I am running a trinity RNASeq Assembly software on Ubuntu server and the following error is occuring for Pair-end reads input.
can't locate auto/threads/error.al in @INC (@INC contains:
I checked for threads library and it's already in the perl library.
Any thoughts on this?
$ perl -V
Summary of my perl5 (revision 5 version 8 subversion 8) configuration:
Platform:
osname=linux, osvers=2.6.9-42.0.3.elsmp, archname=x86_64-linux-thread-multi
uname='linux builder6.centos.org 2.6.9-42.0.3.elsmp #1 smp fri oct 6 06:28:26 cdt 2006 x86_64 x86_64 x86_64 gnulinux '
config_args='-des -Doptimize=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -Dversion=5.8.8 -Dmyhostname=localhost -Dperladmin=root@localhost -Dcc=gcc -Dcf_by=Red Hat, Inc. -Dinstallprefix=/usr -Dprefix=/usr -Dlibpth=/usr/local/lib64
/lib64 /usr/lib64 -Dprivlib=/usr/lib/perl5/5.8.8
-Dsitelib=/usr/lib/perl5/site_perl/5.8.8 -Dvendorlib=/usr/lib/perl5/vendor_perl/5.8.8 -Darchlib=/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi -Dsitearch=/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi -Dvendorarch=/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
-Darchname=x86_64-linux -Dvendorprefix=/usr -Dsiteprefix=/usr -Duseshrplib -Dusethreads -Duseithreads -Duselargefiles -Dd_dosuid -Dd_semctl_semun -Di_db -Ui_ndbm -Di_gdbm -Di_shadow -Di_syslog -Dman3ext=3pm -Duseperlio -Dinstallusrbinperl=n -Ubincompat5005 -Uversiononly -Dpager=/usr/bin/less -isr -Dd_gethostent_r_proto -Ud_endhostent_r_proto -Ud_sethostent_r_proto -Ud_endprotoent_r_proto -Ud_setprotoent_r_proto -Ud_endservent_r_proto -Ud_setservent_r_proto -Dinc_version_list=5.8.7 5.8.6 5.8.5 -Dscriptdir=/usr/bin'
hint=recommended, useposix=true, d_sigaction=define
usethreads=define use5005threads=undef 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 -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm',
optimize='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic',
cppflags='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -I/usr/include/gdbm'
ccversion='', gccversion='4.1.1 20070105 (Red Hat 4.1.1-52)', 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 =''
libpth=/usr/local/lib64 /lib64 /usr/lib64
libs=-lresolv -lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lpthread -lc
perllibs=-lresolv -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc
libc=, so=so, useshrplib=true, libperl=libperl.so
gnulibc_version='2.5' Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E -Wl,-rpath,/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE'
cccdlflags='-fPIC', lddlflags='-shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic'
Characteristics of this binary (from libperl): Compile-time
options: MULTIPLICITY PERL_IMPLICIT_CONTEXT
PERL_MALLOC_WRAP USE_64_BIT_ALL USE_64_BIT_INT
USE_ITHREADS USE_LARGE_FILES USE_PERLIO
USE_REENTRANT_API Built under linux Compiled at Nov 8 2007 06:49:06 %ENV:
PERL5LIB="/fs/home/anuphap/usr/lib/perl5:/fs/home/anuphap/usr/lib/perl5/site_perl:/fs/home/anuphap/usr/lib64/perl5:/fs/home/anuphap/usr/lib64/perl5/site_perl"
@INC:
/fs/home/anuphap/usr/lib/perl5/5.8.8
/fs/home/anuphap/usr/lib/perl5
/fs/home/anuphap/usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
/fs/home/anuphap/usr/lib/perl5/site_perl/5.8.8
/fs/home/anuphap/usr/lib/perl5/site_perl
/fs/home/anuphap/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi
/fs/home/anuphap/usr/lib64/perl5/5.8.8
/fs/home/anuphap/usr/lib64/perl5
/fs/home/anuphap/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
/fs/home/anuphap/usr/lib64/perl5/site_perl/5.8.8
/fs/home/anuphap/usr/lib64/perl5/site_perl
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
/usr/lib64/perl5/site_perl/5.8.7/x86_64-linux-thread-multi
/usr/lib64/perl5/site_perl/5.8.6/x86_64-linux-thread-multi
/usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.8
/usr/lib/perl5/site_perl/5.8.7
/usr/lib/perl5/site_perl/5.8.6
/usr/lib/perl5/site_perl/5.8.5
/usr/lib/perl5/site_perl
/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
/usr/lib64/perl5/vendor_perl/5.8.7/x86_64-linux-thread-multi
/usr/lib64/perl5/vendor_perl/5.8.6/x86_64-linux-thread-multi
/usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.8
/usr/lib/perl5/vendor_perl/5.8.7
/usr/lib/perl5/vendor_perl/5.8.6
/usr/lib/perl5/vendor_perl/5.8.5
/usr/lib/perl5/vendor_perl
/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi
/usr/lib/perl5/5.8.8
You need to install a version of Perl that has threads support. How to install:
Read both INSTALL and README.yoursystem for more detailed information.