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

Chris Fields cjfields at uiuc.edu
Fri Jul 18 14:53:03 EDT 2008


On Jul 18, 2008, at 1:38 PM, Alicia Amadoz wrote:

> Hi,
>
> I have tried >telnet www.ncbi.nlm.nih.gov 80 and it gives what you  
> said,
>
> $ telnet www.ncbi.nlm.nih.gov 80
> Trying 130.14.29.110...
> Connected to www.ncbi.nlm.nih.gov.
> Escape character is '^]'.
>
> I don't know exactly who gives the output message with the error. It  
> creates a file as my
> script is launched. The file is called "delete" and is like de  
> STDERR/STDOUT of the script. I
> haven't programmed anything to create this file, but I can say that  
> the message of error is
> given just after this line:
>
> my $submit = $remote->submit_blast($query_filepath."/". 
> $query_filename);

 From the original script you appear to be running things from a PHP  
environment, so maybe it has something to do with that, e.g. maybe you  
need to set other env. settings (like a proxy) in order to connect.

You can test this; in the same script, try using another module which  
makes remote connections.  For instance, try the following to see if  
you have a similar error:

use Bio::DB::GenBank;

my $gb = Bio::DB::GenBank->new();

my $seqio = $gb->get_Stream_by_id([qw(J00522 AF303112 2981014)]);

while (my $seq = $seqio->next_seq) {
     print $seq->accession_number."\n";
}

> So, I don't know if the message is given by bioperl functions or by  
> the ncbi.

By LWP, actually.  The BLAST request is retrieved using the RID and if  
there is an error flag, either due to connection issues or from a  
problem on their server, an exception is thrown with the proper  
message which the module catches and converts into the relevant  
display message.

> Any help at this point? Thanks a lot in advance.
>
> Regards,
> Alicia


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