[ensembl-dev] Sus scrofa is not a valid species name?

[Bert Overduin]

Alexander,

I am afraid we lost a few synonyms from the db, so 'pig' and 'sus scrofa'
won't work. This will be fixed in v68. In the meantime please use
'sus_scrofa' or 'swine'.

Cheers,
Bert

On Sat, Jun 9, 2012 at 11:47 PM, Alexander Pico <apico at gladstone.ucsf.edu>wrote:

> Hi,
>
> I'm getting errors on some version 67 (and genomes 14) databases where the
> species name is not accepted by the Registry:
>
> -------------------- WARNING ----------------------
> MSG: Sus scrofa is not a valid species name (check DB and API version)
> FILE: Bio/EnsEMBL/Registry.pm LINE: 1172
> CALLED BY: Bio/EnsEMBL/Registry.pm  LINE: 957
> Ensembl API version = 67
> ---------------------------------------------------
>
> -------------------- EXCEPTION --------------------
> MSG: Can not find internal name for species 'Sus scrofa'
> STACK Bio::EnsEMBL::Registry::get_adaptor
> /home/socr/c/users2/apico/src/ensembl/modules/Bio/EnsEMBL/Registry.pm:959
> STACK toplevel Ensembl_ETL_Device_v18_local.pl:425
> Ensembl API version = 67
> ---------------------------------------------------
>
> I'm seeing these errors for the following species databases:
> glycine_max_core_14_67_1
> mycobacterium_collection_core_14_67_4
> solanum_lycopersicum_core_14_67_240
> sus_scrofa_core_67_102
> bacillus_collection_core_14_67_4
> escherichia_collection_core_14_67_5
>
> And here is the version of Registry.pm I'm working with:
> ===================================================================
> File: Registry.pm          Status: Up-to-date
>   Working revision:    1.224
>   Repository revision:    1.224
> /cvsroot/ensembl/ensembl/modules/Bio/EnsEMBL/Registry.pm,v
>   Commit Identifier:    UMuKMdXcvEHkrB1w
>   Sticky Tag:        branch-ensembl-67 (branch: 1.224.2)
>   Sticky Date:        (none)
>   Sticky Options:    (none)
>
> And guesses?
>  - Alex
>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe):
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>



-- 
Bert Overduin, Ph.D.
Vertebrate Genomics Team

EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom

http://www.ebi.ac.uk/~bert

Ensembl browser: http://www.ensembl.org

Mailing lists: http://www.ensembl.org/info/about/contact/mailing.html

Blog: http://www.ensembl.info

YouTube: http://www.youtube.com/user/EnsemblHelpdesk
Facebook: http://www.facebook.com/Ensembl.org
Twitter: http://twitter.com/Ensembl
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20120610/731ad295/attachment.html>