[Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103"

[sheetal gosrani]

Adding some more details on OS and BioPerl version

OS:
sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a
Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 07:54:58
UTC 2010 i686 GNU/Linux

Perl :  v5.10.1 (*) built for i486-linux-gnu-thread-multi

BioPerl Version :
sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl -MBio::Root::Version -e
'print $Bio::Root::Version::VERSION,"\n"'
1.006001

Attached is the error that I get while running the RemoteBlast.

Thanks,
Sheetal

On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani
<sheetu.piscean at gmail.com>wrote:

> Hi,
>
> I am trying to run RemoteBlast to blastx sequences on 'nr' database. Here
> is the complete script :
>   #Remote-blast "factory object" creation and blast-parameter
> initialization
>
>   use Bio::Tools::Run::RemoteBlast;
>   use strict;
>   my $prog = 'blastx';
>   my $db   = 'nr/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);
>
>   $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx';
>
>   #$v is just to turn on and off the messages
>   my $v = 0;
>
>   my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , -format => 'fasta'
> );
>
>   while (my $input = $str->next_seq()){
>     #Blast a sequence against a database:
>
>     #Alternatively, you could  pass in a file with many
>     #sequences rather than loop through sequence one at a time
>     #Remove the loop starting 'while (my $input = $str->next_seq())'
>     #and swap the two lines below for an example of that.
>     my $r = $factory->submit_blast($input);
>     #my $r = $factory->submit_blast('amino.fa');
>
>     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 ) {
>             print "removing rid as rc is < 0";
>             $factory->remove_rid($rid);
>           }
>           print STDERR "." if ( $v > 0 );
>           sleep 5;
>         } else {
>           my $result = $rc->next_result();
>           #save the output
>           print "saving to file";
>           my $filename = "contig_236.out"; #$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";
>             }
>           }
>         }
>       }
>     }
>   }
>
> But when I run this, I get an error in html format which says "Cannot
> accept request, error code: -103". Attaching the error file for reference.
> Can you please help me with debugging this error? Your help is much
> appreciated.
>
> Also, informing about the previous error that I fixed by adding this line:
> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; The error that
> I was getting prior to adding this line was :
> --------------------- WARNING ---------------------
> MSG: <hr><p id="blastErr"><font color="red">An error has occurred on the
> server, The server is unable to format right now, please try again in a few
> minutes.  If the problem  (Informational Message: No alias or index file
> found for protein database [nr/nt] in search path
> [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists
> -  Contact Blast-help at ncbi.nlm.nih.gov and include your RID:
> 4CF5MY9101P</font></p><hr>
>
> It kinda took me a while to find out the 2 requirements<http://www.bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast>
>
> # 1) set your database like this:
>  -database => 'cdsearch/cdd', # c.f. http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for other cdd database options
>
>
> # 2) add this line before submitting the job:
> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast';
>
> I think it will be great if you can add this to the synopsis section of
> RemoteBlast.pm
>
> Thanks,
> Sheetal
>
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