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

Fri Jul 18 02:12:10 UTC 2008

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;
>
> ..
>
>
>
>
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign