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

[Chris Fields]

Okay, so it appears there are overall connection issues (i.e. this  
isn't just a RemoteBlast issue).  The fact that you can ping from  
command line also makes me think it isn't a proxy issue.  I'm not  
familiar with PHP myself, but I would think it only allows user- 
defined processes to access network connections, so that's my next  
guess.

Out of curiosity, is there any particular reason you are using PHP?

chris

On Jul 21, 2008, at 10:24 AM, Alicia Amadoz wrote:

> Hi,
>
> I have tried what you suggested and what I get is another error:
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: WebDBSeqI Request Error:
> 500 Can't connect to eutils.ncbi.nlm.nih.gov:80 (Bad hostname  
> 'eutils.ncbi.nlm.nih.gov')
> Content-Type: text/plain
> Client-Date: Mon, 21 Jul 2008 15:07:39 GMT
> Client-Warning: Internal response
>
> 500 Can't connect to eutils.ncbi.nlm.nih.gov:80 (Bad hostname  
> 'eutils.ncbi.nlm.nih.gov')
>
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/lib/perl5/vendor_perl/5.8.8/Bio/ 
> Root/Root.pm:359
> STACK: Bio::DB::WebDBSeqI::_stream_request
> /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/WebDBSeqI.pm:758
> STACK: Bio::DB::WebDBSeqI::get_seq_stream
> /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/WebDBSeqI.pm:454
> STACK: Bio::DB::WebDBSeqI::get_Stream_by_id
> /usr/lib/perl5/vendor_perl/5.8.8/Bio/DB/WebDBSeqI.pm:275
> STACK: /var/www/html/perl-cgi//remote_blast_ncbi.pl:48
> -----------------------------------------------------------
>
> in line 48 of my script is,
>
> my $seqio = $gb->get_Stream_by_id([qw(J00522 AF303112 2981014)]);
>
>> 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.
>
> I am going to check again php.info but I have no idea what can it be.
>
> Thanks again for your help.
> Alicia
>
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign