[Bioperl-l] Eutilities epost/efetch problem

Kristine Briedis KBriedis at accelrys.com
Tue May 12 17:19:39 UTC 2009

Hi Warren,

We've noticed the same EFetch error.  I emailed NCBI and will let you know what they say.


Kristine Briedis, Ph.D.
Bioinformatics Software Engineer
Accelrys, Inc.
10188 Telesis Court, Suite 100
San Diego, CA 92121  USA
kbriedis at accelrys.com

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Warren Gallin
Sent: Monday, May 11, 2009 6:36 PM
To: BioPerl List
Subject: [Bioperl-l] Eutilities epost/efetch problem

Hi folks,

	Something started failing for me this morning that had been working reliably for the last week,

	I post an array of gi numbers, a history is successfully returned, but when I try to use efetch to get the records, it fails with the

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Response Error
Not Found
STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.8.8/Bio/Root/Root.pm:368
STACK: Bio::DB::GenericWebAgent::get_Response /Library/Perl/5.8.8/Bio/
STACK: 090507_Stable_gb_update.pl:238

	I'm running the efetch inside an eval and letting it try a total of 6  
times with a 5 sedond sleep in between, but the error is consistent.

	So I consider two possibilities:
	1) Has something changed on the Entrez server recently?  Has anyone  
else started having this kind of problem?

	2) Have I inserted some subtle flaw into my code that would lead to a  
failure of efetch.

	I am attaching two text files, one with the code chunklet that is  
doing this and the other the output from the script.

	Any help or suggestions are profoundly appreciated.

Warren Gallin

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