[Bioperl-l] Eutilities epost/efetch problem

[Robert Buels]

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?

Rob

-- 
Robert Buels
Bioinformatics Analyst, Sol Genomics Network
Boyce Thompson Institute for Plant Research
Tower Rd
Ithaca, NY  14853
Tel: 503-889-8539
rmb32 at cornell.edu
http://www.sgn.cornell.edu



Chris Fields wrote:
> Same here (no error).  Just ran the below.
>
> chris
>
> #!/usr/bin/perl -w
>
> use strict;
> use warnings;
> use Bio::DB::EUtilities;
>
> my @gi_number = qw(
> 41395563
> 31618162
> 81831839
> 54038971
> );
>
> 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.
>>
>> Cheers,
>> Kristine
>>
>>
>> -----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.
>>
>> chris
>>
>> 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.
>>>
>>> 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
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
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