[Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103"
sheetal gosrani
sheetu.piscean at gmail.com
Wed Jul 21 21:49:25 UTC 2010
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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