[Bioperl-l] bl2seq memory problem?

[Steven Cannon]

Hello -

I am running into a problem with bl2seq. It chokes on about the 250th 
query, regardless of data set. I have seen this with v.1.02 and with 
v.1.2 (after adding WrapperBase.pm back in). I am on OS X, v. 10.1.5. 
Here is a bit of code that produces the problem, and the error message. 
The input in this case was a fasta file with ~ 40 protein sequences, 
though as I say, I see the problem with various data sets. Any 
suggestions?

Thanks - Steve Cannon

#!/usr/bin/perl -w
# A little script to test bl2seq
# Blasts all seqs in a fasta file against all
# Steven Cannon, March 2003, based on bptutorial.pl
use strict;
use Bio::SeqIO;
use Bio::Tools::BPbl2seq;
use Bio::Tools::Run::StandAloneBlast;
unless(@ARGV) { die "usage: perl $0 <path_to_fasta_input_file>\n" }
my $infile = $ARGV[0];
print "Input file: $infile\n";
my $factory = Bio::Tools::Run::StandAloneBlast->new('program' => 
'blastp');
my $in1 = Bio::SeqIO->new(-file=>"$infile" , '-format' => 'Fasta', );
my $counter = 0;
while (my $seq1 = $in1->next_seq() ) {
   my $seq1_id = $seq1->display_id();
   my $in2 = Bio::SeqIO->new(-file=>"$infile" , '-format' => 'Fasta', );
   while (my $seq2 = $in2->next_seq() ) {
     $counter++;
     my $seq2_id = $seq2->display_id();
     print "$counter\t$seq2_id\t$seq2_id\t";
     my $bl2seq_report = $factory->bl2seq($seq1, $seq2);
     while (my $hsp = $bl2seq_report->next_feature) {
       my $P = $hsp->P;
       print "$P\n";
       last; # we care only about the top HSP
     }
   }
}

... and the error message, near the 246th - 249th successful blast query 
(differs slightly with program context, but seems to be 
data-independent):

247     At4g21760_10527x        At4g21760_10527x        1e-65
248     At4g22100_10673x        At4g22100_10673x        [bl2seq] 
WARNING:  [000.000]  Unable to open BLOSUM62
[bl2seq] WARNING:  [000.000]  BlastScoreBlkMatFill returned non-zero 
status
[bl2seq] WARNING:  [000.000]  SetUpBlastSearch failed.

------------- EXCEPTION  -------------
MSG:  No hit object found for bl2seq report

STACK Bio::Tools::BPbl2seq::next_feature 
/Library/Perl/Bio/Tools/BPbl2seq.pm:231
STACK toplevel bl2seq0.02d.pl:27

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