[Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103"
sheetal gosrani
sheetu.piscean at gmail.com
Fri Jul 23 13:04:59 EDT 2010
I did remove that line but doesn't help. I still keep getting this error:
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:
4KJE1YJ601N</font></p><hr>
Any pointers ??
- Sheetal
On Thu, Jul 22, 2010 at 6:52 PM, Chris Fields <cjfields at illinois.edu> wrote:
> Removing this line from your original script worked for me:
>
> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx';
>
> This is set via '-prog' parameter.
>
> chris
>
> On Jul 22, 2010, at 7:30 PM, sheetal gosrani wrote:
>
> > Yes the error is still occurring. I have emailed to Blast-help as well
> and they have to say that "there is something wrong with the URL, didn't
> give any specifics".
> >
> > Also changing the parameter SERVICE to 'plain' (by default it is set to
> plain, I guess this value is for standard blast pgm. like blastp, blastx,
> etc) gives me this error :
> > 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/blast1:/blast/db/disk.blast/blast1::])
> persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID:
> 4H2Y96KZ012 I have sent an email today to blast-help for this error.
> >
> > Adding below the email conversation with blast-help for debugging further
> :
> > On Thu, Jul 22, 2010 at 6:20 AM, Wayne Matten <mattenw at mail.nih.gov>
> wrote:
> > Sheetal,
> >
> > You are right about the query syntax, but your URL has some errors. The
> URL below works; note that order of parameters does not matter.
> >
> > Best regards,
> > Wayne
> >
> >
> http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=%3EContig_236+%0A%0DAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&CMD=Put&FILTER=L&PROGRAM=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&FORMAT_TYPE=Text
> >
> > On Jul 21, 2010, at 2:57 PM, sheetal gosrani wrote:
> >
> > Thank you Wayne. I tried with the sequence beginning immediately after
> "QUERY=", (called as bare sequence) but still I get the same error.
> >
> > The documentation on your URLAPI says that Query can have Accession(s),
> gi(S) or FASTA sequence. The format of the query for FASTA sequence is as
> shown:
> > http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml Thus for FASTA
> sequence, the query has description/definition followed by actual sequence.
> In that case, the format of my POST request match the requirement.
> >
> > Can you help me figure out why am I still getting error : "Cannot accept
> request, error code: -103" ? Attaching the log file having Query as bare
> sequence and FASTA sequence for your reference. Your help is much
> appreciated.
> >
> > Thanks,
> > Sheetal
> >
> > On Wed, Jul 21, 2010 at 7:45 AM, Wayne Matten <mattenw at mail.nih.gov>
> wrote:
> > Hello,
> >
> > Our URLAPI, which your script should, but may or may not use, requires
> that the sequence begin immediately after "QUERY=". Your example shows a
> definition line preceding the sequence. You can get documentation on our
> URLAPI on this page (Web service interface):
> >
> >
> http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo
> >
> > Best regards,
> > Wayne
> >
> > _~___~___~__~__~_~
> > Wayne Matten, PhD
> > NCBI Public Services
> > mattenw at mail.nih.gov
> >
> >
> > On Jul 20, 2010, at 4:49 PM, sheetal gosrani wrote:
> >
> > Hello,
> >
> > I am trying to use blastx program with 'nr' database in my Bioperl script
> remotely. While I do so, I get this error :
> > Cannot accept request, error code: -103
> >
> > The request that I send is :
> > POST http://blast.ncbi.nlm.nih.gov/Blast.cgi User-Agent:
> bioperl-Bio_Tools_Run_
> >> RemoteBlast/1.006001 Content-Length: 1945 Content-Type:
> application/x-www-form-urlencoded
> DATABASE=nr%2Fnt&QUERY=%3EContig_236+%0AAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGTCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastx
> >>
> >> Can you please help me debug it.
> >>
> >> Thanks and Regards,
> >> Sheetal
> >
> > Thanks
> > Sheetal
> >
> > On Thu, Jul 22, 2010 at 4:54 PM, Chris Fields <cjfields at illinois.edu>
> wrote:
> > 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
> > >>
> > > <log.html>_______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>
>
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