[Bioperl-l] Questions: CoreLib [001.000] 1>: Failed to allocate 10000 bytes

[Jiang Holly]

Hi,
I've written a program to do local blast and extract information on the gene 
near to the hits.The program works well with fly genome,but it fail to work 
with human genome.Following error is suggested:

[NULL_Caption] FATAL ERROR: CoreLib [001.000] 1>: Failed to allocate 10000 
bytes
Is that due to the large datasize?
You are appratiated to help!


#! /usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;
use Bio::Seq;
use Bio::Tools::Run::StandAloneBlast;
use Bio::SearchIO;

my $bits=200;
my $infile=\"#defined inflie\";
my $database=\'##\';


open(OU,\">defined outfile\") or die \"cannot open output.\\n\";
print OU \"\\#Input :\\t\\t $infile\\n\";
print OU \"\\#Bits Limit:\\t$bits\\n\";
my @params=(\'database\' =>$database,
\'program\' =>\'blastn\',
\'e\' =>\'10\',
\'W\' =>\'15\',
\'_READMETHOD\' =>\'Blast\');

my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
my $io=Bio::SeqIO->new(\'-file\' => $infile,
\'-format\' =>\'fasta\');
my $Oinseq;

while($Oinseq=$io->next_seq)
{
my $blast_report = $factory->blastall($Oinseq);
print \"blast\\n\";

my $hsptable;
my $searchio = new Bio::SearchIO(\'-file\' => $blast_report->file);
my $blast_result = $searchio->next_result;
while (my $hit=$blast_result->next_hit)
{ my $hitbits = $hit->bits();
$hitbits =~s/^e/1e/;
next if ($hitbits<=$bits);

while (my $hsp=$hit->next_hsp())
{ my $hspbits=$hsp->bits();
$hspbits=~s/^e/1e/;

if ($hspbits<=$bits)
{next;}
else
{$hsptable->{$hit->accession}->{$hsp->hstart}=$hsp->hend;
print\"hash\\n\";}
}
}
my $count=1;
my $acc;
my $hsphash;
my $hspst;
my $hspend;
my $eq;
my $aseq;
my $cseq;
my $Oseq;
my $read=1;
my $write=1;
my $bgene;
my $hgene;
while(($acc,$hsphash)=each %$hsptable)
{
my $ino = Bio::SeqIO->new(\'-file\'=>\"F:/data/$database/$acc.gbk\",
\'-format\'=>\'genbank\');
my $Oseq = $ino->next_seq;
print \" read $read\\n\";
my @feat=$Oseq->get_SeqFeatures();
print \"features\\n\";
$read++;


while(($hspst,$hspend)= each %$hsphash)
{ print OU \"#$count ACC: $acc\\tStart: $hspst\\tEnd: $hspend#\\n\";

$count++;
foreach my $feat(@feat)
{
if ($feat->primary_tag eq \'CDS\')
{ my $featend = $feat->end;
my $featstart = $feat->start;
if( ($hspst-$featend)>=0)
{ $bgene=\'\';
if ($feat->has_tag(\'gene\'))
{$bgene= join(\'\',$feat->each_tag_value(\'gene\'));
next;}
}
if (($hspend-$featstart)<=0)
{ $hgene=\'\';
if ($feat->has_tag(\'gene\'))
{$hgene= join(\'\',$feat->each_tag_value(\'gene\'));
last;}
}
}
}
#$eq=$Oseq->subseq($hspst-100,$hspend+100);
print OU \"$bgene and $hgene\\n\";
# print OU \"$eq \\n\\n\";

}
}

}






_______________________________________________
Bioperl-l mailing list
Bioperl-l at portal.open-bio.org
http://portal.open-bio.org/mailman/listinfo/bioperl

_________________________________________________________________
Tired of spam? Get advanced junk mail protection with MSN 8. 
http://join.msn.com/?page=features/junkmail