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

Robert Bradbury robert.bradbury at gmail.com
Sat Nov 21 13:26:05 EST 2009


It sounds like NCBI may be counting frequency of requests, how much data
they send or something similar.  Are you delaying the time between fetches?
 The code I've seen typically sleeps for a few seconds each time around a
loop.  You might try longer delays between fetches and see if that gets you
any more data.

Alternatively perhaps the libraries aren't reusing the TCP/IP connection
properly.  Is there a difference between the amount of memory on the
machines?  Have you watched the size of the process to see if it grows over
time?  I think the bug which prevented me from fetching a not-so-large
genome from a few months ago (eating up 3GB of memory in the process) has
not been resolved.  If so that could be your problem.

Robert

On Fri, Nov 20, 2009 at 12:44 PM, Alessandra
<alessandra.bilardi at gmail.com>wrote:
>
>
> 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
>


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