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_to_fasta to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_capillary_to_pairs to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_deinterleave to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_to_quasr_primers_file to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_reverse_complement to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_insert_or_delete_bases to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_to_tiling_bam to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_replace_bases to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_expand_nucleotides to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_merge to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_scaffolds_to_contigs to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_chunker to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_get_ids to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_to_random_subset to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_filter to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_to_mira_xml to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_interleave to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_translate to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_make_random_contigs to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_get_seq_flanking_gaps to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_trim_Ns_at_end to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_to_perfect_reads to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_to_fake_qual to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_sequence_trim to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_extend_gaps to 775 changing mode of /build/buildd/fastaq-1.5.0/debian/fastaq/usr/bin/fastaq_long_read_simulate to 775 dh_installdocs -O--buildsystem=pybuild install -g 0 -o 0 -d debian/fastaq/usr/share/doc/fastaq install -g 0 -o 0 -m 644 -p debian/copyright debian/fastaq/usr/share/doc/fastaq/copyright dh_installchangelogs -O--buildsystem=pybuild install -o 0 -g 0 -p -m644 debian/changelog debian/fastaq/usr/share/doc/fastaq/changelog.Debian debian/rules override_dh_installman make[1]: Entering directory '/build/buildd/fastaq-1.5.0' mkdir -p /build/buildd/fastaq-1.5.0/debian/man /build/buildd/fastaq-1.5.0/debian/usage_to_man Creating manpages Manpage creation complete dh_installman -- install -d debian/fastaq/usr/share/man/man1/ install -p -m644 debian/man/fastaq_capillary_to_pairs.1 debian/fastaq/usr/share/man/man1/fastaq_capillary_to_pairs.1 install -p -m644 debian/man/fastaq_chunker.1 debian/fastaq/usr/share/man/man1/fastaq_chunker.1 install -p -m644 debian/man/fastaq_count_sequences.1 debian/fastaq/usr/share/man/man1/fastaq_count_sequences.1 install -p -m644 debian/man/fastaq_deinterleave.1 debian/fastaq/usr/share/man/man1/fastaq_deinterleave.1 install -p -m644 debian/man/fastaq_enumerate_names.1 debian/fastaq/usr/share/man/man1/fastaq_enumerate_names.1 install -p -m644 debian/man/fastaq_expand_nucleotides.1 debian/fastaq/usr/share/man/man1/fastaq_expand_nucleotides.1 install -p -m644 debian/man/fastaq_extend_gaps.1 debian/fastaq/usr/share/man/man1/fastaq_extend_gaps.1 install -p -m644 debian/man/fastaq_fasta_to_fastq.1 debian/fastaq/usr/share/man/man1/fastaq_fasta_to_fastq.1 install -p -m644 debian/man/fastaq_filter.1 debian/fastaq/usr/share/man/man1/fastaq_filter.1 install -p -m644 debian/man/fastaq_get_ids.1 debian/fastaq/usr/share/man/man1/fastaq_get_ids.1 install -p -m644 debian/man/fastaq_get_seq_flanking_gaps.1 debian/fastaq/usr/share/man/man1/fastaq_get_seq_flanking_gaps.1 install -p -m644 debian/man/fastaq_insert_or_delete_bases.1 debian/fastaq/usr/share/man/man1/fastaq_insert_or_delete_bases.1 install -p -m644 debian/man/fastaq_interleave.1 debian/fastaq/usr/share/man/man1/fastaq_interleave.1 install -p -m644 debian/man/fastaq_long_read_simulate.1 debian/fastaq/usr/share/man/man1/fastaq_long_read_simulate.1 install -p -m644 debian/man/fastaq_make_random_contigs.1 debian/fastaq/usr/share/man/man1/fastaq_make_random_contigs.1 install -p -m644 debian/man/fastaq_merge.1 debian/fastaq/usr/share/man/man1/fastaq_merge.1 install -p -m644 debian/man/fastaq_replace_bases.1 debian/fastaq/usr/share/man/man1/fastaq_replace_bases.1 install -p -m644 debian/man/fastaq_reverse_complement.1 debian/fastaq/usr/share/man/man1/fastaq_reverse_complement.1 install -p -m644 debian/man/fastaq_scaffolds_to_contigs.1 debian/fastaq/usr/share/man/man1/fastaq_scaffolds_to_contigs.1 install -p -m644 debian/man/fastaq_search_for_seq.1 debian/fastaq/usr/share/man/man1/fastaq_search_for_seq.1 install -p -m644 debian/man/fastaq_sequence_trim.1 debian/fastaq/usr/share/man/man1/fastaq_sequence_trim.1 install -p -m644 debian/man/fastaq_split_by_base_count.1 debian/fastaq/usr/share/man/man1/fastaq_split_by_base_count.1 install -p -m644 debian/man/fastaq_strip_illumina_suffix.1 debian/fastaq/usr/share/man/man1/fastaq_strip_illumina_suffix.1 install -p -m644 debian/man/fastaq_to_fake_qual.1 debian/fastaq/usr/share/man/man1/fastaq_to_fake_qual.1 install -p -m644 debian/man/fastaq_to_fasta.1 debian/fastaq/usr/share/man/man1/fastaq_to_fasta.1 install -p -m644 debian/man/fastaq_to_mira_xml.1 debian/fastaq/usr/share/man/man1/fastaq_to_mira_xml.1 install -p -m644 debian/man/fastaq_to_orfs_gff.1 debian/fastaq/usr/share/man/man1/fastaq_to_orfs_gff.1 install -p -m644 debian/man/fastaq_to_perfect_reads.1 debian/fastaq/usr/share/man/man1/fastaq_to_perfect_reads.1 install -p -m644 debian/man/fastaq_to_quasr_primers_file.1 debian/fastaq/usr/share/man/man1/fastaq_to_quasr_primers_file.1 install -p -m644 debian/man/fastaq_to_random_subset.1 debian/fastaq/usr/share/man/man1/fastaq_to_random_subset.1 install -p -m644 debian/man/fastaq_to_tiling_bam.1 debian/fastaq/usr/share/man/man1/fastaq_to_tiling_bam.1 install -p -m644 debian/man/fastaq_to_unique_by_id.1 debian/fastaq/usr/share/man/man1/fastaq_to_unique_by_id.1 install -p -m644 debian/man/fastaq_translate.1 debian/fastaq/usr/share/man/man1/fastaq_translate.1 install -p -m644 debian/man/fastaq_trim_ends.1 debian/fastaq/usr/share/man/man1/fastaq_trim_ends.1 install -p -m644 debian/man/fastaq_trim_Ns_at_end.1 debian/fastaq/usr/share/man/man1/fastaq_trim_Ns_at_end.1 man --recode UTF-8 ./fastaq_split_by_base_count\.1 > fastaq_split_by_base_count\.1\.new chmod 644 fastaq_split_by_base_count.1.new mv -f fastaq_split_by_base_count.1.new fastaq_split_by_base_count.1 man --recode UTF-8 ./fastaq_long_read_simulate\.1 > fastaq_long_read_simulate\.1\.new chmod 644 fastaq_long_read_simulate.1.new mv -f fastaq_long_read_simulate.1.new fastaq_long_read_simulate.1 man --recode UTF-8 ./fastaq_to_fasta\.1 > fastaq_to_fasta\.1\.new chmod 644 fastaq_to_fasta.1.new mv -f fastaq_to_fasta.1.new fastaq_to_fasta.1 man --recode UTF-8 ./fastaq_to_quasr_primers_file\.1 > fastaq_to_quasr_primers_file\.1\.new chmod 644 fastaq_to_quasr_primers_file.1.new mv -f fastaq_to_quasr_primers_file.1.new fastaq_to_quasr_primers_file.1 man --recode UTF-8 ./fastaq_translate\.1 > fastaq_translate\.1\.new chmod 644 fastaq_translate.1.new mv -f fastaq_translate.1.new fastaq_translate.1 man --recode UTF-8 ./fastaq_interleave\.1 > fastaq_interleave\.1\.new chmod 644 fastaq_interleave.1.new mv -f fastaq_interleave.1.new fastaq_interleave.1 man --recode UTF-8 ./fastaq_trim_ends\.1 > fastaq_trim_ends\.1\.new chmod 644 fastaq_trim_ends.1.new mv -f fastaq_trim_ends.1.new fastaq_trim_ends.1 man --recode UTF-8 ./fastaq_to_mira_xml\.1 > fastaq_to_mira_xml\.1\.new chmod 644 fastaq_to_mira_xml.1.new mv -f fastaq_to_mira_xml.1.new fastaq_to_mira_xml.1 man --recode UTF-8 ./fastaq_fasta_to_fastq\.1 > fastaq_fasta_to_fastq\.1\.new chmod 644 fastaq_fasta_to_fastq.1.new mv -f fastaq_fasta_to_fastq.1.new fastaq_fasta_to_fastq.1 man --recode UTF-8 ./fastaq_get_ids\.1 > fastaq_get_ids\.1\.new chmod 644 fastaq_get_ids.1.new mv -f fastaq_get_ids.1.new fastaq_get_ids.1 man --recode UTF-8 ./fastaq_extend_gaps\.1 > fastaq_extend_gaps\.1\.new chmod 644 fastaq_extend_gaps.1.new mv -f fastaq_extend_gaps.1.new fastaq_extend_gaps.1 man --recode UTF-8 ./fastaq_count_sequences\.1 > fastaq_count_sequences\.1\.new chmod 644 fastaq_count_sequences.1.new mv -f fastaq_count_sequences.1.new fastaq_count_sequences.1 man --recode UTF-8 ./fastaq_to_tiling_bam\.1 > fastaq_to_tiling_bam\.1\.new chmod 644 fastaq_to_tiling_bam.1.new mv -f fastaq_to_tiling_bam.1.new fastaq_to_tiling_bam.1 man --recode UTF-8 ./fastaq_trim_Ns_at_end\.1 > fastaq_trim_Ns_at_end\.1\.new chmod 644 fastaq_trim_Ns_at_end.1.new mv -f fastaq_trim_Ns_at_end.1.new fastaq_trim_Ns_at_end.1 man --recode UTF-8 ./fastaq_to_unique_by_id\.1 > fastaq_to_unique_by_id\.1\.new chmod 644 fastaq_to_unique_by_id.1.new mv -f fastaq_to_unique_by_id.1.new fastaq_to_unique_by_id.1 man --recode UTF-8 ./fastaq_strip_illumina_suffix\.1 > fastaq_strip_illumina_suffix\.1\.new chmod 644 fastaq_strip_illumina_suffix.1.new mv -f fastaq_strip_illumina_suffix.1.new fastaq_strip_illumina_suffix.1 man --recode UTF-8 ./fastaq_to_perfect_reads\.1 > fastaq_to_perfect_reads\.1\.new chmod 644 fastaq_to_perfect_reads.1.new mv -f fastaq_to_perfect_reads.1.new fastaq_to_perfect_reads.1 man --recode UTF-8 ./fastaq_search_for_seq\.1 > fastaq_search_for_seq\.1\.new chmod 644 fastaq_search_for_seq.1.new mv -f fastaq_search_for_seq.1.new fastaq_search_for_seq.1 man --recode UTF-8 ./fastaq_replace_bases\.1 > fastaq_replace_bases\.1\.new chmod 644 fastaq_replace_bases.1.new mv -f fastaq_replace_bases.1.new fastaq_replace_bases.1 man --recode UTF-8 ./fastaq_to_fake_qual\.1 > fastaq_to_fake_qual\.1\.new chmod 644 fastaq_to_fake_qual.1.new mv -f fastaq_to_fake_qual.1.new fastaq_to_fake_qual.1 man --recode UTF-8 ./fastaq_reverse_complement\.1 > fastaq_reverse_complement\.1\.new chmod 644 fastaq_reverse_complement.1.new mv -f fastaq_reverse_complement.1.new fastaq_reverse_complement.1 man --recode UTF-8 ./fastaq_get_seq_flanking_gaps\.1 > fastaq_get_seq_flanking_gaps\.1\.new chmod 644 fastaq_get_seq_flanking_gaps.1.new mv -f fastaq_get_seq_flanking_gaps.1.new fastaq_get_seq_flanking_gaps.1 man --recode UTF-8 ./fastaq_merge\.1 > fastaq_merge\.1\.new chmod 644 fastaq_merge.1.new mv -f fastaq_merge.1.new fastaq_merge.1 man --recode UTF-8 ./fastaq_scaffolds_to_contigs\.1 > fastaq_scaffolds_to_contigs\.1\.new chmod 644 fastaq_scaffolds_to_contigs.1.new mv -f fastaq_scaffolds_to_contigs.1.new fastaq_scaffolds_to_contigs.1 man --recode UTF-8 ./fastaq_deinterleave\.1 > fastaq_deinterleave\.1\.new chmod 644 fastaq_deinterleave.1.new mv -f fastaq_deinterleave.1.new fastaq_deinterleave.1 man --recode UTF-8 ./fastaq_to_random_subset\.1 > fastaq_to_random_subset\.1\.new chmod 644 fastaq_to_random_subset.1.new mv -f fastaq_to_random_subset.1.new fastaq_to_random_subset.1 man --recode UTF-8 ./fastaq_insert_or_delete_bases\.1 > fastaq_insert_or_delete_bases\.1\.new chmod 644 fastaq_insert_or_delete_bases.1.new mv -f fastaq_insert_or_delete_bases.1.new fastaq_insert_or_delete_bases.1 man --recode UTF-8 ./fastaq_chunker\.1 > fastaq_chunker\.1\.new chmod 644 fastaq_chunker.1.new mv -f fastaq_chunker.1.new fastaq_chunker.1 man --recode UTF-8 ./fastaq_to_orfs_gff\.1 > fastaq_to_orfs_gff\.1\.new chmod 644 fastaq_to_orfs_gff.1.new mv -f fastaq_to_orfs_gff.1.new fastaq_to_orfs_gff.1 man --recode UTF-8 ./fastaq_filter\.1 > fastaq_filter\.1\.new chmod 644 fastaq_filter.1.new mv -f fastaq_filter.1.new fastaq_filter.1 man --recode UTF-8 ./fastaq_make_random_contigs\.1 > fastaq_make_random_contigs\.1\.new chmod 644 fastaq_make_random_contigs.1.new mv -f fastaq_make_random_contigs.1.new fastaq_make_random_contigs.1 man --recode UTF-8 ./fastaq_enumerate_names\.1 > fastaq_enumerate_names\.1\.new chmod 644 fastaq_enumerate_names.1.new mv -f fastaq_enumerate_names.1.new fastaq_enumerate_names.1 man --recode UTF-8 ./fastaq_capillary_to_pairs\.1 > fastaq_capillary_to_pairs\.1\.new chmod 644 fastaq_capillary_to_pairs.1.new mv -f fastaq_capillary_to_pairs.1.new fastaq_capillary_to_pairs.1 man --recode UTF-8 ./fastaq_sequence_trim\.1 > fastaq_sequence_trim\.1\.new chmod 644 fastaq_sequence_trim.1.new mv -f fastaq_sequence_trim.1.new fastaq_sequence_trim.1 man --recode UTF-8 ./fastaq_expand_nucleotides\.1 > fastaq_expand_nucleotides\.1\.new chmod 644 fastaq_expand_nucleotides.1.new mv -f fastaq_expand_nucleotides.1.new fastaq_expand_nucleotides.1 make[1]: Leaving directory '/build/buildd/fastaq-1.5.0' dh_python3 -O--buildsystem=pybuild D: dh_python3 dh_python3:149: version: 1.20140511-1 D: dh_python3 dh_python3:150: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild'] D: dh_python3 dh_python3:151: options: {'package': None, 'arch': None, 'compile_all': False, 'verbose': False, 'shebang': None, 'skip_private': False, 'no_shebang_rewrite': False, 'depends': None, 'no_ext_rename': False, 'regexpr': None, 'suggests': None, 'ignore_shebangs': False, 'clean_dbg_pkg': True, 'requires': None, 'vrange': None, 'no_package': None, 'guess_deps': True, 'O': '--buildsystem=pybuild', 'recommends': None} D: dh_python3 dh_python3:152: args: [] D: dh_python3 dh_python3:154: supported Python versions: 3.4 (default=3.4) D: dh_python3 debhelper:98: source=fastaq, binary packages=['fastaq'] D: dh_python3 dh_python3:171: processing package fastaq... D: dh_python3 fs:47: moving files from debian/fastaq/usr/lib/python3.4/dist-packages to debian/fastaq/usr/lib/python3/dist-packages/ D: dh_python3 fs:219: package fastaq details = {'compile': True, 'ext_vers': set(), 'private_dirs': {}, 'shebangs': {/usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3}, 'public_vers': {Version('3')}, 'ext_no_version': set(), 'nsp.txt': set(), 'requires.txt': {'debian/fastaq/usr/lib/python3/dist-packages/Fastaq-1.5.0.egg-info/requires.txt'}} D: dh_python3 depends:107: generating dependencies for package fastaq D: dh_python3 pydist:119: trying to guess dependency for nose >= 1.3 (python=None) D: dh_python3 pydist:158: invoking dpkg -S *python3/*/[Nn][Oo][Ss][Ee]-?*\.egg-info D: dh_python3 depends:236: D={'python3:any (>= 3.3.2-2~)', 'python3', 'python3-nose'}; R=[]; S=[]; E=[], B=[]; RT=[] dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild cd debian/fastaq chmod a-x usr/share/man/man1/fastaq_split_by_base_count.1 usr/share/man/man1/fastaq_long_read_simulate.1 usr/share/man/man1/fastaq_to_fasta.1 usr/share/man/man1/fastaq_to_quasr_primers_file.1 usr/share/man/man1/fastaq_translate.1 usr/share/man/man1/fastaq_interleave.1 usr/share/man/man1/fastaq_trim_ends.1 usr/share/man/man1/fastaq_to_mira_xml.1 usr/share/man/man1/fastaq_fasta_to_fastq.1 usr/share/man/man1/fastaq_get_ids.1 usr/share/man/man1/fastaq_extend_gaps.1 usr/share/man/man1/fastaq_count_sequences.1 usr/share/man/man1/fastaq_to_tiling_bam.1 usr/share/man/man1/fastaq_trim_Ns_at_end.1 usr/share/man/man1/fastaq_to_unique_by_id.1 usr/share/man/man1/fastaq_strip_illumina_suffix.1 usr/share/man/man1/fastaq_to_perfect_reads.1 usr/share/man/man1/fastaq_search_for_seq.1 usr/share/man/man1/fastaq_replace_bases.1 usr/share/man/man1/fastaq_to_fake_qual.1 usr/share/man/man1/fastaq_reverse_complement.1 usr/share/man/man1/fastaq_get_seq_flanking_gaps.1 usr/share/man/man1/fastaq_merge.1 usr/share/man/man1/fastaq_scaffolds_to_contigs.1 usr/share/man/man1/fastaq_deinterleave.1 usr/share/man/man1/fastaq_to_random_subset.1 usr/share/man/man1/fastaq_insert_or_delete_bases.1 usr/share/man/man1/fastaq_chunker.1 usr/share/man/man1/fastaq_to_orfs_gff.1 usr/share/man/man1/fastaq_filter.1 usr/share/man/man1/fastaq_make_random_contigs.1 usr/share/man/man1/fastaq_enumerate_names.1 usr/share/man/man1/fastaq_capillary_to_pairs.1 usr/share/man/man1/fastaq_sequence_trim.1 usr/share/man/man1/fastaq_expand_nucleotides.1 usr/share/doc/fastaq/changelog.Debian gzip -9nf usr/share/man/man1/fastaq_split_by_base_count.1 usr/share/man/man1/fastaq_long_read_simulate.1 usr/share/man/man1/fastaq_to_fasta.1 usr/share/man/man1/fastaq_to_quasr_primers_file.1 usr/share/man/man1/fastaq_translate.1 usr/share/man/man1/fastaq_interleave.1 usr/share/man/man1/fastaq_trim_ends.1 usr/share/man/man1/fastaq_to_mira_xml.1 usr/share/man/man1/fastaq_fasta_to_fastq.1 usr/share/man/man1/fastaq_get_ids.1 usr/share/man/man1/fastaq_extend_gaps.1 usr/share/man/man1/fastaq_count_sequences.1 usr/share/man/man1/fastaq_to_tiling_bam.1 usr/share/man/man1/fastaq_trim_Ns_at_end.1 usr/share/man/man1/fastaq_to_unique_by_id.1 usr/share/man/man1/fastaq_strip_illumina_suffix.1 usr/share/man/man1/fastaq_to_perfect_reads.1 usr/share/man/man1/fastaq_search_for_seq.1 usr/share/man/man1/fastaq_replace_bases.1 usr/share/man/man1/fastaq_to_fake_qual.1 usr/share/man/man1/fastaq_reverse_complement.1 usr/share/man/man1/fastaq_get_seq_flanking_gaps.1 usr/share/man/man1/fastaq_merge.1 usr/share/man/man1/fastaq_scaffolds_to_contigs.1 usr/share/man/man1/fastaq_deinterleave.1 usr/share/man/man1/fastaq_to_random_subset.1 usr/share/man/man1/fastaq_insert_or_delete_bases.1 usr/share/man/man1/fastaq_chunker.1 usr/share/man/man1/fastaq_to_orfs_gff.1 usr/share/man/man1/fastaq_filter.1 usr/share/man/man1/fastaq_make_random_contigs.1 usr/share/man/man1/fastaq_enumerate_names.1 usr/share/man/man1/fastaq_capillary_to_pairs.1 usr/share/man/man1/fastaq_sequence_trim.1 usr/share/man/man1/fastaq_expand_nucleotides.1 usr/share/doc/fastaq/changelog.Debian cd '/build/buildd/fastaq-1.5.0' dh_fixperms -O--buildsystem=pybuild find debian/fastaq -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/fastaq ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/fastaq/usr/share/doc -type f ! -regex 'debian/fastaq/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644 find debian/fastaq/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755 find debian/fastaq/usr/share/man debian/fastaq/usr/man/ debian/fastaq/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/fastaq -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/fastaq/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/fastaq/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/fastaq -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/fastaq/usr/lib/x86_64-linux-gnu/perl5/5.20 debian/fastaq/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X find debian/fastaq/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x find debian/fastaq/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w dh_installdeb -O--buildsystem=pybuild install -o 0 -g 0 -d debian/fastaq/DEBIAN printf '#!/bin/sh set -e ' > debian/fastaq/DEBIAN/postinst cat debian/fastaq.postinst.debhelper >> debian/fastaq/DEBIAN/postinst chown 0:0 debian/fastaq/DEBIAN/postinst chmod 755 debian/fastaq/DEBIAN/postinst printf '#!/bin/sh set -e ' > debian/fastaq/DEBIAN/prerm cat debian/fastaq.prerm.debhelper >> debian/fastaq/DEBIAN/prerm chown 0:0 debian/fastaq/DEBIAN/prerm chmod 755 debian/fastaq/DEBIAN/prerm dh_gencontrol -O--buildsystem=pybuild echo misc:Depends= >> debian/fastaq.substvars dpkg-gencontrol -pfastaq -ldebian/changelog -Tdebian/fastaq.substvars -Pdebian/fastaq dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe chmod 644 debian/fastaq/DEBIAN/control chown 0:0 debian/fastaq/DEBIAN/control dh_md5sums -O--buildsystem=pybuild (cd debian/fastaq >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null chmod 644 debian/fastaq/DEBIAN/md5sums chown 0:0 debian/fastaq/DEBIAN/md5sums dh_builddeb -O--buildsystem=pybuild dpkg-deb --build debian/fastaq .. INFO: pkgstriptranslations version 121 pkgstriptranslations: processing fastaq (in debian/fastaq); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/fastaq/DEBIAN/control, package fastaq, directory debian/fastaq pkgstripfiles: PNG optimization for package fastaq took 0 s dpkg-deb: warning: 'debian/fastaq/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `fastaq' in `../fastaq_1.5.0-1_all.deb'. dpkg-genchanges -b -mUbuntu/amd64 Build Daemon >../fastaq_1.5.0-1_amd64.changes dpkg-genchanges: binary-only upload (no source code included) dpkg-source --after-build fastaq-1.5.0 dpkg-buildpackage: binary-only upload (no source included) ****************************************************************************** Build finished at 20141026-0103 chroot-autobuild/build/buildd/fastaq_1.5.0-1_all.deb: new debian package, version 2.0. size 49882 bytes: control archive= 5357 bytes. 5181 bytes, 163 lines control 5994 bytes, 81 lines md5sums 156 bytes, 9 lines * postinst #!/bin/sh 385 bytes, 12 lines * prerm #!/bin/sh Package: fastaq Version: 1.5.0-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 169 Depends: python3:any (>= 3.3.2-2~), python3, python3-nose Section: science Priority: optional Homepage: https://github.com/sanger-pathogens/Fastaq Description: FASTA and FASTQ file manipulation tools A collection of scripts that perform useful and common fasta/q manipulation tasks. . All scripts automatically detect whether the input is a FASTA or FASTQ file. . Input and output files can be gzipped. . fastaq_capillary_to_pairs - Given a fasta/q file of capillary reads, makes an interleaved file of read pairs . fastaq_chunker - Splits a multi fasta/q file into separate files. Splits sequences into chunks of a fixed size. . fastaq_count_sequences - Counts the number of sequences in a fasta/q file . fastaq_deinterleave - Deinterleaves fasta/q file, so that reads are written alternately between two output files . fastaq_enumerate_names - Renames sequences in a file, calling them 1,2,3... . fastaq_expand_nucleotides - Makes all combinations of sequences in input file by using all possibilities of redundant bases. e.g. ART could be AAT or AGT. . fastaq_extend_gaps - Extends the length of all gaps (and trims the start/end of sequences) in a fasta/q file. . fastaq_fasta_to_fastq - Given a fasta and qual file, makes a fastq file. . fastaq_filter - Filters a fasta/q file by sequence length and/or by name matching a regular expression. . fastaq_get_ids - Gets IDs from each sequence in a fasta or fastq file. . fastaq_get_seq_flanking_gaps - Gets the sequences either side of gaps in a fasta/q file. . fastaq_insert_or_delete_bases - Deletes or inserts bases at given position(s) from a fasta/q file. . fastaq_interleave - Interleaves two fasta/q files, so that reads are written alternately first/second in output file. . fastaq_long_read_simulate - Simulates long reads from a fasta/q file. Can optionally make insertions into the reads, like pacbio does. . fastaq_make_random_contigs - Makes a multi-fasta file of random sequences, all of the same length. Each base has equal chance of being A,C,G or T . fastaq_merge - Converts multi fasta/q file to single sequence file, preserving original order of sequences. . fastaq_replace_bases - Replaces all occurences of one letter with another in a fasta/q file. . fastaq_reverse_complement - Reverse complements all sequences in a fasta/q file . fastaq_scaffolds_to_contigs - Creates a file of contigs from a file of scaffolds - i.e. breaks at every gap in the input. . fastaq_search_for_seq - Searches for an exact match on a given string and its reverese complement, in every sequences of a fasta/q file. Case insensitive. Guaranteed to find all hits. . fastaq_sequence_trim - Trims sequences off the start of all sequences in a pair of fasta/q files, whenever there is a perfect match. Only keeps a read pair if both reads of the pair are at least a minimum length after any trimming. . fastaq_split_by_base_count - Splits a multi fasta/q file into separate files. Does not split sequences. Puts up to max_bases into each split file. The exception is that any sequence longer than max_bases is put into its own file. . fastaq_strip_illumina_suffix - Strips /1 or /2 off the end of every read name in a fasta/q file. . fastaq_to_fake_qual - Makes fake quality scores file from a fasta/q file. . fastaq_to_fasta - Converts sequence file to FASTA format. . fastaq_to_mira_xml - Creates an xml file from a fasta/q file of reads, for use with Mira assembler. . fastaq_to_orfs_gff - Writes a GFF file of open reading frames from a fasta/q file . fastaq_to_perfect_reads - Makes perfect paired end fastq reads from a fasta/q file, with insert sizes sampled from a normal distribution. Read orientation is innies. Output is an interleaved fastq file. . fastaq_to_quasr_primers_file - Converts a fasta/q file to QUASR primers format: just the sequence on each line and its reverse complement, tab separated. . fastaq_to_random_subset - Takes a random subset of reads from a fasta/q file and optionally the corresponding read from a mates file. Ouptut is interleaved if mates file given. . fastaq_to_tiling_bam - Takes a fasta/q file. Makes a BAM file containing perfect (unpaired) reads tiling the whole genome. . fastaq_to_unique_by_id - Removes duplicate sequences from a fasta/q file, based on their names. If the same name is found more than once, then the longest sequence is kept. Order of sequences is preserved in output. . fastaq_translate - Translates all sequences in a fasta or fastq file. Output is always fasta format . fastaq_trim_ends - Trims set number of bases off each sequence in a fasta/q file . fastaq_trim_Ns_at_end - Trims any Ns off each sequence in a fasta/q file. Does nothing to gaps in the middle, just trims the ends . A developer API is also provided by this package. There are plenty of examples in tasks.py chroot-autobuild/build/buildd/fastaq_1.5.0-1_all.deb: drwxr-xr-x root/root 0 2014-10-26 01:03 ./ drwxr-xr-x root/root 0 2014-10-26 01:03 ./usr/ drwxr-xr-x root/root 0 2014-10-26 01:03 ./usr/lib/ drwxr-xr-x root/root 0 2014-10-26 01:03 ./usr/lib/python3/ drwxr-xr-x root/root 0 2014-10-26 01:03 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2014-10-26 01:03 ./usr/lib/python3/dist-packages/fastaq/ -rw-r--r-- root/root 21149 2014-10-14 15:57 ./usr/lib/python3/dist-packages/fastaq/sequences.py -rw-r--r-- root/root 23051 2014-10-14 15:57 ./usr/lib/python3/dist-packages/fastaq/tasks.py -rw-r--r-- root/root 76 2014-10-14 15:57 ./usr/lib/python3/dist-packages/fastaq/__init__.py -rw-r--r-- root/root 3504 2014-10-14 15:57 ./usr/lib/python3/dist-packages/fastaq/intervals.py -rw-r--r-- root/root 2277 2014-10-14 15:57 ./usr/lib/python3/dist-packages/fastaq/utils.py drwxr-xr-x root/root 0 2014-10-26 01:03 ./usr/lib/python3/dist-packages/Fastaq-1.5.0.egg-info/ -rw-r--r-- root/root 12 2014-10-26 01:03 ./usr/lib/python3/dist-packages/Fastaq-1.5.0.egg-info/requires.txt -rw-r--r-- root/root 7 2014-10-26 01:03 ./usr/lib/python3/dist-packages/Fastaq-1.5.0.egg-info/top_level.txt -rw-r--r-- root/root 1 2014-10-26 01:03 ./usr/lib/python3/dist-packages/Fastaq-1.5.0.egg-info/dependency_links.txt -rw-r--r-- root/root 2326 2014-10-26 01:03 ./usr/lib/python3/dist-packages/Fastaq-1.5.0.egg-info/PKG-INFO drwxr-xr-x root/root 0 2014-10-26 01:03 ./usr/bin/ -rwxr-xr-x root/root 469 2014-10-26 01:03 ./usr/bin/fastaq_strip_illumina_suffix -rwxr-xr-x root/root 346 2014-10-26 01:03 ./usr/bin/fastaq_count_sequences -rwxr-xr-x root/root 619 2014-10-26 01:03 ./usr/bin/fastaq_to_orfs_gff -rwxr-xr-x root/root 579 2014-10-26 01:03 ./usr/bin/fastaq_fasta_to_fastq -rwxr-xr-x root/root 570 2014-10-26 01:03 ./usr/bin/fastaq_to_unique_by_id -rwxr-xr-x root/root 971 2014-10-26 01:03 ./usr/bin/fastaq_enumerate_names -rwxr-xr-x root/root 689 2014-10-26 01:03 ./usr/bin/fastaq_trim_ends -rwxr-xr-x root/root 720 2014-10-26 01:03 ./usr/bin/fastaq_search_for_seq -rwxr-xr-x root/root 915 2014-10-26 01:03 ./usr/bin/fastaq_split_by_base_count -rwxr-xr-x root/root 848 2014-10-26 01:03 ./usr/bin/fastaq_to_fasta -rwxr-xr-x root/root 675 2014-10-26 01:03 ./usr/bin/fastaq_capillary_to_pairs -rwxr-xr-x root/root 794 2014-10-26 01:03 ./usr/bin/fastaq_deinterleave -rwxr-xr-x root/root 499 2014-10-26 01:03 ./usr/bin/fastaq_to_quasr_primers_file -rwxr-xr-x root/root 453 2014-10-26 01:03 ./usr/bin/fastaq_reverse_complement -rwxr-xr-x root/root 3987 2014-10-26 01:03 ./usr/bin/fastaq_insert_or_delete_bases -rwxr-xr-x root/root 2830 2014-10-26 01:03 ./usr/bin/fastaq_to_tiling_bam -rwxr-xr-x root/root 596 2014-10-26 01:03 ./usr/bin/fastaq_replace_bases -rwxr-xr-x root/root 604 2014-10-26 01:03 ./usr/bin/fastaq_expand_nucleotides -rwxr-xr-x root/root 654 2014-10-26 01:03 ./usr/bin/fastaq_merge -rwxr-xr-x root/root 660 2014-10-26 01:03 ./usr/bin/fastaq_scaffolds_to_contigs -rwxr-xr-x root/root 1088 2014-10-26 01:03 ./usr/bin/fastaq_chunker -rwxr-xr-x root/root 417 2014-10-26 01:03 ./usr/bin/fastaq_get_ids -rwxr-xr-x root/root 1387 2014-10-26 01:03 ./usr/bin/fastaq_to_random_subset -rwxr-xr-x root/root 1318 2014-10-26 01:03 ./usr/bin/fastaq_filter -rwxr-xr-x root/root 469 2014-10-26 01:03 ./usr/bin/fastaq_to_mira_xml -rwxr-xr-x root/root 620 2014-10-26 01:03 ./usr/bin/fastaq_interleave -rwxr-xr-x root/root 644 2014-10-26 01:03 ./usr/bin/fastaq_translate -rwxr-xr-x root/root 1299 2014-10-26 01:03 ./usr/bin/fastaq_make_random_contigs -rwxr-xr-x root/root 747 2014-10-26 01:03 ./usr/bin/fastaq_get_seq_flanking_gaps -rwxr-xr-x root/root 503 2014-10-26 01:03 ./usr/bin/fastaq_trim_Ns_at_end -rwxr-xr-x root/root 3985 2014-10-26 01:03 ./usr/bin/fastaq_to_perfect_reads -rwxr-xr-x root/root 567 2014-10-26 01:03 ./usr/bin/fastaq_to_fake_qual -rwxr-xr-x root/root 1297 2014-10-26 01:03 ./usr/bin/fastaq_sequence_trim -rwxr-xr-x root/root 779 2014-10-26 01:03 ./usr/bin/fastaq_extend_gaps -rwxr-xr-x root/root 3248 2014-10-26 01:03 ./usr/bin/fastaq_long_read_simulate drwxr-xr-x root/root 0 2014-10-26 01:03 ./usr/share/ drwxr-xr-x root/root 0 2014-10-26 01:03 ./usr/share/man/ drwxr-xr-x root/root 0 2014-10-26 01:03 ./usr/share/man/man1/ -rw-r--r-- root/root 690 2014-10-26 01:03 ./usr/share/man/man1/fastaq_search_for_seq.1.gz -rw-r--r-- root/root 673 2014-10-26 01:03 ./usr/share/man/man1/fastaq_expand_nucleotides.1.gz -rw-r--r-- root/root 769 2014-10-26 01:03 ./usr/share/man/man1/fastaq_chunker.1.gz -rw-r--r-- root/root 594 2014-10-26 01:03 ./usr/share/man/man1/fastaq_to_fake_qual.1.gz -rw-r--r-- root/root 834 2014-10-26 01:03 ./usr/share/man/man1/fastaq_make_random_contigs.1.gz -rw-r--r-- root/root 877 2014-10-26 01:03 ./usr/share/man/man1/fastaq_to_perfect_reads.1.gz -rw-r--r-- root/root 749 2014-10-26 01:03 ./usr/share/man/man1/fastaq_to_tiling_bam.1.gz -rw-r--r-- root/root 632 2014-10-26 01:03 ./usr/share/man/man1/fastaq_get_seq_flanking_gaps.1.gz -rw-r--r-- root/root 642 2014-10-26 01:03 ./usr/share/man/man1/fastaq_to_unique_by_id.1.gz -rw-r--r-- root/root 600 2014-10-26 01:03 ./usr/share/man/man1/fastaq_strip_illumina_suffix.1.gz -rw-r--r-- root/root 629 2014-10-26 01:03 ./usr/share/man/man1/fastaq_merge.1.gz -rw-r--r-- root/root 1194 2014-10-26 01:03 ./usr/share/man/man1/fastaq_long_read_simulate.1.gz -rw-r--r-- root/root 619 2014-10-26 01:03 ./usr/share/man/man1/fastaq_to_orfs_gff.1.gz -rw-r--r-- root/root 698 2014-10-26 01:03 ./usr/share/man/man1/fastaq_to_random_subset.1.gz -rw-r--r-- root/root 683 2014-10-26 01:03 ./usr/share/man/man1/fastaq_to_fasta.1.gz -rw-r--r-- root/root 650 2014-10-26 01:03 ./usr/share/man/man1/fastaq_scaffolds_to_contigs.1.gz -rw-r--r-- root/root 590 2014-10-26 01:03 ./usr/share/man/man1/fastaq_to_mira_xml.1.gz -rw-r--r-- root/root 660 2014-10-26 01:03 ./usr/share/man/man1/fastaq_deinterleave.1.gz -rw-r--r-- root/root 604 2014-10-26 01:03 ./usr/share/man/man1/fastaq_trim_ends.1.gz -rw-r--r-- root/root 712 2014-10-26 01:03 ./usr/share/man/man1/fastaq_enumerate_names.1.gz -rw-r--r-- root/root 611 2014-10-26 01:03 ./usr/share/man/man1/fastaq_translate.1.gz -rw-r--r-- root/root 709 2014-10-26 01:03 ./usr/share/man/man1/fastaq_extend_gaps.1.gz -rw-r--r-- root/root 605 2014-10-26 01:03 ./usr/share/man/man1/fastaq_replace_bases.1.gz -rw-r--r-- root/root 573 2014-10-26 01:03 ./usr/share/man/man1/fastaq_reverse_complement.1.gz -rw-r--r-- root/root 606 2014-10-26 01:03 ./usr/share/man/man1/fastaq_trim_Ns_at_end.1.gz -rw-r--r-- root/root 700 2014-10-26 01:03 ./usr/share/man/man1/fastaq_capillary_to_pairs.1.gz -rw-r--r-- root/root 615 2014-10-26 01:03 ./usr/share/man/man1/fastaq_interleave.1.gz -rw-r--r-- root/root 724 2014-10-26 01:03 ./usr/share/man/man1/fastaq_split_by_base_count.1.gz -rw-r--r-- root/root 573 2014-10-26 01:03 ./usr/share/man/man1/fastaq_fasta_to_fastq.1.gz -rw-r--r-- root/root 615 2014-10-26 01:03 ./usr/share/man/man1/fastaq_to_quasr_primers_file.1.gz -rw-r--r-- root/root 555 2014-10-26 01:03 ./usr/share/man/man1/fastaq_get_ids.1.gz -rw-r--r-- root/root 756 2014-10-26 01:03 ./usr/share/man/man1/fastaq_filter.1.gz -rw-r--r-- root/root 545 2014-10-26 01:03 ./usr/share/man/man1/fastaq_count_sequences.1.gz -rw-r--r-- root/root 901 2014-10-26 01:03 ./usr/share/man/man1/fastaq_insert_or_delete_bases.1.gz -rw-r--r-- root/root 759 2014-10-26 01:03 ./usr/share/man/man1/fastaq_sequence_trim.1.gz drwxr-xr-x root/root 0 2014-10-26 01:03 ./usr/share/doc/ drwxr-xr-x root/root 0 2014-10-26 01:03 ./usr/share/doc/fastaq/ -rw-r--r-- root/root 991 2014-10-23 18:29 ./usr/share/doc/fastaq/copyright -rw-r--r-- root/root 159 2014-10-23 18:29 ./usr/share/doc/fastaq/changelog.Debian.gz fastaq_1.5.0-1_amd64.changes: Format: 1.8 Date: Thu, 23 Oct 2014 20:23:54 +0200 Source: fastaq Binary: fastaq Architecture: all Version: 1.5.0-1 Distribution: vivid-proposed Urgency: medium Maintainer: Ubuntu/amd64 Build Daemon Changed-By: Jorge Soares Description: fastaq - FASTA and FASTQ file manipulation tools Closes: 766321 Changes: fastaq (1.5.0-1) unstable; urgency=medium . * Initial release (Closes: #766321) Checksums-Sha1: fe30f9c8606fc19f6364a12017d0678be9b2f018 49882 fastaq_1.5.0-1_all.deb Checksums-Sha256: bec56edfd9e52979c92e27922079a3c940099859e8f01a1d0e18afde7b6dbfb0 49882 fastaq_1.5.0-1_all.deb Files: 5788bfac50b4f9deab0574b2ca0db408 49882 science optional fastaq_1.5.0-1_all.deb ****************************************************************************** Built successfully ****************************************************************************** Finished at 20141026-0103 Build needed 00:00:22, 2352k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-6503219'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-6503219/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-6503219'] Unmounting chroot for build PACKAGEBUILD-6503219... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-6503219'] Removing build PACKAGEBUILD-6503219