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

[Andreas Kahari]

On Wed, Jul 23, 2008 at 01:03:04PM +0200, Alicia Amadoz wrote:
> 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

Probably a chroot'ed httpd without the proper /etc/resolv.conf in its
chroot.  I hope they fixed it properly and not by un-chroot'ing it...


Andreas

> 
> > 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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-- 
Andreas Kähäri, Ensembl Software Developer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, United Kingdom