[Bioperl-l] Newbie StandAloneBlast - too many files?

[Brian Osborne]

Keith,

Which Bioperl version? Various people have been saying this problem is fixed
in version 1.2.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at bioperl.org [mailto:bioperl-l-bounces at bioperl.org]On
Behalf Of Keith Anthony Boroevich
Sent: Wednesday, February 12, 2003 4:05 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Newbie StandAloneBlast - too many files?

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::StandAloneBla
st=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::StandAloneBlas
t=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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