[Bioperl-l] Bio_Tools_Run_RemoteBlast error: 500 Can't connect to www.ncbi.nlm.nih.gov:80

Fri Jul 18 08:25:08 UTC 2008

Hi Chris,

Thank you very much for your comment.

The thing is that my script doesn't run in the most recent version of bioperl (1.5.2) and it 
works with the previous version (1.4). So, I would like to know if anything related to 
Bio::Tools:Run::RemoteBlast has changed that could throw me the error of 

> > 500 Can't connect to www.ncbi.nlm.nih.gov:80 (Bad hostname 'www.ncbi.nlm.nih.gov 
> > ')

Or anyone has an idea of why it gives this error?

Thank you very much in advance.
Alicia

> You need to update to a recent version of bioperl (1.4 is too old).
> 
> chris
> 
> On Jul 17, 2008, at 4:17 AM, Alicia Amadoz wrote:
> 
> > Hi,
> >
> > I am installing my bioperl script into a new server and I have an  
> > error that I don't know how
> > to solve. Once I have launched my script at the new server, it  
> > appears a file named "delete"
> > that has the following error:
> >
> > -------------------- WARNING ---------------------
> > MSG: req was POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
> > User-Agent: bioperl-Bio_Tools_Run_RemoteBlast/1.005002102
> > Content-Length: 610
> > Content-Type: application/x-www-form-urlencoded
> >
> > DATABASE=nr&QUERY=%3Ee3768n+ 
> > %0Aggtgcccactggggagtcctagcgggcatagcgtatttctccatggtg
> > gggaactgggcgaaggtcctgctagtgctgttgttgtttgccggcgtcgatgcggaaacctacatcaccggg
> > 
ggggccgtcgccaaggccgcgcttggattcactgggtttttcacttcgggccccaagcaggacatccagctaatcaactccaacgg
> > cagttggcacatcaatcgtactgccttgaactgtaatgcgagcctcgaaaccggctggatagcgg
> > 
ggctcctctatcacaacagattcaactcttcaggctgccccgagaggatggccagctgtagacccctcgccgacttcgaccagggct
> > ggggccctatcagctacgccaacggaagcggccccgatcaccgcccc&COMPOSITION_BASE
> > D_STATISTICS 
> > =off&EXPECT=10&SERVICE=plain&FORMAT_OBJECT=Alignment&ALIGNMENTS=
> > Pairwise 
> > &CMD=Put&FILTER=m&DESCRIPTIONS=100&PROGRAM=blastn&ALIGNMENT_VIEW=P
> > a
> > irwise
> >
> > <HTML>
> > <HEAD><TITLE>An Error Occurred</TITLE></HEAD>
> > <BODY>
> > <H1>An Error Occurred</H1>
> > 500 Can't connect to www.ncbi.nlm.nih.gov:80 (Bad hostname 'www.ncbi.nlm.nih.gov 
> > ')
> > </BODY>
> > </HTML>
> >
> > ---------------------------------------------------
> >
> > My script works ok in my current machine, a fedora 5 with bioperl  
> > 1.4 installed through
> > cpan. The new server is a fedora 8 and we installed bioperl and  
> > bioperl run 1.5.2 through
> > yumex installer. Both machines have perl 5.8.8 installed.
> >
> > Any idea of how to solve this error?? Thank you very much in advance.
> >
> > Alicia
> >
> > Here you are a part of my script:
> >
> > #!/usr/bin/perl
> >
> > use Bio::Seq;
> > use Bio::SeqIO;
> > use Bio::SearchIO;
> > use Bio::DB::GenBank;
> > use Bio::Tools::Run::RemoteBlast;
> > use POSIX;
> > use strict;
> > use File::Copy;
> >
> > # Blast using RemoteBlast
> > # get php variables
> >
> > my $query_filename = $ARGV[0];
> > my $query_filepath = $ARGV[1];
> > my $database = $ARGV[2];
> > my $program = $ARGV[3];
> > my $ALIGNMENTS = $ARGV[5];
> > my $ALIGNMENT_VIEW = $ARGV[5];
> > my $DESCRIPTIONS = $ARGV[6];
> > my $EXPECT = $ARGV[7];
> > # maybe "novar" variables
> > my $FILTER_1 = $ARGV[8];
> > my $FILTER_2 = $ARGV[9];
> > my $LCASE_MASK = $ARGV[10];
> > my $MEGABLAST = $ARGV[11];
> > my $UNGAPPED_ALIGNMENT = $ARGV[12];
> > my $user_name = $ARGV[13];
> > my $perlfunc_path = $ARGV[14];
> > my $input = $ARGV[15];
> > my $format = $ARGV[16];
> >
> > my $ENTREZ_QUERY = $ARGV[17];
> >
> > my @params = ('-prog' => $program, '-data' => $database, '-expect'  
> > => $EXPECT, '-
> > readmethod' => 'SearchIO');
> >
> > my $remote = Bio::Tools::Run::RemoteBlast->new(@params);
> > # change query parameters
> > $Bio::Tools::Run::RemoteBlast::HEADER{'ALIGNMENTS'} = $ALIGNMENTS;
> > $Bio::Tools::Run::RemoteBlast::HEADER{'ALIGNMENT_VIEW'} =  
> > $ALIGNMENT_VIEW;
> > $Bio::Tools::Run::RemoteBlast::HEADER{'DESCRIPTIONS'} = $DESCRIPTIONS;
> >
> > ..
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Marie-Claude Hofmann
> College of Veterinary Medicine
> University of Illinois Urbana-Champaign
> 
> 
> 
> 
> 
> 