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perl-module-version
DBI - 1.627
DBD::mysql - 4.023
Raw
perl-pfam-ensembl-log
LSF Batch summary
Time Fri May 17 19:09:26 2013 (1368788966)
Job ID input ID analysis ID
20 chunk.543 Pfam
Running job 20
Module is ProteinAnnotation/Hmmpfam
Input id is chunk.543
Analysis is Pfam
Files are /home/u00wly00/ensembl_pipeline/protein_annotation/output/Pfam/2/chunk.543.Pfam.459.out /home/u00wly00/ensembl_pipeline/protein_annotation/output/Pfam/2/chunk.543.Pfam.459.err
Running:/home/u00wly00/ensembl_pipeline/prg/hmmer-3.0/bin/hmmscan --acc --noali --cut_ga --cpu 1 /home/u00wly00/ensembl_pipeline/db/pfam/Pfam-A.hmm /home/u00wly00/ensembl_pipeline/protein_annotation/chunks/chunk.543 > /tmp/Pfam.results.6121.60491.out
*** stack smashing detected ***: perl terminated
======= Backtrace: =========
/lib64/libc.so.6(__fortify_fail+0x37)[0x2ada30694877]
/lib64/libc.so.6(__fortify_fail+0x0)[0x2ada30694840]
/home/u00wly00/perl5/perlbrew/perls/perl-5.16.3/lib/site_perl/5.16.3/x86_64-linux-thread-multi/auto/DBD/mysql/mysql.so(+0xbd48)[0x2ada31b6ad48]
/home/u00wly00/perl5/perlbrew/perls/perl-5.16.3/lib/site_perl/5.16.3/x86_64-linux-thread-multi/auto/DBD/mysql/mysql.so(+0x126f2)[0x2ada31b716f2]
/home/u00wly00/perl5/perlbrew/perls/perl-5.16.3/lib/site_perl/5.16.3/x86_64-linux-thread-multi/auto/DBI/DBI.so(XS_DBI_dispatch+0xc79)[0x2ada3091c4a9]
perl(Perl_pp_entersub+0x602)[0x4a68e2]
perl(Perl_runops_standard+0x16)[0x49f086]
perl(perl_run+0x402)[0x43cbf2]
perl(main+0x123)[0x41ed33]
/lib64/libc.so.6(__libc_start_main+0xe6)[0x2ada305c7bc6]
perl[0x41ea85]
======= Memory map: ========
00400000-00571000 r-xp 00000000 1d8:db410 61356822 /home/u00wly00/perl5/perlbrew/perls/perl-5.16.3/bin/perl
00770000-00771000 r--p 00170000 1d8:db410 61356822 /home/u00wly00/perl5/perlbrew/perls/perl-5.16.3/bin/perl
00771000-00776000 rw-p 00171000 1d8:db410 61356822 /home/u00wly00/perl5/perlbrew/perls/perl-5.16.3/bin/perl
00776000-01f3e000 rw-p 00000000 00:00 0 [heap]
2ada2f6b9000-2ada2f6d8000 r-xp 00000000 08:03 79905035 /lib64/ld-2.11.1.so
2ada2f6d8000-2ada2f6d9000 rw-p 00000000 00:00 0
2ada2f6d9000-2ada2f6da000 r--p 00000000 08:03 16630469 /usr/lib/locale/zh_TW.utf8/LC_IDENTIFICATION
2ada2f6da000-2ada2f6e1000 r--s 00000000 08:03 16630986 /usr/lib64/gconv/gconv-modules.cache
2ada2f6e1000-2ada2f6e2000 r--p 00000000 08:03 16630971 /usr/lib/locale/zh_TW.utf8/LC_MEASUREMENT
2ada2f6e2000-2ada2f6e3000 r--p 00000000 08:03 16630826 /usr/lib/locale/zh_TW.utf8/LC_TELEPHONE
2ada2f6e3000-2ada2f6e4000 r--p 00000000 08:03 16630467 /usr/lib/locale/zh_TW.utf8/LC_ADDRESS
2ada2f6e4000-2ada2f6e5000 r--p 00000000 08:03 16630753 /usr/lib/locale/zh_TW.utf8/LC_NAME
2ada2f6e5000-2ada2f6e6000 r--p 00000000 08:03 16630968 /usr/lib/locale/zh_TW.utf8/LC_PAPER
2ada2f6e6000-2ada2f6e7000 r--p 00000000 08:03 16630754 /usr/lib/locale/zh_TW.utf8/LC_MESSAGES/SYS_LC_MESSAGES
2ada2f6e7000-2ada2f6e8000 r--p 00000000 08:03 16630827 /usr/lib/locale/zh_TW.utf8/LC_MONETARY
2ada2f6e8000-2ada2f805000 r--p 00000000 08:03 16630985 /usr/lib/locale/zh_TW.utf8/LC_COLLATE
2ada2f805000-2ada2f806000 r--p 00000000 08:03 16630470 /usr/lib/locale/zh_TW.utf8/LC_TIME
2ada2f806000-2ada2f807000 r--p 00000000 08:03 16630934 /usr/lib/locale/zh_TW.utf8/LC_NUMERIC
2ada2f807000-2ada2f846000 r--p 00000000 08:03 16630755 /usr/lib/locale/zh_TW.utf8/LC_CTYPE
2ada2f8d7000-2ada2f8d8000 r--p 0001e000 08:03 79905035 /lib64/ld-2.11.1.so
2ada2f8d8000-2ada2f8d9000 rw-p 0001f000 08:03 79905035 /lib64/ld-2.11.1.so
2ada2f8d9000-2ada2f8da000 rw-p 00000000 00:00 0
2ada2f8da000-2ada2f8ef000 r-xp 00000000 08:03 79904787 /lib64/libnsl-2.11.1.so
2ada2f8ef000-2ada2faee000 ---p 00015000 08:03 79904787 /lib64/libnsl-2.11.1.so
2ada2faee000-2ada2faef000 r--p 00014000 08:03 79904787 /lib64/libnsl-2.11.1.so
2ada2faef000-2ada2faf0000 rw-p 00015000 08:03 79904787 /lib64/libnsl-2.11.1.so
2ada2faf0000-2ada2faf3000 rw-p 00000000 00:00 0
2ada2faf3000-2ada2faf5000 r-xp 00000000 08:03 79904782 /lib64/libdl-2.11.1.so
2ada2faf5000-2ada2fcf5000 ---p 00002000 08:03 79904782 /lib64/libdl-2.11.1.so
2ada2fcf5000-2ada2fcf6000 r--p 00002000 08:03 79904782 /lib64/libdl-2.11.1.so
2ada2fcf6000-2ada2fcf7000 rw-p 00003000 08:03 79904782 /lib64/libdl-2.11.1.so
2ada2fcf7000-2ada2fd4c000 r-xp 00000000 08:03 79904784 /lib64/libm-2.11.1.so
2ada2fd4c000-2ada2ff4b000 ---p 00055000 08:03 79904784 /lib64/libm-2.11.1.so
2ada2ff4b000-2ada2ff4c000 r--p 00054000 08:03 79904784 /lib64/libm-2.11.1.so
2ada2ff4c000-2ada2ff4d000 rw-p 00055000 08:03 79904784 /lib64/libm-2.11.1.so
2ada2ff4d000-2ada2ff59000 r-xp 00000000 08:03 79904780 /lib64/libcrypt-2.11.1.so
2ada2ff59000-2ada30158000 ---p 0000c000 08:03 79904780 /lib64/libcrypt-2.11.1.so
2ada30158000-2ada30159000 r--p 0000b000 08:03 79904780 /lib64/libcrypt-2.11.1.so
2ada30159000-2ada3015a000 rw-p 0000c000 08:03 79904780 /lib64/libcrypt-2.11.1.so
2ada3015a000-2ada30189000 rw-p 00000000 00:00 0
2ada30189000-2ada3018b000 r-xp 00000000 08:03 79904810 /lib64/libutil-2.11.1.so
2ada3018b000-2ada3038a000 ---p 00002000 08:03 79904810 /lib64/libutil-2.11.1.so
2ada3038a000-2ada3038b000 r--p 00001000 08:03 79904810 /lib64/libutil-2.11.1.so
2ada3038b000-2ada3038c000 rw-p 00002000 08:03 79904810 /lib64/libutil-2.11.1.so
2ada3038c000-2ada303a3000 r-xp 00000000 08:03 79904802 /lib64/libpthread-2.11.1.so
2ada303a3000-2ada305a3000 ---p 00017000 08:03 79904802 /lib64/libpthread-2.11.1.so
2ada305a3000-2ada305a4000 r--p 00017000 08:03 79904802 /lib64/libpthread-2.11.1.so
2ada305a4000-2ada305a5000 rw-p 00018000 08:03 79904802 /lib64/libpthread-2.11.1.so
2ada305a5000-2ada305a9000 rw-p 00000000 00:00 0
2ada305a9000-2ada306fe000 r-xp 00000000 08:03 79904776 /lib64/libc-2.11.1.so
2ada306fe000-2ada308fd000 ---p 00155000 08:03 79904776 /lib64/libc-2.11.1.so
2ada308fd000-2ada30901000 r--p 00154000 08:03 79904776 /lib64/libc-2.11.1.so
2ada30901000-2ada30902000 rw-p 00158000 08:03 79904776 /lib64/libc-2.11.1.so
2ada30902000-2ada30909000 rw-p 00000000 00:00 0
2ada30909000-2ada30927000 r-xp 00000000 1d8:db410 62412036 /home/u00wly00/perl5/perlbrew/perls/perl-5.16.3/lib/site_perl/5.16.3/x86_64-linux-thread-multi/auto/DBI/DBI.so
2ada30927000-2ada30b26000 ---p 0001e000 1d8:db410 62412036 /home/u00wly00/perl5/perlbrew/perls/perl-5.16.3/lib/site_perl/5.16.3/x86_64-linux-thread-multi/auto/DBI/DBI.so已經終止
u00wly00@alps1:~/ensembl_pipeline/protein_annotation>
Raw
suse-gcc-perl-version
u00wly00@alps1:~> gcc -v
使用內建 specs。
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib64/gcc/x86_64-suse-linux/4.7/lto-wrapper
目的：x86_64-suse-linux
配置為：../configure --prefix=/usr --infodir=/usr/share/info --mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 --enable-languages=c,c++,objc,fortran,obj-c++,java,ada --enable-checking=release --with-gxx-include-dir=/usr/include/c++/4.7 --enable-ssp --disable-libssp --disable-libitm --disable-plugin --with-bugurl=http://bugs.opensuse.org/ --with-pkgversion='SUSE Linux' --disable-libgcj --disable-libmudflap --with-slibdir=/lib64 --with-system-zlib --enable-__cxa_atexit --enable-libstdcxx-allocator=new --disable-libstdcxx-pch --enable-version-specific-runtime-libs --enable-linker-build-id --program-suffix=-4.7 --enable-linux-futex --without-system-libunwind --with-arch-32=i586 --with-tune=generic --build=x86_64-suse-linux
執行緒模型：posix
gcc version 4.7.2 20130108 [gcc-4_7-branch revision 195012] (SUSE Linux)
u00wly00@alps1:~> perl -V
Summary of my perl5 (revision 5 version 16 subversion 3) configuration:
Platform:
osname=linux, osvers=2.6.32.12-0.7-default, archname=x86_64-linux-thread-multi
uname='linux alps1 2.6.32.12-0.7-default #1 smp 2010-05-20 11:14:20 +0200 x86_64 x86_64 x86_64 gnulinux '
config_args='-de -Dprefix=/home/u00wly00/perl5/perlbrew/perls/perl-5.16.3 -Dcc=gcc -Dnoextensions=ODBM_File -Dusethreads -Duse64bitint -Aeval:scriptdir=/home/u00wly00/perl5/perlbrew/perls/perl-5.16.3/bin'
hint=recommended, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='gcc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2',
cppflags='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion='', gccversion='4.7.2 20130108 [gcc-4_7-branch revision 195012]', gccosandvers=''
intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16
ivtype='long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
alignbytes=8, prototype=define
Linker and Libraries:
ld='gcc', ldflags =' -fstack-protector -L/usr/local/lib'
libpth=/usr/local/lib /lib/../lib64 /usr/lib/../lib64 /lib /usr/lib /lib64 /usr/lib64 /usr/local/lib64
libs=-lnsl -lgdbm -ldl -lm -lcrypt -lutil -lpthread -lc -lgdbm_compat
perllibs=-lnsl -ldl -lm -lcrypt -lutil -lpthread -lc
libc=/lib/libc-2.11.1.so, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.11.1'
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
cccdlflags='-fPIC', lddlflags='-shared -O2 -L/usr/local/lib -fstack-protector'
Characteristics of this binary (from libperl):
Compile-time options: HAS_TIMES MULTIPLICITY PERLIO_LAYERS
PERL_DONT_CREATE_GVSV PERL_IMPLICIT_CONTEXT
PERL_MALLOC_WRAP PERL_PRESERVE_IVUV USE_64_BIT_ALL
USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
USE_LOCALE USE_LOCALE_COLLATE USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC USE_PERLIO USE_PERL_ATOF
USE_REENTRANT_API
Built under linux
Compiled at May 17 2013 15:03:58
%ENV:
PERLBREW_BASHRC_VERSION="0.63"
PERLBREW_HOME="/home/u00wly00/.perlbrew"
PERLBREW_MANPATH="/home/u00wly00/perl5/perlbrew/perls/perl-5.16.3/man"
PERLBREW_PATH="/home/u00wly00/perl5/perlbrew/bin:/home/u00wly00/perl5/perlbrew/perls/perl-5.16.3/bin"
PERLBREW_PERL="perl-5.16.3"
PERLBREW_ROOT="/home/u00wly00/perl5/perlbrew"
PERLBREW_VERSION="0.63"
@INC:
/home/u00wly00/perl5/perlbrew/perls/perl-5.16.3/lib/site_perl/5.16.3/x86_64-linux-thread-multi
/home/u00wly00/perl5/perlbrew/perls/perl-5.16.3/lib/site_perl/5.16.3
/home/u00wly00/perl5/perlbrew/perls/perl-5.16.3/lib/5.16.3/x86_64-linux-thread-multi
/home/u00wly00/perl5/perlbrew/perls/perl-5.16.3/lib/5.16.3
.
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