subread →
1.5.0-p1+dfsg-2 →
armhf → 2016-01-27 22:52:11
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bm-wb-01
╔══════════════════════════════════════════════════════════════════════════════╗
║ subread 1.5.0-p1+dfsg-2 (armhf) 27 Jan 2016 22:25 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: subread
Version: 1.5.0-p1+dfsg-2
Source Version: 1.5.0-p1+dfsg-2
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/subread-XGHppp/subread-1.5.0-p1+dfsg' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/subread-XGHppp' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-66ae269b-0524-4801-b769-e52827da5469' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [8651 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [10.7 MB]
Fetched 19.4 MB in 21s (905 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
─────────
Checking available source versions...
Download source files with APT
──────────────────────────────
Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'subread' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/subread.git
Please use:
git clone git://anonscm.debian.org/debian-med/subread.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 20.1 MB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main subread 1.5.0-p1+dfsg-2 (dsc) [2245 B]
Get:2 http://172.17.0.1/private stretch-staging/main subread 1.5.0-p1+dfsg-2 (tar) [20.1 MB]
Get:3 http://172.17.0.1/private stretch-staging/main subread 1.5.0-p1+dfsg-2 (diff) [6764 B]
Fetched 20.1 MB in 2s (9587 kB/s)
Download complete and in download only mode
Check architectures
───────────────────
Check dependencies
──────────────────
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-Dq1IPq/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Get:1 file:/«BUILDDIR»/resolver-Dq1IPq/apt_archive ./ InRelease
Ign:1 file:/«BUILDDIR»/resolver-Dq1IPq/apt_archive ./ InRelease
Get:2 file:/«BUILDDIR»/resolver-Dq1IPq/apt_archive ./ Release [2119 B]
Get:2 file:/«BUILDDIR»/resolver-Dq1IPq/apt_archive ./ Release [2119 B]
Get:3 file:/«BUILDDIR»/resolver-Dq1IPq/apt_archive ./ Release.gpg [299 B]
Get:3 file:/«BUILDDIR»/resolver-Dq1IPq/apt_archive ./ Release.gpg [299 B]
Get:4 file:/«BUILDDIR»/resolver-Dq1IPq/apt_archive ./ Sources [208 B]
Get:5 file:/«BUILDDIR»/resolver-Dq1IPq/apt_archive ./ Packages [525 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 5 not upgraded.
Need to get 0 B/768 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 file:/«BUILDDIR»/resolver-Dq1IPq/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [768 B]
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12670 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) ...
W: No sandbox user '_apt' on the system, can not drop privileges
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, 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, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-subread-dummy' in '/«BUILDDIR»/resolver-bsPnjd/apt_archive/sbuild-build-depends-subread-dummy.deb'.
OK
Get:1 file:/«BUILDDIR»/resolver-bsPnjd/apt_archive ./ InRelease
Ign:1 file:/«BUILDDIR»/resolver-bsPnjd/apt_archive ./ InRelease
Get:2 file:/«BUILDDIR»/resolver-bsPnjd/apt_archive ./ Release [2119 B]
Get:2 file:/«BUILDDIR»/resolver-bsPnjd/apt_archive ./ Release [2119 B]
Get:3 file:/«BUILDDIR»/resolver-bsPnjd/apt_archive ./ Release.gpg [299 B]
Get:3 file:/«BUILDDIR»/resolver-bsPnjd/apt_archive ./ Release.gpg [299 B]
Get:4 file:/«BUILDDIR»/resolver-bsPnjd/apt_archive ./ Sources [324 B]
Get:5 file:/«BUILDDIR»/resolver-bsPnjd/apt_archive ./ Packages [580 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install subread build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autotools-dev bsdmainutils debhelper dh-strip-nondeterminism file gettext
gettext-base groff-base help2man intltool-debian libarchive-zip-perl
libcroco3 libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libicu55
liblocale-gettext-perl libmagic1 libpipeline1 libtimedate-perl libunistring0
libxml2 man-db po-debconf zlib1g-dev
Suggested packages:
wamerican | wordlist whois vacation dh-make gettext-doc autopoint
libasprintf-dev libgettextpo-dev groff less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autotools-dev bsdmainutils debhelper dh-strip-nondeterminism file gettext
gettext-base groff-base help2man intltool-debian libarchive-zip-perl
libcroco3 libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libicu55
liblocale-gettext-perl libmagic1 libpipeline1 libtimedate-perl libunistring0
libxml2 man-db po-debconf sbuild-build-depends-subread-dummy zlib1g-dev
0 upgraded, 26 newly installed, 0 to remove and 5 not upgraded.
Need to get 16.8 MB/16.8 MB of archives.
After this operation, 58.6 MB of additional disk space will be used.
Get:1 file:/«BUILDDIR»/resolver-bsPnjd/apt_archive ./ sbuild-build-depends-subread-dummy 0.invalid.0 [816 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf liblocale-gettext-perl armhf 1.07-1+b1 [18.0 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-5 [1083 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.6 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.25-2 [250 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.7-2 [111 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libicu55 armhf 55.1-7 [7380 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.3+dfsg1-1 [800 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20150820.1 [71.7 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libffi6 armhf 3.2.1-4 [18.5 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.46.2-3 [2482 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.7-2 [1400 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.56-2 [94.9 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.014-1 [10.6 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.014-1 [7472 B]
Get:24 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160115 [827 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf help2man armhf 1.47.3 [154 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 16.8 MB in 2s (8001 kB/s)
Selecting previously unselected package liblocale-gettext-perl.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12670 files and directories currently installed.)
Preparing to unpack .../liblocale-gettext-perl_1.07-1+b1_armhf.deb ...
Unpacking liblocale-gettext-perl (1.07-1+b1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../groff-base_1.22.3-5_armhf.deb ...
Unpacking groff-base (1.22.3-5) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../bsdmainutils_9.0.6_armhf.deb ...
Unpacking bsdmainutils (9.0.6) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../libpipeline1_1.4.1-2_armhf.deb ...
Unpacking libpipeline1:armhf (1.4.1-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../man-db_2.7.5-1_armhf.deb ...
Unpacking man-db (2.7.5-1) ...
Selecting previously unselected package libunistring0:armhf.
Preparing to unpack .../libunistring0_0.9.3-5.2_armhf.deb ...
Unpacking libunistring0:armhf (0.9.3-5.2) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../libmagic1_1%3a5.25-2_armhf.deb ...
Unpacking libmagic1:armhf (1:5.25-2) ...
Selecting previously unselected package file.
Preparing to unpack .../file_1%3a5.25-2_armhf.deb ...
Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.7-2_armhf.deb ...
Unpacking gettext-base (0.19.7-2) ...
Selecting previously unselected package libicu55:armhf.
Preparing to unpack .../libicu55_55.1-7_armhf.deb ...
Unpacking libicu55:armhf (55.1-7) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../libxml2_2.9.3+dfsg1-1_armhf.deb ...
Unpacking libxml2:armhf (2.9.3+dfsg1-1) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../autotools-dev_20150820.1_all.deb ...
Unpacking autotools-dev (20150820.1) ...
Selecting previously unselected package libffi6:armhf.
Preparing to unpack .../libffi6_3.2.1-4_armhf.deb ...
Unpacking libffi6:armhf (3.2.1-4) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../libglib2.0-0_2.46.2-3_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.46.2-3) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../libcroco3_0.6.11-1_armhf.deb ...
Unpacking libcroco3:armhf (0.6.11-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../gettext_0.19.7-2_armhf.deb ...
Unpacking gettext (0.19.7-2) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.4) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../po-debconf_1.0.19_all.deb ...
Unpacking po-debconf (1.0.19) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../libarchive-zip-perl_1.56-2_all.deb ...
Unpacking libarchive-zip-perl (1.56-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../libfile-stripnondeterminism-perl_0.014-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (0.014-1) ...
Selecting previously unselected package libtimedate-perl.
Preparing to unpack .../libtimedate-perl_2.3000-2_all.deb ...
Unpacking libtimedate-perl (2.3000-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../dh-strip-nondeterminism_0.014-1_all.deb ...
Unpacking dh-strip-nondeterminism (0.014-1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../debhelper_9.20160115_all.deb ...
Unpacking debhelper (9.20160115) ...
Selecting previously unselected package help2man.
Preparing to unpack .../help2man_1.47.3_armhf.deb ...
Unpacking help2man (1.47.3) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Selecting previously unselected package sbuild-build-depends-subread-dummy.
Preparing to unpack .../sbuild-build-depends-subread-dummy.deb ...
Unpacking sbuild-build-depends-subread-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.21-6) ...
Setting up liblocale-gettext-perl (1.07-1+b1) ...
Setting up groff-base (1.22.3-5) ...
Setting up bsdmainutils (9.0.6) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up libmagic1:armhf (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.7-2) ...
Setting up libicu55:armhf (55.1-7) ...
Setting up libxml2:armhf (2.9.3+dfsg1-1) ...
Setting up autotools-dev (20150820.1) ...
Setting up libffi6:armhf (3.2.1-4) ...
Setting up libglib2.0-0:armhf (2.46.2-3) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.11-1) ...
Setting up gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.19) ...
Setting up libarchive-zip-perl (1.56-2) ...
Setting up libfile-stripnondeterminism-perl (0.014-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up help2man (1.47.3) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up debhelper (9.20160115) ...
Setting up sbuild-build-depends-subread-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.014-1) ...
Processing triggers for libc-bin (2.21-6) ...
W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25.90.20160101-2 dpkg-dev_1.18.4 g++-5_5.3.1-5+rpi1 gcc-5_5.3.1-5+rpi1 libc6-dev_2.21-6 libstdc++-5-dev_5.3.1-5+rpi1 libstdc++6_5.3.1-5+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.113+nmu3 apt_1.2 autotools-dev_20150820.1 base-files_9.5+rpi1 base-passwd_3.5.39 bash_4.3-14 binutils_2.25.90.20160101-2 bsdmainutils_9.0.6 bsdutils_1:2.27.1-1 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-5+rpi1 dash_0.5.7-4 debconf_1.5.58 debfoster_2.7-2 debhelper_9.20160115 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-3 dmsetup_2:1.02.114-1 dpkg_1.18.4 dpkg-dev_1.18.4 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.6.0-2 g++_4:5.3.1-1+rpi1 g++-5_5.3.1-5+rpi1 gcc_4:5.3.1-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-3 gcc-4.9-base_4.9.3-10 gcc-5_5.3.1-5+rpi1 gcc-5-base_5.3.1-5+rpi1 gettext_0.19.7-2 gettext-base_0.19.7-2 gnupg_1.4.20-1 gpgv_1.4.20-1 grep_2.22-1 groff-base_1.22.3-5 gzip_1.6-4 help2man_1.47.3 hostname_3.16 init_1.24 init-system-helpers_1.24 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-6+rpi1 kmod_21-1 libacl1_2.2.52-2 libapparmor1_2.10-2+b3 libapt-pkg5.0_1.2 libarchive-zip-perl_1.56-2 libasan2_5.3.1-5+rpi1 libatomic1_5.3.1-5+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1 libaudit1_1:2.4.5-1 libblkid1_2.27.1-1 libbz2-1.0_1.0.6-8 libc-bin_2.21-6 libc-dev-bin_2.21-6 libc6_2.21-6 libc6-dev_2.21-6 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-5+rpi1 libcomerr2_1.42.13-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.6-1 libdebconfclient0_0.201 libdevmapper1.02.1_2:1.02.114-1 libdpkg-perl_1.18.4 libdrm2_2.4.66-2 libfakeroot_1.20.2-1 libfdisk1_2.27.1-1 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.014-1 libgc1c2_1:7.4.2-7.3 libgcc-5-dev_5.3.1-5+rpi1 libgcc1_1:5.3.1-5+rpi1 libgcrypt20_1.6.4-4 libgdbm3_1.8.3-13.1 libglib2.0-0_2.46.2-3 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.3.1-5+rpi1 libgpg-error0_1.21-1 libicu55_55.1-7 libisl15_0.15-3 libklibc_2.0.4-6+rpi1 libkmod2_21-1 liblocale-gettext-perl_1.07-1+b1 liblz4-1_0.0~r131-1 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-1 libmpc3_1.0.3-1 libmpfr4_3.1.3-2 libncurses5_6.0+20151024-2 libncursesw5_6.0+20151024-2 libpam-modules_1.1.8-3.2 libpam-modules-bin_1.1.8-3.2 libpam-runtime_1.1.8-3.2 libpam0g_1.1.8-3.2 libpcre3_2:8.38-1 libperl5.22_5.22.1-4 libpipeline1_1.4.1-2 libpng12-0_1.2.54-1 libprocps5_2:3.3.11-3 libreadline6_6.3-8+b3 libseccomp2_2.2.3-2 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libsmartcols1_2.27.1-1 libss2_1.42.13-1 libstdc++-5-dev_5.3.1-5+rpi1 libstdc++6_5.3.1-5+rpi1 libsystemd0_228-4 libtimedate-perl_2.3000-2 libtinfo5_6.0+20151024-2 libubsan0_5.3.1-5+rpi1 libudev1_228-4 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-28 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-1 libxml2_2.9.3+dfsg1-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.2 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.04-0.1 mawk_1.3.3-17 mount_2.27.1-1 multiarch-support_2.21-6 nano_2.4.3-1 ncurses-base_6.0+20151024-2 ncurses-bin_6.0+20151024-2 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.1-4 perl-base_5.22.1-4 perl-modules-5.22_5.22.1-4 po-debconf_1.0.19 procps_2:3.3.11-3 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_228-4 systemd-sysv_228-4 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 tar_1.28-2.1 tzdata_2015g-1 udev_228-4 util-linux_2.27.1-1 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 Jan 18 12:26:14 2016 UTC using RSA key ID 1B5228B0
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./subread_1.5.0-p1+dfsg-2.dsc
dpkg-source: info: extracting subread in subread-1.5.0-p1+dfsg
dpkg-source: info: unpacking subread_1.5.0-p1+dfsg.orig.tar.gz
dpkg-source: info: unpacking subread_1.5.0-p1+dfsg-2.debian.tar.xz
dpkg-source: info: applying syntax_err.patch
dpkg-source: info: applying arch_specific_flags.patch
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
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=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-66ae269b-0524-4801-b769-e52827da5469
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package subread
dpkg-buildpackage: source version 1.5.0-p1+dfsg-2
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build subread-1.5.0-p1+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-1.5.0-p1+dfsg'
cd src; make -f Makefile.Linux clean
make[2]: Entering directory '/«BUILDDIR»/subread-1.5.0-p1+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 core-bigtable.o seek-zlib.o
make[2]: Leaving directory '/«BUILDDIR»/subread-1.5.0-p1+dfsg/src'
dh_clean
make[1]: Leaving directory '/«BUILDDIR»/subread-1.5.0-p1+dfsg'
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_update_autotools_config -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/«BUILDDIR»/subread-1.5.0-p1+dfsg'
cd src; make -f Makefile.Linux
make[2]: Entering directory '/«BUILDDIR»/subread-1.5.0-p1+dfsg/src'
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core.o core.c
core.c: In function 'print_in_box':
core.c:139:7: 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:834:19: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
gzFile * rawfp = gzopen(fname, "r");
^
core.c:845:25: warning: passing argument 1 of 'gzgets' from incompatible pointer type [-Wincompatible-pointer-types]
char * bufr =gzgets(rawfp, linebuff, 3000);
^
In file included from subread.h:26:0,
from core.c:43:
/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:856:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(rawfp);
^
In file included from subread.h:26:0,
from core.c:43:
/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 'calc_tlen':
core.c:1451:16: warning: variable 'section_start' set but not used [-Wunused-but-set-variable]
unsigned int section_start = smaller_head_pos, section_end = 0;
^
core.c: In function 'do_iteration_one':
core.c:2075:6: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
int ret;
^
core.c: In function 'write_realignments_for_fragment':
core.c:2286:21: warning: variable 'raw_r2' set but not used [-Wunused-but-set-variable]
mapping_result_t * raw_r2 = NULL;
^
core.c:2283:21: warning: variable 'raw_r1' set but not used [-Wunused-but-set-variable]
mapping_result_t * raw_r1 = NULL;
^
core.c: In function 'do_iteration_two':
core.c:2352:6: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
int ret;
^
core.c: In function 'do_voting':
core.c:2896:9: 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:2815:6: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
int ret, xk1;
^
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-junction.o core-junction.c
core-junction.c: In function 'copy_vote_to_alignment_res':
core-junction.c:1022:12: warning: variable 'current_piece_minor_score' set but not used [-Wunused-but-set-variable]
int i,j, current_piece_minor_score = 0;
^
core-junction.c: In function 'finalise_explain_CIGAR':
core-junction.c:2331:10: warning: variable 'is_front_search' set but not used [-Wunused-but-set-variable]
int is_front_search = 0;
^
core-junction.c:2467:94: warning: variable 'total_coverage_length' set but not used [-Wunused-but-set-variable]
int final_qual = 0, applied_mismatch = 0, non_clipped_length = 0, total_indel_length = 0, total_coverage_length = 0, final_MATCH = 0;
^
core-junction.c:2447:28: warning: variable 'isCigarOK' set but not used [-Wunused-but-set-variable]
int mismatch_bases = 0, isCigarOK = 0;
^
core-junction.c:2266:23: warning: variable 'tmp_cigar_exonic' set but not used [-Wunused-but-set-variable]
char tmp_cigar[120], tmp_cigar_exonic[120];
^
core-junction.c: In function 'find_translocation_brk_PQR':
core-junction.c:4883:23: warning: variable 'candBrkPlist' set but not used [-Wunused-but-set-variable]
chromosome_event_t * candBrkPlist [_PQR_LIST_SIZE];
^
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-indel.o core-indel.c
core-indel.c: In function 'find_new_indels':
core-indel.c:1580:9: 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:2927:41: warning: variable 'best_right' set but not used [-Wunused-but-set-variable]
int best_edge_score = -1, best_left, best_right;
^
core-indel.c:2927:30: 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:3026:24: 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:3304:3: 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:3305:3: 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:3306:3: 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:3383:3: 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:3384:3: 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:3385:3: 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:3747:3: 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:3748:3: 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:3749:3: 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=\""1.5.0-p1"\" -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sambam-file.o sambam-file.c
sambam-file.c: In function 'PBam_get_next_zchunk':
sambam-file.c:346:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&ID1, 1, 1, bam_fp);
^
sambam-file.c:347:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&ID2, 1, 1, bam_fp);
^
sambam-file.c:348:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&CM, 1, 1, bam_fp);
^
sambam-file.c:349:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&FLG, 1, 1, bam_fp);
^
sambam-file.c:358:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&XLEN,1, 2, bam_fp );
^
sambam-file.c:366:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SI1, 1, 1, bam_fp);
^
sambam-file.c:367:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SI2, 1, 1, bam_fp);
^
sambam-file.c:368:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SLEN, 1, 2, bam_fp);
^
sambam-file.c:372:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&BSIZE_MID, 1,2 , bam_fp);
^
sambam-file.c:384:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(buffer, 1, CDATA_READING, bam_fp);
^
sambam-file.c:388:3: 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=\""1.5.0-p1"\" -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sublog.o sublog.c
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-algorithms.o gene-algorithms.c
gene-algorithms.c: In function 'show_cigar':
gene-algorithms.c:757:6: warning: variable 'last_end' set but not used [-Wunused-but-set-variable]
int last_end=0, last_offset = 0, cursor = 0;
^
gene-algorithms.c:756:9: 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:1169:28: 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:1718:6: 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:2359:7: 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=\""1.5.0-p1"\" -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-files.o input-files.c
input-files.c: In function 'f_subr_open':
input-files.c:52:10: warning: implicit declaration of function 'fopen64' [-Wimplicit-function-declaration]
return fopen64(fname, mode);
^
input-files.c:52:10: warning: return makes pointer from integer without a cast [-Wint-conversion]
input-files.c: In function 'SAM_pairer_read_SAM_MB':
input-files.c:2531:12: warning: variable 'last' set but not used [-Wunused-but-set-variable]
int nch, last=-1;
^
input-files.c: In function 'SAM_pairer_get_next_read_BIN':
input-files.c:2709:11: warning: variable 'ref_name' set but not used [-Wunused-but-set-variable]
char ref_name[MAX_CHROMOSOME_NAME_LEN];
^
input-files.c: In function 'fix_write_block':
input-files.c:4008:23: warning: variable 'retbam' set but not used [-Wunused-but-set-variable]
int x1, bam_len = 0, retbam;
^
input-files.c: In function 'SAM_nosort_run_once':
input-files.c:4458:9: warning: variable 'ref_name' set but not used [-Wunused-but-set-variable]
char ref_name[MAX_CHROMOSOME_NAME_LEN];
^
input-files.c: In function 'geinput_next_char':
input-files.c:508:5: 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 'SAM_pairer_writer_reset':
input-files.c:3349:2: warning: ignoring return value of 'ftruncate', declared with attribute warn_unused_result [-Wunused-result]
ftruncate(fileno(bam_main -> bam_fp), 0);
^
input-files.c: In function 'SAM_pairer_osr_next_name':
input-files.c:3558:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 2, fp);
^
input-files.c:3570:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 2, fp);
^
input-files.c: In function 'SAM_pairer_osr_next_bin':
input-files.c:3580:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 2, fp);
^
input-files.c:3584:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 2, fp);
^
input-files.c:3587:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(bin, 1, rlen, fp);
^
input-files.c: In function 'fix_load_next_block':
input-files.c:3984:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(bam_buf, 1, bsize - xlen - 19, in);
^
input-files.c: In function 'sort_SAM_finalise':
input-files.c:4767:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_name_len, 2,1 , bbfp);
^
input-files.c:4773:6: 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:4776:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len,2,1,bbfp);
^
input-files.c:4782:6: 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:4835:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_name_len, 2,1 , bbfp);
^
input-files.c:4841:6: 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:4845:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, 2,1 , bbfp);
^
input-files.c:4848:6: 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=\""1.5.0-p1"\" -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sorted-hashtable.o sorted-hashtable.c
sorted-hashtable.c: In function 'gehash_load_option':
sorted-hashtable.c:1264:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(magic_chars,1,8,fp);
^
sorted-hashtable.c:1269:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_key, 2, 1, fp);
^
sorted-hashtable.c:1272:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_length, 2, 1, fp);
^
sorted-hashtable.c:1276:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(result ,option_length,1,fp);
^
sorted-hashtable.c: In function 'gehash_load':
sorted-hashtable.c:1303:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(magic_chars,1,8,fp);
^
sorted-hashtable.c:1326:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_key, 2, 1, fp);
^
sorted-hashtable.c:1329:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_length, 2, 1, fp);
^
sorted-hashtable.c:1332:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&(the_table -> index_gap),2,1,fp);
^
sorted-hashtable.c:1334:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&(the_table -> padding),2,1,fp);
^
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -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 -Wdate-time -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=\""1.5.0-p1"\" -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 -Wdate-time -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=\""1.5.0-p1"\" -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -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 -Wdate-time -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=\""1.5.0-p1"\" -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 -Wdate-time -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=\""1.5.0-p1"\" -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c
core-bigtable.c: In function 'bigtable_readonly_result':
core-bigtable.c:70:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(write_ptr, loadjunc?sizeof(subjunc_result_t):sizeof(mapping_result_t), 1, global_context -> bigtable_cache_file_fp);
^
core-bigtable.c: In function 'bigtable_retrieve_cache':
core-bigtable.c:219:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread( current_cache -> big_margin_data , sizeof(short) * 3 * global_context -> config.big_margin_record_size , 1, global_context -> bigtable_cache_file_fp );
^
core-bigtable.c:220:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread( current_cache -> alignment_res , sizeof(mapping_result_t) * global_context -> config.multi_best_reads , 1, global_context -> bigtable_cache_file_fp );
^
core-bigtable.c:223:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread( current_cache -> subjunc_res , sizeof(subjunc_result_t) * global_context -> config.multi_best_reads , 1, global_context -> bigtable_cache_file_fp);
^
core-bigtable.c:229:5: warning: ignoring return value of 'ftruncate', declared with attribute warn_unused_result [-Wunused-result]
ftruncate(fileno(global_context -> bigtable_cache_file_fp), new_file_size);
^
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c
gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o repair read-repair.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 core-bigtable.o seek-zlib.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=\""1.5.0-p1"\" -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 core-bigtable.o seek-zlib.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
readSummary.c: In function 'calc_junctions_from_cigar':
readSummary.c:341:15: warning: variable 'right_boundary' set but not used [-Wunused-but-set-variable]
unsigned int right_boundary = 0;
^
readSummary.c: In function 'readSummary':
readSummary.c:3899:9: warning: variable 'curchr_name' set but not used [-Wunused-but-set-variable]
char * curchr_name, * fasta_contigs_fname;
^
readSummary.c:3898:15: warning: variable 'curpos' set but not used [-Wunused-but-set-variable]
long curchr, curpos;
^
readSummary.c:3898:7: warning: variable 'curchr' set but not used [-Wunused-but-set-variable]
long curchr, curpos;
^
readSummary.c: In function 'load_feature_info':
readSummary.c:834:10: warning: 'token_temp' may be used uninitialized in this function [-Wmaybe-uninitialized]
char * token_temp, *chro_name;
^
readSummary.c:898:10: 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=\""1.5.0-p1"\" -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 core-bigtable.o seek-zlib.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=\""1.5.0-p1"\" -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 core-bigtable.o seek-zlib.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=\""1.5.0-p1"\" -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 core-bigtable.o seek-zlib.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
index-builder.c: In function 'scan_gene_index':
index-builder.c:456:19: 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=\""1.5.0-p1"\" -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 core-bigtable.o seek-zlib.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=\""1.5.0-p1"\" -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 core-bigtable.o seek-zlib.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=\""1.5.0-p1"\" -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 core-bigtable.o seek-zlib.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=\""1.5.0-p1"\" -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 core-bigtable.o seek-zlib.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=\""1.5.0-p1"\" -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 core-bigtable.o seek-zlib.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=\""1.5.0-p1"\" -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 core-bigtable.o seek-zlib.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=\""1.5.0-p1"\" -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 core-bigtable.o seek-zlib.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
mkdir -p ../bin/utilities
mv subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/
mv repair coverageCount propmapped qualityScores removeDup subread-fullscan ../bin/utilities
###########################################################
# #
# Installation finished. #
# #
# Generated executables were copied to directory ../bin/ #
# #
###########################################################
make[2]: Leaving directory '/«BUILDDIR»/subread-1.5.0-p1+dfsg/src'
dh_auto_build
make[1]: Leaving directory '/«BUILDDIR»/subread-1.5.0-p1+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/«BUILDDIR»/subread-1.5.0-p1+dfsg'
debian/tests/subread-tests /«BUILDDIR»/subread-1.5.0-p1+dfsg
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p1
//========================== 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/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p1
//=========================== indexBuilder setting ===========================\\
|| ||
|| Index name : tmp/small1 ||
|| Index space : base-space ||
|| Memory : 3000 Mbytes ||
|| Repeat threshold : 100 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=318.0k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=359.9k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=401.9k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=430.6k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=459.8k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=485.3k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=505.0k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=526.9k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=545.7k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=562.6k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=581.5k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=593.4k bps/s, total=0m ||
|| 2 uninformative subreads were found. ||
|| These subreads were excluded from index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=219.3k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=228.3k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=243.4k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=239.4k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=241.9k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=258.7k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=275.0k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=277.6k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=283.9k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=298.4k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=314.2k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=328.2k 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/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p1
//============================= 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 ||
|| ||
|| All subreads : 14 ||
|| Min read1 votes : 1 ||
|| Min read2 votes : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| ||
|| Allowed mismatch : 3 bases ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : no ||
|| Hamming distance : no ||
|| Quality scores : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (27-Jan-2016 22:33:44) ======================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [2,41] ||
|| Load the 1-th index block... ||
|| Map fragments... ||
|| 41% completed, 0.4 mins elapsed, rate=1.4k fragments per second ||
|| 48% completed, 0.5 mins elapsed, rate=1.4k fragments per second ||
|| 54% completed, 0.5 mins elapsed, rate=1.4k fragments per second ||
|| 61% completed, 0.5 mins elapsed, rate=1.5k fragments per second ||
|| Finish the 16052 fragments... ||
|| 77% completed, 0.5 mins elapsed, rate=0.4k fragments per second ||
|| 87% completed, 0.5 mins elapsed, rate=0.4k fragments per second ||
|| 97% completed, 0.5 mins elapsed, rate=0.5k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 16052 fragments ||
|| Mapped : 15914 fragments (99.1%) ||
|| Correctly paired : 14375 fragments ||
|| Junctions : 407 ||
|| Indels : 187 ||
|| ||
|| Running time : 3.4 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p1
//============================= 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 ||
|| ||
|| All subreads : 14 ||
|| Min read1 votes : 1 ||
|| Min read2 votes : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| ||
|| Allowed mismatch : 3 bases ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : no ||
|| Hamming distance : no ||
|| Quality scores : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (27-Jan-2016 22:37:08) ======================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [2,41] ||
|| Load the 1-th index block... ||
|| Map fragments... ||
|| 41% completed, 0.4 mins elapsed, rate=1.3k fragments per second ||
|| 48% completed, 0.4 mins elapsed, rate=1.4k fragments per second ||
|| 54% completed, 0.4 mins elapsed, rate=1.4k fragments per second ||
|| 61% completed, 0.4 mins elapsed, rate=1.5k fragments per second ||
|| Finish the 16052 fragments... ||
|| 77% completed, 0.5 mins elapsed, rate=0.4k fragments per second ||
|| 87% completed, 0.5 mins elapsed, rate=0.4k fragments per second ||
|| 97% completed, 0.6 mins elapsed, rate=0.5k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 16052 fragments ||
|| Mapped : 15915 fragments (99.1%) ||
|| Correctly paired : 14344 fragments ||
|| Junctions : 402 ||
|| Fusions : 92 ||
|| Indels : 188 ||
|| ||
|| Running time : 2.4 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p1
//=========================== indexBuilder setting ===========================\\
|| ||
|| Index name : tmp/small1 ||
|| Index space : base-space ||
|| Memory : 100 Mbytes ||
|| Repeat threshold : 100 repeats ||
|| Distance to next subread : 1 ||
|| ||
|| 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=128.2k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=169.7k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=206.6k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=222.3k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=245.6k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=268.8k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=287.6k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=307.9k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=325.7k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=341.3k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=358.6k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=363.3k bps/s, total=0m ||
|| 52 uninformative subreads were found. ||
|| These subreads were excluded from index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=82.2k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=102.0k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=121.9k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=135.6k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=153.8k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=171.4k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=188.2k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=204.0k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=215.7k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=226.3k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=239.2k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=251.0k 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/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p1
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| 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 / 10 ||
|| Allowed mismatch : 3 bases ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : no ||
|| Hamming distance : yes ||
|| Quality scores : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (27-Jan-2016 22:39:40) ======================\\
|| ||
|| The input file contains base space reads. ||
|| WARNING - The specified Phred score offset (33) seems incorrect. ||
|| ASCII values of the quality scores of read bases included in ||
|| the first 3000 reads were found to be within the range of ||
|| [73,73]. ||
|| ||
|| Load the 1-th index block... ||
|| Map reads... ||
|| 33% completed, 0.3 mins elapsed, rate=2.7k reads per second ||
|| 39% completed, 0.3 mins elapsed, rate=3.0k reads per second ||
|| 46% completed, 0.3 mins elapsed, rate=3.2k reads per second ||
|| 53% completed, 0.3 mins elapsed, rate=3.3k reads per second ||
|| 60% completed, 0.3 mins elapsed, rate=3.4k reads per second ||
|| Finish the 19998 reads... ||
|| 74% completed, 0.3 mins elapsed, rate=0.8k reads per second ||
|| 83% completed, 0.3 mins elapsed, rate=0.9k reads per second ||
|| 91% completed, 0.3 mins elapsed, rate=1.0k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 reads ||
|| Mapped : 19997 reads (100.0%) ||
|| Indels : 7 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 2.0 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p1
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| 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 / 10 ||
|| Allowed mismatch : 3 bases ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : yes ||
|| Hamming distance : yes ||
|| Quality scores : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (27-Jan-2016 22:41:43) ======================\\
|| ||
|| The input file contains base space reads. ||
|| WARNING - The specified Phred score offset (33) seems incorrect. ||
|| ASCII values of the quality scores of read bases included in ||
|| the first 3000 reads were found to be within the range of ||
|| [73,73]. ||
|| ||
|| Load the 1-th index block... ||
|| Map reads... ||
|| 33% completed, 0.2 mins elapsed, rate=3.3k reads per second ||
|| 39% completed, 0.2 mins elapsed, rate=3.4k reads per second ||
|| 46% completed, 0.2 mins elapsed, rate=3.6k reads per second ||
|| 53% completed, 0.2 mins elapsed, rate=3.8k reads per second ||
|| 60% completed, 0.2 mins elapsed, rate=3.9k reads per second ||
|| Finish the 19998 reads... ||
|| 74% completed, 0.3 mins elapsed, rate=1.0k reads per second ||
|| 83% completed, 0.3 mins elapsed, rate=1.0k reads per second ||
|| 91% completed, 0.3 mins elapsed, rate=1.1k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 reads ||
|| Mapped : 18758 reads (93.8%) ||
|| Indels : 5 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 1.5 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p1
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| 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 ||
|| ||
|| All subreads : 10 ||
|| Min read1 votes : 3 ||
|| Min read2 votes : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| ||
|| Allowed mismatch : 3 bases ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : no ||
|| Hamming distance : yes ||
|| Quality scores : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (27-Jan-2016 22:43:13) ======================\\
|| ||
|| The input file contains base space reads. ||
|| WARNING - The specified Phred score offset (33) seems incorrect. ||
|| ASCII values of the quality scores of read bases included in ||
|| the first 3000 reads were found to be within the range of ||
|| [73,73]. ||
|| ||
|| Load the 1-th index block... ||
|| Map fragments... ||
|| 33% completed, 0.3 mins elapsed, rate=1.7k fragments per second ||
|| 39% completed, 0.3 mins elapsed, rate=1.8k fragments per second ||
|| 46% completed, 0.3 mins elapsed, rate=1.9k fragments per second ||
|| 53% completed, 0.3 mins elapsed, rate=2.0k fragments per second ||
|| 60% completed, 0.3 mins elapsed, rate=2.0k fragments per second ||
|| Finish the 19998 fragments... ||
|| 74% completed, 0.3 mins elapsed, rate=0.7k fragments per second ||
|| 83% completed, 0.4 mins elapsed, rate=0.8k fragments per second ||
|| 91% completed, 0.4 mins elapsed, rate=0.8k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 fragments ||
|| Mapped : 19998 fragments (100.0%) ||
|| Correctly paired : 19554 fragments ||
|| Indels : 23 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 1.5 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p1
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| 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 ||
|| ||
|| All subreads : 10 ||
|| Min read1 votes : 3 ||
|| Min read2 votes : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| ||
|| Allowed mismatch : 3 bases ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : yes ||
|| Hamming distance : yes ||
|| Quality scores : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (27-Jan-2016 22:44:42) ======================\\
|| ||
|| The input file contains base space reads. ||
|| WARNING - The specified Phred score offset (33) seems incorrect. ||
|| ASCII values of the quality scores of read bases included in ||
|| the first 3000 reads were found to be within the range of ||
|| [73,73]. ||
|| ||
|| Load the 1-th index block... ||
|| Map fragments... ||
|| 33% completed, 0.3 mins elapsed, rate=1.5k fragments per second ||
|| 39% completed, 0.3 mins elapsed, rate=1.6k fragments per second ||
|| 46% completed, 0.3 mins elapsed, rate=1.7k fragments per second ||
|| 53% completed, 0.3 mins elapsed, rate=1.8k fragments per second ||
|| 60% completed, 0.3 mins elapsed, rate=1.9k fragments per second ||
|| Finish the 19998 fragments... ||
|| 74% completed, 0.4 mins elapsed, rate=0.7k fragments per second ||
|| 83% completed, 0.4 mins elapsed, rate=0.8k fragments per second ||
|| 91% completed, 0.4 mins elapsed, rate=0.8k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 fragments ||
|| Mapped : 19216 fragments (96.1%) ||
|| Correctly paired : 18830 fragments ||
|| Indels : 22 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 2.2 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p1
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| 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 ||
|| ||
|| All subreads : 10 ||
|| Min read1 votes : 3 ||
|| Min read2 votes : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| ||
|| Allowed mismatch : 3 bases ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : no ||
|| Hamming distance : yes ||
|| Quality scores : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (27-Jan-2016 22:46:57) ======================\\
|| ||
|| The input file contains base space reads. ||
|| WARNING - The specified Phred score offset (33) seems incorrect. ||
|| ASCII values of the quality scores of read bases included in ||
|| the first 3000 reads were found to be within the range of ||
|| [50,50]. ||
|| ||
|| Load the 1-th index block... ||
|| Map fragments... ||
|| 33% completed, 0.2 mins elapsed, rate=2.0k fragments per second ||
|| 39% completed, 0.3 mins elapsed, rate=2.1k fragments per second ||
|| 46% completed, 0.3 mins elapsed, rate=2.2k fragments per second ||
|| 53% completed, 0.3 mins elapsed, rate=2.2k fragments per second ||
|| 60% completed, 0.3 mins elapsed, rate=2.3k fragments per second ||
|| Finish the 20000 fragments... ||
|| 74% completed, 0.3 mins elapsed, rate=0.8k fragments per second ||
|| 83% completed, 0.3 mins elapsed, rate=0.9k fragments per second ||
|| 91% completed, 0.3 mins elapsed, rate=0.9k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 20000 fragments ||
|| Mapped : 19568 fragments (97.8%) ||
|| Correctly paired : 14442 fragments ||
|| Indels : 63 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 1.3 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p1
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| 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 ||
|| ||
|| All subreads : 10 ||
|| Min read1 votes : 3 ||
|| Min read2 votes : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| ||
|| Allowed mismatch : 3 bases ||
|| 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 (27-Jan-2016 22:48:15) ======================\\
|| ||
|| The input file contains base space reads. ||
|| WARNING - The specified Phred score offset (33) seems incorrect. ||
|| ASCII values of the quality scores of read bases included in ||
|| the first 3000 reads were found to be within the range of ||
|| [50,50]. ||
|| ||
|| Load the 1-th index block... ||
|| Map fragments... ||
|| 34% completed, 0.2 mins elapsed, rate=2.8k fragments per second ||
|| 40% completed, 0.2 mins elapsed, rate=2.9k fragments per second ||
|| 48% completed, 0.3 mins elapsed, rate=3.0k fragments per second ||
|| 53% completed, 0.3 mins elapsed, rate=2.9k fragments per second ||
|| 59% completed, 0.3 mins elapsed, rate=3.0k fragments per second ||
|| 67% completed, 0.3 mins elapsed, rate=3.0k fragments per second ||
|| Finish the 20001 fragments... ||
|| 75% completed, 0.3 mins elapsed, rate=0.8k fragments per second ||
|| 83% completed, 0.3 mins elapsed, rate=0.9k fragments per second ||
|| 92% completed, 0.3 mins elapsed, rate=0.9k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 20001 fragments ||
|| Mapped : 19528 fragments (97.6%) ||
|| Correctly paired : 14071 fragments ||
|| Indels : 179 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 1.3 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p1
//============================= 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 (27-Jan-2016 22:49:32) ======================\\
|| ||
|| Split BAM file into ./temp-snps-025607-2FE9F960-* ... ||
|| 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-1.5.0-p1+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-1.5.0-p1+dfsg'
find /«BUILDDIR»/subread-1.5.0-p1+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \;
mkdir -p /«BUILDDIR»/subread-1.5.0-p1+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-1.5.0-p1+dfsg/bin/subread-align | debian/filter.pl > /«BUILDDIR»/subread-1.5.0-p1+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-1.5.0-p1+dfsg/bin/subread-buildindex | debian/filter.pl > /«BUILDDIR»/subread-1.5.0-p1+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-1.5.0-p1+dfsg/bin/subjunc | debian/filter.pl > /«BUILDDIR»/subread-1.5.0-p1+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-1.5.0-p1+dfsg/bin/featureCounts | debian/filter.pl > /«BUILDDIR»/subread-1.5.0-p1+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-1.5.0-p1+dfsg/bin/exactSNP | debian/filter.pl > /«BUILDDIR»/subread-1.5.0-p1+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-1.5.0-p1+dfsg/bin/subindel | debian/filter.pl > /«BUILDDIR»/subread-1.5.0-p1+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-1.5.0-p1+dfsg/bin/utilities/subread-fullscan | debian/filter.pl > /«BUILDDIR»/subread-1.5.0-p1+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-1.5.0-p1+dfsg/bin/utilities/coverageCount | debian/filter.pl > /«BUILDDIR»/subread-1.5.0-p1+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-1.5.0-p1+dfsg/bin/utilities/propmapped | debian/filter.pl > /«BUILDDIR»/subread-1.5.0-p1+dfsg/debian/subread/usr/share/man/man1/propmapped.1;
for i in removeDup repair qualityScores ; do \
help2man --no-info --help-option="''" --no-discard-stderr --name='a component of subread suite' /«BUILDDIR»/subread-1.5.0-p1+dfsg/bin/utilities/$i | debian/filter.pl > /«BUILDDIR»/subread-1.5.0-p1+dfsg/debian/subread/usr/share/man/man1/$i.1; \
done
dh_auto_install
make[1]: Leaving directory '/«BUILDDIR»/subread-1.5.0-p1+dfsg'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
debian/rules override_dh_compress
make[1]: Entering directory '/«BUILDDIR»/subread-1.5.0-p1+dfsg'
dh_compress -X.pdf -Xtest.tar.xz
make[1]: Leaving directory '/«BUILDDIR»/subread-1.5.0-p1+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
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-dbgsym' in '../subread-dbgsym_1.5.0-p1+dfsg-2_armhf.deb'.
dpkg-deb: building package 'subread' in '../subread_1.5.0-p1+dfsg-2_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../subread_1.5.0-p1+dfsg-2_armhf.changes
dpkg-genchanges: warning: package subread-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build subread-1.5.0-p1+dfsg
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20160127-2251
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
subread_1.5.0-p1+dfsg-2_armhf.changes:
──────────────────────────────────────
Format: 1.8
Date: Mon, 18 Jan 2016 12:03:41 +0100
Source: subread
Binary: subread subread-data
Architecture: armhf
Version: 1.5.0-p1+dfsg-2
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard 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 (1.5.0-p1+dfsg-2) unstable; urgency=medium
.
* d/control: remove hurd-i386 and mipsel due to failing tests
Checksums-Sha1:
c98f64f8b4ed13a58c19aa1f64a7138d00aab2e5 5086280 subread-dbgsym_1.5.0-p1+dfsg-2_armhf.deb
6930feecf209ebc3a77536f7f8c9f34c26a9ba14 423560 subread_1.5.0-p1+dfsg-2_armhf.deb
Checksums-Sha256:
3342ccf9294359084638ed801d673aedac1de18428593351399958992f24bcce 5086280 subread-dbgsym_1.5.0-p1+dfsg-2_armhf.deb
fce50eecb19e2e57f7d2f4105b35b14e20607baf0525458134522627173ff5b8 423560 subread_1.5.0-p1+dfsg-2_armhf.deb
Files:
bb2be3c287ee0b8cb063359adb98cdfa 5086280 debug extra subread-dbgsym_1.5.0-p1+dfsg-2_armhf.deb
18b8404760c751ee37ee7145de944ba5 423560 science optional subread_1.5.0-p1+dfsg-2_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
subread-dbgsym_1.5.0-p1+dfsg-2_armhf.deb
────────────────────────────────────────
new debian package, version 2.0.
size 5086280 bytes: control archive=1096 bytes.
886 bytes, 13 lines control
1272 bytes, 12 lines md5sums
Package: subread-dbgsym
Source: subread
Version: 1.5.0-p1+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5702
Depends: subread (= 1.5.0-p1+dfsg-2)
Section: debug
Priority: extra
Homepage: http://sourceforge.net/projects/subread/
Description: Debug symbols for subread
Auto-Built-Package: debug-symbols
Build-Ids: 018e6ff6859ce70f9e62744e61fbcd1cb1c288dc 0ec4db8b53e2ecf0d1cae06dd93cd57fbb05438e 608f4995a0070999bf74945deb212de5f799c5be 780b92b1a8e8b0be4748026145e94fb35261e069 80bd4b9a57752efc8b09e50cb2ce2d5eddb9d589 9c9e5d51525941c10872e8b1b7662f35824f2f2b 9e8e72bc37e3a19ee5e174c2ceb7e23da52eae5a a007d02da8d92bd574fa334da72a26eaac3a9744 a7ea49b238d2f533a4dbcffd6cc2e6d75fde1717 a9f371d4bc2245685be783cd5d55ffdc9624ecfb d942587f03261e79d3c96fea92e02dd602d22d73 e88bca62fc5be2c6da75a6fed5059376a0cf463e
drwxr-xr-x root/root 0 2016-01-27 22:51 ./
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/lib/
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/lib/debug/.build-id/01/
-rw-r--r-- root/root 498780 2016-01-27 22:50 ./usr/lib/debug/.build-id/01/8e6ff6859ce70f9e62744e61fbcd1cb1c288dc.debug
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/lib/debug/.build-id/0e/
-rw-r--r-- root/root 474532 2016-01-27 22:50 ./usr/lib/debug/.build-id/0e/c4db8b53e2ecf0d1cae06dd93cd57fbb05438e.debug
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/lib/debug/.build-id/60/
-rw-r--r-- root/root 476296 2016-01-27 22:50 ./usr/lib/debug/.build-id/60/8f4995a0070999bf74945deb212de5f799c5be.debug
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/lib/debug/.build-id/78/
-rw-r--r-- root/root 476240 2016-01-27 22:50 ./usr/lib/debug/.build-id/78/0b92b1a8e8b0be4748026145e94fb35261e069.debug
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/lib/debug/.build-id/80/
-rw-r--r-- root/root 472532 2016-01-27 22:50 ./usr/lib/debug/.build-id/80/bd4b9a57752efc8b09e50cb2ce2d5eddb9d589.debug
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/lib/debug/.build-id/9c/
-rw-r--r-- root/root 473972 2016-01-27 22:50 ./usr/lib/debug/.build-id/9c/9e5d51525941c10872e8b1b7662f35824f2f2b.debug
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/lib/debug/.build-id/9e/
-rw-r--r-- root/root 477456 2016-01-27 22:50 ./usr/lib/debug/.build-id/9e/8e72bc37e3a19ee5e174c2ceb7e23da52eae5a.debug
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/lib/debug/.build-id/a0/
-rw-r--r-- root/root 473952 2016-01-27 22:50 ./usr/lib/debug/.build-id/a0/07d02da8d92bd574fa334da72a26eaac3a9744.debug
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/lib/debug/.build-id/a7/
-rw-r--r-- root/root 543568 2016-01-27 22:50 ./usr/lib/debug/.build-id/a7/ea49b238d2f533a4dbcffd6cc2e6d75fde1717.debug
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/lib/debug/.build-id/a9/
-rw-r--r-- root/root 476644 2016-01-27 22:50 ./usr/lib/debug/.build-id/a9/f371d4bc2245685be783cd5d55ffdc9624ecfb.debug
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/lib/debug/.build-id/d9/
-rw-r--r-- root/root 476676 2016-01-27 22:50 ./usr/lib/debug/.build-id/d9/42587f03261e79d3c96fea92e02dd602d22d73.debug
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/lib/debug/.build-id/e8/
-rw-r--r-- root/root 489676 2016-01-27 22:50 ./usr/lib/debug/.build-id/e8/8bca62fc5be2c6da75a6fed5059376a0cf463e.debug
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/share/
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-01-27 22:50 ./usr/share/doc/subread-dbgsym -> subread
subread_1.5.0-p1+dfsg-2_armhf.deb
─────────────────────────────────
new debian package, version 2.0.
size 423560 bytes: control archive=1395 bytes.
626 bytes, 14 lines control
1819 bytes, 28 lines md5sums
Package: subread
Version: 1.5.0-p1+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5530
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 2016-01-27 22:50 ./
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/bin/
-rwxr-xr-x root/root 485636 2016-01-27 22:50 ./usr/bin/exactSNP
-rwxr-xr-x root/root 543220 2016-01-27 22:50 ./usr/bin/featureCounts
-rwxr-xr-x root/root 456980 2016-01-27 22:50 ./usr/bin/subindel
-rwxr-xr-x root/root 461860 2016-01-27 22:50 ./usr/bin/subjunc
-rwxr-xr-x root/root 461780 2016-01-27 22:50 ./usr/bin/subread-align
-rwxr-xr-x root/root 477420 2016-01-27 22:50 ./usr/bin/subread-buildindex
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/lib/
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/lib/subread/
-rwxr-xr-x root/root 456980 2016-01-27 22:50 ./usr/lib/subread/coverageCount
-rwxr-xr-x root/root 456980 2016-01-27 22:50 ./usr/lib/subread/propmapped
-rwxr-xr-x root/root 457092 2016-01-27 22:50 ./usr/lib/subread/qualityScores
-rwxr-xr-x root/root 452836 2016-01-27 22:50 ./usr/lib/subread/removeDup
-rwxr-xr-x root/root 452836 2016-01-27 22:50 ./usr/lib/subread/repair
-rwxr-xr-x root/root 452836 2016-01-27 22:50 ./usr/lib/subread/subread-fullscan
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/share/
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/share/doc/subread/
-rw-r--r-- root/root 500 2016-01-18 11:06 ./usr/share/doc/subread/README.Debian
-rw-r--r-- root/root 3670 2015-12-18 03:05 ./usr/share/doc/subread/README.txt
-rw-r--r-- root/root 1324 2016-01-18 11:06 ./usr/share/doc/subread/changelog.Debian.gz
-rw-r--r-- root/root 1137 2016-01-18 11:06 ./usr/share/doc/subread/copyright
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/share/man/
drwxr-xr-x root/root 0 2016-01-27 22:50 ./usr/share/man/man1/
-rw-r--r-- root/root 600 2016-01-27 22:50 ./usr/share/man/man1/coverageCount.1.gz
-rw-r--r-- root/root 1177 2016-01-27 22:50 ./usr/share/man/man1/exactSNP.1.gz
-rw-r--r-- root/root 2234 2016-01-27 22:50 ./usr/share/man/man1/featureCounts.1.gz
-rw-r--r-- root/root 463 2016-01-27 22:50 ./usr/share/man/man1/propmapped.1.gz
-rw-r--r-- root/root 569 2016-01-27 22:50 ./usr/share/man/man1/qualityScores.1.gz
-rw-r--r-- root/root 500 2016-01-27 22:50 ./usr/share/man/man1/removeDup.1.gz
-rw-r--r-- root/root 481 2016-01-27 22:50 ./usr/share/man/man1/repair.1.gz
-rw-r--r-- root/root 351 2016-01-27 22:50 ./usr/share/man/man1/subindel.1.gz
-rw-r--r-- root/root 1531 2016-01-27 22:50 ./usr/share/man/man1/subjunc.1.gz
-rw-r--r-- root/root 1621 2016-01-27 22:50 ./usr/share/man/man1/subread-align.1.gz
-rw-r--r-- root/root 766 2016-01-27 22:50 ./usr/share/man/man1/subread-buildindex.1.gz
-rw-r--r-- root/root 380 2016-01-27 22:50 ./usr/share/man/man1/subread-fullscan.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 103992
Build-Time: 1354
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 182
Job: subread_1.5.0-p1+dfsg-2
Machine Architecture: armhf
Package: subread
Package-Time: 1585
Source-Version: 1.5.0-p1+dfsg-2
Space: 103992
Status: successful
Version: 1.5.0-p1+dfsg-2
────────────────────────────────────────────────────────────────────────────────
Finished at 20160127-2251
Build needed 00:26:25, 103992k disc space