subread →
1.4.6-p3+dfsg-2 →
armhf → 2015-05-27 05:46:44
sbuild (Debian sbuild) 0.64.1 (13 Oct 2013) on testbuildd.raspbian.org
╔══════════════════════════════════════════════════════════════════════════════╗
║ subread 1.4.6-p3+dfsg-2 (armhf) 27 May 2015 05:33 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: subread
Version: 1.4.6-p3+dfsg-2
Source Version: 1.4.6-p3+dfsg-2
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/subread-jXm2O8/subread-1.4.6-p3+dfsg' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/subread-jXm2O8' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-9a214019-b101-47e8-8e97-5c7e8fa1d29e' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 stretch-staging/main Sources [7904 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [9688 kB]
Ign http://172.17.0.1 stretch-staging/main Translation-en
Fetched 17.6 MB in 33s (521 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
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Checking available source versions...
Download source files with APT
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Reading package lists...
Building dependency tree...
NOTICE: 'subread' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/subread.git
Need to get 13.9 MB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main subread 1.4.6-p3+dfsg-2 (dsc) [2279 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main subread 1.4.6-p3+dfsg-2 (tar) [13.9 MB]
Get:3 http://172.17.0.1/private/ stretch-staging/main subread 1.4.6-p3+dfsg-2 (diff) [6684 B]
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Download complete and in download only mode
Check arch
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-8ctp7V/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 51 not upgraded.
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After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
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(Reading database ... 11998 files and directories currently installed.)
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Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), zlib1g-dev, help2man
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), zlib1g-dev, help2man
dpkg-deb: building package `sbuild-build-depends-subread-dummy' in `/«BUILDDIR»/resolver-9TMfOQ/apt_archive/sbuild-build-depends-subread-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install subread build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils debhelper file gettext gettext-base groff-base help2man
intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libmagic1
libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
Suggested packages:
wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser
libmail-box-perl
Recommended packages:
curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libglib2.0-data shared-mime-info xdg-user-dirs xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils debhelper file gettext gettext-base groff-base help2man
intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libmagic1
libpipeline1 libunistring0 libxml2 man-db po-debconf
sbuild-build-depends-subread-dummy zlib1g-dev
0 upgraded, 20 newly installed, 0 to remove and 51 not upgraded.
Need to get 8726 kB/8727 kB of archives.
After this operation, 24.7 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ stretch-staging/main libpipeline1 armhf 1.4.0-1 [24.0 kB]
Get:2 http://172.17.0.1/private/ stretch-staging/main groff-base armhf 1.22.3-1 [1085 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
Get:4 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.0.2-5 [972 kB]
Get:5 http://172.17.0.1/private/ stretch-staging/main libasprintf0c2 armhf 0.19.4-1 [31.5 kB]
Get:6 http://172.17.0.1/private/ stretch-staging/main libmagic1 armhf 1:5.22+15-2 [244 kB]
Get:7 http://172.17.0.1/private/ stretch-staging/main libxml2 armhf 2.9.1+dfsg1-5 [703 kB]
Get:8 http://172.17.0.1/private/ stretch-staging/main libffi6 armhf 3.1-2 [18.1 kB]
Get:9 http://172.17.0.1/private/ stretch-staging/main libglib2.0-0 armhf 2.44.1-1 [2314 kB]
Get:10 http://172.17.0.1/private/ stretch-staging/main libcroco3 armhf 0.6.8-3 [121 kB]
Get:11 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:12 http://172.17.0.1/private/ stretch-staging/main file armhf 1:5.22+15-2 [59.9 kB]
Get:13 http://172.17.0.1/private/ stretch-staging/main gettext-base armhf 0.19.4-1 [117 kB]
Get:14 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.4-1 [1168 kB]
Get:15 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.2 [25.9 kB]
Get:16 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:17 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20150507 [824 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main help2man armhf 1.46.6 [142 kB]
Get:19 http://172.17.0.1/private/ stretch-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-2 [199 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 8726 kB in 4s (1784 kB/s)
Selecting previously unselected package libpipeline1:armhf.
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Preparing to unpack .../libpipeline1_1.4.0-1_armhf.deb ...
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Unpacking libglib2.0-0:armhf (2.44.1-1) ...
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Setting up libpipeline1:armhf (1.4.0-1) ...
Setting up groff-base (1.22.3-1) ...
Setting up bsdmainutils (9.0.6) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.7.0.2-5) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:armhf (0.19.4-1) ...
Setting up libmagic1:armhf (1:5.22+15-2) ...
Setting up libxml2:armhf (2.9.1+dfsg1-5) ...
Setting up libffi6:armhf (3.1-2) ...
Setting up libglib2.0-0:armhf (2.44.1-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.8-3) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up file (1:5.22+15-2) ...
Setting up gettext-base (0.19.4-1) ...
Setting up gettext (0.19.4-1) ...
Setting up intltool-debian (0.35.0+20060710.2) ...
Setting up po-debconf (1.0.18) ...
Setting up debhelper (9.20150507) ...
Setting up help2man (1.46.6) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2) ...
Setting up sbuild-build-depends-subread-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-18) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25-5 dpkg-dev_1.17.25 g++-4.9_4.9.2-10 gcc-4.9_4.9.2-10 libc6-dev_2.19-18 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 linux-libc-dev_3.16.7-ckt4-1+rpi1
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.9.8 base-files_8+rpi1 base-passwd_3.5.37 bash_4.3-11 binutils_2.25-5 bsdmainutils_9.0.6 bsdutils_1:2.25.2-6 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:4.9.2-2 cpp-4.9_4.9.2-10 dash_0.5.7-4 debconf_1.5.56 debconf-i18n_1.5.56 debfoster_2.7-2 debhelper_9.20150507 debianutils_4.4 diffutils_1:3.3-1 dmsetup_2:1.02.90-2.2 dpkg_1.17.25 dpkg-dev_1.17.25 e2fslibs_1.42.12-1.1 e2fsprogs_1.42.12-1.1 fakeroot_1.20.2-1 file_1:5.22+15-2 findutils_4.4.2-9 g++_4:4.9.2-2 g++-4.9_4.9.2-10 gcc_4:4.9.2-2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.4-1 gcc-4.9_4.9.2-10 gcc-4.9-base_4.9.2-10 gettext_0.19.4-1 gettext-base_0.19.4-1 gnupg_1.4.18-7 gpgv_1.4.18-7 grep_2.20-4.1 groff-base_1.22.3-1 gzip_1.6-4 help2man_1.46.6 hostname_3.15 init_1.22 init-system-helpers_1.22 initramfs-tools_0.120 initscripts_2.88dsf-59 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.2 klibc-utils_2.0.4-2+rpi1 kmod_18-3 libacl1_2.2.52-2 libapt-pkg4.12_1.0.9.8 libasan1_4.9.2-10 libasprintf0c2_0.19.4-1 libatomic1_4.9.2-10 libattr1_1:2.4.47-2 libaudit-common_1:2.4-1 libaudit1_1:2.4-1 libblkid1_2.25.2-6 libbz2-1.0_1.0.6-7 libc-bin_2.19-18 libc-dev-bin_2.19-18 libc6_2.19-18 libc6-dev_2.19-18 libcap2_1:2.24-8 libcap2-bin_1:2.24-8 libcloog-isl4_0.18.2-1 libcomerr2_1.42.12-1.1 libcroco3_0.6.8-3 libcryptsetup4_2:1.6.6-5 libdb5.3_5.3.28-9 libdbus-1-3_1.8.16-1 libdebconfclient0_0.192 libdevmapper1.02.1_2:1.02.90-2.2 libdpkg-perl_1.17.25 libdrm2_2.4.58-2 libfakeroot_1.20.2-1 libffi6_3.1-2 libgc1c2_1:7.2d-6.4 libgcc-4.9-dev_4.9.2-10 libgcc1_1:4.9.2-10 libgcrypt20_1.6.3-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.44.1-1 libgmp10_2:6.0.0+dfsg-6+rpi1 libgomp1_4.9.2-10 libgpg-error0_1.17-3 libisl10_0.12.2-2 libklibc_2.0.4-2+rpi1 libkmod2_18-3 liblocale-gettext-perl_1.05-8+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.22+15-2 libmount1_2.25.2-6 libmpc3_1.0.2-1 libmpfr4_3.1.2-2 libncurses5_5.9+20140913-1 libncursesw5_5.9+20140913-1 libnih-dbus1_1.0.3-4.3 libnih1_1.0.3-4.3 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpcre3_2:8.35-3.3 libpipeline1_1.4.0-1 libpng12-0_1.2.50-2 libprocps3_2:3.3.9-9 libreadline6_6.3-8 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libslang2_2.3.0-2 libsmartcols1_2.25.2-6 libss2_1.42.12-1.1 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 libsystemd0_215-17 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140913-1 libubsan0_4.9.2-10 libudev1_215-17 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-25 libustr-1.0-1_1.0.4-3 libuuid1_2.25.2-6 libxml2_2.9.1+dfsg1-5 linux-libc-dev_3.16.7-ckt4-1+rpi1 login_1:4.2-3 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.1 makedev_2.3.1-93 man-db_2.7.0.2-5 mawk_1.3.3-17 mount_2.25.2-6 mountall_2.54 multiarch-support_2.19-18 ncurses-base_5.9+20140913-1 ncurses-bin_5.9+20140913-1 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-3 perl-base_5.20.2-3 perl-modules_5.20.2-3 plymouth_0.9.0-9 po-debconf_1.0.18 procps_2:3.3.9-9 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-subread-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 startpar_0.59-3 systemd_215-17 systemd-sysv_215-17 sysv-rc_2.88dsf-59 sysvinit-utils_2.88dsf-59 tar_1.27.1-2 tzdata_2015c-1 udev_215-17 util-linux_2.25.2-6 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-2 zlib1g-dev_1:1.2.8.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Thu May 21 19:44:28 2015 UTC using RSA key ID 1B5228B0
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./subread_1.4.6-p3+dfsg-2.dsc
dpkg-source: info: extracting subread in subread-1.4.6-p3+dfsg
dpkg-source: info: unpacking subread_1.4.6-p3+dfsg.orig.tar.xz
dpkg-source: info: unpacking subread_1.4.6-p3+dfsg-2.debian.tar.xz
dpkg-source: info: applying arch_specific_flags.patch
dpkg-source: info: applying fix_syntax.patch
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=111
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-9a214019-b101-47e8-8e97-5c7e8fa1d29e
SCHROOT_UID=106
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package subread
dpkg-buildpackage: source version 1.4.6-p3+dfsg-2
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build subread-1.4.6-p3+dfsg
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
debian/rules override_dh_clean
make[1]: Entering directory '/«BUILDDIR»/subread-1.4.6-p3+dfsg'
cd src; make -f Makefile.Linux clean
make[2]: Entering directory '/«BUILDDIR»/subread-1.4.6-p3+dfsg/src'
rm -f core featureCounts exactSNP removeDup subread-buildindex core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o
make[2]: Leaving directory '/«BUILDDIR»/subread-1.4.6-p3+dfsg/src'
dh_clean
make[1]: Leaving directory '/«BUILDDIR»/subread-1.4.6-p3+dfsg'
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/«BUILDDIR»/subread-1.4.6-p3+dfsg'
cd src; make -f Makefile.Linux
make[2]: Entering directory '/«BUILDDIR»/subread-1.4.6-p3+dfsg/src'
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o core.o core.c
core.c: In function 'print_in_box':
core.c:91:7: warning: variable 'is_R_linebreak' set but not used [-Wunused-but-set-variable]
char is_R_linebreak=0, * content, *out_line_buff;
^
core.c: In function 'convert_GZ_to_FQ':
core.c:775:25: warning: passing argument 1 of 'gzgets' from incompatible pointer type
char * bufr =gzgets(rawfp, linebuff, 3000);
^
In file included from sambam-file.h:23:0,
from core.h:47,
from core.c:42:
/usr/include/zlib.h:1372:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
core.c:786:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(rawfp);
^
In file included from sambam-file.h:23:0,
from core.h:47,
from core.c:42:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
core.c: In function 'convert_read_to_tmp':
core.c:1094:7: warning: variable 'current_repeated_times' set but not used [-Wunused-but-set-variable]
int current_repeated_times;
^
core.c: In function 'do_voting':
core.c:2985:9: warning: variable 'allsubreads_for_each_gap' set but not used [-Wunused-but-set-variable]
int allsubreads_for_each_gap [GENE_SLIDING_STEP], noninformative_subreads_for_each_gap[GENE_SLIDING_STEP];
^
core.c: In function 'split_read_files':
core.c:3314:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(read_line_buf, 3000, global_context->input_reads.first_read_file.input_fp);
^
core.c:3316:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(read_line_buf2, 3000, global_context->input_reads.second_read_file.input_fp);
^
core.c:3345:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(read_line_buf, 3000, global_context->input_reads.first_read_file.input_fp);
^
core.c:3346:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(read_line_buf2, 3000, global_context->input_reads.second_read_file.input_fp);
^
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o core-junction.o core-junction.c
core-junction.c: In function 'search_events_to_back':
core-junction.c:388:6: warning: variable 'move_start' set but not used [-Wunused-but-set-variable]
int move_start = read_tail_pos - global_context -> config.realignment_minimum_variant_distance;
^
core-junction.c: In function 'finalise_explain_CIGAR':
core-junction.c:1769:23: warning: variable 'tmp_cigar_exonic' set but not used [-Wunused-but-set-variable]
char tmp_cigar[120], tmp_cigar_exonic[120];
^
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o core-indel.o core-indel.c
core-indel.c: In function 'find_new_indels':
core-indel.c:1486:9: warning: variable 'best_j' set but not used [-Wunused-but-set-variable]
int best_j=0, best_score=-99999, is_ambiguous_indel= 0;
^
core-indel.c: In function 'full_indel_alignment':
core-indel.c:2828:41: warning: variable 'best_right' set but not used [-Wunused-but-set-variable]
int best_edge_score = -1, best_left, best_right;
^
core-indel.c:2828:30: warning: variable 'best_left' set but not used [-Wunused-but-set-variable]
int best_edge_score = -1, best_left, best_right;
^
core-indel.c: In function 'find_potential_ultralong_indels':
core-indel.c:2933:24: warning: variable 'best_c2_location' set but not used [-Wunused-but-set-variable]
int best_match = -1, best_c2_location = -1;
^
core-indel.c: In function 'finalise_pileup_file':
core-indel.c:3211:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, sizeof(short), 1, tmp_fp);
^
core-indel.c:3212:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_text, sizeof(char), read_len, tmp_fp);
^
core-indel.c:3213:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qual_text, sizeof(char), read_len, tmp_fp);
^
core-indel.c:3290:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, sizeof(short), 1, tmp_fp);
^
core-indel.c:3291:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_text, sizeof(char), read_len, tmp_fp);
^
core-indel.c:3292:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qual_text, sizeof(char), read_len, tmp_fp);
^
core-indel.c: In function 'finalise_pileup_file_by_debrujin':
core-indel.c:3647:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, sizeof(short), 1, tmp_fp);
^
core-indel.c:3648:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_text, sizeof(char), read_len, tmp_fp);
^
core-indel.c:3649:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qual_text, sizeof(char), read_len, tmp_fp);
^
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o sambam-file.o sambam-file.c
sambam-file.c: In function 'PBam_get_next_zchunk':
sambam-file.c:324:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&ID1, 1, 1, bam_fp);
^
sambam-file.c:325:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&ID2, 1, 1, bam_fp);
^
sambam-file.c:326:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&CM, 1, 1, bam_fp);
^
sambam-file.c:327:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&FLG, 1, 1, bam_fp);
^
sambam-file.c:336:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&XLEN,1, 2, bam_fp );
^
sambam-file.c:344:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SI1, 1, 1, bam_fp);
^
sambam-file.c:345:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SI2, 1, 1, bam_fp);
^
sambam-file.c:346:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SLEN, 1, 2, bam_fp);
^
sambam-file.c:350:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&BSIZE_MID, 1,2 , bam_fp);
^
sambam-file.c:362:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(buffer, 1, CDATA_READING, bam_fp);
^
sambam-file.c:366:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&real_len, 4, 1, bam_fp);
^
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o sublog.o sublog.c
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o gene-algorithms.o gene-algorithms.c
gene-algorithms.c: In function 'show_cigar':
gene-algorithms.c:747:6: warning: variable 'last_end' set but not used [-Wunused-but-set-variable]
int last_end=0, last_offset = 0, cursor = 0;
^
gene-algorithms.c:746:9: warning: variable 'is_error' set but not used [-Wunused-but-set-variable]
int i, is_error = 0;
^
gene-algorithms.c: In function 'match_chro_indel':
gene-algorithms.c:1159:28: warning: variable 'last_section_indels' set but not used [-Wunused-but-set-variable]
int last_section_end = 0, last_section_indels=0;
^
gene-algorithms.c: In function 'search_DP_branch':
gene-algorithms.c:1703:6: warning: variable 'table_mask2_j_1' set but not used [-Wunused-but-set-variable]
int table_mask2_j_1 = 0, table_mask2_i_1 = 0;
^
gene-algorithms.c: In function 'final_mapping_quality':
gene-algorithms.c:2344:7: warning: variable 'is_match_begin' set but not used [-Wunused-but-set-variable]
int is_match_begin = 0;
^
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o input-files.o input-files.c
input-files.c: In function 'f_subr_open':
input-files.c:46:3: warning: implicit declaration of function 'fopen64' [-Wimplicit-function-declaration]
return fopen64(fname, mode);
^
input-files.c:46:3: warning: return makes pointer from integer without a cast
input-files.c: In function 'geinput_next_char':
input-files.c:442:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(out_buf, 1999,input->input_fp);
^
input-files.c: In function 'sort_SAM_finalise':
input-files.c:2188:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_name_len, 2,1 , bbfp);
^
input-files.c:2194:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_name, 1, read_name_len, bbfp);
^
input-files.c:2197:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len,2,1,bbfp);
^
input-files.c:2203:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(new_line_mem, 1, read_len, bbfp);
^
input-files.c:2256:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_name_len, 2,1 , bbfp);
^
input-files.c:2262:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_name_buf, 1, read_name_len, bbfp);
^
input-files.c:2266:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, 2,1 , bbfp);
^
input-files.c:2269:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_line_buf, 1, read_len, bbfp);
^
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o sorted-hashtable.o sorted-hashtable.c
sorted-hashtable.c: In function 'gehash_load':
sorted-hashtable.c:1249:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(magic_chars,1,8,fp);
^
sorted-hashtable.c:1272:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_key, 2, 1, fp);
^
sorted-hashtable.c:1275:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_length, 2, 1, fp);
^
sorted-hashtable.c:1278:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&(the_table -> index_gap),2,1,fp);
^
sorted-hashtable.c: In function 'gehash_go_q_tolerable':
sorted-hashtable.c:510:22: warning: array subscript is above array bounds [-Warray-bounds]
mutation_stack[j] = 0;
^
sorted-hashtable.c: In function 'gehash_go_q_CtoT':
sorted-hashtable.c:591:22: warning: array subscript is above array bounds [-Warray-bounds]
mutation_stack[j] = 0;
^
sorted-hashtable.c:609:22: warning: array subscript is above array bounds [-Warray-bounds]
error_pos_stack[j] = error_pos_stack[i] + (j-i);
^
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o gene-value-index.o gene-value-index.c
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o exon-algorithms.o exon-algorithms.c
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.c
long-hashtable.c: In function 'lnhash_create':
long-hashtable.c:43:45: warning: large integer implicitly truncated to unsigned type [-Woverflow]
the_table -> key_repeated_numbers = malloc(sizeof(short) * 0x100000000llu);
^
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
readSummary.c: In function 'readSummary':
readSummary.c:2917:9: warning: variable 'curchr_name' set but not used [-Wunused-but-set-variable]
char * curchr_name;
^
readSummary.c:2916:15: warning: variable 'curpos' set but not used [-Wunused-but-set-variable]
long curchr, curpos;
^
readSummary.c:2916:7: warning: variable 'curchr' set but not used [-Wunused-but-set-variable]
long curchr, curpos;
^
readSummary.c: In function 'load_feature_info':
readSummary.c:568:49: warning: 'token_temp' may be used uninitialized in this function [-Wmaybe-uninitialized]
ret_features[xk1].is_negative_strand = ('-' ==strand_str[0]);
^
readSummary.c:499:40: warning: 'token_temp' may be used uninitialized in this function [-Wmaybe-uninitialized]
chro_name[CHROMOSOME_NAME_LENGTH-1]=0;
^
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
index-builder.c: In function 'scan_gene_index':
index-builder.c:449:19: warning: variable 'table_no' set but not used [-Wunused-but-set-variable]
int file_number, table_no, i ,j;
^
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subtools subtools.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
qualityScores.c: In function 'finalise_qs_context':
qualityScores.c:82:12: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(qs_context -> gzfq_reader);
^
In file included from qualityScores.c:24:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
qualityScores.c: In function 'rewind_qs_file':
qualityScores.c:275:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(qs_context -> gzfq_reader);
^
In file included from qualityScores.c:24:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
qualityScores.c:282:29: warning: assignment from incompatible pointer type
qs_context -> gzfq_reader = gzopen(qs_context->input_name, "rb");
^
qualityScores.c: In function 'start_qs_context':
qualityScores.c:313:29: warning: assignment from incompatible pointer type
qs_context -> gzfq_reader = gzopen(qs_context->input_name, "rb");
^
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o coverageCount coverage_calc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
gcc -fsigned-char -O2 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o globalReassembly global-reassembly.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm
global-reassembly.c: In function 'GRA_trim_reads':
global-reassembly.c:415:7: warning: variable 'in_flags_1' set but not used [-Wunused-but-set-variable]
int in_flags_1= -1, is_second_read = 0;
^
global-reassembly.c: In function 'GRA_reassemble_reads_LR':
global-reassembly.c:1435:14: warning: variable 'target_votes' set but not used [-Wunused-but-set-variable]
int mm=0, target_votes=0, new_bases_len;
^
mkdir -p ../bin/utilities
mv subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/
mv globalReassembly coverageCount propmapped qualityScores removeDup subread-fullscan subtools ../bin/utilities
make[2]: Leaving directory '/«BUILDDIR»/subread-1.4.6-p3+dfsg/src'
dh_auto_build
make[1]: Leaving directory '/«BUILDDIR»/subread-1.4.6-p3+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/«BUILDDIR»/subread-1.4.6-p3+dfsg'
debian/tests/subread-tests /«BUILDDIR»/subread-1.4.6-p3+dfsg
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6-p3
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 SAM file ||
|| P data/test-minimum.sam ||
|| ||
|| Output file : test-minimum.FC ||
|| Annotations : data/test-minimum.GTF (GTF) ||
|| ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| Strand specific : no ||
|| Multimapping reads : not counted ||
|| Multi-overlapping reads : not counted ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================================= Running ==================================\\
|| ||
|| Load annotation file data/test-minimum.GTF ... ||
|| Features : 23 ||
|| Meta-features : 7 ||
|| Chromosomes : 3 ||
|| ||
|| Process SAM file data/test-minimum.sam... ||
|| Paired-end reads are included. ||
|| Assign reads to features... ||
|| Total reads : 998 ||
|| Successfully assigned reads : 389 (39.0%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Read assignment finished. ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6-p3
//=========================== indexBuilder setting ===========================\\
|| ||
|| Index name : tmp/small1 ||
|| Index space : base-space ||
|| Memory : 3000 Mbytes ||
|| Repeat threshold : 24 repeats ||
|| Distance to next subread : 3 ||
|| ||
|| Input files : 1 file in total ||
|| o ../chr901.fa ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================================= Running ==================================\\
|| ||
|| Check the integrity of provided reference sequences ... ||
|| There were 4 notes for reference sequences. ||
|| The notes can be found in the log file, 'tmp/small1.log'. ||
|| Scan uninformative subreads in reference sequences ... ||
|| 8%, 0 mins elapsed, rate=43.5k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=84.9k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=124.2k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=161.5k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=197.0k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=230.7k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=262.6k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=293.1k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=322.1k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=349.6k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=375.9k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=401.0k bps/s, total=0m ||
|| 95 uninformative subreads were found. ||
|| These subreads were excluded from index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=209.3k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=220.4k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=235.6k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=249.3k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=263.0k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=277.1k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=291.8k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=306.5k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=321.5k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=335.7k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=351.3k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=365.0k bps/s, total=0m ||
|| Save current index block... ||
|| [ 0.0% finished ] ||
|| [ 10.0% finished ] ||
|| [ 20.0% finished ] ||
|| [ 30.0% finished ] ||
|| [ 40.0% finished ] ||
|| [ 50.0% finished ] ||
|| [ 60.0% finished ] ||
|| [ 70.0% finished ] ||
|| [ 80.0% finished ] ||
|| [ 90.0% finished ] ||
|| [ 100.0% finished ] ||
|| ||
|| Total running time: 0.1 minutes. ||
|| Index tmp/small1 was successfully built! ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6-p3
//============================= subjunc setting ==============================\\
|| ||
|| Function : Read alignment + Junction detection (RNA-Seq) ||
|| Threads : 1 ||
|| Input file 1 : data/junction-reads-A.fq ||
|| Input file 2 : data/junction-reads-B.fq ||
|| Output file : junctions.sam (SAM) ||
|| Index name : tmp/small1 ||
|| Phred offset : 33 ||
|| ||
|| Min read1 votes : 1 ||
|| Min read2 votes : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : no ||
|| Hamming distance : no ||
|| Quality scores : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (27-May-2015 05:42:34) ======================\\
|| ||
|| The input file contains base space reads. ||
|| Load the 1-th index block... ||
|| Map fragments... ||
|| 37% completed, 0 mins elapsed, total=16k frags, rate=2.2k/s ||
|| 43% completed, 0 mins elapsed, total=16k frags, rate=2.2k/s ||
|| 49% completed, 0 mins elapsed, total=16k frags, rate=2.2k/s ||
|| 55% completed, 0 mins elapsed, total=16k frags, rate=2.2k/s ||
|| Detect indels and junctions... ||
|| 60% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 62% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 63% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 64% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 65% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 66% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 67% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 68% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 69% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| Realign fragments... ||
|| 70% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 72% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 73% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 74% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 75% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 76% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 77% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 78% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 79% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 16052 fragments were processed. Save the mapping results for them... ||
|| 81% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 84% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 86% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 88% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 90% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 92% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 94% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 96% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 98% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 16052 fragments ||
|| Mapped : 15906 fragments (99.1%) ||
|| Correctly paired : 13038 fragments ||
|| Junctions : 405 ||
|| Indels : 179 ||
|| ||
|| Running time : 0.2 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6-p3
//============================= subjunc setting ==============================\\
|| ||
|| Function : Read alignment + Junction/Fusion detection (RNA-Seq) ||
|| Threads : 1 ||
|| Input file 1 : data/junction-reads-A.fq ||
|| Input file 2 : data/junction-reads-B.fq ||
|| Output file : junctionsNfusions.bam (BAM) ||
|| Index name : tmp/small1 ||
|| Phred offset : 33 ||
|| ||
|| Min read1 votes : 1 ||
|| Min read2 votes : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : no ||
|| Hamming distance : no ||
|| Quality scores : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (27-May-2015 05:42:48) ======================\\
|| ||
|| The input file contains base space reads. ||
|| Load the 1-th index block... ||
|| Map fragments... ||
|| 37% completed, 0 mins elapsed, total=16k frags, rate=2.1k/s ||
|| 43% completed, 0 mins elapsed, total=16k frags, rate=2.1k/s ||
|| 49% completed, 0 mins elapsed, total=16k frags, rate=2.1k/s ||
|| 55% completed, 0 mins elapsed, total=16k frags, rate=2.1k/s ||
|| Detect indels and junctions... ||
|| 60% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 62% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 63% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 64% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 65% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 66% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 67% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 68% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 69% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| Realign fragments... ||
|| 70% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 72% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 73% completed, 0 mins elapsed, total=16k frags, rate=1.2k/s ||
|| 74% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 75% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 76% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 77% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 78% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 79% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 16052 fragments were processed. Save the mapping results for them... ||
|| 81% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 84% completed, 0 mins elapsed, total=16k frags, rate=1.1k/s ||
|| 86% completed, 0 mins elapsed, total=16k frags, rate=1.0k/s ||
|| 88% completed, 0 mins elapsed, total=16k frags, rate=1.0k/s ||
|| 90% completed, 0 mins elapsed, total=16k frags, rate=1.0k/s ||
|| 92% completed, 0 mins elapsed, total=16k frags, rate=1.0k/s ||
|| 94% completed, 0 mins elapsed, total=16k frags, rate=1.0k/s ||
|| 96% completed, 0 mins elapsed, total=16k frags, rate=1.0k/s ||
|| 98% completed, 0 mins elapsed, total=16k frags, rate=1.0k/s ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 16052 fragments ||
|| Mapped : 15904 fragments (99.1%) ||
|| Correctly paired : 12889 fragments ||
|| Junctions : 415 ||
|| Fusions : 92 ||
|| Indels : 160 ||
|| ||
|| Running time : 0.3 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6-p3
//=========================== indexBuilder setting ===========================\\
|| ||
|| Index name : tmp/small1 ||
|| Index space : base-space ||
|| Memory : 100 Mbytes ||
|| Repeat threshold : 24 repeats ||
|| Distance to next subread : 3 ||
|| ||
|| Input files : 1 file in total ||
|| o ../chr901.fa ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================================= Running ==================================\\
|| ||
|| Check the integrity of provided reference sequences ... ||
|| There were 4 notes for reference sequences. ||
|| The notes can be found in the log file, 'tmp/small1.log'. ||
|| Scan uninformative subreads in reference sequences ... ||
|| 8%, 0 mins elapsed, rate=45.2k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=88.2k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=128.9k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=167.6k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=204.2k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=239.1k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=272.2k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=303.7k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=333.6k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=361.9k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=389.0k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=414.9k bps/s, total=0m ||
|| 95 uninformative subreads were found. ||
|| These subreads were excluded from index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=214.2k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=225.8k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=241.0k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=255.8k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=270.7k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=286.1k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=302.0k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=317.7k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=334.2k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=349.2k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=365.6k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=380.0k bps/s, total=0m ||
|| Save current index block... ||
|| [ 0.0% finished ] ||
|| [ 10.0% finished ] ||
|| [ 20.0% finished ] ||
|| [ 30.0% finished ] ||
|| [ 40.0% finished ] ||
|| [ 50.0% finished ] ||
|| [ 60.0% finished ] ||
|| [ 70.0% finished ] ||
|| [ 80.0% finished ] ||
|| [ 90.0% finished ] ||
|| [ 100.0% finished ] ||
|| ||
|| Total running time: 0.1 minutes. ||
|| Index tmp/small1 was successfully built! ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6-p3
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment ||
|| Threads : 1 ||
|| Input file : data/test-noerror-r1.fq ||
|| Output file : tmp/test-tmp.sam1 (SAM) ||
|| Index name : tmp/small1 ||
|| Phred offset : 33 ||
|| ||
|| Min votes : 3 ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : no ||
|| Hamming distance : yes ||
|| Quality scores : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (27-May-2015 05:43:12) ======================\\
|| ||
|| The input file contains base space reads. ||
|| Load the 1-th index block... ||
|| Map reads... ||
|| 29% completed, 0 mins elapsed, total=20k reads, rate=4.8k/s ||
|| 35% completed, 0 mins elapsed, total=20k reads, rate=4.8k/s ||
|| 42% completed, 0 mins elapsed, total=20k reads, rate=4.8k/s ||
|| 48% completed, 0 mins elapsed, total=20k reads, rate=4.8k/s ||
|| 54% completed, 0 mins elapsed, total=19k reads, rate=4.8k/s ||
|| Detect indels... ||
|| 60% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 61% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 62% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 63% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 64% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 65% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 66% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 67% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 68% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| Realign reads... ||
|| 70% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 71% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 72% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 73% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 74% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 75% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 76% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 77% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 78% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 19998 reads were processed. Save the mapping results for them... ||
|| 81% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 83% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 85% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 87% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 89% completed, 0 mins elapsed, total=19k reads, rate=2.4k/s ||
|| 91% completed, 0 mins elapsed, total=19k reads, rate=2.4k/s ||
|| 93% completed, 0 mins elapsed, total=19k reads, rate=2.4k/s ||
|| 95% completed, 0 mins elapsed, total=19k reads, rate=2.4k/s ||
|| 97% completed, 0 mins elapsed, total=19k reads, rate=2.4k/s ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 reads ||
|| Mapped : 19967 reads (99.8%) ||
|| Indels : 7 ||
|| ||
|| Running time : 0.1 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6-p3
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment ||
|| Threads : 1 ||
|| Input file : data/test-noerror-r1.fq ||
|| Output file : tmp/test-tmp.sam2 (SAM) ||
|| Index name : tmp/small1 ||
|| Phred offset : 33 ||
|| ||
|| Min votes : 3 ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : yes ||
|| Hamming distance : yes ||
|| Quality scores : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (27-May-2015 05:43:21) ======================\\
|| ||
|| The input file contains base space reads. ||
|| Load the 1-th index block... ||
|| Map reads... ||
|| 29% completed, 0 mins elapsed, total=20k reads, rate=4.8k/s ||
|| 35% completed, 0 mins elapsed, total=20k reads, rate=4.8k/s ||
|| 42% completed, 0 mins elapsed, total=20k reads, rate=4.8k/s ||
|| 48% completed, 0 mins elapsed, total=20k reads, rate=4.8k/s ||
|| 54% completed, 0 mins elapsed, total=19k reads, rate=4.8k/s ||
|| Detect indels... ||
|| 60% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 61% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 62% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 63% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 64% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 65% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 66% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 67% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 68% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| Realign reads... ||
|| 70% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 71% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 72% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 73% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 74% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 75% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 76% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 77% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 78% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 19998 reads were processed. Save the mapping results for them... ||
|| 81% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 83% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 85% completed, 0 mins elapsed, total=19k reads, rate=2.3k/s ||
|| 87% completed, 0 mins elapsed, total=19k reads, rate=2.4k/s ||
|| 89% completed, 0 mins elapsed, total=19k reads, rate=2.4k/s ||
|| 91% completed, 0 mins elapsed, total=19k reads, rate=2.4k/s ||
|| 93% completed, 0 mins elapsed, total=19k reads, rate=2.4k/s ||
|| 95% completed, 0 mins elapsed, total=19k reads, rate=2.4k/s ||
|| 97% completed, 0 mins elapsed, total=19k reads, rate=2.4k/s ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 reads ||
|| Mapped : 18817 reads (94.1%) ||
|| Indels : 7 ||
|| ||
|| Running time : 0.1 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6-p3
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment ||
|| Threads : 1 ||
|| Input file 1 : data/test-noerror-r1.fq ||
|| Input file 2 : data/test-noerror-r2.fq ||
|| Output file : tmp/test-tmp.sam3 (SAM) ||
|| Index name : tmp/small1 ||
|| Phred offset : 33 ||
|| ||
|| Min read1 votes : 3 ||
|| Min read2 votes : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : no ||
|| Hamming distance : yes ||
|| Quality scores : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (27-May-2015 05:43:30) ======================\\
|| ||
|| The input file contains base space reads. ||
|| Load the 1-th index block... ||
|| Map fragments... ||
|| 29% completed, 0 mins elapsed, total=20k frags, rate=2.4k/s ||
|| 35% completed, 0 mins elapsed, total=20k frags, rate=2.4k/s ||
|| 42% completed, 0 mins elapsed, total=20k frags, rate=2.4k/s ||
|| 48% completed, 0 mins elapsed, total=20k frags, rate=2.4k/s ||
|| 54% completed, 0 mins elapsed, total=19k frags, rate=2.4k/s ||
|| Detect indels... ||
|| 60% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 61% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 62% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 63% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 64% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 65% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 66% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 67% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 68% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| Realign fragments... ||
|| 70% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 71% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 72% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 73% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 74% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 75% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 76% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 77% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 78% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 19998 fragments were processed. Save the mapping results for them... ||
|| 81% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 83% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 85% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 87% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 89% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 91% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 93% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 95% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 97% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 fragments ||
|| Mapped : 19990 fragments (100.0%) ||
|| Correctly paired : 19469 fragments ||
|| Indels : 7 ||
|| ||
|| Running time : 0.2 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6-p3
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment ||
|| Threads : 1 ||
|| Input file 1 : data/test-noerror-r1.fq ||
|| Input file 2 : data/test-noerror-r2.fq ||
|| Output file : tmp/test-tmp.sam4 (SAM) ||
|| Index name : tmp/small1 ||
|| Phred offset : 33 ||
|| ||
|| Min read1 votes : 3 ||
|| Min read2 votes : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : yes ||
|| Hamming distance : yes ||
|| Quality scores : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (27-May-2015 05:43:44) ======================\\
|| ||
|| The input file contains base space reads. ||
|| Load the 1-th index block... ||
|| Map fragments... ||
|| 29% completed, 0 mins elapsed, total=20k frags, rate=2.3k/s ||
|| 35% completed, 0 mins elapsed, total=20k frags, rate=2.3k/s ||
|| 42% completed, 0 mins elapsed, total=20k frags, rate=2.3k/s ||
|| 48% completed, 0 mins elapsed, total=20k frags, rate=2.3k/s ||
|| 54% completed, 0 mins elapsed, total=19k frags, rate=2.3k/s ||
|| Detect indels... ||
|| 60% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 61% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 62% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 63% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 64% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 65% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 66% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 67% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 68% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| Realign fragments... ||
|| 70% completed, 0 mins elapsed, total=19k frags, rate=1.5k/s ||
|| 71% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 72% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 73% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 74% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 75% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 76% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 77% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 78% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 19998 fragments were processed. Save the mapping results for them... ||
|| 81% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 83% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 85% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 87% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 89% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 91% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 93% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 95% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| 97% completed, 0 mins elapsed, total=19k frags, rate=1.4k/s ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 fragments ||
|| Mapped : 19513 fragments (97.6%) ||
|| Correctly paired : 19009 fragments ||
|| Indels : 7 ||
|| ||
|| Running time : 0.2 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6-p3
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment ||
|| Threads : 1 ||
|| Input file 1 : data/test-error-r1.fq ||
|| Input file 2 : data/test-error-r2.fq ||
|| Output file : tmp/test-tmp.sam5 (SAM) ||
|| Index name : tmp/small1 ||
|| Phred offset : 33 ||
|| ||
|| Min read1 votes : 3 ||
|| Min read2 votes : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : no ||
|| Hamming distance : yes ||
|| Quality scores : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (27-May-2015 05:43:58) ======================\\
|| ||
|| The input file contains base space reads. ||
|| Load the 1-th index block... ||
|| Map fragments... ||
|| 29% completed, 0 mins elapsed, total=20k frags, rate=2.5k/s ||
|| 35% completed, 0 mins elapsed, total=20k frags, rate=2.5k/s ||
|| 42% completed, 0 mins elapsed, total=20k frags, rate=2.5k/s ||
|| 48% completed, 0 mins elapsed, total=20k frags, rate=2.5k/s ||
|| 54% completed, 0 mins elapsed, total=20k frags, rate=2.5k/s ||
|| Detect indels... ||
|| 60% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 61% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 62% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 63% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 64% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 65% completed, 0 mins elapsed, total=20k frags, rate=1.6k/s ||
|| 67% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 68% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 69% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| Realign fragments... ||
|| 70% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 71% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 72% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 73% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 74% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 75% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 77% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 78% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 79% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 20000 fragments were processed. Save the mapping results for them... ||
|| 81% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 83% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 85% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 87% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 89% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 91% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 94% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 96% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 98% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 20000 fragments ||
|| Mapped : 19528 fragments (97.6%) ||
|| Correctly paired : 14234 fragments ||
|| Indels : 13 ||
|| ||
|| Running time : 0.2 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6-p3
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment ||
|| Threads : 1 ||
|| Input file 1 : data/test-err-mut-r1.fq.gz ||
|| Input file 2 : data/test-err-mut-r2.fq.gz ||
|| Output file : tmp/test-tmp.sam6 (SAM) ||
|| Index name : tmp/small1 ||
|| Phred offset : 33 ||
|| ||
|| Min read1 votes : 3 ||
|| Min read2 votes : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| ||
|| Max indels : 5 ||
|| # of Best mapping : 1 ||
|| Unique mapping : no ||
|| Hamming distance : yes ||
|| Quality scores : no ||
|| Read group name : MyTestGroup ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (27-May-2015 05:44:12) ======================\\
|| ||
|| Decompress data/test-err-mut-r1.fq.gz... ||
|| The input file contains base space reads. ||
|| Decompress data/test-err-mut-r2.fq.gz... ||
|| Load the 1-th index block... ||
|| Map fragments... ||
|| 29% completed, 0 mins elapsed, total=20k frags, rate=2.4k/s ||
|| 35% completed, 0 mins elapsed, total=20k frags, rate=2.4k/s ||
|| 41% completed, 0 mins elapsed, total=20k frags, rate=2.5k/s ||
|| 48% completed, 0 mins elapsed, total=20k frags, rate=2.5k/s ||
|| 54% completed, 0 mins elapsed, total=20k frags, rate=2.5k/s ||
|| Detect indels... ||
|| 60% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 61% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 62% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 63% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 64% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 65% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 67% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 68% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| 69% completed, 0 mins elapsed, total=20k frags, rate=1.5k/s ||
|| Realign fragments... ||
|| 70% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 71% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 72% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 73% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 74% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 75% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 77% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 78% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 79% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 20001 fragments were processed. Save the mapping results for them... ||
|| 81% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 83% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 85% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 87% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 89% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 91% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 94% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 96% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| 98% completed, 0 mins elapsed, total=20k frags, rate=1.4k/s ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 20001 fragments ||
|| Mapped : 19497 fragments (97.5%) ||
|| Correctly paired : 13881 fragments ||
|| Indels : 113 ||
|| ||
|| Running time : 0.2 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6-p3
//============================= exactSNP setting =============================\\
|| ||
|| Input file : data/test-in.BAM (BAM) ||
|| Output file : test-out.VCF ||
|| Reference genome : ../chr901.fa ||
|| ||
|| Threads : 1 ||
|| Min supporting reads : 1 ||
|| Min pct. of supporting reads : 0.0% ||
|| Min base quality score : 13 ||
|| Number of trimmed bases : 3 ||
|| ||
|| Q value cutoff : 10E-12.0 ||
|| P value upper bound : 0.00500 ||
|| Flanking windows size : 5 ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (27-May-2015 05:44:27) ======================\\
|| ||
|| Split BAM file into ./temp-snps-009358-7F883AB8-* ... ||
|| processed block chr901@999950 by thread 1/1 [block number=1/1] ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed reads : 50204 ||
|| Reported SNPs : 415 ||
|| Reported indels : 21 ||
|| ||
|| Running time : 0.1 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
make[1]: Leaving directory '/«BUILDDIR»/subread-1.4.6-p3+dfsg'
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/«BUILDDIR»/subread-1.4.6-p3+dfsg'
find /«BUILDDIR»/subread-1.4.6-p3+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \;
mkdir -p /«BUILDDIR»/subread-1.4.6-p3+dfsg/debian/subread/usr/share/man/man1
help2man --no-info --help-option="''" --no-discard-stderr --name='an accurate and efficient aligner for mapping both genomic \
DNA-seq reads and RNA-seq reads (for the purpose of expression analysis)' \
/«BUILDDIR»/subread-1.4.6-p3+dfsg/bin/subread-align | debian/filter.pl > /«BUILDDIR»/subread-1.4.6-p3+dfsg/debian/subread/usr/share/man/man1/subread-align.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='builds an base-space or color-space index using the reference sequences' \
/«BUILDDIR»/subread-1.4.6-p3+dfsg/bin/subread-buildindex | debian/filter.pl > /«BUILDDIR»/subread-1.4.6-p3+dfsg/debian/subread/usr/share/man/man1/subread-buildindex.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='an RNA-seq aligner suitable for all purposes of RNA-seq analyses' \
/«BUILDDIR»/subread-1.4.6-p3+dfsg/bin/subjunc | debian/filter.pl > /«BUILDDIR»/subread-1.4.6-p3+dfsg/debian/subread/usr/share/man/man1/subjunc.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='a highly efficient and accurate read summarization program' \
/«BUILDDIR»/subread-1.4.6-p3+dfsg/bin/featureCounts | debian/filter.pl > /«BUILDDIR»/subread-1.4.6-p3+dfsg/debian/subread/usr/share/man/man1/featureCounts.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='a SNP caller that discovers SNPs by testing signals against local background noises' \
/«BUILDDIR»/subread-1.4.6-p3+dfsg/bin/exactSNP | debian/filter.pl > /«BUILDDIR»/subread-1.4.6-p3+dfsg/debian/subread/usr/share/man/man1/exactSNP.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='detect short and long indels' \
/«BUILDDIR»/subread-1.4.6-p3+dfsg/bin/subindel | debian/filter.pl > /«BUILDDIR»/subread-1.4.6-p3+dfsg/debian/subread/usr/share/man/man1/subindel.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='scans the entire genome and reports all matches of a specified sequence' \
/«BUILDDIR»/subread-1.4.6-p3+dfsg/bin/utilities/subread-fullscan | debian/filter.pl > /«BUILDDIR»/subread-1.4.6-p3+dfsg/debian/subread/usr/share/man/man1/subread-fullscan.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='counting the coverage of mapped reads at each location on the entire reference genome' \
/«BUILDDIR»/subread-1.4.6-p3+dfsg/bin/utilities/coverageCount | debian/filter.pl > /«BUILDDIR»/subread-1.4.6-p3+dfsg/debian/subread/usr/share/man/man1/coverageCount.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='calculate the proportion of mapped reads/fragments' \
/«BUILDDIR»/subread-1.4.6-p3+dfsg/bin/utilities/propmapped | debian/filter.pl > /«BUILDDIR»/subread-1.4.6-p3+dfsg/debian/subread/usr/share/man/man1/propmapped.1;
for i in globalReassembly removeDup qualityScores subtools ; do \
help2man --no-info --help-option="''" --no-discard-stderr --name='a component of subread suite' /«BUILDDIR»/subread-1.4.6-p3+dfsg/bin/utilities/$i | debian/filter.pl > /«BUILDDIR»/subread-1.4.6-p3+dfsg/debian/subread/usr/share/man/man1/$i.1; \
done
dh_auto_install
make[1]: Leaving directory '/«BUILDDIR»/subread-1.4.6-p3+dfsg'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
debian/rules override_dh_compress
make[1]: Entering directory '/«BUILDDIR»/subread-1.4.6-p3+dfsg'
dh_compress -X.pdf -Xtest.tar.xz
make[1]: Leaving directory '/«BUILDDIR»/subread-1.4.6-p3+dfsg'
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package `subread' in `../subread_1.4.6-p3+dfsg-2_armhf.deb'.
dpkg-genchanges -B -mRaspbian nitrogen6x test autobuilder <root@raspbian.org> >../subread_1.4.6-p3+dfsg-2_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build subread-1.4.6-p3+dfsg
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20150527-0546
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
subread_1.4.6-p3+dfsg-2_armhf.changes:
──────────────────────────────────────
Format: 1.8
Date: Thu, 21 May 2015 20:56:14 +0200
Source: subread
Binary: subread subread-data
Architecture: armhf
Version: 1.4.6-p3+dfsg-2
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian nitrogen6x test autobuilder <root@raspbian.org>
Changed-By: Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
Description:
subread - toolkit for processing next-gen sequencing data
subread-data - data files for subread package
Changes:
subread (1.4.6-p3+dfsg-2) unstable; urgency=medium
.
* d/changelog: upload to unstable, forgot to include the amd64 architecture
in d/contorl
* d/control: added amd64 to Architecture
Checksums-Sha1:
b80b66026ef9130694370d19da8205c86dcda82e 355542 subread_1.4.6-p3+dfsg-2_armhf.deb
Checksums-Sha256:
60b972eee1cfb07edc4eb5df91dad6566f3cf32e893ef3cf3709c5a9c66ac485 355542 subread_1.4.6-p3+dfsg-2_armhf.deb
Files:
e4a87c90556a45ce336710d03ea725e0 355542 science optional subread_1.4.6-p3+dfsg-2_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
subread_1.4.6-p3+dfsg-2_armhf.deb
─────────────────────────────────
new debian package, version 2.0.
size 355542 bytes: control archive=1534 bytes.
626 bytes, 14 lines control
1965 bytes, 30 lines md5sums
Package: subread
Version: 1.4.6-p3+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4621
Depends: libc6 (>= 2.15), zlib1g (>= 1:1.2.3.3)
Section: science
Priority: optional
Homepage: http://sourceforge.net/projects/subread/
Description: toolkit for processing next-gen sequencing data
Subread aligner can be used to align both gDNA-seq and RNA-seq reads.
Subjunc aligner was specified designed for the detection of exon-exon
junction. For the mapping of RNA-seq reads, Subread performs local
alignments and Subjunc performs global alignments.
drwxr-xr-x root/root 0 2015-05-27 05:46 ./
drwxr-xr-x root/root 0 2015-05-27 05:45 ./usr/
drwxr-xr-x root/root 0 2015-05-27 05:45 ./usr/share/
drwxr-xr-x root/root 0 2015-05-27 05:45 ./usr/share/man/
drwxr-xr-x root/root 0 2015-05-27 05:46 ./usr/share/man/man1/
-rw-r--r-- root/root 2263 2015-05-27 05:45 ./usr/share/man/man1/subread-align.1.gz
-rw-r--r-- root/root 763 2015-05-27 05:45 ./usr/share/man/man1/subread-buildindex.1.gz
-rw-r--r-- root/root 2179 2015-05-27 05:45 ./usr/share/man/man1/subjunc.1.gz
-rw-r--r-- root/root 2523 2015-05-27 05:45 ./usr/share/man/man1/featureCounts.1.gz
-rw-r--r-- root/root 1174 2015-05-27 05:45 ./usr/share/man/man1/exactSNP.1.gz
-rw-r--r-- root/root 345 2015-05-27 05:45 ./usr/share/man/man1/subindel.1.gz
-rw-r--r-- root/root 287 2015-05-27 05:45 ./usr/share/man/man1/subread-fullscan.1.gz
-rw-r--r-- root/root 267 2015-05-27 05:45 ./usr/share/man/man1/coverageCount.1.gz
-rw-r--r-- root/root 464 2015-05-27 05:45 ./usr/share/man/man1/propmapped.1.gz
-rw-r--r-- root/root 342 2015-05-27 05:45 ./usr/share/man/man1/globalReassembly.1.gz
-rw-r--r-- root/root 268 2015-05-27 05:45 ./usr/share/man/man1/removeDup.1.gz
-rw-r--r-- root/root 318 2015-05-27 05:45 ./usr/share/man/man1/qualityScores.1.gz
-rw-r--r-- root/root 255 2015-05-27 05:45 ./usr/share/man/man1/subtools.1.gz
drwxr-xr-x root/root 0 2015-05-27 05:45 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-05-27 05:46 ./usr/share/doc/subread/
-rw-r--r-- root/root 3670 2014-10-15 04:44 ./usr/share/doc/subread/README.txt
-rw-r--r-- root/root 500 2015-05-21 18:58 ./usr/share/doc/subread/README.Debian
-rw-r--r-- root/root 1287 2015-05-21 18:58 ./usr/share/doc/subread/copyright
-rw-r--r-- root/root 1032 2015-05-21 18:58 ./usr/share/doc/subread/changelog.Debian.gz
drwxr-xr-x root/root 0 2015-05-27 05:46 ./usr/bin/
-rwxr-xr-x root/root 374940 2015-05-27 05:46 ./usr/bin/exactSNP
-rwxr-xr-x root/root 420188 2015-05-27 05:46 ./usr/bin/featureCounts
-rwxr-xr-x root/root 350380 2015-05-27 05:46 ./usr/bin/subindel
-rwxr-xr-x root/root 359180 2015-05-27 05:46 ./usr/bin/subjunc
-rwxr-xr-x root/root 359180 2015-05-27 05:46 ./usr/bin/subread-align
-rwxr-xr-x root/root 366724 2015-05-27 05:46 ./usr/bin/subread-buildindex
drwxr-xr-x root/root 0 2015-05-27 05:45 ./usr/lib/
drwxr-xr-x root/root 0 2015-05-27 05:46 ./usr/lib/subread/
-rwxr-xr-x root/root 350364 2015-05-27 05:46 ./usr/lib/subread/coverageCount
-rwxr-xr-x root/root 371036 2015-05-27 05:46 ./usr/lib/subread/globalReassembly
-rwxr-xr-x root/root 354476 2015-05-27 05:46 ./usr/lib/subread/propmapped
-rwxr-xr-x root/root 354588 2015-05-27 05:46 ./usr/lib/subread/qualityScores
-rwxr-xr-x root/root 350332 2015-05-27 05:46 ./usr/lib/subread/removeDup
-rwxr-xr-x root/root 350332 2015-05-27 05:46 ./usr/lib/subread/subread-fullscan
-rwxr-xr-x root/root 350428 2015-05-27 05:46 ./usr/lib/subread/subtools
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 85828
Build-Time: 565
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 165
Job: subread_1.4.6-p3+dfsg-2
Machine Architecture: armhf
Package: subread
Package-Time: 805
Source-Version: 1.4.6-p3+dfsg-2
Space: 85828
Status: successful
Version: 1.4.6-p3+dfsg-2
────────────────────────────────────────────────────────────────────────────────
Finished at 20150527-0546
Build needed 00:13:25, 85828k disc space