[Bioperl-l] Bio::DB::EUtilities question

Alessandra alessandra.bilardi at gmail.com
Fri Nov 20 12:44:18 EST 2009


Hi all,

I'm testing Bio::DB::EUtilities - webagent which interacts with and
retrieves data from NCBI's eUtils. My perl script works but it works
only if I request less than ~450 times get_Response function.. else I
have got this error message:

------------- EXCEPTION -------------
MSG: Response Error
Can't connect to eutils.ncbi.nlm.nih.gov:80 (connect: No route to host)
STACK Bio::DB::GenericWebAgent::get_Response
/usr/local/share/perl/5.10.0/Bio/DB/GenericWebAgent.pm:215
STACK toplevel ./wget4gbk.pl:77
-------------------------------------

wget4gbk.pl lines 76-77 are:
my $req = Bio::DB::EUtilities->new(-db => 'genome', -eutil =>
'esummary', -retmode => $mode, -rettype => $type, -id => $id);
my $entry = $req->get_Response;

I run perl script more ten times and this error arrives random time at
the range 300-600 requests. If I use another system to request data,
then I can to do ~ 10000 requests, without errors. Had I to set
EUtilities object with particular parameters?

Can you help me about random exception error?

Best,

-- 
 Alessandra Bilardi, Ph. D.
----
 CRIBI, University of Padova, Italy
 http://www.linkedin.com/in/bilardi
----


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