subread →
1.6.2+dfsg-1 →
armhf → 2018-05-21 05:41:34
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd
+==============================================================================+
| subread 1.6.2+dfsg-1 (armhf) Mon, 21 May 2018 04:55:35 +0000 |
+==============================================================================+
Package: subread
Version: 1.6.2+dfsg-1
Source Version: 1.6.2+dfsg-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-c2017091-8557-4f0b-9ad1-a3576e854090' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.7 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.5 MB]
Fetched 23.3 MB in 28s (838 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...
NOTICE: 'subread' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/subread.git
Please use:
git clone https://salsa.debian.org/med-team/subread.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 15.8 MB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main subread 1.6.2+dfsg-1 (dsc) [2196 B]
Get:2 http://172.17.0.1/private buster-staging/main subread 1.6.2+dfsg-1 (tar) [15.8 MB]
Get:3 http://172.17.0.1/private buster-staging/main subread 1.6.2+dfsg-1 (diff) [8572 B]
Fetched 15.8 MB in 5s (3401 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/subread-rDzi0K/subread-1.6.2+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/subread-rDzi0K' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-vfHoRk/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-vfHoRk/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-vfHoRk/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-vfHoRk/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-vfHoRk/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-vfHoRk/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-vfHoRk/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-vfHoRk/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (3343 B/s)
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 packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 54 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-vfHoRk/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15721 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.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
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in amd64 arm64 armel armhf i386 kfreebsd-amd64 kfreebsd-i386 ppc64el all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: bc, debhelper (>= 11), help2man, python, zlib1g-dev
Filtered Build-Depends: bc, debhelper (>= 11), help2man, python, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-subread-dummy' in '/<<BUILDDIR>>/resolver-vfHoRk/apt_archive/sbuild-build-depends-subread-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-subread-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-vfHoRk/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-vfHoRk/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-vfHoRk/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-vfHoRk/apt_archive ./ Sources [509 B]
Get:5 copy:/<<BUILDDIR>>/resolver-vfHoRk/apt_archive ./ Packages [589 B]
Fetched 2431 B in 1s (3727 B/s)
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 packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libnss-systemd
libpam-systemd libsasl2-modules openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bc bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3
libfile-stripnondeterminism-perl libglib2.0-0 libicu57
liblocale-gettext-perl libmagic-mgc libmagic1 libncursesw6 libpipeline1
libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2
libtimedate-perl libtinfo6 libtool libxml2 m4 man-db mime-support po-debconf
python python-minimal python2.7 python2.7-minimal zlib1g zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libgpm2 libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bc bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3
libfile-stripnondeterminism-perl libglib2.0-0 libicu57
liblocale-gettext-perl libmagic-mgc libmagic1 libncursesw6 libpipeline1
libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2
libtimedate-perl libtinfo6 libtool libxml2 m4 man-db mime-support po-debconf
python python-minimal python2.7 python2.7-minimal
sbuild-build-depends-subread-dummy zlib1g-dev
The following packages will be upgraded:
zlib1g
1 upgraded, 44 newly installed, 0 to remove and 53 not upgraded.
Need to get 15.5 MB/23.8 MB of archives.
After this operation, 81.8 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-vfHoRk/apt_archive ./ sbuild-build-depends-subread-dummy 0.invalid.0 [876 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf liblocale-gettext-perl armhf 1.07-3+b2 [18.3 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf zlib1g armhf 1:1.2.11.dfsg-1 [87.3 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.3-2 [1146 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.15-1 [393 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.15-1 [1077 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.15~rc1-1 [41.1 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libtinfo6 armhf 6.1+20180210-3 [307 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libncursesw6 armhf 6.1+20180210-3 [103 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.15-1 [1841 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.15-1 [298 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.15~rc1-1 [20.5 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.15~rc1-1 [155 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf bc armhf 1.07.1-2 [101 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.33-2 [234 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.33-2 [106 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.33-2 [64.7 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3.1 [736 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 17 [16.5 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.041-1 [19.9 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.041-1 [12.0 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.1-2 [2754 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.2.1 [1013 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf help2man armhf 1.47.6 [169 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package liblocale-gettext-perl.
(Reading database ... 15721 files and directories currently installed.)
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Unpacking libbsd0:armhf (0.8.7-1) ...
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Unpacking groff-base (1.22.3-10) ...
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Unpacking zlib1g:armhf (1:1.2.11.dfsg-1) over (1:1.2.8.dfsg-5) ...
Setting up zlib1g:armhf (1:1.2.11.dfsg-1) ...
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Setting up libpython2.7-minimal:armhf (2.7.15-1) ...
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Setting up mime-support (3.60) ...
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Setting up libglib2.0-0:armhf (2.56.1-2) ...
No schema files found: removed existing output file.
Setting up libtinfo6:armhf (6.1+20180210-3) ...
Setting up gettext-base (0.19.8.1-6) ...
Setting up libpipeline1:armhf (1.5.0-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-9) ...
Setting up libbsd0:armhf (0.8.7-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-6.1) ...
Setting up libmagic-mgc (1:5.33-2) ...
Setting up libmagic1:armhf (1:5.33-2) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Processing triggers for libc-bin (2.27-3+rpi1) ...
Setting up autotools-dev (20180224.1) ...
Setting up liblocale-gettext-perl (1.07-3+b2) ...
Setting up bsdmainutils (11.1.2) ...
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 bc (1.07.1-2) ...
Setting up autopoint (0.19.8.1-6) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (0.041-1) ...
Setting up gettext (0.19.8.1-6) ...
Setting up libncursesw6:armhf (6.1+20180210-3) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.33-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up automake (1:1.15.1-3.1) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up help2man (1.47.6) ...
Setting up man-db (2.8.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libpython2.7-stdlib:armhf (2.7.15-1) ...
Setting up libtool (2.4.6-2.1) ...
Setting up po-debconf (1.0.20) ...
Setting up python2.7 (2.7.15-1) ...
Setting up libpython-stdlib:armhf (2.7.15~rc1-1) ...
Setting up python (2.7.15~rc1-1) ...
Setting up dh-strip-nondeterminism (0.041-1) ...
Setting up debhelper (11.2.1) ...
Setting up dh-autoreconf (17) ...
Setting up sbuild-build-depends-subread-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-3+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.30-15+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-12 gcc-7_7.3.0-12 libc6-dev_2.27-3+rpi1 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180414-1+rpi1 linux-libc-dev_4.15.17-1+rpi1
Package versions: adduser_3.117 apt_1.6.1 autoconf_2.69-11 automake_1:1.15.1-3.1 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-2+b1 bc_1.07.1-2 binutils_2.30-15+rpi1 binutils-arm-linux-gnueabihf_2.30-15+rpi1 binutils-common_2.30-15+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.31.1-0.5 build-essential_12.4+b1 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.3.0-12 dash_0.5.8-2.10 dbus_1.12.6-2 dbus-user-session_1.12.6-2 debconf_1.5.66 debhelper_11.2.1 debianutils_4.8.4 dh-autoreconf_17 dh-strip-nondeterminism_0.041-1 diffutils_1:3.6-1 dirmngr_2.2.5-1 dmsetup_2:1.02.145-4.1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 e2fslibs_1.44.1-2 e2fsprogs_1.44.1-2 e2fsprogs-l10n_1.44.1-2 fakeroot_1.22-2 fdisk_2.31.1-0.5 file_1:5.33-2 findutils_4.6.0+git+20171230-2 g++_4:7.2.0-1d1 g++-7_7.3.0-12 gcc_4:7.2.0-1d1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1 gcc-5-base_5.5.0-8 gcc-7_7.3.0-12 gcc-7-base_7.3.0-12 gcc-8-base_8-20180414-1+rpi1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gnupg_2.2.5-1 gnupg-agent_2.2.5-1 gnupg-l10n_2.2.5-1 gnupg-utils_2.2.5-1 gpg_2.2.5-1 gpg-agent_2.2.5-1 gpg-wks-client_2.2.5-1 gpg-wks-server_2.2.5-1 gpgconf_2.2.5-1 gpgsm_2.2.5-1 gpgv_2.2.5-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 help2man_1.47.6 hostname_3.20 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.12-4 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-2 libasan4_7.3.0-12 libassuan0_2.5.1-2 libatomic1_8-20180414-1+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.2-1 libaudit1_1:2.8.2-1 libbinutils_2.30-15+rpi1 libblkid1_2.31.1-0.5 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3+rpi1 libc-dev-bin_2.27-3+rpi1 libc6_2.27-3+rpi1 libc6-dev_2.27-3+rpi1 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.2 libcc1-0_8-20180414-1+rpi1 libcilkrts5_7.3.0-12 libcom-err2_1.44.1-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.6-2 libdebconfclient0_0.243 libdevmapper1.02.1_2:1.02.145-4.1 libdpkg-perl_1.19.0.5 libdrm-common_2.4.91-2+rpi1 libdrm2_2.4.91-2+rpi1 libexpat1_2.2.5-3 libext2fs2_1.44.1-2 libfakeroot_1.22-2 libfdisk1_2.31.1-0.5 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.041-1 libgcc-7-dev_7.3.0-12 libgcc1_1:8-20180414-1+rpi1 libgcrypt20_1.8.2-2 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libglib2.0-0_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8-20180414-1+rpi1 libgpg-error0_1.29-4 libhogweed4_3.4-1 libicu57_57.1-9 libidn11_1.33-2.2 libidn2-0_2.0.4-1.1 libip4tc0_1.6.2-1 libisl15_0.18-4 libjson-c3_0.12.1-1.3 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblocale-gettext-perl_1.07-3+b2 liblz4-1_1.8.1.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.33-2 libmagic1_1:5.33-2 libmount1_2.31.1-0.5 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1-1 libncursesw5_6.1-1 libncursesw6_6.1+20180210-3 libnettle6_3.4-1 libnpth0_1.5-3 libnss-systemd_238-4 libp11-kit0_0.23.10-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_238-4 libpam0g_1.1.8-3.7 libpcre3_2:8.39-9 libperl5.24_5.24.1-7 libperl5.26_5.26.2-2 libpipeline1_1.5.0-1 libplymouth4_0.9.3-2 libpng16-16_1.6.34-1 libprocps6_2:3.3.14-1 libpython-stdlib_2.7.15~rc1-1 libpython2.7-minimal_2.7.15-1 libpython2.7-stdlib_2.7.15-1 libreadline7_7.0-3 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.12-2 libsmartcols1_2.31.1-0.5 libsqlite3-0_3.23.1-1 libss2_1.44.1-2 libssl1.1_1.1.0h-2 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180414-1+rpi1 libsystemd0_238-4 libtasn1-6_4.13-2 libtext-charwidth-perl_0.04-7.1 libtext-iconv-perl_1.7-5+b9 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.1-1 libtinfo6_6.1+20180210-3 libtool_2.4.6-2.1 libubsan0_7.3.0-12 libudev1_238-4 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.31.1-0.5 libxml2_2.9.4+dfsg1-6.1 libzstd1_1.3.3+dfsg-2+rpi1 linux-base_4.5 linux-libc-dev_4.15.17-1+rpi1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.3-2 mawk_1.3.3-17 mime-support_3.60 mount_2.31.1-0.5 multiarch-support_2.27-3+rpi1 nano_2.9.5-1 ncurses-base_6.1-1 ncurses-bin_6.1-1 netbase_5.4 openssl_1.1.0h-2 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-2 perl-base_5.26.2-2 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-3 pinentry-curses_1.1.0-1 plymouth_0.9.3-2 po-debconf_1.0.20 procps_2:3.3.14-1 python_2.7.15~rc1-1 python-minimal_2.7.15~rc1-1 python2.7_2.7.15-1 python2.7-minimal_2.7.15-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-subread-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_238-4 systemd-sysv_238-4 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2018d-1 udev_238-4 util-linux_2.31.1-0.5 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Fri May 18 18:10:08 2018 UTC
gpgv: using RSA key 1CF792111B5228B0
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./subread_1.6.2+dfsg-1.dsc
dpkg-source: info: extracting subread in /<<BUILDDIR>>/subread-1.6.2+dfsg
dpkg-source: info: unpacking subread_1.6.2+dfsg.orig.tar.xz
dpkg-source: info: unpacking subread_1.6.2+dfsg-1.debian.tar.xz
dpkg-source: info: applying typo.patch
dpkg-source: info: applying fix_ftbfs_kfreebsd.patch
dpkg-source: info: applying arch_specific_flags.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-c2017091-8557-4f0b-9ad1-a3576e854090
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package subread
dpkg-buildpackage: info: source version 1.6.2+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build subread-1.6.2+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
debian/rules override_dh_clean
make[1]: Entering directory '/<<BUILDDIR>>/subread-1.6.2+dfsg'
cd src; make -f Makefile.Linux clean
make[2]: Entering directory '/<<BUILDDIR>>/subread-1.6.2+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-1.6.2+dfsg/src'
dh_clean
make[1]: Leaving directory '/<<BUILDDIR>>/subread-1.6.2+dfsg'
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/subread-1.6.2+dfsg'
cd src; make -f Makefile.Linux
make[2]: Entering directory '/<<BUILDDIR>>/subread-1.6.2+dfsg/src'
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core.o core.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-junction.o core-junction.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-indel.o core-indel.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sambam-file.o sambam-file.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sublog.o sublog.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-algorithms.o gene-algorithms.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -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:51:10: warning: implicit declaration of function 'fopen64'; did you mean 'gzopen64'? [-Wimplicit-function-declaration]
return fopen64(fname, mode);
^~~~~~~
gzopen64
input-files.c:51:10: warning: return makes pointer from integer without a cast [-Wint-conversion]
return fopen64(fname, mode);
^~~~~~~~~~~~~~~~~~~~
input-files.c: In function 'SAM_nosort_run_once':
input-files.c:5169:10: warning: argument 1 value '4294967295' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
char * header_txt = malloc(max(1000000,pairer->BAM_l_text));
^~~~~~~~~~
In file included from input-files.c:24:0:
/usr/include/stdlib.h:539:14: note: in a call to allocation function 'malloc' declared here
extern void *malloc (size_t __size) __THROW __attribute_malloc__ __wur;
^~~~~~
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sorted-hashtable.o sorted-hashtable.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-value-index.o gene-value-index.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o exon-algorithms.o exon-algorithms.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -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 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o detectionCall detection-calls.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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
In file included from detection-calls.c:8:0:
detection-calls.c: In function 'DTCprint_lentab_items':
detection-calls.c:160:16: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=]
SUBREADprintf("%s => %ld\n", (char*)key, hashed_obj - NULL);
^
subread.h:125:44: note: in definition of macro 'SUBREADprintf'
#define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__)
^~~~~~~~~~~
echo " " > longread-one/make.version
rm -f longread-one/*.o
cd longread-one && make
make[3]: Entering directory '/<<BUILDDIR>>/subread-1.6.2+dfsg/src/longread-one'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.2"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMsorted-hashtable.o LRMsorted-hashtable.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.2"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMbase-index.o LRMbase-index.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.2"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMchro-event.o LRMchro-event.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.2"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMhelper.o LRMhelper.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.2"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMseek-zlib.o LRMseek-zlib.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.2"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMfile-io.o LRMfile-io.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.2"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMhashtable.o LRMhashtable.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.2"\" -fmessage-length=0 -ggdb -o LRM longread-mapping.c LRMsorted-hashtable.o LRMbase-index.o LRMchro-event.o LRMhelper.o LRMseek-zlib.o LRMfile-io.o LRMhashtable.o -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
make[3]: Leaving directory '/<<BUILDDIR>>/subread-1.6.2+dfsg/src/longread-one'
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o txUnique tx-unique.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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
SUBindel.c: In function 'load_global_context_forindel':
SUBindel.c:66:24: warning: '.reads' directive writing 6 bytes into a region of size between 1 and 300 [-Wformat-overflow=]
sprintf(tmp_fname, "%s.reads", context->config.index_prefix);
^~~~~~
In file included from /usr/include/stdio.h:862:0,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 7 and 306 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SUBindel.c:75:25: warning: '.00.c.tab' directive writing 9 bytes into a region of size between 1 and 300 [-Wformat-overflow=]
sprintf(tmp_fname, "%s.00.c.tab", context->config.index_prefix);
^~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 10 and 309 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SUBindel.c:77:25: warning: '.00.b.tab' directive writing 9 bytes into a region of size between 1 and 300 [-Wformat-overflow=]
sprintf(tmp_fname, "%s.00.b.tab", context->config.index_prefix);
^~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 10 and 309 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SUBindel.c:87:26: warning: '%02d' directive writing between 2 and 11 bytes into a region of size between 0 and 299 [-Wformat-overflow=]
sprintf(tmp_fname, "%s.%02d.%c.tab", context->config.index_prefix, context->index_block_number, context->config.space_type == GENE_SPACE_COLOR?'c':'b');
^~~~
In file included from /usr/include/stdio.h:862:0,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 10 and 318 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SUBindel.c: In function 'load_indexes_forindel':
SUBindel.c:110:26: warning: '%02d' directive writing between 2 and 10 bytes into a region of size between 0 and 299 [-Wformat-overflow=]
sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b');
^~~~
SUBindel.c:110:22: note: directive argument in the range [0, 2147483647]
sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b');
^~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 12 and 319 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.2"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o flattenGTF flattenAnnotations.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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
mkdir -p ../bin/utilities
mv longread-one/LRM longread-one/sublong
mv longread-one/sublong subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/
mv detectionCall repair coverageCount propmapped qualityScores removeDup subread-fullscan txUnique flattenGTF ../bin/utilities
###########################################################
# #
# Installation successfully completed. #
# #
# Generated executables were copied to directory ../bin/ #
# #
###########################################################
make[2]: Leaving directory '/<<BUILDDIR>>/subread-1.6.2+dfsg/src'
dh_auto_build -- CC=arm-linux-gnueabihf-gcc
make[1]: Leaving directory '/<<BUILDDIR>>/subread-1.6.2+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/subread-1.6.2+dfsg'
debian/tests/subread-tests /<<BUILDDIR>>/subread-1.6.2+dfsg
[2J[0;0H[30;47m
**************************************************
**************************************************
*** ***
*** This script will test the major functions ***
*** in our package, including the index build- ***
*** er, subread-align, subjunc, featureCounts ***
*** and exactSNP. ***
*** ***
*** Test will start in seconds. ***
*** ***
**************************************************
**************************************************
[13;26H[33;44m9[13;26H8[13;26H7[13;26H6[13;26H5[13;26H4[13;26H3[13;26H2[13;26H1[13;26H0[0m[2J[0,0H
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.2
//=========================== indexBuilder setting ===========================\\
|| ||
|| Index name : small1 ||
|| Index space : base-space ||
|| One block index : yes ||
|| 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, '../small1.log'. ||
|| Scan uninformative subreads in reference sequences ... ||
|| 8%, 0 mins elapsed, rate=107.4k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=135.5k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=163.5k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=185.0k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=204.1k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=222.9k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=237.9k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=255.1k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=269.7k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=256.8k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=271.6k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=280.8k bps/s, total=0m ||
|| 52 uninformative subreads were found. ||
|| These subreads were excluded from index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=70.7k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=86.6k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=103.2k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=114.6k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=130.3k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=146.0k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=161.5k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=176.4k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=190.6k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=203.9k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=217.0k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=229.2k 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: 0.2 minutes. ||
|| Index ../small1 was successfully built! ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.2
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file : test-noerror-r1.fq ||
|| Output file : test-tmp.sam (SAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 64 ||
|| Min votes : 3 / 10 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================ Running (21-May-2018 05:11:33, pid=15422) =================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [9,9] ||
|| Load the 1-th index block... ||
|| 33% completed, 0.3 mins elapsed, rate=2.2k reads per second ||
|| 39% completed, 0.3 mins elapsed, rate=2.3k reads per second ||
|| 46% completed, 0.3 mins elapsed, rate=2.5k reads per second ||
|| 53% completed, 0.3 mins elapsed, rate=2.7k reads per second ||
|| 60% completed, 0.3 mins elapsed, rate=2.8k reads per second ||
|| 74% completed, 0.4 mins elapsed, rate=0.7k reads per second ||
|| 83% completed, 0.4 mins elapsed, rate=0.8k reads per second ||
|| 91% completed, 0.4 mins elapsed, rate=0.8k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 reads ||
|| Mapped : 18759 reads (93.8%), wherein ||
|| Uniquely mapped : 18759 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 1239 ||
|| ||
|| Indels : 3 ||
|| ||
|| Running time : 2.6 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.2
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file : test-noerror-r1.fq ||
|| Output file : test-tmp.sam (SAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 64 ||
|| Min votes : 3 / 10 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================ Running (21-May-2018 05:14:18, pid=15455) =================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [9,9] ||
|| Load the 1-th index block... ||
|| 33% completed, 0.3 mins elapsed, rate=2.1k reads per second ||
|| 39% completed, 0.3 mins elapsed, rate=2.4k reads per second ||
|| 46% completed, 0.3 mins elapsed, rate=2.6k reads per second ||
|| 53% completed, 0.3 mins elapsed, rate=2.9k reads per second ||
|| 60% completed, 0.3 mins elapsed, rate=3.1k reads per second ||
|| 74% completed, 0.3 mins elapsed, rate=0.7k reads per second ||
|| 83% completed, 0.3 mins elapsed, rate=0.8k reads per second ||
|| 91% completed, 0.4 mins elapsed, rate=0.9k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 reads ||
|| Mapped : 18759 reads (93.8%), wherein ||
|| Uniquely mapped : 18759 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 1239 ||
|| ||
|| Indels : 3 ||
|| ||
|| Running time : 3.0 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.2
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : test-noerror-r1.fq ||
|| Input file 2 : test-noerror-r2.fq ||
|| Output file : test-tmp.sam (SAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 64 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================ Running (21-May-2018 05:17:26, pid=15819) =================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [9,9] ||
|| Load the 1-th index block... ||
|| 33% completed, 0.3 mins elapsed, rate=1.8k fragments per second ||
|| 39% completed, 0.3 mins elapsed, rate=2.0k fragments per second ||
|| 46% completed, 0.3 mins elapsed, rate=2.1k 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 ||
|| 74% completed, 0.4 mins elapsed, rate=0.7k fragments per second ||
|| 83% completed, 0.4 mins elapsed, rate=0.7k 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%), wherein ||
|| Uniquely mapped : 19216 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 782 ||
|| ||
|| Correctly paired : 18831 fragments ||
|| Not mapped in pairs : 385 fragments, wherein ||
|| Only one end mapped : 0 fragments ||
|| Multi-chromosomes : 0 fragments ||
|| Different strands : 0 fragments ||
|| Not in PE distance : 385 fragments ||
|| Abnormal order : 0 fragments ||
|| ||
|| Indels : 14 ||
|| ||
|| Running time : 3.0 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.2
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : test-noerror-r1.fq ||
|| Input file 2 : test-noerror-r2.fq ||
|| Output file : test-tmp.sam (SAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 64 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================ Running (21-May-2018 05:20:35, pid=16231) =================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [9,9] ||
|| Load the 1-th index block... ||
|| 33% completed, 0.4 mins elapsed, rate=2.2k fragments per second ||
|| 39% completed, 0.4 mins elapsed, rate=2.4k fragments per second ||
|| 46% completed, 0.4 mins elapsed, rate=2.5k fragments per second ||
|| 53% completed, 0.4 mins elapsed, rate=2.6k fragments per second ||
|| 60% completed, 0.4 mins elapsed, rate=2.7k fragments per second ||
|| 74% completed, 0.4 mins elapsed, rate=0.6k fragments per second ||
|| 83% completed, 0.4 mins elapsed, rate=0.7k fragments per second ||
|| 91% completed, 0.4 mins elapsed, rate=0.7k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 fragments ||
|| Mapped : 19216 fragments (96.1%), wherein ||
|| Uniquely mapped : 19216 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 782 ||
|| ||
|| Correctly paired : 18831 fragments ||
|| Not mapped in pairs : 385 fragments, wherein ||
|| Only one end mapped : 0 fragments ||
|| Multi-chromosomes : 0 fragments ||
|| Different strands : 0 fragments ||
|| Not in PE distance : 385 fragments ||
|| Abnormal order : 0 fragments ||
|| ||
|| Indels : 14 ||
|| ||
|| Running time : 2.9 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.2
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : test-error-r1.fq ||
|| Input file 2 : test-error-r2.fq ||
|| Output file : test-tmp.sam (SAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 64 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================ Running (21-May-2018 05:23:39, pid=16263) =================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [-14,-14] ||
|| Load the 1-th index block... ||
|| 33% completed, 0.4 mins elapsed, rate=1.7k fragments per second ||
|| 39% completed, 0.4 mins elapsed, rate=1.8k fragments per second ||
|| 46% completed, 0.4 mins elapsed, rate=2.0k fragments per second ||
|| 53% completed, 0.4 mins elapsed, rate=2.1k fragments per second ||
|| 60% completed, 0.4 mins elapsed, rate=2.2k fragments per second ||
|| 74% completed, 0.5 mins elapsed, rate=0.6k fragments per second ||
|| 83% completed, 0.5 mins elapsed, rate=0.6k fragments per second ||
|| 91% completed, 0.5 mins elapsed, rate=0.6k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 20000 fragments ||
|| Mapped : 18697 fragments (93.5%), wherein ||
|| Uniquely mapped : 18697 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 1303 ||
|| ||
|| Correctly paired : 13917 fragments ||
|| Not mapped in pairs : 4780 fragments, wherein ||
|| Only one end mapped : 4503 fragments ||
|| Multi-chromosomes : 0 fragments ||
|| Different strands : 0 fragments ||
|| Not in PE distance : 273 fragments ||
|| Abnormal order : 4 fragments ||
|| ||
|| Indels : 32 ||
|| ||
|| Running time : 3.1 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.2
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : test-err-mut-r1.fq.gz ||
|| Input file 2 : test-err-mut-r2.fq.gz ||
|| Output file : test-tmp.sam (SAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 64 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| Read group name : MyTestGroup ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================ Running (21-May-2018 05:26:51, pid=16625) =================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [-14,-14] ||
|| Load the 1-th index block... ||
|| 34% completed, 0.3 mins elapsed, rate=1.6k fragments per second ||
|| 40% completed, 0.3 mins elapsed, rate=1.8k fragments per second ||
|| 48% completed, 0.4 mins elapsed, rate=1.9k fragments per second ||
|| 53% completed, 0.4 mins elapsed, rate=2.0k fragments per second ||
|| 59% completed, 0.4 mins elapsed, rate=2.1k fragments per second ||
|| 67% completed, 0.4 mins elapsed, rate=2.2k fragments per second ||
|| 75% completed, 0.4 mins elapsed, rate=0.6k fragments per second ||
|| 83% completed, 0.4 mins elapsed, rate=0.7k fragments per second ||
|| 92% completed, 0.4 mins elapsed, rate=0.7k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 20001 fragments ||
|| Mapped : 18659 fragments (93.3%), wherein ||
|| Uniquely mapped : 18659 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 1342 ||
|| ||
|| Correctly paired : 13558 fragments ||
|| Not mapped in pairs : 5101 fragments, wherein ||
|| Only one end mapped : 4786 fragments ||
|| Multi-chromosomes : 0 fragments ||
|| Different strands : 0 fragments ||
|| Not in PE distance : 310 fragments ||
|| Abnormal order : 5 fragments ||
|| ||
|| Indels : 164 ||
|| ||
|| Running time : 2.9 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
ac8ddfc3a7a5c396a2f6200361a10cf2 ../small1.00.b.array
3b39eb4b0aad6902d8a1be198cf2478d ../small1.00.b.tab
*************************************************
*** SINGLE-END READS NO ERROR ******
*************************************************
unmatched= 0 ; matched= 18759 ; unmapped= 1239 ; reads= 19998 ;NN= 0
accuracy= 1.0 ; sensitivity= 0.93804380438
paired_match= 0 ; paired= 0.0
*************************************************
*** SINGLE-END READS NO ERROR NO DUP ******
*************************************************
unmatched= 0 ; matched= 18759 ; unmapped= 1239 ; reads= 19998 ;NN= 0
accuracy= 1.0 ; sensitivity= 0.93804380438
paired_match= 0 ; paired= 0.0
*************************************************
*** READS WITH NO ERROR ******
*************************************************
unmatched= 0 ; matched= 38432 ; unmapped= 1564 ; reads= 39996 ;NN= 0
accuracy= 1.0 ; sensitivity= 0.960896089609
paired_match= 38432 ; paired= 1.0
*************************************************
*** READS NO ERROR, NO DUPLICATED REPORT ******
*************************************************
unmatched= 0 ; matched= 38432 ; unmapped= 1564 ; reads= 39996 ;NN= 0
accuracy= 1.0 ; sensitivity= 0.960896089609
paired_match= 38432 ; paired= 1.0
*************************************************
*** READS WITH ONLY SEQUENCING ERROR ******
*************************************************
unmatched= 10 ; matched= 32881 ; unmapped= 7109 ; reads= 40000 ;NN= 0
accuracy= 0.999695965462 ; sensitivity= 0.822275
paired_match= 28378 ; paired= 0.863051610352
*************************************************
*** READS WITH SEQUENCING ERROR AND MUTATION ***
*** SUBREAD IS RUN WITH LONG INDEL DETECTION ***
*************************************************
unmatched= 13 ; matched= 32517 ; unmapped= 7470 ; reads= 40002 ;NN= 0
accuracy= 0.99960036889 ; sensitivity= 0.813209339533
paired_match= 27734 ; paired= 0.852907709813
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.2
//=========================== indexBuilder setting ===========================\\
|| ||
|| Index name : 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, '../small1.log'. ||
|| Scan uninformative subreads in reference sequences ... ||
|| 8%, 0 mins elapsed, rate=249.5k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=288.3k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=325.9k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=352.7k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=379.4k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=402.8k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=421.1k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=442.0k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=460.0k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=476.9k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=495.4k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=507.3k bps/s, total=0m ||
|| 2 uninformative subreads were found. ||
|| These subreads were excluded from index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=176.5k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=185.1k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=198.7k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=211.7k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=224.9k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=238.7k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=252.9k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=267.6k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=282.7k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=297.3k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=313.4k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=327.8k 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 ../small1 was successfully built! ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.2
//============================= subjunc setting ==============================\\
|| ||
|| Function : Read alignment + Junction detection (RNA-Seq) ||
|| Input file 1 : junction-reads-A.fq ||
|| Input file 2 : junction-reads-B.fq ||
|| Output file : junctions.sam (SAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 14 ||
|| Min read1 vote : 1 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================ Running (21-May-2018 05:30:01, pid=16659) =================\\
|| ||
|| 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... ||
|| 41% completed, 0.6 mins elapsed, rate=1.4k fragments per second ||
|| 48% completed, 0.6 mins elapsed, rate=1.5k fragments per second ||
|| 54% completed, 0.6 mins elapsed, rate=1.5k fragments per second ||
|| 61% completed, 0.6 mins elapsed, rate=1.6k fragments per second ||
|| 77% completed, 0.6 mins elapsed, rate=0.3k fragments per second ||
|| 87% completed, 0.6 mins elapsed, rate=0.4k fragments per second ||
|| 97% completed, 0.6 mins elapsed, rate=0.4k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 16052 fragments ||
|| Mapped : 15251 fragments (95.0%), wherein ||
|| Uniquely mapped : 15251 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 801 ||
|| ||
|| Correctly paired : 13854 fragments ||
|| Not mapped in pairs : 1397 fragments, wherein ||
|| Only one end mapped : 966 fragments ||
|| Multi-chromosomes : 0 fragments ||
|| Different strands : 37 fragments ||
|| Not in PE distance : 332 fragments ||
|| Abnormal order : 62 fragments ||
|| ||
|| Junctions : 416 ||
|| Indels : 183 ||
|| ||
|| Running time : 4.6 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.2
//============================= subjunc setting ==============================\\
|| ||
|| Function : Read alignment + Junction/Fusion detection (RNA-Seq) ||
|| Input file 1 : junction-reads-A.fq ||
|| Input file 2 : junction-reads-B.fq ||
|| Output file : junctionsNfusions.bam (BAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 28 ||
|| Min read1 vote : 1 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================ Running (21-May-2018 05:34:40, pid=17039) =================\\
|| ||
|| 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... ||
|| 41% completed, 0.7 mins elapsed, rate=0.8k fragments per second ||
|| 48% completed, 0.7 mins elapsed, rate=0.8k fragments per second ||
|| 54% completed, 0.7 mins elapsed, rate=0.9k fragments per second ||
|| 61% completed, 0.7 mins elapsed, rate=0.9k fragments per second ||
|| 77% completed, 0.8 mins elapsed, rate=0.3k fragments per second ||
|| 87% completed, 0.8 mins elapsed, rate=0.3k fragments per second ||
|| 97% completed, 0.8 mins elapsed, rate=0.3k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 16052 fragments ||
|| Mapped : 15234 fragments (94.9%), wherein ||
|| Uniquely mapped : 15234 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 818 ||
|| ||
|| Correctly paired : 13757 fragments ||
|| Not mapped in pairs : 1477 fragments, wherein ||
|| Only one end mapped : 1013 fragments ||
|| Multi-chromosomes : 0 fragments ||
|| Different strands : 35 fragments ||
|| Not in PE distance : 366 fragments ||
|| Abnormal order : 63 fragments ||
|| ||
|| Junctions : 434 ||
|| Fusions : 92 ||
|| Indels : 182 ||
|| ||
|| Running time : 4.8 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
================================================================================
FeatureCounts Basic Test
http://subread.sourceforge.net/
================================================================================
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.2
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 SAM file ||
|| P test-minimum.sam ||
|| ||
|| Output file : test-minimum.FC ||
|| Summary : test-minimum.FC.summary ||
|| Annotation : test-minimum.GTF (GTF) ||
|| Dir for temp files : result ||
|| ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| Multimapping reads : not counted ||
|| Multi-overlapping reads : not counted ||
|| Min overlapping bases : 1 ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================================= Running ==================================\\
|| ||
|| Load annotation file test-minimum.GTF ... ||
|| Features : 23 ||
|| Meta-features : 7 ||
|| Chromosomes/contigs : 3 ||
|| ||
|| Process SAM file 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. ||
|| ||
|| Summary of counting results can be found in file "result/test-minimum.FC. ||
|| summary" ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
================================================================================
Basic Test finished.
The results are in result/test-minimum.FC
================================================================================
================================================================================
FeatureCounts Chromosome Name Aliases Tests
http://subread.sourceforge.net/
================================================================================
Testing chromosome aliases ... [[32mPASS[0m]
================================================================================
FeatureCounts Chromosome Name Inference Tests
http://subread.sourceforge.net/
================================================================================
Testing automatic inference of chromosome names ... [[32mPASS[0m]
================================================================================
FeatureCounts Corner Case Tests
http://subread.sourceforge.net/
================================================================================
Testing indel reads ... [[32mPASS[0m]
Testing junction reads ... [[32mPASS[0m]
Testing paired-end reads (fragment counting) ... [[32mPASS[0m]
Testing paired-end reads (fragment counting, both ends mapped) ... [[32mPASS[0m]
Testing multi-overlapping reads ... [[32mPASS[0m]
Testing feature-level summarization ... [[32mPASS[0m]
Testing gene-level summarization ... [[32mPASS[0m]
Testing multi-mapping reads ... [[32mPASS[0m]
Testing multi-mapping reads (primary only) ... [[32mPASS[0m]
Testing both ends mapped ... [[32mPASS[0m]
Testing disallowing chimeric fragments ... [[32mPASS[0m]
Testing Allowing multi-mapped reads ... [[32mPASS[0m]
Testing not sorting input file ... [[32mPASS[0m]
Testing minimum overlapping length ... [[32mPASS[0m]
Testing minimum overlapping fraction ... [[32mPASS[0m]
Testing Largest Overlapping ... [[32mPASS[0m]
Testing paired-end distance ... [[32mPASS[0m]
Testing Read to position (5' end) ... [[32mPASS[0m]
Testing Read to position (3' end) ... [[32mPASS[0m]
Testing Read extension to the 3' end ... [[32mPASS[0m]
Testing Read extension to the 5' end ... [[32mPASS[0m]
Testing Low maxOPs value ... [[32mPASS[0m]
Testing minimum mapping quality ... [[32mPASS[0m]
Testing Ignoring duplicated reads ... [[32mPASS[0m]
Testing Fraction counting ... [[32mPASS[0m]
Testing Advanced fractions ... [[32mPASS[0m]
Testing Junction counting ... [[32mPASS[0m,[32mPASS[0m]
Skipping Junction counting (with genome).
Testing GTF format annotations ... [[32mPASS[0m]
Testing SAF format annotations ... [[32mPASS[0m]
Testing SAM format input ... [[32mPASS[0m]
Testing BAM format input ... [[32mPASS[0m]
Testing unstranded read summarization ... [[32mPASS[0m]
Testing stranded read summarization ... [[32mPASS[0m]
Testing reversely stranded read summarization ... [[32mPASS[0m]
Testing Ignoring duplicate fragments ... [[32mPASS[0m]
Testing Junction reads only ... [[32mPASS[0m]
Testing Exonic reads only ... [[32mPASS[0m]
Testing intron_between ... [[32mPASS[0m]
Testing intron_between ... [[32mPASS[0m]
Testing intron_between ... [[32mPASS[0m]
Testing intron_between ... [[32mPASS[0m]
Testing across_genes ... [[32mPASS[0m]
Testing across_genes ... [[32mPASS[0m]
Testing across_genes ... [[32mPASS[0m]
Testing across_genes ... [[32mPASS[0m]
Testing across_intron ... [[32mPASS[0m]
Testing across_intron ... [[32mPASS[0m]
Testing across_intron ... [[32mPASS[0m]
Testing across_intron ... [[32mPASS[0m]
../../bin/exactSNP -g ../chr901.fa -o result/test-out.VCF -i data/test-in.BAM -b
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.2
//============================= exactSNP setting =============================\\
|| ||
|| Input file : 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 (21-May-2018 05:39:34) ======================\\
|| ||
|| Split BAM file into result/temp-snps-018224-001F7BB4154E-* ... ||
|| 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/ ======================//
[30;47m
**************************************************
**************************************************
*** ***
*** Test finished. ***
*** ***
*** Should there be any error, please visit ***
*** [34mhttp://subread.sourceforge.net/[0;30;47m for more ***
*** information. ***
*** ***
**************************************************
**************************************************
[0m
make[1]: Leaving directory '/<<BUILDDIR>>/subread-1.6.2+dfsg'
create-stamp debian/debhelper-build-stamp
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-1.6.2+dfsg'
find /<<BUILDDIR>>/subread-1.6.2+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \;
mkdir -p /<<BUILDDIR>>/subread-1.6.2+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-1.6.2+dfsg/bin/subread-align | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.2+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-1.6.2+dfsg/bin/subread-buildindex | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.2+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-1.6.2+dfsg/bin/subjunc | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.2+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-1.6.2+dfsg/bin/featureCounts | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.2+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-1.6.2+dfsg/bin/exactSNP | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.2+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-1.6.2+dfsg/bin/subindel | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.2+dfsg/debian/subread/usr/share/man/man1/subindel.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='long-read aligner that is designed based on seed-and-vote' \
/<<BUILDDIR>>/subread-1.6.2+dfsg/bin/sublong| debian/filter.pl > /<<BUILDDIR>>/subread-1.6.2+dfsg/debian/subread/usr/share/man/man1/sublong.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='scans the entire genome and reports all matches of a specified sequence' \
/<<BUILDDIR>>/subread-1.6.2+dfsg/bin/utilities/subread-fullscan | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.2+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-1.6.2+dfsg/bin/utilities/coverageCount | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.2+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-1.6.2+dfsg/bin/utilities/propmapped | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.2+dfsg/debian/subread/usr/share/man/man1/propmapped.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='retrieve Phred score for read bases' \
/<<BUILDDIR>>/subread-1.6.2+dfsg/bin/utilities/qualityScores| debian/filter.pl > /<<BUILDDIR>>/subread-1.6.2+dfsg/debian/subread/usr/share/man/man1/qualityScores.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='Find reads that are from the same pair in the input and then place them next \
to each other in the output. A dummy read is added for each singleton read that does not have a pair. \
The output file is compatible with featureCounts program' \
/<<BUILDDIR>>/subread-1.6.2+dfsg/bin/utilities/repair| debian/filter.pl > /<<BUILDDIR>>/subread-1.6.2+dfsg/debian/subread/usr/share/man/man1/repair.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='Remove duplicated reads' \
/<<BUILDDIR>>/subread-1.6.2+dfsg/bin/utilities/removeDup| debian/filter.pl > /<<BUILDDIR>>/subread-1.6.2+dfsg/debian/subread/usr/share/man/man1/removeDup.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='Flatten features included in a GTF annotation and save the modified annotation \
to a SAF format file.' \
/<<BUILDDIR>>/subread-1.6.2+dfsg/bin/utilities/flattenGTF| debian/filter.pl > /<<BUILDDIR>>/subread-1.6.2+dfsg/debian/subread/usr/share/man/man1/flattenGTF.1;
dh_auto_install
make[1]: Leaving directory '/<<BUILDDIR>>/subread-1.6.2+dfsg'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/subread/usr/lib/subread/coverageCount debian/subread/usr/bin/subread-align debian/subread/usr/lib/subread/qualityScores debian/subread/usr/bin/sublong debian/subread/usr/bin/subindel debian/subread/usr/bin/exactSNP debian/subread/usr/bin/subjunc debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/repair debian/subread/usr/bin/featureCounts debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/removeDup debian/subread/usr/bin/subread-buildindex were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'subread' in '../subread_1.6.2+dfsg-1_armhf.deb'.
dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_1.6.2+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../subread_1.6.2+dfsg-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build subread-1.6.2+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-05-21T05:41:12Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
subread_1.6.2+dfsg-1_armhf.changes:
-----------------------------------
Format: 1.8
Date: Fri, 18 May 2018 19:07:58 +0200
Source: subread
Binary: subread subread-data
Architecture: armhf
Version: 1.6.2+dfsg-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Alexandre Mestiashvili <mestia@debian.org>
Description:
subread - toolkit for processing next-gen sequencing data
subread-data - data files for subread package
Changes:
subread (1.6.2+dfsg-1) unstable; urgency=medium
.
* New upstream version 1.6.2+dfsg
* d/control:
- bump Policy to 4.1.4
- update uploader's email in d/{control,copyright}
- bump compat to 11
* Remove --parallel from dh invocation in d/rules
* Generate man page for flattenGTF with help2man
* Install new binary flattenGTF
* Refresh and update patches
Checksums-Sha1:
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78d832b61f0af4906f60d00366ddbb901b473ad8 5065 subread_1.6.2+dfsg-1_armhf.buildinfo
ec785ec654df31d209288997a9bc31c19b419fda 413108 subread_1.6.2+dfsg-1_armhf.deb
Checksums-Sha256:
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Files:
5bbd38a99b0d2ea9ff1eb1fb596dc817 5846548 debug optional subread-dbgsym_1.6.2+dfsg-1_armhf.deb
a44c2933fc351a214e323f7cbfb002d4 5065 science optional subread_1.6.2+dfsg-1_armhf.buildinfo
41ab82f32387eb6fa5e104e8531c6dc1 413108 science optional subread_1.6.2+dfsg-1_armhf.deb
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| Package contents |
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subread-dbgsym_1.6.2+dfsg-1_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 5846548 bytes: control archive=1248 bytes.
955 bytes, 12 lines control
1590 bytes, 15 lines md5sums
Package: subread-dbgsym
Source: subread
Version: 1.6.2+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7112
Depends: subread (= 1.6.2+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for subread
Build-Ids: 0217956f818bda42a0d3a4f192d345cf63358010 06a0653f3986d1d4bb4d1b5cd5eb061ea0c6a118 10fd0834c8caaad57f14563322af92198846e14f 1c11d2990e53717d47ff7b9ad3c2cd0ad40714e1 3b9460441915612c799243371c913cced5c3ce48 4bfa96b15c20c5cc1e75da0d6cd7c760d6165140 6fc2df58b90cbc776fb33f8a6562411123c85788 8acc7202ab6aa92443bc7b6434aeb0c0f2ce83b0 9d9310f4714348f11abcb2066e73996578f0831a 9f0354d613cb5516bce7cb4fe14a7ced1d9fb4ce bb1c931a8d659a3215ea61ec9429f84b138c1474 c453b090337160050a155319dffe4e783f51d411 cd4657f30787c39c0d01fafb7a30f97d2639f2e4 e2cbb2eca3c1b0f250872e6ecce9b09b3ebb5ec2 fd113365016f83c5c53c16f35e67a32d5a61186b
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drwxr-xr-x root/root 0 2018-05-18 17:07 ./usr/share/
drwxr-xr-x root/root 0 2018-05-18 17:07 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-05-18 17:07 ./usr/share/doc/subread-dbgsym -> subread
subread_1.6.2+dfsg-1_armhf.deb
------------------------------
new Debian package, version 2.0.
size 413108 bytes: control archive=1568 bytes.
622 bytes, 14 lines control
2124 bytes, 33 lines md5sums
Package: subread
Version: 1.6.2+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5085
Depends: libc6 (>= 2.7), 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 2018-05-18 17:07 ./
drwxr-xr-x root/root 0 2018-05-18 17:07 ./usr/
drwxr-xr-x root/root 0 2018-05-18 17:07 ./usr/bin/
-rwxr-xr-x root/root 375076 2018-05-18 17:07 ./usr/bin/exactSNP
-rwxr-xr-x root/root 449204 2018-05-18 17:07 ./usr/bin/featureCounts
-rwxr-xr-x root/root 350516 2018-05-18 17:07 ./usr/bin/subindel
-rwxr-xr-x root/root 363700 2018-05-18 17:07 ./usr/bin/subjunc
-rwxr-xr-x root/root 62968 2018-05-18 17:07 ./usr/bin/sublong
-rwxr-xr-x root/root 363620 2018-05-18 17:07 ./usr/bin/subread-align
-rwxr-xr-x root/root 366860 2018-05-18 17:07 ./usr/bin/subread-buildindex
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-rwxr-xr-x root/root 354612 2018-05-18 17:07 ./usr/lib/subread/coverageCount
-rwxr-xr-x root/root 350468 2018-05-18 17:07 ./usr/lib/subread/flattenGTF
-rwxr-xr-x root/root 354612 2018-05-18 17:07 ./usr/lib/subread/propmapped
-rwxr-xr-x root/root 354724 2018-05-18 17:07 ./usr/lib/subread/qualityScores
-rwxr-xr-x root/root 350468 2018-05-18 17:07 ./usr/lib/subread/removeDup
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-rwxr-xr-x root/root 350468 2018-05-18 17:07 ./usr/lib/subread/subread-fullscan
-rwxr-xr-x root/root 354564 2018-05-18 17:07 ./usr/lib/subread/txUnique
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-rw-r--r-- root/root 500 2018-05-18 17:07 ./usr/share/doc/subread/README.Debian
-rw-r--r-- root/root 3850 2018-05-15 03:14 ./usr/share/doc/subread/README.txt
-rw-r--r-- root/root 2630 2018-05-18 17:07 ./usr/share/doc/subread/changelog.Debian.gz
-rw-r--r-- root/root 1130 2018-05-18 17:07 ./usr/share/doc/subread/copyright
drwxr-xr-x root/root 0 2018-05-18 17:07 ./usr/share/man/
drwxr-xr-x root/root 0 2018-05-18 17:07 ./usr/share/man/man1/
-rw-r--r-- root/root 591 2018-05-18 17:07 ./usr/share/man/man1/coverageCount.1.gz
-rw-r--r-- root/root 1159 2018-05-18 17:07 ./usr/share/man/man1/exactSNP.1.gz
-rw-r--r-- root/root 3408 2018-05-18 17:07 ./usr/share/man/man1/featureCounts.1.gz
-rw-r--r-- root/root 455 2018-05-18 17:07 ./usr/share/man/man1/flattenGTF.1.gz
-rw-r--r-- root/root 470 2018-05-18 17:07 ./usr/share/man/man1/propmapped.1.gz
-rw-r--r-- root/root 575 2018-05-18 17:07 ./usr/share/man/man1/qualityScores.1.gz
-rw-r--r-- root/root 478 2018-05-18 17:07 ./usr/share/man/man1/removeDup.1.gz
-rw-r--r-- root/root 600 2018-05-18 17:07 ./usr/share/man/man1/repair.1.gz
-rw-r--r-- root/root 367 2018-05-18 17:07 ./usr/share/man/man1/subindel.1.gz
-rw-r--r-- root/root 2303 2018-05-18 17:07 ./usr/share/man/man1/subjunc.1.gz
-rw-r--r-- root/root 554 2018-05-18 17:07 ./usr/share/man/man1/sublong.1.gz
-rw-r--r-- root/root 2377 2018-05-18 17:07 ./usr/share/man/man1/subread-align.1.gz
-rw-r--r-- root/root 703 2018-05-18 17:07 ./usr/share/man/man1/subread-buildindex.1.gz
-rw-r--r-- root/root 365 2018-05-18 17:07 ./usr/share/man/man1/subread-fullscan.1.gz
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| Post Build |
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+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 118308
Build-Time: 2048
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 621
Job: subread_1.6.2+dfsg-1
Machine Architecture: armhf
Package: subread
Package-Time: 2737
Source-Version: 1.6.2+dfsg-1
Space: 118308
Status: successful
Version: 1.6.2+dfsg-1
--------------------------------------------------------------------------------
Finished at 2018-05-21T05:41:12Z
Build needed 00:45:37, 118308k disc space