[Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103"
sheetal gosrani
sheetu.piscean at gmail.com
Fri Jul 23 18:15:51 UTC 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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