[Bioperl-l] Eutilities epost/efetch problem

[Kristine Briedis]

Hi Warren,

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

Cheers,
Kristine


===============================
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
error:


------------- 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/
DB/GenericWebAgent.pm:215
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