[Bioperl-l] Newbie StandAloneBlast - too many files?
Keith Anthony Boroevich
kaboroev at sfu.ca
Wed Feb 12 01:04:34 EST 2003
hi,
i am running looped stand alone blast of 88 100pb sequences and around
the 80th or so sequence i recieve the error...
>Uncaught exception from user code:
>Error in tempfile() using /tmp/XXXXXXXXXX: Could not create temp file
/tmp/K6eorI51Yw: Too many open files at
/usr/lib/perl5/site_perl/5.6.1/Bio/Root/IO.pm line 614
>Carp::croak('Error in tempfile() using /tmp/XXXXXXXXXX: Could not
create temp...') called at /usr/lib/perl5/5.6.1/File/Temp.pm line 1052
>File::Temp::tempfile('UNLINK', 1, 'DIR', '/tmp') called at
/usr/lib/perl5/site_perl/5.6.1/Bio/Root/IO.pm line 614
>Bio::Root::IO::tempfile('Bio::Root::IO=HASH(0x8c5989c)') called at
/usr/lib/perl5/site_perl/5.6.1/Bio/Tools/Run/StandAloneBlast.pm line 706
>
>Bio::Tools::Run::StandAloneBlast::_setinput('Bio::Tools::Run::StandAloneBlast=HASH(0x8c47024)', 'blastall', 'Bio::Seq=HASH(0x8f91528)') called at /usr/lib/perl5/site_perl/5.6.1/Bio/Tools/Run/StandAloneBlast.pm line 483
>
>Bio::Tools::Run::StandAloneBlast::blastall('Bio::Tools::Run::StandAloneBlast=HASH(0x8c47024)', 'Bio::Seq=HASH(0x8f91528)') called at ../bce.pl line 115
>
>[2]+ Exit 24 ../bce.pl orangutan.fas
>orangutan.blast (wd: ~/mager/primate)
this however is only my testing set and i will "hopefully" be running
hundreds to thousands of 100bp sequences through this. Any suggestions
would be gratly appriciated
Keith
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