[Bioperl-l] RE: problem connecting to remote blast
Stefan Kirov
skirov at utk.edu
Thu Oct 2 10:20:59 EDT 2003
Did you try to run your search from the web interface as well? Did it
work? Looking at the error you get I guess something might be wrong with
your test.txt file: format violation, size, etc. Try it from the web
interface (or if you have the db and blastn locally) to validate the input.
Good luck
Stefan
Jason Stajich wrote:
>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
>_______________________________________________
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>
>
--
Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
1060 Commerce Park, Oak Ridge
TN 37830-8026
USA
tel +865 576 5120
fax +865 241 1965
e-mail: skirov at utk.edu
sao at ornl.gov
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