[Bioperl-l] Eutilities epost/efetch problem
KBriedis at accelrys.com
Tue May 12 14:42:33 EDT 2009
I'm not getting the error anymore. NCBI must have fixed something.
From: Chris Fields [mailto:cjfields at illinois.edu]
Sent: Tuesday, May 12, 2009 11:36 AM
To: Kristine Briedis
Cc: Warren Gallin; BioPerl List
Subject: Re: [Bioperl-l] Eutilities epost/efetch problem
Not showing up in tests, so this may be something very specific that
changed. I'll try to reproduce it.
On May 12, 2009, at 12:19 PM, Kristine Briedis wrote:
> 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
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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