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

[Alexander Pico]

Great. That worked for pig. But I¹m now stuck on the bacteria collections,
specifically:

escherichia_shigella_collection
bacillus_collection
mycobacterium_collection

I¹ve tried the above, plus Œescherichia_coli¹ (which used to work) and
ŒEscherichia coli¹.  Any suggestions for these species in v67?

Thanks!
 - Alex



On 6/10/12 1:40 AM, "Bert Overduin" <bert at ebi.ac.uk> wrote:

> 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
>> 
>> 
>> 
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> 
> 

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