[Bioperl-l] StandAloneFasta and Too many open files

[Dimitar Kenanov]

Hi guys,
yesterday i got the following error:

     'Too many open files at 
/usr/lib64/perl5/site_perl/5.10.0/Bio/Tools/Run/Alignment/StandAloneFasta.pm 
line 380'

from the following code:
------------
     my $ssout="my_seq_out.txt";
     print "SS:$tquery:\n:$tseq:\n";
     my @sargs=(
         'q' => '',
         'E' => '1',
         'w' => '100',
         'O' => "$ssout",
         'program' => "ssearch36",
         );
     my $fac_ss=Bio::Tools::Run::Alignment::StandAloneFasta->new(@sargs);
     $fac_ss->library($tmpseq);
     my @sreport=$fac_ss->run($tqtmp);

   foreach my $sr (@sreport){
       while(my $result=$sr->next_result){
           while(my $hit=$result->next_hit){
               while(my $hsp=$hit->next_hsp){
                   my $iden=$hsp->frac_identical;
                   $rv3=$iden;
#               print "IDEN:$iden:$rv1\n";
               }
           }
       }
   }
--------------------
I am using that code over several thousands of HSPs for which i get the 
sequence and then 'ssearch36' with it against another sequence. I was 
digging around the module StandAloneFasta but couldnt get where the 
problem is. There should be somewhere many opened filehandles but do not 
know where. I checked the module but couldnt find such filehandles. May 
be the problem is in the base modules.
I also checked and my script for left open filehandles and i have not. I 
found only that i can actually close SeqIO streams with '$stream->close' 
which i didnt see on the web documentation. So something positive out of 
this :) So i closed all my SeqIO streams and i still had the same problem.
Next i commented out the above code and rewrote my script into the 
following:
--------------
     my $ssout="my_seq_out.txt";
     my @sargs=("ssearch36 -q -E 1 -d 1 $tqtmp $tmpseq > $ssout");
     system(@sargs) == 0 or die "system @sargs failed: $!";

     my $sreport=Bio::SearchIO->new(-file => $ssout, -format => 'fasta');
     while(my $result=$sreport->next_result){
#    print Dumper($result);
         while(my $hit=$result->next_hit){
             while(my $hsp=$hit->next_hsp){

             my $iden=$hsp->frac_identical;
             $rv3=$iden;
#            print "IDEN:$iden:$rv1\n";
             }
         }
     }
---------------
Fortunately this code overcame the error message with too many 
filehandles. So the problem was indeed coming from the module or the 
modules behind it.

I have also read that one can change the number of how many files can be 
opened on the system but i didnt want to mess with that for now because 
i do not know what could be the implications of that.

Ok that is it. I just wanted to inform about my experience and to report 
the problem.

Cheers
Dimitar

-- 
Dimitar Kenanov
Postdoctoral research fellow
Protein Sequence Analysis Group
Bioinformatics Institute
A*STAR, Singapore
tel: +65 6478 8514