[Bioperl-l] RE: problem connecting to remote blast

[Jason Stajich]

I really don't know - i don't really have time to debug this for you I'm
sorry - please post your question to the bioperl list.

On Mon, 29 Sep 2003, 010381P GOH PHUAY CHENG wrote:

> hi,
> i have already remove the entrez query part but i still encountered the same
> warning.
>
> 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,
>          '-expect' => $e_val,
>          '-readmethod' => 'SearchIO' );
>   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";
>             }
>           }
>         }
>       }
>     }
>   }
>
> -------------------- 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: 1064815728-21972-271666.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>
>
>
> ---------------------------------------------------
>
>
>
>
> -----Original Message-----
> From:	Jason Stajich [mailto:jason at cgt.duhs.duke.edu]
> Sent:	Mon 9/29/2003 9:32 AM
> To:	010381P GOH PHUAY CHENG
> Cc:
> Subject:	Re: problem connecting to remote blast
>
> I suppose it might be because you specified an entrez query for homo
> sapiens on the ecoli db - that is not going to return any hits.  remove
> the entrez query part perhaps.
>
> please post your questions to the bioperl list in the future -
> bioperl-l at bioperl.org
>
> Thanks,
> -jason
>
> On Mon, 29 Sep 2003, 010381P GOH PHUAY CHENG wrote:
>
> > hi Jason,
> > i encountered some problems running the remote blast.could u please check
> for
> > me wats wrong with my codes. Thanks.
> >
> > phuay cheng
> >
> > -------------------- 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: 1064796976-1676-2574126.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>
> >
> >
> > ---------------------------------------------------
> >
> > #!/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,
> >          '-readmethod' => 'SearchIO' );
> >   my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
> >
> >   $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens
> > [ORGN]';
> >
> >   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";
> >             }
> >           }
> >         }
> >       }
> >     }
> >   }
> >
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>
>
>
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu