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<TITLE>Re: [ensembl-dev] Sus scrofa is not a valid species name?</TITLE>
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<FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>Great. That worked for pig. But I’m now stuck on the bacteria collections, specifically:<BR>
<BR>
escherichia_shigella_collection<BR>
bacillus_collection<BR>
mycobacterium_collection<BR>
<BR>
I’ve tried the above, plus ‘escherichia_coli’ (which used to work) and ‘Escherichia coli’. Any suggestions for these species in v67?<BR>
<BR>
Thanks!<BR>
- Alex<BR>
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On 6/10/12 1:40 AM, "Bert Overduin" <<a href="bert@ebi.ac.uk">bert@ebi.ac.uk</a>> wrote:<BR>
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</SPAN></FONT><BLOCKQUOTE><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>Alexander,<BR>
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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'.<BR>
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Cheers,<BR>
Bert<BR>
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On Sat, Jun 9, 2012 at 11:47 PM, Alexander Pico <<a href="apico@gladstone.ucsf.edu">apico@gladstone.ucsf.edu</a>> wrote:<BR>
</SPAN></FONT><BLOCKQUOTE><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>Hi,<BR>
<BR>
I'm getting errors on some version 67 (and genomes 14) databases where the<BR>
species name is not accepted by the Registry:<BR>
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-------------------- WARNING ----------------------<BR>
MSG: Sus scrofa is not a valid species name (check DB and API version)<BR>
FILE: Bio/EnsEMBL/Registry.pm LINE: 1172<BR>
CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 957<BR>
Ensembl API version = 67<BR>
---------------------------------------------------<BR>
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-------------------- EXCEPTION --------------------<BR>
MSG: Can not find internal name for species 'Sus scrofa'<BR>
STACK Bio::EnsEMBL::Registry::get_adaptor<BR>
/home/socr/c/users2/apico/src/ensembl/modules/Bio/EnsEMBL/Registry.pm:959<BR>
STACK toplevel Ensembl_ETL_Device_v18_local.pl:425<BR>
Ensembl API version = 67<BR>
---------------------------------------------------<BR>
<BR>
I'm seeing these errors for the following species databases:<BR>
glycine_max_core_14_67_1<BR>
mycobacterium_collection_core_14_67_4<BR>
solanum_lycopersicum_core_14_67_240<BR>
sus_scrofa_core_67_102<BR>
bacillus_collection_core_14_67_4<BR>
escherichia_collection_core_14_67_5<BR>
<BR>
And here is the version of Registry.pm I'm working with:<BR>
===================================================================<BR>
File: Registry.pm Status: Up-to-date<BR>
Working revision: 1.224<BR>
Repository revision: 1.224<BR>
/cvsroot/ensembl/ensembl/modules/Bio/EnsEMBL/Registry.pm,v<BR>
Commit Identifier: UMuKMdXcvEHkrB1w<BR>
Sticky Tag: branch-ensembl-67 (branch: 1.224.2)<BR>
Sticky Date: (none)<BR>
Sticky Options: (none)<BR>
<BR>
And guesses?<BR>
- Alex<BR>
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