[Bioperl-l] Can't find Carp/Heavy.pm using BPbl2seq module

[Gisel, Andreas]

James,
thanks for the hint! Since I am new in Perl/Bioperl I don't now how to be sure that the files created by a Bioperl modul gets closed again. I am using the modul

my $factory = Bio::Tools::Run::StandAloneBlast->new(	'prog' => 'blastn',
									'outfile' => 'bl2seq.out');

that creats the file 'bl2seq.out'. When is this file closed again or do I have to close it???

Thanks

Andreas



-----Original Message-----
From: JDiggans@genelogic.com [mailto:JDiggans@genelogic.com]
Sent: Monday, June 24, 2002 9:14 PM
To: Gisel, Andreas
Cc: bioperl-l@bioperl.org
Subject: Re: [Bioperl-l] Can't find Carp/Heavy.pm using BPbl2seq module



I've run into this before; chances are you're opening too many files and
are running out of available file handles by the time you reach the 60th
iteration. Make sure you're closing the BLAST report file handles after
parsing each one. You can check/adjust how many file handles your processes
can have open by using the 'limit' UNIX command (IF you're on a Unix
machine).

HTH,
-j

-------------------------------------------------
James Diggans
Bioinformatics Programmer
Gene Logic, Inc.
Phone: 301.987.1756
FAX: 301.987.1701





                                                                                                                     
                      "Gisel, Andreas"                                                                               
                      <Andreas.Gisel@fm        To:       <bioperl-l@bioperl.org>                                     
                      i.ch>                    cc:                                                                   
                      Sent by:                 Subject:  [Bioperl-l] Can't find Carp/Heavy.pm using BPbl2seq module  
                      bioperl-l-admin@b                                                                              
                      ioperl.org                                                                                     
                                                                                                                     
                                                                                                                     
                      06/19/2002 08:28                                                                               
                      AM                                                                                             
                                                                                                                     
                                                                                                                     




Dear Bioperl users

I am new in the Perl/Bioperl world and run into the following problem I
don't know how to solve:

I am using Bio::Tools::Run::StandAloneBlast and Bio::Tools::BPbl2seq for
alignments between two DNA sequences (see below part of the script). The
modules run in a loop and work fin until the 60th loop and the I get an
error 'can't find Carp/Heavy.pm'. I checked and Carp/Heavy.pm it is at the
place where it should be!!

What is the problem and how can I solve it??

Thousand Thanks

Andreas Gisel