[Bioperl-l] HELP PLEASE. (too many open file problem)

[Gudmundur Arni Thorisson]

   See the discussion a couple of days ago on this topic  ('too many open 
files'). According to Jason's mail on this issue, the 
Bio::Tools::Run::StandAloneBlast tempfile-problem has been eliminated in 
recent Bioperl release (or was that just in bioperl-live CVS, Jason, not 
in the current release?)


                    Mummi

On Friday, November 8, 2002, at 06:32 AM, Perl yang wrote:

> Dear bioperl people,
>
> Part of scripts of mine:
>
> @params = ('program'  => 'blastp',
>              'outfile' => 'bl2seq.out');
> $factory =
> Bio::Tools::Run::StandAloneBlast->new(@params);
>
> FOR LOOP{
> $report = $factory->bl2seq( $input1, $input2);
> $hsp = $report->next_feature;
> print $hsp->percent;
> }
>
> The following is what people post before. I have the
> exactly same error message. 'can't find Carp/Heavy.pm'
>
> Which file handles should I close? and How?
>
> Many thanks. I appreciate your help very much.
>
> Peter
>
>
>
>
> ----------------------------------------------------
> 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
>
> -----------------------------------------------
> 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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