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

[Chris Fields]

The errors reported seem to indicate problems on the NCBI server, not problems with the script.  Is this still occurring?

chris

On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote:

> 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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