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

[Gisel, Andreas]

I tried to explicitly close the filehandling for this bl2seq.out file but my Perl knowledge is too poor to find out the name of this filehandle.

Originally I was reading the bl2seq.out file with the Bio::Tools::BPbl2seq module but I also tried with the Bio::AlignIO but I have the same problem except that it stops after half of the cycles than with BPbl2seq and I got a different error message:

------------- EXCEPTION  -------------
MSG: Could not open bl2seq.out for reading: Too many open files
STACK Bio::Root::IO::_initialize_io /usr/local/lib/perl5/site_perl/5.6.1/Bio/Root/IO.pm:244
STACK Bio::AlignIO::_initialize /usr/local/lib/perl5/site_perl/5.6.1/Bio/AlignIO.pm:357
STACK Bio::AlignIO::new /usr/local/lib/perl5/site_perl/5.6.1/Bio/AlignIO.pm:293
STACK Bio::AlignIO::new /usr/local/lib/perl5/site_perl/5.6.1/Bio/AlignIO.pm:306
STACK toplevel standaloneblast3a.pl:80
--------------------------------------

and line 80 is:

    74                  my $factory = Bio::Tools::Run::StandAloneBlast->new(    'prog' => 'blastn',
    75                                                                          'outfile' => 'bl2seq.out');
    76
    77                  print "A4 $count\n";
    78                  my $bl2seq_report = $factory->bl2seq($seq1, $seq2);
    79
    80                  my $str = Bio::AlignIO->new(-file=> 'bl2seq.out','-format' => 'bl2seq');
    81                  my $aln = $str->next_aln();
    82                  print"Length: ", $aln->length,"\n";


Thanks

Andreas


-----Original Message-----
From: Jason Stajich [mailto:jason@cgt.mc.duke.edu]
Sent: Thursday, July 04, 2002 8:24 PM
To: Gisel, Andreas
Cc: JDiggans@genelogic.com; bioperl-l@bioperl.org
Subject: RE: [Bioperl-l] Can't find Carp/Heavy.pm using BPbl2seq module


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
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>

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