[Bioperl-l] load_seqdatabase error with a specific locus from genbank

[Johann PELLET]

Hie Hilmar,

I am very sorry, I checked my GenBank file, and you are right It's  
corrupted :-(

grep EU608407 genbankFile

AUTHORS   Bonhoeffer,S., Chappey,C., Parkin,N.T., Whitcomb,LOCUS        
EU608407                1212 bp    DNA     linear   VRL 20-APR-2008
ACCESSION   EU608407
VERSION     EU608407.1  GI:183190953


So I have downloaded EU608407 and I have loaded it alone with  
load_sequence.pl without problems. Same for EU608559.

Thanks again Johann

Le 9 avr. 09 à 05:51, Hilmar Lapp a écrit :

>
> On Apr 8, 2009, at 11:35 PM, Hilmar Lapp wrote:
>
>>
>> On Apr 8, 2009, at 11:29 AM, Johann PELLET wrote:
>>
>>> [...]
>>> and finally EU608407 and EU608559  made a crash:
>>>
>>> [...]
>>> --------------------- WARNING ---------------------
>>> MSG: Unexpected error in feature table for  Skipping feature,  
>>> attempting to recover
>>> ---------------------------------------------------
>>> #######...14 times ...############
>>
>> I would assume that you figured out that this was triggered by or  
>> affected EU608407? Would you mind sharing how?
>
> Looking at EU608407, it most likely wasn't the culprit or stumbling  
> stone. It must have been triggered before that.
>
>> [...]
>> So are there other sequences associated with that PubMed ID?
>
> To answer my own question, it's indeed EU608407 that's from the same  
> PubMed ID, and so am I correct in assuming that you didn't get the  
> exception for that record, which would mean that the reference was  
> properly inserted when that sequence was loaded.
>
> The second occurrence of the same PubMed ID should have actually  
> triggered a successful lookup of the previously inserted record,  
> which would then have skipped the insert. The fact that that didn't  
> happen suggests that the PubMed ID also wasn't properly extracted  
> from the Genbank record. So my first suspicion remains that your  
> file is corrupted.
>
> Otherwise, if you download this record:
> http://www.ncbi.nlm.nih.gov/nuccore/183191257
>
> in GenBank format and try to load it alone, it should yield the same  
> error. Can you indeed reproduce the problem in that way?
>
> 	-hilmar
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>