subread →
1.4.6-p5+dfsg-1 →
armhf → 2015-09-14 07:17:16
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on testbuildd.raspbian.org
╔══════════════════════════════════════════════════════════════════════════════╗
║ subread 1.4.6-p5+dfsg-1 (armhf) 14 Sep 2015 06:56 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: subread
Version: 1.4.6-p5+dfsg-1
Source Version: 1.4.6-p5+dfsg-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/subread-XhpX2o/subread-1.4.6-p5+dfsg' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/subread-XhpX2o' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-bef777ac-b41a-4c48-ac57-790e00a4bd48' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 stretch-staging/main Sources [8329 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [10.2 MB]
Ign http://172.17.0.1 stretch-staging/main Translation-en
Fetched 18.6 MB in 35s (523 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
─────────
Checking available source versions...
Download source files with APT
──────────────────────────────
Reading package lists...
Building dependency tree...
NOTICE: 'subread' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/subread.git
Need to get 14.4 MB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main subread 1.4.6-p5+dfsg-1 (dsc) [2300 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main subread 1.4.6-p5+dfsg-1 (tar) [14.4 MB]
Get:3 http://172.17.0.1/private/ stretch-staging/main subread 1.4.6-p5+dfsg-1 (diff) [6936 B]
Fetched 14.4 MB in 5s (2615 kB/s)
Download complete and in download only mode
Check architectures
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Check dependencies
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-q7Wqpg/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded.
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(Reading database ... 11953 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), help2man, texlive-latex-extra, zlib1g-dev
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), help2man, texlive-latex-extra, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-subread-dummy' in '/«BUILDDIR»/resolver-ueeSxq/apt_archive/sbuild-build-depends-subread-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install subread build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils debhelper file fontconfig-config fonts-dejavu-core gettext
gettext-base groff-base help2man intltool-debian libasprintf0v5
libavahi-client3 libavahi-common-data libavahi-common3 libcroco3 libcups2
libcupsfilters1 libcupsimage2 libexpat1 libffi6 libfontconfig1 libfreetype6
libglib2.0-0 libgnutls-deb0-28 libgraphite2-3 libgs9 libgs9-common
libgssapi-krb5-2 libharfbuzz-icu0 libharfbuzz0b libhogweed4 libice6 libicu55
libidn11 libijs-0.35 libjbig0 libjbig2dec0 libjpeg62-turbo libk5crypto3
libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblcms2-2 libmagic1
libnettle6 libopenjpeg5 libp11-kit0 libpaper-utils libpaper1 libpipeline1
libpixman-1-0 libpoppler46 libpotrace0 libptexenc1 libpython-stdlib
libpython2.7-minimal libpython2.7-stdlib libsm6 libsqlite3-0 libssl1.0.0
libsynctex1 libtasn1-6 libtexlua52 libtexluajit2 libtiff5 libtrio2
libunistring0 libx11-6 libx11-data libxau6 libxaw7 libxcb1 libxdmcp6
libxext6 libxi6 libxml2 libxmu6 libxpm4 libxt6 libzzip-0-13 man-db
mime-support po-debconf poppler-data preview-latex-style python
python-minimal python2.7 python2.7-minimal t1utils tex-common texlive-base
texlive-binaries texlive-latex-base texlive-latex-extra
texlive-latex-recommended texlive-pictures ucf x11-common xdg-utils
zlib1g-dev
Suggested packages:
wamerican wordlist whois vacation dh-make gettext-doc groff cups-common
gnutls-bin krb5-doc krb5-user liblcms2-utils less www-browser
libmail-box-perl poppler-utils ghostscript fonts-japanese-mincho
fonts-ipafont-mincho fonts-japanese-gothic fonts-ipafont-gothic
fonts-arphic-ukai fonts-arphic-uming fonts-nanum python-doc python-tk
python2.7-doc binfmt-support gv postscript-viewer xpdf-reader pdf-viewer
perl-tk libspreadsheet-parseexcel-perl python-pygments libfile-which-perl
texlive-pstricks dot2tex libtcltk-ruby gvfs-bin
Recommended packages:
curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libglib2.0-data shared-mime-info xdg-user-dirs fonts-droid krb5-locales
xml-core libmail-sendmail-perl lmodern ruby wish texlive-latex-base-doc
texlive-latex-extra-doc texlive-fonts-recommended
texlive-latex-recommended-doc prosper prerex texlive-pictures-doc
libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils
x11-xserver-utils
The following NEW packages will be installed:
bsdmainutils debhelper file fontconfig-config fonts-dejavu-core gettext
gettext-base groff-base help2man intltool-debian libasprintf0v5
libavahi-client3 libavahi-common-data libavahi-common3 libcroco3 libcups2
libcupsfilters1 libcupsimage2 libexpat1 libffi6 libfontconfig1 libfreetype6
libglib2.0-0 libgnutls-deb0-28 libgraphite2-3 libgs9 libgs9-common
libgssapi-krb5-2 libharfbuzz-icu0 libharfbuzz0b libhogweed4 libice6 libicu55
libidn11 libijs-0.35 libjbig0 libjbig2dec0 libjpeg62-turbo libk5crypto3
libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblcms2-2 libmagic1
libnettle6 libopenjpeg5 libp11-kit0 libpaper-utils libpaper1 libpipeline1
libpixman-1-0 libpoppler46 libpotrace0 libptexenc1 libpython-stdlib
libpython2.7-minimal libpython2.7-stdlib libsm6 libsqlite3-0 libssl1.0.0
libsynctex1 libtasn1-6 libtexlua52 libtexluajit2 libtiff5 libtrio2
libunistring0 libx11-6 libx11-data libxau6 libxaw7 libxcb1 libxdmcp6
libxext6 libxi6 libxml2 libxmu6 libxpm4 libxt6 libzzip-0-13 man-db
mime-support po-debconf poppler-data preview-latex-style python
python-minimal python2.7 python2.7-minimal
sbuild-build-depends-subread-dummy t1utils tex-common texlive-base
texlive-binaries texlive-latex-base texlive-latex-extra
texlive-latex-recommended texlive-pictures ucf x11-common xdg-utils
zlib1g-dev
0 upgraded, 103 newly installed, 0 to remove and 1 not upgraded.
Need to get 85.8 MB/85.8 MB of archives.
After this operation, 335 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ stretch-staging/main groff-base armhf 1.22.3-1 [1085 kB]
Get:2 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main libpipeline1 armhf 1.4.1-1 [23.9 kB]
Get:4 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.2-1 [973 kB]
Get:5 http://172.17.0.1/private/ stretch-staging/main libasprintf0v5 armhf 0.19.5.1-1 [32.0 kB]
Get:6 http://172.17.0.1/private/ stretch-staging/main libmagic1 armhf 1:5.22+15-2 [244 kB]
Get:7 http://172.17.0.1/private/ stretch-staging/main libtasn1-6 armhf 4.5-2 [43.9 kB]
Get:8 http://172.17.0.1/private/ stretch-staging/main libxml2 armhf 2.9.1+dfsg1-5 [703 kB]
Get:9 http://172.17.0.1/private/ stretch-staging/main libpython2.7-minimal armhf 2.7.10-3 [380 kB]
Get:10 http://172.17.0.1/private/ stretch-staging/main python2.7-minimal armhf 2.7.10-3 [1163 kB]
Get:11 http://172.17.0.1/private/ stretch-staging/main python-minimal armhf 2.7.9-1 [40.1 kB]
Get:12 http://172.17.0.1/private/ stretch-staging/main mime-support all 3.59 [36.4 kB]
Get:13 http://172.17.0.1/private/ stretch-staging/main libexpat1 armhf 2.1.0-7 [59.8 kB]
Get:14 http://172.17.0.1/private/ stretch-staging/main libffi6 armhf 3.2.1-3 [18.5 kB]
Get:15 http://172.17.0.1/private/ stretch-staging/main libsqlite3-0 armhf 3.8.11.1-1 [391 kB]
Get:16 http://172.17.0.1/private/ stretch-staging/main libssl1.0.0 armhf 1.0.2d-1 [882 kB]
Get:17 http://172.17.0.1/private/ stretch-staging/main libpython2.7-stdlib armhf 2.7.10-3 [1815 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main python2.7 armhf 2.7.10-3 [259 kB]
Get:19 http://172.17.0.1/private/ stretch-staging/main libpython-stdlib armhf 2.7.9-1 [19.6 kB]
Get:20 http://172.17.0.1/private/ stretch-staging/main python armhf 2.7.9-1 [151 kB]
Get:21 http://172.17.0.1/private/ stretch-staging/main libavahi-common-data armhf 0.6.31-5 [98.8 kB]
Get:22 http://172.17.0.1/private/ stretch-staging/main libavahi-common3 armhf 0.6.31-5 [48.0 kB]
Get:23 http://172.17.0.1/private/ stretch-staging/main libavahi-client3 armhf 0.6.31-5 [50.6 kB]
Get:24 http://172.17.0.1/private/ stretch-staging/main libglib2.0-0 armhf 2.44.1-1.1 [2312 kB]
Get:25 http://172.17.0.1/private/ stretch-staging/main libcroco3 armhf 0.6.8-3 [121 kB]
Get:26 http://172.17.0.1/private/ stretch-staging/main libfreetype6 armhf 2.5.2-4 [412 kB]
Get:27 http://172.17.0.1/private/ stretch-staging/main ucf all 3.0030 [69.7 kB]
Get:28 http://172.17.0.1/private/ stretch-staging/main fonts-dejavu-core all 2.35-1 [1064 kB]
Get:29 http://172.17.0.1/private/ stretch-staging/main fontconfig-config all 2.11.0-6.3 [273 kB]
Get:30 http://172.17.0.1/private/ stretch-staging/main libfontconfig1 armhf 2.11.0-6.3 [311 kB]
Get:31 http://172.17.0.1/private/ stretch-staging/main libgraphite2-3 armhf 1.2.4-3 [48.2 kB]
Get:32 http://172.17.0.1/private/ stretch-staging/main libjbig0 armhf 2.1-3.1 [27.5 kB]
Get:33 http://172.17.0.1/private/ stretch-staging/main liblcms2-2 armhf 2.6-3 [113 kB]
Get:34 http://172.17.0.1/private/ stretch-staging/main libpaper1 armhf 1.1.24+nmu4 [21.4 kB]
Get:35 http://172.17.0.1/private/ stretch-staging/main libpixman-1-0 armhf 0.32.6-3 [422 kB]
Get:36 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:37 http://172.17.0.1/private/ stretch-staging/main libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:38 http://172.17.0.1/private/ stretch-staging/main libxdmcp6 armhf 1:1.1.2-1 [25.0 kB]
Get:39 http://172.17.0.1/private/ stretch-staging/main libxcb1 armhf 1.10-3+b1 [40.6 kB]
Get:40 http://172.17.0.1/private/ stretch-staging/main libx11-data all 2:1.6.3-1 [128 kB]
Get:41 http://172.17.0.1/private/ stretch-staging/main libx11-6 armhf 2:1.6.3-1 [678 kB]
Get:42 http://172.17.0.1/private/ stretch-staging/main libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:43 http://172.17.0.1/private/ stretch-staging/main libxi6 armhf 2:1.7.4-1+b2 [74.2 kB]
Get:44 http://172.17.0.1/private/ stretch-staging/main x11-common all 1:7.7+9 [287 kB]
Get:45 http://172.17.0.1/private/ stretch-staging/main libice6 armhf 2:1.0.9-1+b1 [51.9 kB]
Get:46 http://172.17.0.1/private/ stretch-staging/main libsm6 armhf 2:1.2.2-1+b1 [31.2 kB]
Get:47 http://172.17.0.1/private/ stretch-staging/main libxt6 armhf 1:1.1.4-1+b1 [154 kB]
Get:48 http://172.17.0.1/private/ stretch-staging/main libxmu6 armhf 2:1.1.2-1 [50.8 kB]
Get:49 http://172.17.0.1/private/ stretch-staging/main libzzip-0-13 armhf 0.13.62-3 [51.3 kB]
Get:50 http://172.17.0.1/private/ stretch-staging/main poppler-data all 0.4.7-3 [1470 kB]
Get:51 http://172.17.0.1/private/ stretch-staging/main libtrio2 armhf 1.16+dfsg1-3 [39.0 kB]
Get:52 http://172.17.0.1/private/ stretch-staging/main file armhf 1:5.22+15-2 [59.9 kB]
Get:53 http://172.17.0.1/private/ stretch-staging/main gettext-base armhf 0.19.5.1-1 [118 kB]
Get:54 http://172.17.0.1/private/ stretch-staging/main libnettle6 armhf 3.1.1-4 [200 kB]
Get:55 http://172.17.0.1/private/ stretch-staging/main libhogweed4 armhf 3.1.1-4 [126 kB]
Get:56 http://172.17.0.1/private/ stretch-staging/main libp11-kit0 armhf 0.23.1-3 [94.2 kB]
Get:57 http://172.17.0.1/private/ stretch-staging/main libgnutls-deb0-28 armhf 3.3.17-1 [646 kB]
Get:58 http://172.17.0.1/private/ stretch-staging/main libkeyutils1 armhf 1.5.9-7 [11.5 kB]
Get:59 http://172.17.0.1/private/ stretch-staging/main libkrb5support0 armhf 1.13.2+dfsg-2 [55.9 kB]
Get:60 http://172.17.0.1/private/ stretch-staging/main libk5crypto3 armhf 1.13.2+dfsg-2 [109 kB]
Get:61 http://172.17.0.1/private/ stretch-staging/main libkrb5-3 armhf 1.13.2+dfsg-2 [260 kB]
Get:62 http://172.17.0.1/private/ stretch-staging/main libgssapi-krb5-2 armhf 1.13.2+dfsg-2 [130 kB]
Get:63 http://172.17.0.1/private/ stretch-staging/main libidn11 armhf 1.32-1 [168 kB]
Get:64 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.5.1-1 [1386 kB]
Get:65 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.2 [25.9 kB]
Get:66 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:67 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20150811 [817 kB]
Get:68 http://172.17.0.1/private/ stretch-staging/main help2man armhf 1.47.1 [150 kB]
Get:69 http://172.17.0.1/private/ stretch-staging/main libcups2 armhf 2.0.3-10 [264 kB]
Get:70 http://172.17.0.1/private/ stretch-staging/main libcupsimage2 armhf 2.0.3-10 [117 kB]
Get:71 http://172.17.0.1/private/ stretch-staging/main libjpeg62-turbo armhf 1:1.4.1-2 [103 kB]
Get:72 http://172.17.0.1/private/ stretch-staging/main libtiff5 armhf 4.0.5-1 [200 kB]
Get:73 http://172.17.0.1/private/ stretch-staging/main libcupsfilters1 armhf 1.0.71-1 [101 kB]
Get:74 http://172.17.0.1/private/ stretch-staging/main libijs-0.35 armhf 0.35-11 [16.1 kB]
Get:75 http://172.17.0.1/private/ stretch-staging/main libjbig2dec0 armhf 0.12-2 [51.0 kB]
Get:76 http://172.17.0.1/private/ stretch-staging/main libgs9-common all 9.16~dfsg-2 [2983 kB]
Get:77 http://172.17.0.1/private/ stretch-staging/main libgs9 armhf 9.16~dfsg-2 [1699 kB]
Get:78 http://172.17.0.1/private/ stretch-staging/main libharfbuzz0b armhf 1.0.1-1+b1 [501 kB]
Get:79 http://172.17.0.1/private/ stretch-staging/main libicu55 armhf 55.1-4 [7378 kB]
Get:80 http://172.17.0.1/private/ stretch-staging/main libharfbuzz-icu0 armhf 1.0.1-1+b1 [390 kB]
Get:81 http://172.17.0.1/private/ stretch-staging/main libkpathsea6 armhf 2015.20150524.37493-6 [148 kB]
Get:82 http://172.17.0.1/private/ stretch-staging/main libpaper-utils armhf 1.1.24+nmu4 [17.2 kB]
Get:83 http://172.17.0.1/private/ stretch-staging/main libopenjpeg5 armhf 1:1.5.2-3.1 [93.6 kB]
Get:84 http://172.17.0.1/private/ stretch-staging/main libpoppler46 armhf 0.26.5-4 [1084 kB]
Get:85 http://172.17.0.1/private/ stretch-staging/main libpotrace0 armhf 1.12-1 [22.9 kB]
Get:86 http://172.17.0.1/private/ stretch-staging/main libptexenc1 armhf 2015.20150524.37493-6 [53.3 kB]
Get:87 http://172.17.0.1/private/ stretch-staging/main libsynctex1 armhf 2015.20150524.37493-6 [55.9 kB]
Get:88 http://172.17.0.1/private/ stretch-staging/main libtexlua52 armhf 2015.20150524.37493-6 [84.2 kB]
Get:89 http://172.17.0.1/private/ stretch-staging/main libtexluajit2 armhf 2015.20150524.37493-6 [185 kB]
Get:90 http://172.17.0.1/private/ stretch-staging/main libxpm4 armhf 1:3.5.11-1+b1 [42.4 kB]
Get:91 http://172.17.0.1/private/ stretch-staging/main libxaw7 armhf 2:1.0.13-1 [164 kB]
Get:92 http://172.17.0.1/private/ stretch-staging/main tex-common all 6.03 [563 kB]
Get:93 http://172.17.0.1/private/ stretch-staging/main preview-latex-style all 11.87-3+deb8u1 [318 kB]
Get:94 http://172.17.0.1/private/ stretch-staging/main t1utils armhf 1.38-4 [50.1 kB]
Get:95 http://172.17.0.1/private/ stretch-staging/main xdg-utils all 1.1.0~rc3+git20150907-1 [68.0 kB]
Get:96 http://172.17.0.1/private/ stretch-staging/main texlive-binaries armhf 2015.20150524.37493-6 [6798 kB]
Get:97 http://172.17.0.1/private/ stretch-staging/main texlive-base all 2015.20150823-1 [17.9 MB]
Get:98 http://172.17.0.1/private/ stretch-staging/main texlive-latex-base all 2015.20150823-1 [985 kB]
Get:99 http://172.17.0.1/private/ stretch-staging/main texlive-latex-recommended all 2015.20150823-1 [8363 kB]
Get:100 http://172.17.0.1/private/ stretch-staging/main texlive-pictures all 2015.20150823-1 [3145 kB]
Get:101 http://172.17.0.1/private/ stretch-staging/main texlive-latex-extra all 2015.20150823-1 [9731 kB]
Get:102 http://172.17.0.1/private/ stretch-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
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update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
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Setting up libnettle6:armhf (3.1.1-4) ...
Setting up libhogweed4:armhf (3.1.1-4) ...
Setting up libp11-kit0:armhf (0.23.1-3) ...
Setting up libgnutls-deb0-28:armhf (3.3.17-1) ...
Setting up libkeyutils1:armhf (1.5.9-7) ...
Setting up libkrb5support0:armhf (1.13.2+dfsg-2) ...
Setting up libk5crypto3:armhf (1.13.2+dfsg-2) ...
Setting up libkrb5-3:armhf (1.13.2+dfsg-2) ...
Setting up libgssapi-krb5-2:armhf (1.13.2+dfsg-2) ...
Setting up libidn11:armhf (1.32-1) ...
Setting up gettext (0.19.5.1-1) ...
Setting up intltool-debian (0.35.0+20060710.2) ...
Setting up po-debconf (1.0.18) ...
Setting up debhelper (9.20150811) ...
Setting up help2man (1.47.1) ...
Setting up libcups2:armhf (2.0.3-10) ...
Setting up libjpeg62-turbo:armhf (1:1.4.1-2) ...
Setting up libtiff5:armhf (4.0.5-1) ...
Setting up libijs-0.35:armhf (0.35-11) ...
Setting up libjbig2dec0 (0.12-2) ...
Setting up libgs9-common (9.16~dfsg-2) ...
Setting up libharfbuzz0b:armhf (1.0.1-1+b1) ...
Setting up libicu55:armhf (55.1-4) ...
Setting up libharfbuzz-icu0:armhf (1.0.1-1+b1) ...
Setting up libkpathsea6 (2015.20150524.37493-6) ...
Setting up libpaper-utils (1.1.24+nmu4) ...
Setting up libopenjpeg5:armhf (1:1.5.2-3.1) ...
Setting up libpoppler46:armhf (0.26.5-4) ...
Setting up libpotrace0 (1.12-1) ...
Setting up libptexenc1 (2015.20150524.37493-6) ...
Setting up libsynctex1 (2015.20150524.37493-6) ...
Setting up libtexlua52 (2015.20150524.37493-6) ...
Setting up libtexluajit2 (2015.20150524.37493-6) ...
Setting up libxpm4:armhf (1:3.5.11-1+b1) ...
Setting up libxaw7:armhf (2:1.0.13-1) ...
Setting up tex-common (6.03) ...
update-language: texlive-base not installed and configured, doing nothing!
Setting up preview-latex-style (11.87-3+deb8u1) ...
update-language: texlive-base not installed and configured, doing nothing!
Regenerating '/var/lib/texmf/fmtutil.cnf-DEBIAN'... done.
Regenerating '/var/lib/texmf/fmtutil.cnf-TEXLIVEDIST'... done.
update-fmtutil has updated the following file(s):
/var/lib/texmf/fmtutil.cnf-DEBIAN
/var/lib/texmf/fmtutil.cnf-TEXLIVEDIST
If you want to activate the changes in the above file(s),
you should run fmtutil-sys or fmtutil.
Setting up t1utils (1.38-4) ...
Setting up xdg-utils (1.1.0~rc3+git20150907-1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up libcupsimage2:armhf (2.0.3-10) ...
Setting up libcupsfilters1:armhf (1.0.71-1) ...
Setting up libgs9 (9.16~dfsg-2) ...
Setting up texlive-binaries (2015.20150524.37493-6) ...
update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode
update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode
Processing triggers for tex-common (6.03) ...
update-language: texlive-base not installed and configured, doing nothing!
texlive-base is not ready, skipping fmtutil-sys --all call
Setting up texlive-base (2015.20150823-1) ...
/usr/bin/tl-paper: setting paper size for dvips to a4.
/usr/bin/tl-paper: setting paper size for dvipdfmx to a4.
/usr/bin/tl-paper: setting paper size for xdvi to a4.
/usr/bin/tl-paper: setting paper size for pdftex to a4.
Processing triggers for tex-common (6.03) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Building format(s) --all.
This may take some time... done.
Setting up texlive-latex-base (2015.20150823-1) ...
Processing triggers for tex-common (6.03) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Building format(s) --all.
This may take some time... done.
Setting up texlive-latex-recommended (2015.20150823-1) ...
Setting up texlive-pictures (2015.20150823-1) ...
Processing triggers for tex-common (6.03) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Setting up texlive-latex-extra (2015.20150823-1) ...
Processing triggers for tex-common (6.03) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Setting up sbuild-build-depends-subread-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-19) ...
Processing triggers for systemd (225-1) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25.1-1 dpkg-dev_1.18.2 g++-5_5.2.1-16+rpi1 gcc-5_5.2.1-16+rpi1 libc6-dev_2.19-19 libstdc++-5-dev_5.2.1-16+rpi1 libstdc++6_5.2.1-16+rpi1 linux-libc-dev_3.16.7-ckt4-1+rpi1+b2
Package versions: adduser_3.113+nmu3 apt_1.0.10.2 base-files_9.4+rpi1 base-passwd_3.5.38 bash_4.3-14 binutils_2.25.1-1 bsdmainutils_9.0.6 bsdutils_1:2.26.2-9 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:5.2.1-4+rpi2 cpp-5_5.2.1-16+rpi1 dash_0.5.7-4 debconf_1.5.57 debconf-i18n_1.5.57 debfoster_2.7-2 debhelper_9.20150811 debianutils_4.5.1 diffutils_1:3.3-1 dmsetup_2:1.02.104-1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.22+15-2 findutils_4.4.2-9 fontconfig-config_2.11.0-6.3 fonts-dejavu-core_2.35-1 g++_4:5.2.1-4+rpi2 g++-5_5.2.1-16+rpi1 gcc_4:5.2.1-4+rpi2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.4-4 gcc-4.9-base_4.9.3-4 gcc-5_5.2.1-16+rpi1 gcc-5-base_5.2.1-16+rpi1 gettext_0.19.5.1-1 gettext-base_0.19.5.1-1 gnupg_1.4.19-5 gpgv_1.4.19-5 grep_2.21-2 groff-base_1.22.3-1 gzip_1.6-4 help2man_1.47.1 hostname_3.16 init_1.23 init-system-helpers_1.23 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.2 klibc-utils_2.0.4-2+rpi1 kmod_21-1 libacl1_2.2.52-2 libapparmor1_2.9.2-3 libapt-pkg4.16_1.0.10.2 libasan2_5.2.1-16+rpi1 libasprintf0v5_0.19.5.1-1 libatomic1_5.2.1-16+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.4-1 libaudit1_1:2.4.4-1 libavahi-client3_0.6.31-5 libavahi-common-data_0.6.31-5 libavahi-common3_0.6.31-5 libblkid1_2.26.2-9 libbz2-1.0_1.0.6-8 libc-bin_2.19-19 libc-dev-bin_2.19-19 libc6_2.19-19 libc6-dev_2.19-19 libcap2_1:2.24-11 libcap2-bin_1:2.24-11 libcc1-0_5.2.1-16+rpi1 libcomerr2_1.42.13-1 libcroco3_0.6.8-3 libcryptsetup4_2:1.6.6-5 libcups2_2.0.3-10 libcupsfilters1_1.0.71-1 libcupsimage2_2.0.3-10 libdb5.3_5.3.28-11 libdbus-1-3_1.8.20-1 libdebconfclient0_0.195 libdevmapper1.02.1_2:1.02.104-1 libdpkg-perl_1.18.2 libdrm2_2.4.64-1 libexpat1_2.1.0-7 libfakeroot_1.20.2-1 libfdisk1_2.26.2-9 libffi6_3.2.1-3 libfontconfig1_2.11.0-6.3 libfreetype6_2.5.2-4 libgc1c2_1:7.2d-6.4 libgcc-5-dev_5.2.1-16+rpi1 libgcc1_1:5.2.1-16+rpi1 libgcrypt20_1.6.3-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.44.1-1.1 libgmp10_2:6.0.0+dfsg-7+rpi1 libgnutls-deb0-28_3.3.17-1 libgomp1_5.2.1-16+rpi1 libgpg-error0_1.19-2 libgraphite2-3_1.2.4-3 libgs9_9.16~dfsg-2 libgs9-common_9.16~dfsg-2 libgssapi-krb5-2_1.13.2+dfsg-2 libharfbuzz-icu0_1.0.1-1+b1 libharfbuzz0b_1.0.1-1+b1 libhogweed4_3.1.1-4 libice6_2:1.0.9-1+b1 libicu55_55.1-4 libidn11_1.32-1 libijs-0.35_0.35-11 libisl13_0.14-2 libjbig0_2.1-3.1 libjbig2dec0_0.12-2 libjpeg62-turbo_1:1.4.1-2 libk5crypto3_1.13.2+dfsg-2 libkeyutils1_1.5.9-7 libklibc_2.0.4-2+rpi1 libkmod2_21-1 libkpathsea6_2015.20150524.37493-6 libkrb5-3_1.13.2+dfsg-2 libkrb5support0_1.13.2+dfsg-2 liblcms2-2_2.6-3 liblocale-gettext-perl_1.05-9 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.22+15-2 libmount1_2.26.2-9 libmpc3_1.0.3-1 libmpfr4_3.1.3-1 libncurses5_6.0+20150810-1 libncursesw5_6.0+20150810-1 libnettle6_3.1.1-4 libnih-dbus1_1.0.3-4.3 libnih1_1.0.3-4.3 libopenjpeg5_1:1.5.2-3.1 libp11-kit0_0.23.1-3 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpaper-utils_1.1.24+nmu4 libpaper1_1.1.24+nmu4 libpcre3_2:8.35-7.1 libpipeline1_1.4.1-1 libpixman-1-0_0.32.6-3 libpng12-0_1.2.50-2+b2 libpoppler46_0.26.5-4 libpotrace0_1.12-1 libprocps4_2:3.3.10-2 libptexenc1_2015.20150524.37493-6 libpython-stdlib_2.7.9-1 libpython2.7-minimal_2.7.10-3 libpython2.7-stdlib_2.7.10-3 libreadline6_6.3-8+b3 libseccomp2_2.2.3-2 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libsm6_2:1.2.2-1+b1 libsmartcols1_2.26.2-9 libsqlite3-0_3.8.11.1-1 libss2_1.42.13-1 libssl1.0.0_1.0.2d-1 libstdc++-5-dev_5.2.1-16+rpi1 libstdc++6_5.2.1-16+rpi1 libsynctex1_2015.20150524.37493-6 libsystemd0_225-1 libtasn1-6_4.5-2 libtexlua52_2015.20150524.37493-6 libtexluajit2_2015.20150524.37493-6 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7.1 libtiff5_4.0.5-1 libtinfo5_6.0+20150810-1 libtrio2_1.16+dfsg1-3 libubsan0_5.2.1-16+rpi1 libudev1_225-1 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.26.2-9 libx11-6_2:1.6.3-1 libx11-data_2:1.6.3-1 libxau6_1:1.0.8-1 libxaw7_2:1.0.13-1 libxcb1_1.10-3+b1 libxdmcp6_1:1.1.2-1 libxext6_2:1.3.3-1 libxi6_2:1.7.4-1+b2 libxml2_2.9.1+dfsg1-5 libxmu6_2:1.1.2-1 libxpm4_1:3.5.11-1+b1 libxt6_1:1.1.4-1+b1 libzzip-0-13_0.13.62-3 linux-libc-dev_3.16.7-ckt4-1+rpi1+b2 login_1:4.2-3 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.2 makedev_2.3.1-93 man-db_2.7.2-1 mawk_1.3.3-17 mime-support_3.59 mount_2.26.2-9 mountall_2.54 multiarch-support_2.19-19 ncurses-base_6.0+20150810-1 ncurses-bin_6.0+20150810-1 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-6 perl-base_5.20.2-6 perl-modules_5.20.2-6 plymouth_0.9.0-9 po-debconf_1.0.18 poppler-data_0.4.7-3 preview-latex-style_11.87-3+deb8u1 procps_2:3.3.10-2 python_2.7.9-1 python-minimal_2.7.9-1 python2.7_2.7.10-3 python2.7-minimal_2.7.10-3 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-subread-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_225-1 systemd-sysv_225-1 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 t1utils_1.38-4 tar_1.28-1 tex-common_6.03 texlive-base_2015.20150823-1 texlive-binaries_2015.20150524.37493-6 texlive-latex-base_2015.20150823-1 texlive-latex-extra_2015.20150823-1 texlive-latex-recommended_2015.20150823-1 texlive-pictures_2015.20150823-1 tzdata_2015f-1 ucf_3.0030 udev_225-1 util-linux_2.26.2-9 x11-common_1:7.7+9 xdg-utils_1.1.0~rc3+git20150907-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Mon Sep 7 12:10:20 2015 UTC using RSA key ID 1B5228B0
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./subread_1.4.6-p5+dfsg-1.dsc
dpkg-source: info: extracting subread in subread-1.4.6-p5+dfsg
dpkg-source: info: unpacking subread_1.4.6-p5+dfsg.orig.tar.xz
dpkg-source: info: unpacking subread_1.4.6-p5+dfsg-1.debian.tar.xz
dpkg-source: info: applying arch_specific_flags.patch
dpkg-source: info: applying fix_syntax.patch
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=111
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-bef777ac-b41a-4c48-ac57-790e00a4bd48
SCHROOT_UID=106
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package subread
dpkg-buildpackage: source version 1.4.6-p5+dfsg-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build subread-1.4.6-p5+dfsg
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
debian/rules override_dh_clean
make[1]: Entering directory '/«BUILDDIR»/subread-1.4.6-p5+dfsg'
cd src; make -f Makefile.Linux clean
make[2]: Entering directory '/«BUILDDIR»/subread-1.4.6-p5+dfsg/src'
rm -f core featureCounts exactSNP removeDup subread-buildindex core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o
make[2]: Leaving directory '/«BUILDDIR»/subread-1.4.6-p5+dfsg/src'
dh_clean
make[1]: Leaving directory '/«BUILDDIR»/subread-1.4.6-p5+dfsg'
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/«BUILDDIR»/subread-1.4.6-p5+dfsg'
cd src; make -f Makefile.Linux
make[2]: Entering directory '/«BUILDDIR»/subread-1.4.6-p5+dfsg/src'
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o core.o core.c
core.c: In function 'print_in_box':
core.c:91:7: warning: variable 'is_R_linebreak' set but not used [-Wunused-but-set-variable]
char is_R_linebreak=0, * content, *out_line_buff;
^
core.c: In function 'convert_GZ_to_FQ':
core.c:775:25: warning: passing argument 1 of 'gzgets' from incompatible pointer type [-Wincompatible-pointer-types]
char * bufr =gzgets(rawfp, linebuff, 3000);
^
In file included from sambam-file.h:23:0,
from core.h:47,
from core.c:42:
/usr/include/zlib.h:1372:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
core.c:786:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(rawfp);
^
In file included from sambam-file.h:23:0,
from core.h:47,
from core.c:42:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
core.c: In function 'convert_read_to_tmp':
core.c:1094:7: warning: variable 'current_repeated_times' set but not used [-Wunused-but-set-variable]
int current_repeated_times;
^
core.c: In function 'do_voting':
core.c:2985:9: warning: variable 'allsubreads_for_each_gap' set but not used [-Wunused-but-set-variable]
int allsubreads_for_each_gap [GENE_SLIDING_STEP], noninformative_subreads_for_each_gap[GENE_SLIDING_STEP];
^
core.c: In function 'split_read_files':
core.c:3314:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(read_line_buf, 3000, global_context->input_reads.first_read_file.input_fp);
^
core.c:3316:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(read_line_buf2, 3000, global_context->input_reads.second_read_file.input_fp);
^
core.c:3345:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(read_line_buf, 3000, global_context->input_reads.first_read_file.input_fp);
^
core.c:3346:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(read_line_buf2, 3000, global_context->input_reads.second_read_file.input_fp);
^
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o core-junction.o core-junction.c
core-junction.c: In function 'search_events_to_back':
core-junction.c:388:6: warning: variable 'move_start' set but not used [-Wunused-but-set-variable]
int move_start = read_tail_pos - global_context -> config.realignment_minimum_variant_distance;
^
core-junction.c: In function 'finalise_explain_CIGAR':
core-junction.c:1769:23: warning: variable 'tmp_cigar_exonic' set but not used [-Wunused-but-set-variable]
char tmp_cigar[120], tmp_cigar_exonic[120];
^
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o core-indel.o core-indel.c
core-indel.c: In function 'find_new_indels':
core-indel.c:1486:9: warning: variable 'best_j' set but not used [-Wunused-but-set-variable]
int best_j=0, best_score=-99999, is_ambiguous_indel= 0;
^
core-indel.c: In function 'full_indel_alignment':
core-indel.c:2828:41: warning: variable 'best_right' set but not used [-Wunused-but-set-variable]
int best_edge_score = -1, best_left, best_right;
^
core-indel.c:2828:30: warning: variable 'best_left' set but not used [-Wunused-but-set-variable]
int best_edge_score = -1, best_left, best_right;
^
core-indel.c: In function 'find_potential_ultralong_indels':
core-indel.c:2933:24: warning: variable 'best_c2_location' set but not used [-Wunused-but-set-variable]
int best_match = -1, best_c2_location = -1;
^
core-indel.c: In function 'finalise_pileup_file':
core-indel.c:3211:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, sizeof(short), 1, tmp_fp);
^
core-indel.c:3212:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_text, sizeof(char), read_len, tmp_fp);
^
core-indel.c:3213:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qual_text, sizeof(char), read_len, tmp_fp);
^
core-indel.c:3290:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, sizeof(short), 1, tmp_fp);
^
core-indel.c:3291:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_text, sizeof(char), read_len, tmp_fp);
^
core-indel.c:3292:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qual_text, sizeof(char), read_len, tmp_fp);
^
core-indel.c: In function 'finalise_pileup_file_by_debrujin':
core-indel.c:3647:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, sizeof(short), 1, tmp_fp);
^
core-indel.c:3648:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_text, sizeof(char), read_len, tmp_fp);
^
core-indel.c:3649:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qual_text, sizeof(char), read_len, tmp_fp);
^
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o sambam-file.o sambam-file.c
sambam-file.c: In function 'PBam_get_next_zchunk':
sambam-file.c:324:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&ID1, 1, 1, bam_fp);
^
sambam-file.c:325:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&ID2, 1, 1, bam_fp);
^
sambam-file.c:326:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&CM, 1, 1, bam_fp);
^
sambam-file.c:327:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&FLG, 1, 1, bam_fp);
^
sambam-file.c:336:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&XLEN,1, 2, bam_fp );
^
sambam-file.c:344:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SI1, 1, 1, bam_fp);
^
sambam-file.c:345:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SI2, 1, 1, bam_fp);
^
sambam-file.c:346:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SLEN, 1, 2, bam_fp);
^
sambam-file.c:350:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&BSIZE_MID, 1,2 , bam_fp);
^
sambam-file.c:362:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(buffer, 1, CDATA_READING, bam_fp);
^
sambam-file.c:366:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&real_len, 4, 1, bam_fp);
^
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o sublog.o sublog.c
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o gene-algorithms.o gene-algorithms.c
gene-algorithms.c: In function 'show_cigar':
gene-algorithms.c:747:6: warning: variable 'last_end' set but not used [-Wunused-but-set-variable]
int last_end=0, last_offset = 0, cursor = 0;
^
gene-algorithms.c:746:9: warning: variable 'is_error' set but not used [-Wunused-but-set-variable]
int i, is_error = 0;
^
gene-algorithms.c: In function 'match_chro_indel':
gene-algorithms.c:1159:28: warning: variable 'last_section_indels' set but not used [-Wunused-but-set-variable]
int last_section_end = 0, last_section_indels=0;
^
gene-algorithms.c: In function 'search_DP_branch':
gene-algorithms.c:1703:6: warning: variable 'table_mask2_j_1' set but not used [-Wunused-but-set-variable]
int table_mask2_j_1 = 0, table_mask2_i_1 = 0;
^
gene-algorithms.c: In function 'final_mapping_quality':
gene-algorithms.c:2344:7: warning: variable 'is_match_begin' set but not used [-Wunused-but-set-variable]
int is_match_begin = 0;
^
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o input-files.o input-files.c
input-files.c: In function 'f_subr_open':
input-files.c:46:10: warning: implicit declaration of function 'fopen64' [-Wimplicit-function-declaration]
return fopen64(fname, mode);
^
input-files.c:46:10: warning: return makes pointer from integer without a cast [-Wint-conversion]
input-files.c: In function 'geinput_next_char':
input-files.c:442:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(out_buf, 1999,input->input_fp);
^
input-files.c: In function 'sort_SAM_finalise':
input-files.c:2188:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_name_len, 2,1 , bbfp);
^
input-files.c:2194:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_name, 1, read_name_len, bbfp);
^
input-files.c:2197:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len,2,1,bbfp);
^
input-files.c:2203:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(new_line_mem, 1, read_len, bbfp);
^
input-files.c:2256:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_name_len, 2,1 , bbfp);
^
input-files.c:2262:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_name_buf, 1, read_name_len, bbfp);
^
input-files.c:2266:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, 2,1 , bbfp);
^
input-files.c:2269:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_line_buf, 1, read_len, bbfp);
^
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o sorted-hashtable.o sorted-hashtable.c
sorted-hashtable.c: In function 'gehash_load':
sorted-hashtable.c:1249:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(magic_chars,1,8,fp);
^
sorted-hashtable.c:1272:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_key, 2, 1, fp);
^
sorted-hashtable.c:1275:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_length, 2, 1, fp);
^
sorted-hashtable.c:1278:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&(the_table -> index_gap),2,1,fp);
^
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o gene-value-index.o gene-value-index.c
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o exon-algorithms.o exon-algorithms.c
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.c
long-hashtable.c: In function 'lnhash_create':
long-hashtable.c:43:45: warning: large integer implicitly truncated to unsigned type [-Woverflow]
the_table -> key_repeated_numbers = malloc(sizeof(short) * 0x100000000llu);
^
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
readSummary.c: In function 'readSummary':
readSummary.c:3008:9: warning: variable 'curchr_name' set but not used [-Wunused-but-set-variable]
char * curchr_name;
^
readSummary.c:3007:15: warning: variable 'curpos' set but not used [-Wunused-but-set-variable]
long curchr, curpos;
^
readSummary.c:3007:7: warning: variable 'curchr' set but not used [-Wunused-but-set-variable]
long curchr, curpos;
^
readSummary.c: In function 'load_feature_info':
readSummary.c:478:10: warning: 'token_temp' may be used uninitialized in this function [-Wmaybe-uninitialized]
char * token_temp, *chro_name;
^
readSummary.c:542:10: warning: 'token_temp' may be used uninitialized in this function [-Wmaybe-uninitialized]
char * token_temp;
^
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
index-builder.c: In function 'scan_gene_index':
index-builder.c:449:19: warning: variable 'table_no' set but not used [-Wunused-but-set-variable]
int file_number, table_no, i ,j;
^
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subtools subtools.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
qualityScores.c: In function 'finalise_qs_context':
qualityScores.c:82:12: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(qs_context -> gzfq_reader);
^
In file included from qualityScores.c:24:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
qualityScores.c: In function 'rewind_qs_file':
qualityScores.c:275:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(qs_context -> gzfq_reader);
^
In file included from qualityScores.c:24:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
qualityScores.c:282:29: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
qs_context -> gzfq_reader = gzopen(qs_context->input_name, "rb");
^
qualityScores.c: In function 'start_qs_context':
qualityScores.c:313:29: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
qs_context -> gzfq_reader = gzopen(qs_context->input_name, "rb");
^
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o coverageCount coverage_calc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p5"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o globalReassembly global-reassembly.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
global-reassembly.c: In function 'GRA_trim_reads':
global-reassembly.c:415:7: warning: variable 'in_flags_1' set but not used [-Wunused-but-set-variable]
int in_flags_1= -1, is_second_read = 0;
^
global-reassembly.c: In function 'GRA_reassemble_reads_LR':
global-reassembly.c:1435:14: warning: variable 'target_votes' set but not used [-Wunused-but-set-variable]
int mm=0, target_votes=0, new_bases_len;
^
mkdir -p ../bin/utilities
mv subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/
mv globalReassembly coverageCount propmapped qualityScores removeDup subread-fullscan subtools ../bin/utilities
make[2]: Leaving directory '/«BUILDDIR»/subread-1.4.6-p5+dfsg/src'
cd doc && pdflatex -synctex=1 -interaction=nonstopmode SubreadUsersGuide.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(./SubreadUsersGuide.tex
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Chapter 1.
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Chapter 2.
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Chapter 3.
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Chapter 4.
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Chapter 5.
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Chapter 6.
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Chapter 7.
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Chapter 8.
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Chapter 1.
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Chapter 2.
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Chapter 3.
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Chapter 4.
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Chapter 5.
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[]\OT1/cmr/bx/n/17.28 A quick start for \OT1/cmss/bx/n/17.28 fea-ture-Counts \O
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Chapter 7.
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Chapter 8.
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Chapter 1.
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Chapter 2.
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Chapter 3.
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Chapter 4.
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Chapter 5.
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[]\OT1/cmr/bx/n/17.28 Mapping mi-croRNA se-quenc-ing reads (miRNA-seq)
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Chapter 6.
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[]\OT1/cmr/bx/n/17.28 A quick start for \OT1/cmss/bx/n/17.28 fea-ture-Counts \O
T1/cmr/bx/n/17.28 in Bio-con-duc-tor \OT1/cmss/bx/n/17.28 Rsub-
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Chapter 7.
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Chapter 8.
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\OT1/cmtt/m/n/12 http : / / bioinf . wehi . edu . au / RNAseqCaseStudy / data .
tar . gz$ \OT1/cmr/m/n/12 (283MB). Both read data and
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dh_auto_build
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v1.4.6-p5
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 SAM file ||
|| P data/test-minimum.sam ||
|| ||
|| Output file : test-minimum.FC ||
|| Annotations : data/test-minimum.GTF (GTF) ||
|| ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| Strand specific : no ||
|| Multimapping reads : not counted ||
|| Multi-overlapping reads : not counted ||
|| Read orientations : fr ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================================= Running ==================================\\
|| ||
|| Load annotation file data/test-minimum.GTF ... ||
|| Features : 23 ||
|| Meta-features : 7 ||
|| Chromosomes/contigs : 3 ||
|| ||
|| Process SAM file data/test-minimum.sam... ||
|| Paired-end reads are included. ||
|| Assign reads to features... ||
|| Total reads : 998 ||
|| Successfully assigned reads : 389 (39.0%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Read assignment finished. ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
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v1.4.6-p5
//=========================== indexBuilder setting ===========================\\
|| ||
|| Index name : tmp/small1 ||
|| Index space : base-space ||
|| Memory : 3000 Mbytes ||
|| Repeat threshold : 24 repeats ||
|| Distance to next subread : 3 ||
|| ||
|| Input files : 1 file in total ||
|| o ../chr901.fa ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================================= Running ==================================\\
|| ||
|| Check the integrity of provided reference sequences ... ||
|| There were 4 notes for reference sequences. ||
|| The notes can be found in the log file, 'tmp/small1.log'. ||
|| Scan uninformative subreads in reference sequences ... ||
|| 8%, 0 mins elapsed, rate=301.9k bps/s, total=0m ||
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|| 91%, 0 mins elapsed, rate=545.9k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=555.8k bps/s, total=0m ||
|| 95 uninformative subreads were found. ||
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|| Build the index... ||
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|| 41%, 0 mins elapsed, rate=258.7k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=271.1k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=284.5k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=298.2k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=312.6k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=326.0k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=341.1k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=354.0k bps/s, total=0m ||
|| Save current index block... ||
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|| ||
|| Total running time: 0.1 minutes. ||
|| Index tmp/small1 was successfully built! ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
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========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6-p5
//============================= subjunc setting ==============================\\
|| ||
|| Function : Read alignment + Junction detection (RNA-Seq) ||
|| Threads : 1 ||
|| Input file 1 : data/junction-reads-A.fq ||
|| Input file 2 : data/junction-reads-B.fq ||
|| Output file : junctions.sam (SAM) ||
|| Index name : tmp/small1 ||
|| Phred offset : 33 ||
|| ||
|| Min read1 votes : 1 ||
|| Min read2 votes : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : no ||
|| Hamming distance : no ||
|| Quality scores : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (14-Sep-2015 07:14:09) ======================\\
|| ||
|| The input file contains base space reads. ||
|| Load the 1-th index block... ||
|| Map fragments... ||
|| 37% completed, 0 mins elapsed, total=16k frags, rate=2.1k/s ||
|| 43% completed, 0 mins elapsed, total=16k frags, rate=2.1k/s ||
|| 49% completed, 0 mins elapsed, total=16k frags, rate=2.1k/s ||
|| 55% completed, 0 mins elapsed, total=16k frags, rate=2.1k/s ||
|| Detect indels and junctions... ||
|| 60% completed, 0 mins elapsed, total=16k frags, rate=1.7k/s ||
|| 62% completed, 0 mins elapsed, total=16k frags, rate=1.7k/s ||
|| 63% completed, 0 mins elapsed, total=16k frags, rate=1.6k/s ||
|| 64% completed, 0 mins elapsed, total=16k frags, rate=1.6k/s ||
|| 65% completed, 0 mins elapsed, total=16k frags, rate=1.6k/s ||
|| 66% completed, 0 mins elapsed, total=16k frags, rate=1.6k/s ||
|| 67% completed, 0 mins elapsed, total=16k frags, rate=1.6k/s ||
|| 68% completed, 0 mins elapsed, total=16k frags, rate=1.6k/s ||
|| 69% completed, 0 mins elapsed, total=16k frags, rate=1.6k/s ||
|| Realign fragments... ||
|| 70% completed, 0 mins elapsed, total=16k frags, rate=1.5k/s ||
|| 72% completed, 0 mins elapsed, total=16k frags, rate=1.5k/s ||
|| 73% completed, 0 mins elapsed, total=16k frags, rate=1.5k/s ||
|| 74% completed, 0 mins elapsed, total=16k frags, rate=1.5k/s ||
|| 75% completed, 0 mins elapsed, total=16k frags, rate=1.4k/s ||
|| 76% completed, 0 mins elapsed, total=16k frags, rate=1.4k/s ||
|| 77% completed, 0 mins elapsed, total=16k frags, rate=1.4k/s ||
|| 78% completed, 0 mins elapsed, total=16k frags, rate=1.4k/s ||
|| 79% completed, 0 mins elapsed, total=16k frags, rate=1.4k/s ||
|| 16052 fragments were processed. Save the mapping results for them... ||
|| 81% completed, 0 mins elapsed, total=16k frags, rate=1.4k/s ||
|| 84% completed, 0 mins elapsed, total=16k frags, rate=1.4k/s ||
|| 86% completed, 0 mins elapsed, total=16k frags, rate=1.4k/s ||
|| 88% completed, 0 mins elapsed, total=16k frags, rate=1.4k/s ||
|| 90% completed, 0 mins elapsed, total=16k frags, rate=1.4k/s ||
|| 92% completed, 0 mins elapsed, total=16k frags, rate=1.4k/s ||
|| 94% completed, 0 mins elapsed, total=16k frags, rate=1.4k/s ||
|| 96% completed, 0 mins elapsed, total=16k frags, rate=1.4k/s ||
|| 98% completed, 0 mins elapsed, total=16k frags, rate=1.4k/s ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 16052 fragments ||
|| Mapped : 15906 fragments (99.1%) ||
|| Correctly paired : 13038 fragments ||
|| Junctions : 405 ||
|| Indels : 179 ||
|| ||
|| Running time : 0.2 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6-p5
//============================= subjunc setting ==============================\\
|| ||
|| Function : Read alignment + Junction/Fusion detection (RNA-Seq) ||
|| Threads : 1 ||
|| Input file 1 : data/junction-reads-A.fq ||
|| Input file 2 : data/junction-reads-B.fq ||
|| Output file : junctionsNfusions.bam (BAM) ||
|| Index name : tmp/small1 ||
|| Phred offset : 33 ||
|| ||
|| Min read1 votes : 1 ||
|| Min read2 votes : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : no ||
|| Hamming distance : no ||
|| Quality scores : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (14-Sep-2015 07:14:20) ======================\\
|| ||
|| The input file contains base space reads. ||
|| Load the 1-th index block... ||
|| Map fragments... ||
|| 37% completed, 0 mins elapsed, total=16k frags, rate=2.0k/s ||
|| 43% completed, 0 mins elapsed, total=16k frags, rate=2.0k/s ||
|| 49% completed, 0 mins elapsed, total=16k frags, rate=2.0k/s ||
|| 55% completed, 0 mins elapsed, total=16k frags, rate=2.0k/s ||
|| Detect indels and junctions... ||
|| 60% completed, 0 mins elapsed, total=16k frags, rate=1.6k/s ||
|| 62% completed, 0 mins elapsed, total=16k frags, rate=1.6k/s ||
|| 63% completed, 0 mins elapsed, total=16k frags, rate=1.6k/s ||
|| 64% completed, 0 mins elapsed, total=16k frags, rate=1.6k/s ||
|| 65% completed, 0 mins elapsed, total=16k frags, rate=1.6k/s ||
|| 66% completed, 0 mins elapsed, total=16k frags, rate=1.6k/s ||
|| 67% completed, 0 mins elapsed, total=16k frags, rate=1.5k/s ||
|| 68% completed, 0 mins elapsed, total=16k frags, rate=1.5k/s ||
|| 69% completed, 0 mins elapsed, total=16k frags, rate=1.5k/s ||
|| Realign fragments... ||
|| 70% completed, 0 mins elapsed, total=16k frags, rate=1.5k/s ||
|| 72% completed, 0 mins elapsed, total=16k frags, rate=1.5k/s ||
|| 73% completed, 0 mins elapsed, total=16k frags, rate=1.4k/s ||
|| 74% completed, 0 mins elapsed, total=16k frags, rate=1.4k/s ||
|| 75% completed, 0 mins elapsed, total=16k frags, rate=1.4k/s ||
|| 76% completed, 0 mins elapsed, total=16k frags, rate=1.4k/s ||
|| 77% completed, 0 mins elapsed, total=16k frags, rate=1.3k/s ||
|| 78% completed, 0 mins elapsed, total=16k frags, rate=1.3k/s ||
|| 79% completed, 0 mins elapsed, total=16k frags, rate=1.3k/s ||
|| 16052 fragments were processed. Save the mapping results for them... ||
|| 81% completed, 0 mins elapsed, total=16k frags, rate=1.3k/s ||
|| 84% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 86% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 88% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 90% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 92% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 94% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 96% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 98% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 16052 fragments ||
|| Mapped : 15904 fragments (99.1%) ||
|| Correctly paired : 12889 fragments ||
|| Junctions : 415 ||
|| Fusions : 92 ||
|| Indels : 160 ||
|| ||
|| Running time : 0.3 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6-p5
//=========================== indexBuilder setting ===========================\\
|| ||
|| Index name : tmp/small1 ||
|| Index space : base-space ||
|| Memory : 100 Mbytes ||
|| Repeat threshold : 24 repeats ||
|| Distance to next subread : 3 ||
|| ||
|| Input files : 1 file in total ||
|| o ../chr901.fa ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================================= Running ==================================\\
|| ||
|| Check the integrity of provided reference sequences ... ||
|| There were 4 notes for reference sequences. ||
|| The notes can be found in the log file, 'tmp/small1.log'. ||
|| Scan uninformative subreads in reference sequences ... ||
|| 8%, 0 mins elapsed, rate=309.7k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=347.2k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=385.7k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=412.0k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=438.5k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=461.6k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=479.6k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=499.7k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=517.1k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=532.7k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=550.1k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=561.1k bps/s, total=0m ||
|| 95 uninformative subreads were found. ||
|| These subreads were excluded from index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=209.3k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=219.8k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=235.4k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=249.8k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=264.7k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=280.4k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=296.1k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=311.6k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=328.0k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=343.2k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=359.5k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=374.0k bps/s, total=0m ||
|| Save current index block... ||
|| [ 0.0% finished ] ||
|| [ 10.0% finished ] ||
|| [ 20.0% finished ] ||
|| [ 30.0% finished ] ||
|| [ 40.0% finished ] ||
|| [ 50.0% finished ] ||
|| [ 60.0% finished ] ||
|| [ 70.0% finished ] ||
|| [ 80.0% finished ] ||
|| [ 90.0% finished ] ||
|| [ 100.0% finished ] ||
|| ||
|| Total running time: 0.1 minutes. ||
|| Index tmp/small1 was successfully built! ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6-p5
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment ||
|| Threads : 1 ||
|| Input file : data/test-noerror-r1.fq ||
|| Output file : tmp/test-tmp.sam1 (SAM) ||
|| Index name : tmp/small1 ||
|| Phred offset : 33 ||
|| ||
|| Min votes : 3 ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : no ||
|| Hamming distance : yes ||
|| Quality scores : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (14-Sep-2015 07:14:41) ======================\\
|| ||
|| The input file contains base space reads. ||
|| Load the 1-th index block... ||
|| Map reads... ||
|| 29% completed, 0 mins elapsed, total=20k reads, rate=4.6k/s ||
|| 35% completed, 0 mins elapsed, total=20k reads, rate=4.6k/s ||
|| 42% completed, 0 mins elapsed, total=20k reads, rate=4.6k/s ||
|| 48% completed, 0 mins elapsed, total=20k reads, rate=4.6k/s ||
|| 54% completed, 0 mins elapsed, total=19k reads, rate=4.6k/s ||
|| Detect indels... ||
|| 60% completed, 0 mins elapsed, total=19k reads, rate=3.6k/s ||
|| 61% completed, 0 mins elapsed, total=19k reads, rate=3.6k/s ||
|| 62% completed, 0 mins elapsed, total=19k reads, rate=3.6k/s ||
|| 63% completed, 0 mins elapsed, total=19k reads, rate=3.5k/s ||
|| 64% completed, 0 mins elapsed, total=19k reads, rate=3.5k/s ||
|| 65% completed, 0 mins elapsed, total=19k reads, rate=3.5k/s ||
|| 66% completed, 0 mins elapsed, total=19k reads, rate=3.5k/s ||
|| 67% completed, 0 mins elapsed, total=19k reads, rate=3.4k/s ||
|| 68% completed, 0 mins elapsed, total=19k reads, rate=3.4k/s ||
|| Realign reads... ||
|| 70% completed, 0 mins elapsed, total=19k reads, rate=3.3k/s ||
|| 71% completed, 0 mins elapsed, total=19k reads, rate=3.3k/s ||
|| 72% completed, 0 mins elapsed, total=19k reads, rate=3.2k/s ||
|| 73% completed, 0 mins elapsed, total=19k reads, rate=3.2k/s ||
|| 74% completed, 0 mins elapsed, total=19k reads, rate=3.2k/s ||
|| 75% completed, 0 mins elapsed, total=19k reads, rate=3.1k/s ||
|| 76% completed, 0 mins elapsed, total=19k reads, rate=3.1k/s ||
|| 77% completed, 0 mins elapsed, total=19k reads, rate=3.1k/s ||
|| 78% completed, 0 mins elapsed, total=19k reads, rate=3.0k/s ||
|| 19998 reads were processed. Save the mapping results for them... ||
|| 81% completed, 0 mins elapsed, total=19k reads, rate=3.0k/s ||
|| 83% completed, 0 mins elapsed, total=19k reads, rate=3.0k/s ||
|| 85% completed, 0 mins elapsed, total=19k reads, rate=3.0k/s ||
|| 87% completed, 0 mins elapsed, total=19k reads, rate=3.0k/s ||
|| 89% completed, 0 mins elapsed, total=19k reads, rate=3.0k/s ||
|| 91% completed, 0 mins elapsed, total=19k reads, rate=3.0k/s ||
|| 93% completed, 0 mins elapsed, total=19k reads, rate=3.0k/s ||
|| 95% completed, 0 mins elapsed, total=19k reads, rate=3.0k/s ||
|| 97% completed, 0 mins elapsed, total=19k reads, rate=3.0k/s ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 reads ||
|| Mapped : 19967 reads (99.8%) ||
|| Indels : 7 ||
|| ||
|| Running time : 0.1 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6-p5
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment ||
|| Threads : 1 ||
|| Input file : data/test-noerror-r1.fq ||
|| Output file : tmp/test-tmp.sam2 (SAM) ||
|| Index name : tmp/small1 ||
|| Phred offset : 33 ||
|| ||
|| Min votes : 3 ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : yes ||
|| Hamming distance : yes ||
|| Quality scores : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (14-Sep-2015 07:14:48) ======================\\
|| ||
|| The input file contains base space reads. ||
|| Load the 1-th index block... ||
|| Map reads... ||
|| 29% completed, 0 mins elapsed, total=20k reads, rate=4.6k/s ||
|| 35% completed, 0 mins elapsed, total=20k reads, rate=4.6k/s ||
|| 42% completed, 0 mins elapsed, total=20k reads, rate=4.6k/s ||
|| 48% completed, 0 mins elapsed, total=20k reads, rate=4.6k/s ||
|| 54% completed, 0 mins elapsed, total=19k reads, rate=4.6k/s ||
|| Detect indels... ||
|| 60% completed, 0 mins elapsed, total=19k reads, rate=3.6k/s ||
|| 61% completed, 0 mins elapsed, total=19k reads, rate=3.6k/s ||
|| 62% completed, 0 mins elapsed, total=19k reads, rate=3.6k/s ||
|| 63% completed, 0 mins elapsed, total=19k reads, rate=3.5k/s ||
|| 64% completed, 0 mins elapsed, total=19k reads, rate=3.5k/s ||
|| 65% completed, 0 mins elapsed, total=19k reads, rate=3.5k/s ||
|| 66% completed, 0 mins elapsed, total=19k reads, rate=3.5k/s ||
|| 67% completed, 0 mins elapsed, total=19k reads, rate=3.4k/s ||
|| 68% completed, 0 mins elapsed, total=19k reads, rate=3.4k/s ||
|| Realign reads... ||
|| 70% completed, 0 mins elapsed, total=19k reads, rate=3.3k/s ||
|| 71% completed, 0 mins elapsed, total=19k reads, rate=3.3k/s ||
|| 72% completed, 0 mins elapsed, total=19k reads, rate=3.2k/s ||
|| 73% completed, 0 mins elapsed, total=19k reads, rate=3.2k/s ||
|| 74% completed, 0 mins elapsed, total=19k reads, rate=3.2k/s ||
|| 75% completed, 0 mins elapsed, total=19k reads, rate=3.1k/s ||
|| 76% completed, 0 mins elapsed, total=19k reads, rate=3.1k/s ||
|| 77% completed, 0 mins elapsed, total=19k reads, rate=3.1k/s ||
|| 78% completed, 0 mins elapsed, total=19k reads, rate=3.0k/s ||
|| 19998 reads were processed. Save the mapping results for them... ||
|| 81% completed, 0 mins elapsed, total=19k reads, rate=3.0k/s ||
|| 83% completed, 0 mins elapsed, total=19k reads, rate=3.0k/s ||
|| 85% completed, 0 mins elapsed, total=19k reads, rate=3.0k/s ||
|| 87% completed, 0 mins elapsed, total=19k reads, rate=3.0k/s ||
|| 89% completed, 0 mins elapsed, total=19k reads, rate=3.0k/s ||
|| 91% completed, 0 mins elapsed, total=19k reads, rate=3.0k/s ||
|| 93% completed, 0 mins elapsed, total=19k reads, rate=3.0k/s ||
|| 95% completed, 0 mins elapsed, total=19k reads, rate=3.0k/s ||
|| 97% completed, 0 mins elapsed, total=19k reads, rate=3.0k/s ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 reads ||
|| Mapped : 18817 reads (94.1%) ||
|| Indels : 7 ||
|| ||
|| Running time : 0.1 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6-p5
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment ||
|| Threads : 1 ||
|| Input file 1 : data/test-noerror-r1.fq ||
|| Input file 2 : data/test-noerror-r2.fq ||
|| Output file : tmp/test-tmp.sam3 (SAM) ||
|| Index name : tmp/small1 ||
|| Phred offset : 33 ||
|| ||
|| Min read1 votes : 3 ||
|| Min read2 votes : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : no ||
|| Hamming distance : yes ||
|| Quality scores : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (14-Sep-2015 07:14:55) ======================\\
|| ||
|| The input file contains base space reads. ||
|| Load the 1-th index block... ||
|| Map fragments... ||
|| 29% completed, 0 mins elapsed, total=20k frags, rate=2.2k/s ||
|| 35% completed, 0 mins elapsed, total=20k frags, rate=2.2k/s ||
|| 42% completed, 0 mins elapsed, total=20k frags, rate=2.2k/s ||
|| 48% completed, 0 mins elapsed, total=20k frags, rate=2.2k/s ||
|| 54% completed, 0 mins elapsed, total=19k frags, rate=2.2k/s ||
|| Detect indels... ||
|| 60% completed, 0 mins elapsed, total=19k frags, rate=1.9k/s ||
|| 61% completed, 0 mins elapsed, total=19k frags, rate=1.9k/s ||
|| 62% completed, 0 mins elapsed, total=19k frags, rate=1.9k/s ||
|| 63% completed, 0 mins elapsed, total=19k frags, rate=1.9k/s ||
|| 64% completed, 0 mins elapsed, total=19k frags, rate=1.8k/s ||
|| 65% completed, 0 mins elapsed, total=19k frags, rate=1.8k/s ||
|| 66% completed, 0 mins elapsed, total=19k frags, rate=1.8k/s ||
|| 67% completed, 0 mins elapsed, total=19k frags, rate=1.8k/s ||
|| 68% completed, 0 mins elapsed, total=19k frags, rate=1.8k/s ||
|| Realign fragments... ||
|| 70% completed, 0 mins elapsed, total=19k frags, rate=1.7k/s ||
|| 71% completed, 0 mins elapsed, total=19k frags, rate=1.7k/s ||
|| 72% completed, 0 mins elapsed, total=19k frags, rate=1.7k/s ||
|| 73% completed, 0 mins elapsed, total=19k frags, rate=1.6k/s ||
|| 74% completed, 0 mins elapsed, total=19k frags, rate=1.6k/s ||
|| 75% completed, 0 mins elapsed, total=19k frags, rate=1.6k/s ||
|| 76% completed, 0 mins elapsed, total=19k frags, rate=1.6k/s ||
|| 77% completed, 0 mins elapsed, total=19k frags, rate=1.6k/s ||
|| 78% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 19998 fragments were processed. Save the mapping results for them... ||
|| 81% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 83% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 85% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 87% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 89% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 91% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 93% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 95% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 97% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 fragments ||
|| Mapped : 19990 fragments (100.0%) ||
|| Correctly paired : 19469 fragments ||
|| Indels : 7 ||
|| ||
|| Running time : 0.2 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6-p5
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment ||
|| Threads : 1 ||
|| Input file 1 : data/test-noerror-r1.fq ||
|| Input file 2 : data/test-noerror-r2.fq ||
|| Output file : tmp/test-tmp.sam4 (SAM) ||
|| Index name : tmp/small1 ||
|| Phred offset : 33 ||
|| ||
|| Min read1 votes : 3 ||
|| Min read2 votes : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : yes ||
|| Hamming distance : yes ||
|| Quality scores : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (14-Sep-2015 07:15:08) ======================\\
|| ||
|| The input file contains base space reads. ||
|| Load the 1-th index block... ||
|| Map fragments... ||
|| 29% completed, 0 mins elapsed, total=20k frags, rate=2.1k/s ||
|| 35% completed, 0 mins elapsed, total=20k frags, rate=2.1k/s ||
|| 42% completed, 0 mins elapsed, total=20k frags, rate=2.1k/s ||
|| 48% completed, 0 mins elapsed, total=20k frags, rate=2.1k/s ||
|| 54% completed, 0 mins elapsed, total=19k frags, rate=2.1k/s ||
|| Detect indels... ||
|| 60% completed, 0 mins elapsed, total=19k frags, rate=1.8k/s ||
|| 61% completed, 0 mins elapsed, total=19k frags, rate=1.8k/s ||
|| 62% completed, 0 mins elapsed, total=19k frags, rate=1.8k/s ||
|| 63% completed, 0 mins elapsed, total=19k frags, rate=1.8k/s ||
|| 64% completed, 0 mins elapsed, total=19k frags, rate=1.8k/s ||
|| 65% completed, 0 mins elapsed, total=19k frags, rate=1.7k/s ||
|| 66% completed, 0 mins elapsed, total=19k frags, rate=1.7k/s ||
|| 67% completed, 0 mins elapsed, total=19k frags, rate=1.7k/s ||
|| 68% completed, 0 mins elapsed, total=19k frags, rate=1.7k/s ||
|| Realign fragments... ||
|| 70% completed, 0 mins elapsed, total=19k frags, rate=1.7k/s ||
|| 71% completed, 0 mins elapsed, total=19k frags, rate=1.6k/s ||
|| 72% completed, 0 mins elapsed, total=19k frags, rate=1.6k/s ||
|| 73% completed, 0 mins elapsed, total=19k frags, rate=1.6k/s ||
|| 74% completed, 0 mins elapsed, total=19k frags, rate=1.6k/s ||
|| 75% completed, 0 mins elapsed, total=19k frags, rate=1.6k/s ||
|| 76% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 77% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 78% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 19998 fragments were processed. Save the mapping results for them... ||
|| 81% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 83% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 85% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 87% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 89% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 91% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 93% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 95% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 97% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 fragments ||
|| Mapped : 19513 fragments (97.6%) ||
|| Correctly paired : 19009 fragments ||
|| Indels : 7 ||
|| ||
|| Running time : 0.2 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6-p5
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment ||
|| Threads : 1 ||
|| Input file 1 : data/test-error-r1.fq ||
|| Input file 2 : data/test-error-r2.fq ||
|| Output file : tmp/test-tmp.sam5 (SAM) ||
|| Index name : tmp/small1 ||
|| Phred offset : 33 ||
|| ||
|| Min read1 votes : 3 ||
|| Min read2 votes : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : no ||
|| Hamming distance : yes ||
|| Quality scores : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (14-Sep-2015 07:15:21) ======================\\
|| ||
|| The input file contains base space reads. ||
|| Load the 1-th index block... ||
|| Map fragments... ||
|| 29% completed, 0 mins elapsed, total=20k frags, rate=2.3k/s ||
|| 35% completed, 0 mins elapsed, total=20k frags, rate=2.3k/s ||
|| 42% completed, 0 mins elapsed, total=20k frags, rate=2.3k/s ||
|| 48% completed, 0 mins elapsed, total=20k frags, rate=2.3k/s ||
|| 54% completed, 0 mins elapsed, total=20k frags, rate=2.3k/s ||
|| Detect indels... ||
|| 60% completed, 0 mins elapsed, total=20k frags, rate=2.0k/s ||
|| 61% completed, 0 mins elapsed, total=20k frags, rate=2.0k/s ||
|| 62% completed, 0 mins elapsed, total=20k frags, rate=2.0k/s ||
|| 63% completed, 0 mins elapsed, total=20k frags, rate=2.0k/s ||
|| 64% completed, 0 mins elapsed, total=20k frags, rate=2.0k/s ||
|| 65% completed, 0 mins elapsed, total=20k frags, rate=1.9k/s ||
|| 67% completed, 0 mins elapsed, total=20k frags, rate=1.9k/s ||
|| 68% completed, 0 mins elapsed, total=20k frags, rate=1.9k/s ||
|| 69% completed, 0 mins elapsed, total=20k frags, rate=1.9k/s ||
|| Realign fragments... ||
|| 70% completed, 0 mins elapsed, total=20k frags, rate=1.8k/s ||
|| 71% completed, 0 mins elapsed, total=20k frags, rate=1.8k/s ||
|| 72% completed, 0 mins elapsed, total=20k frags, rate=1.8k/s ||
|| 73% completed, 0 mins elapsed, total=20k frags, rate=1.7k/s ||
|| 74% completed, 0 mins elapsed, total=20k frags, rate=1.7k/s ||
|| 75% completed, 0 mins elapsed, total=20k frags, rate=1.7k/s ||
|| 77% completed, 0 mins elapsed, total=20k frags, rate=1.7k/s ||
|| 78% completed, 0 mins elapsed, total=20k frags, rate=1.7k/s ||
|| 79% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 20000 fragments were processed. Save the mapping results for them... ||
|| 81% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 83% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 85% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 87% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 89% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 91% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 94% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 96% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 98% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 20000 fragments ||
|| Mapped : 19528 fragments (97.6%) ||
|| Correctly paired : 14234 fragments ||
|| Indels : 13 ||
|| ||
|| Running time : 0.2 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6-p5
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment ||
|| Threads : 1 ||
|| Input file 1 : data/test-err-mut-r1.fq.gz ||
|| Input file 2 : data/test-err-mut-r2.fq.gz ||
|| Output file : tmp/test-tmp.sam6 (SAM) ||
|| Index name : tmp/small1 ||
|| Phred offset : 33 ||
|| ||
|| Min read1 votes : 3 ||
|| Min read2 votes : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : no ||
|| Hamming distance : yes ||
|| Quality scores : no ||
|| Read group name : MyTestGroup ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (14-Sep-2015 07:15:34) ======================\\
|| ||
|| Decompress data/test-err-mut-r1.fq.gz... ||
|| The input file contains base space reads. ||
|| Decompress data/test-err-mut-r2.fq.gz... ||
|| Load the 1-th index block... ||
|| Map fragments... ||
|| 29% completed, 0 mins elapsed, total=20k frags, rate=2.4k/s ||
|| 35% completed, 0 mins elapsed, total=20k frags, rate=2.4k/s ||
|| 41% completed, 0 mins elapsed, total=20k frags, rate=2.3k/s ||
|| 48% completed, 0 mins elapsed, total=20k frags, rate=2.3k/s ||
|| 54% completed, 0 mins elapsed, total=20k frags, rate=2.3k/s ||
|| Detect indels... ||
|| 60% completed, 0 mins elapsed, total=20k frags, rate=1.9k/s ||
|| 61% completed, 0 mins elapsed, total=20k frags, rate=1.9k/s ||
|| 62% completed, 0 mins elapsed, total=20k frags, rate=1.9k/s ||
|| 63% completed, 0 mins elapsed, total=20k frags, rate=1.9k/s ||
|| 64% completed, 0 mins elapsed, total=20k frags, rate=1.8k/s ||
|| 65% completed, 0 mins elapsed, total=20k frags, rate=1.8k/s ||
|| 67% completed, 0 mins elapsed, total=20k frags, rate=1.8k/s ||
|| 68% completed, 0 mins elapsed, total=20k frags, rate=1.8k/s ||
|| 69% completed, 0 mins elapsed, total=20k frags, rate=1.8k/s ||
|| Realign fragments... ||
|| 70% completed, 0 mins elapsed, total=20k frags, rate=1.7k/s ||
|| 71% completed, 0 mins elapsed, total=20k frags, rate=1.7k/s ||
|| 72% completed, 0 mins elapsed, total=20k frags, rate=1.7k/s ||
|| 73% completed, 0 mins elapsed, total=20k frags, rate=1.7k/s ||
|| 74% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 75% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 77% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 78% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 79% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 20001 fragments were processed. Save the mapping results for them... ||
|| 81% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 83% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 85% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 87% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 89% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 91% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 94% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 96% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 98% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 20001 fragments ||
|| Mapped : 19497 fragments (97.5%) ||
|| Correctly paired : 13881 fragments ||
|| Indels : 113 ||
|| ||
|| Running time : 0.2 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6-p5
//============================= exactSNP setting =============================\\
|| ||
|| Input file : data/test-in.BAM (BAM) ||
|| Output file : test-out.VCF ||
|| Reference genome : ../chr901.fa ||
|| ||
|| Threads : 1 ||
|| Min supporting reads : 1 ||
|| Min pct. of supporting reads : 0.0% ||
|| Min base quality score : 13 ||
|| Number of trimmed bases : 3 ||
|| ||
|| Q value cutoff : 10E-12.0 ||
|| P value upper bound : 0.00500 ||
|| Flanking windows size : 5 ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (14-Sep-2015 07:15:47) ======================\\
|| ||
|| Split BAM file into ./temp-snps-003867-59472E5C-* ... ||
|| processed block chr901@999950 by thread 1/1 [block number=1/1] ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed reads : 50204 ||
|| Reported SNPs : 415 ||
|| Reported indels : 21 ||
|| ||
|| Running time : 0.1 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
make[1]: Leaving directory '/«BUILDDIR»/subread-1.4.6-p5+dfsg'
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/«BUILDDIR»/subread-1.4.6-p5+dfsg'
find /«BUILDDIR»/subread-1.4.6-p5+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \;
mkdir -p /«BUILDDIR»/subread-1.4.6-p5+dfsg/debian/subread/usr/share/man/man1
help2man --no-info --help-option="''" --no-discard-stderr --name='an accurate and efficient aligner for mapping both genomic \
DNA-seq reads and RNA-seq reads (for the purpose of expression analysis)' \
/«BUILDDIR»/subread-1.4.6-p5+dfsg/bin/subread-align | debian/filter.pl > /«BUILDDIR»/subread-1.4.6-p5+dfsg/debian/subread/usr/share/man/man1/subread-align.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='builds an base-space or color-space index using the reference sequences' \
/«BUILDDIR»/subread-1.4.6-p5+dfsg/bin/subread-buildindex | debian/filter.pl > /«BUILDDIR»/subread-1.4.6-p5+dfsg/debian/subread/usr/share/man/man1/subread-buildindex.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='an RNA-seq aligner suitable for all purposes of RNA-seq analyses' \
/«BUILDDIR»/subread-1.4.6-p5+dfsg/bin/subjunc | debian/filter.pl > /«BUILDDIR»/subread-1.4.6-p5+dfsg/debian/subread/usr/share/man/man1/subjunc.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='a highly efficient and accurate read summarization program' \
/«BUILDDIR»/subread-1.4.6-p5+dfsg/bin/featureCounts | debian/filter.pl > /«BUILDDIR»/subread-1.4.6-p5+dfsg/debian/subread/usr/share/man/man1/featureCounts.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='a SNP caller that discovers SNPs by testing signals against local background noises' \
/«BUILDDIR»/subread-1.4.6-p5+dfsg/bin/exactSNP | debian/filter.pl > /«BUILDDIR»/subread-1.4.6-p5+dfsg/debian/subread/usr/share/man/man1/exactSNP.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='detect short and long indels' \
/«BUILDDIR»/subread-1.4.6-p5+dfsg/bin/subindel | debian/filter.pl > /«BUILDDIR»/subread-1.4.6-p5+dfsg/debian/subread/usr/share/man/man1/subindel.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='scans the entire genome and reports all matches of a specified sequence' \
/«BUILDDIR»/subread-1.4.6-p5+dfsg/bin/utilities/subread-fullscan | debian/filter.pl > /«BUILDDIR»/subread-1.4.6-p5+dfsg/debian/subread/usr/share/man/man1/subread-fullscan.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='counting the coverage of mapped reads at each location on the entire reference genome' \
/«BUILDDIR»/subread-1.4.6-p5+dfsg/bin/utilities/coverageCount | debian/filter.pl > /«BUILDDIR»/subread-1.4.6-p5+dfsg/debian/subread/usr/share/man/man1/coverageCount.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='calculate the proportion of mapped reads/fragments' \
/«BUILDDIR»/subread-1.4.6-p5+dfsg/bin/utilities/propmapped | debian/filter.pl > /«BUILDDIR»/subread-1.4.6-p5+dfsg/debian/subread/usr/share/man/man1/propmapped.1;
for i in globalReassembly removeDup qualityScores subtools ; do \
help2man --no-info --help-option="''" --no-discard-stderr --name='a component of subread suite' /«BUILDDIR»/subread-1.4.6-p5+dfsg/bin/utilities/$i | debian/filter.pl > /«BUILDDIR»/subread-1.4.6-p5+dfsg/debian/subread/usr/share/man/man1/$i.1; \
done
dh_auto_install
make[1]: Leaving directory '/«BUILDDIR»/subread-1.4.6-p5+dfsg'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
debian/rules override_dh_compress
make[1]: Entering directory '/«BUILDDIR»/subread-1.4.6-p5+dfsg'
dh_compress -X.pdf -Xtest.tar.xz
make[1]: Leaving directory '/«BUILDDIR»/subread-1.4.6-p5+dfsg'
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'subread' in '../subread_1.4.6-p5+dfsg-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian nitrogen6x test autobuilder <root@raspbian.org> >../subread_1.4.6-p5+dfsg-1_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build subread-1.4.6-p5+dfsg
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20150914-0717
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
subread_1.4.6-p5+dfsg-1_armhf.changes:
──────────────────────────────────────
Format: 1.8
Date: Sat, 05 Sep 2015 12:35:30 +0200
Source: subread
Binary: subread subread-data
Architecture: armhf
Version: 1.4.6-p5+dfsg-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian nitrogen6x test autobuilder <root@raspbian.org>
Changed-By: Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
Description:
subread - toolkit for processing next-gen sequencing data
subread-data - data files for subread package
Changes:
subread (1.4.6-p5+dfsg-1) unstable; urgency=medium
.
* Imported Upstream version 1.4.6-p5+dfsg
* Build and install SubreadUsersGuide.pdf
Checksums-Sha1:
ca7e6947609c1c33d7c43c84d7fab99f18c5383f 972080 subread_1.4.6-p5+dfsg-1_armhf.deb
Checksums-Sha256:
3f42b85c6899d5b224312f8b35f0f2874e349444a029a39dde6eb28406408c77 972080 subread_1.4.6-p5+dfsg-1_armhf.deb
Files:
2eb804e00f0c9ecb1e8b9aa1e72af115 972080 science optional subread_1.4.6-p5+dfsg-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
subread_1.4.6-p5+dfsg-1_armhf.deb
─────────────────────────────────
new debian package, version 2.0.
size 972080 bytes: control archive=1519 bytes.
626 bytes, 14 lines control
2104 bytes, 32 lines md5sums
Package: subread
Version: 1.4.6-p5+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5337
Depends: libc6 (>= 2.15), zlib1g (>= 1:1.2.3.3)
Section: science
Priority: optional
Homepage: http://sourceforge.net/projects/subread/
Description: toolkit for processing next-gen sequencing data
Subread aligner can be used to align both gDNA-seq and RNA-seq reads.
Subjunc aligner was specified designed for the detection of exon-exon
junction. For the mapping of RNA-seq reads, Subread performs local
alignments and Subjunc performs global alignments.
drwxr-xr-x root/root 0 2015-09-14 07:16 ./
drwxr-xr-x root/root 0 2015-09-14 07:16 ./usr/
drwxr-xr-x root/root 0 2015-09-14 07:16 ./usr/bin/
-rwxr-xr-x root/root 387228 2015-09-14 07:16 ./usr/bin/exactSNP
-rwxr-xr-x root/root 428412 2015-09-14 07:16 ./usr/bin/featureCounts
-rwxr-xr-x root/root 354476 2015-09-14 07:16 ./usr/bin/subindel
-rwxr-xr-x root/root 363276 2015-09-14 07:16 ./usr/bin/subjunc
-rwxr-xr-x root/root 363276 2015-09-14 07:16 ./usr/bin/subread-align
-rwxr-xr-x root/root 374916 2015-09-14 07:16 ./usr/bin/subread-buildindex
drwxr-xr-x root/root 0 2015-09-14 07:16 ./usr/lib/
drwxr-xr-x root/root 0 2015-09-14 07:16 ./usr/lib/subread/
-rwxr-xr-x root/root 354460 2015-09-14 07:16 ./usr/lib/subread/coverageCount
-rwxr-xr-x root/root 379228 2015-09-14 07:16 ./usr/lib/subread/globalReassembly
-rwxr-xr-x root/root 354476 2015-09-14 07:16 ./usr/lib/subread/propmapped
-rwxr-xr-x root/root 358684 2015-09-14 07:16 ./usr/lib/subread/qualityScores
-rwxr-xr-x root/root 354428 2015-09-14 07:16 ./usr/lib/subread/removeDup
-rwxr-xr-x root/root 354428 2015-09-14 07:16 ./usr/lib/subread/subread-fullscan
-rwxr-xr-x root/root 354524 2015-09-14 07:16 ./usr/lib/subread/subtools
drwxr-xr-x root/root 0 2015-09-14 07:16 ./usr/share/
drwxr-xr-x root/root 0 2015-09-14 07:16 ./usr/share/doc-base/
-rw-r--r-- root/root 532 2015-09-07 12:03 ./usr/share/doc-base/subread
drwxr-xr-x root/root 0 2015-09-14 07:16 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-09-14 07:16 ./usr/share/doc/subread/
-rw-r--r-- root/root 500 2015-09-07 12:03 ./usr/share/doc/subread/README.Debian
-rw-r--r-- root/root 3670 2014-10-15 04:44 ./usr/share/doc/subread/README.txt
-rw-r--r-- root/root 630602 2015-09-14 07:13 ./usr/share/doc/subread/SubreadUsersGuide.pdf
-rw-r--r-- root/root 1158 2015-09-07 12:03 ./usr/share/doc/subread/changelog.Debian.gz
-rw-r--r-- root/root 1286 2015-09-07 12:03 ./usr/share/doc/subread/copyright
drwxr-xr-x root/root 0 2015-09-14 07:16 ./usr/share/man/
drwxr-xr-x root/root 0 2015-09-14 07:16 ./usr/share/man/man1/
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-rw-r--r-- root/root 270 2015-09-14 07:16 ./usr/share/man/man1/removeDup.1.gz
-rw-r--r-- root/root 348 2015-09-14 07:16 ./usr/share/man/man1/subindel.1.gz
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-rw-r--r-- root/root 2262 2015-09-14 07:16 ./usr/share/man/man1/subread-align.1.gz
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 89208
Build-Time: 437
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 729
Job: subread_1.4.6-p5+dfsg-1
Machine Architecture: armhf
Package: subread
Package-Time: 1238
Source-Version: 1.4.6-p5+dfsg-1
Space: 89208
Status: successful
Version: 1.4.6-p5+dfsg-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20150914-0717
Build needed 00:20:38, 89208k disc space