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

[Jason Stajich]

I find that I have these problems after I run a certain number of
iterations with my new PAML wrapper module - something is definitely not
being cleaned up/released, still to be investigated I guess.

 On Tue, 25 Jun 2002, Gisel, Andreas wrote:

>
> 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
>
>
>
>
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>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu