[Bioperl-l] Eutilities epost/efetch problem
rmb32 at cornell.edu
Tue May 12 15:19:03 EDT 2009
I don't think this is terribly unusual to have Efetch go down. I have
an automated pipeline that uses efetch to cross-check some stuff, and it
goes down every once in a while, sometimes for up to a day or so.
Might consider having a little nicer error message for this case?
Bioinformatics Analyst, Sol Genomics Network
Boyce Thompson Institute for Plant Research
Ithaca, NY 14853
rmb32 at cornell.edu
Chris Fields wrote:
> Same here (no error). Just ran the below.
> #!/usr/bin/perl -w
> use strict;
> use warnings;
> use Bio::DB::EUtilities;
> my @gi_number = qw(
> my $gpeptfactory = Bio::DB::EUtilities->new(
> -eutil => 'epost',
> -db => 'protein',
> -rettype => 'gp',
> -retmode => 'text',
> -tool => 'VKCDB_Update',
> -email => 'wgallin at ualberta.ca',
> -id => \@gi_number,
> -keep_histories => 1);
> my $hist = $gpeptfactory->next_cookie || die "Arghh!";
> $gpeptfactory->set_parameters(-eutil => 'efetch',
> -history => $hist);
> $gpeptfactory->get_Response(-file => '>test.gb');
> On May 12, 2009, at 1:42 PM, Kristine Briedis wrote:
>> Hi Chris,
>> I'm not getting the error anymore. NCBI must have fixed something.
>> -----Original Message-----
>> 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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