[Bioperl-l] problem with remote blast
010381P GOH PHUAY CHENG
010381P at nyp.edu.sg
Mon Sep 29 02:16:45 EDT 2003
hi,
i am trying to connect to the remote blast. but i encountered the following
warnings. could u pls help me.
-------------------- WARNING ---------------------
MSG: <p><!--
QBlastInfoBegin
Status=READY
QBlastInfoEnd
--><p>
<b><FONT color="red">INFO: [blastsrv4.REAL]: Error: Segmentation violation
(or m
emory usage limit was exceeded) SIGSEGV (11).
</FONT></B><p><HR><p>
<PRE>
BLASTN 2.2.6 [Apr-09-2003]
<pre>RID: 1064815996-23369-1254165.BLASTQ3
Query= Test
(560 letters)
<b>No significant similarity found.</b> For reasons why, <A HREF =
"/blast/blast
_FAQs.html#no hits"><b>click here</A>.</b><br><br>
---------------------------------------------------
my codes:
#!/usr/bin/perl -w
use Bio::SeqIO;
use Bio::Tools::Run::RemoteBlast;
use strict;
my $prog = 'blastn';
my $db = 'ecoli.nt';
my $e_val= '1e-10';
my @params = ( '-prog' => $prog,
'-data' => $db,
);
my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};
my $v = 1;
my $str = Bio::SeqIO->new(-file=>'test.txt' , '-format' => 'fasta' );
while (my $input = $str->next_seq()){
#my $r = $factory->submit_blast($input);
my $r = $factory->submit_blast('test.txt');
print STDERR "waiting..." if( $v > 0 );
while ( my @rids = $factory->each_rid ) {
foreach my $rid ( @rids ) {
my $rc = $factory->retrieve_blast($rid);
if( !ref($rc) ) {
if( $rc < 0 ) {
$factory->remove_rid($rid);
}
print STDERR "." if ( $v > 0 );
sleep 5;
} else {
my $result = $rc->next_result();
#save the output
my $filename = $result->query_name()."\.out";
$factory->save_output($filename);
$factory->remove_rid($rid);
print "\nQuery Name: ", $result->query_name(), "\n";
while ( my $hit = $result->next_hit ) {
next unless ( $v > 0);
print "\thit name is ", $hit->name, "\n";
while( my $hsp = $hit->next_hsp ) {
print "\t\tscore is ", $hsp->score, "\n";
}
}
}
}
}
}
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