Alexander,<div><br></div><div>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'.</div>
<div><br></div><div>Cheers,</div><div>Bert<br><br><div class="gmail_quote">On Sat, Jun 9, 2012 at 11:47 PM, Alexander Pico <span dir="ltr"><<a href="mailto:apico@gladstone.ucsf.edu" target="_blank">apico@gladstone.ucsf.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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>
<br>
-------------------- 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>
<br>
-------------------- 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>
<br>
<br>
<br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br>Bert Overduin, Ph.D.<br>Vertebrate Genomics Team<br><br>EMBL - European Bioinformatics Institute<br>Wellcome Trust Genome Campus<br>Hinxton, Cambridge CB10 1SD<br>
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