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

sheetal gosrani sheetu.piscean at gmail.com
Fri Jul 23 14:15:51 EDT 2010


Thanks a lot Chris. It worked for me as well :)

- Sheetal

On Fri, Jul 23, 2010 at 10:36 AM, Chris Fields <cjfields at illinois.edu>wrote:

> I've attached the code and example data that worked.  This is using the
> latest bioperl on github, so maybe it's the version you have installed?
>
> chris
>
> On Fri, 2010-07-23 at 10:04 -0700, sheetal gosrani wrote:
> > 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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