[Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103"
sheetal gosrani
sheetu.piscean at gmail.com
Fri Jul 23 00:30:24 UTC 2010
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<http://blast.ncbi.nlm.nih.gov/Blast.cgiUser-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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