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

Alicia Amadoz Alicia.Amadoz at uv.es
Wed Jul 23 07:03:04 EDT 2008


Hi,

Finally I've been talking with my system administrator and the error was because some 
security configuration of our server. Now it is already solved and works ok Thanks for your 
help and comments.

I am using PHP because our application is developed in PHP and from this application 
different scripts are launched. 

Alicia

> 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
> >
> >
> >
> > _______________________________________________
> > 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
> 
> 
> 
> 
> 
> 


--
***********************************************
Alicia Amadoz Navarro

Evolutionary Genetics Unit
Cavanilles Institute for Biodiversity and Evolutionary
Biology
University of Valencia
Polígono de la Coma s/n,
46980 Paterna (Valencia),
Phone: (+34) 96 354 3687
FAX: (+34) 96 354 3733
e-mail: alicia.amadoz at uv.es
http://www.uv.es/~biodiver/v/index.htm

***********************************************







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