[ensembl-dev] Orthologs in ensembl-genomes...MethodLinkSpeciesSets not found for two species: Bos taurus(Btau_4.0) and Rattus norvegicus(RGSC3.4)

[Niran Abeygunawardena]

Hi,

I'm using branch-ensemblgenomes-5-58 api to access orthologs. For most 
species pairs, it works except for combinations involving these two species:
Bos taurus(Btau_4.0) and Rattus norvegicus(RGSC3.4)


For example, I get the following error from my attached scripts:
-------------------- WARNING ----------------------
MSG: No Bio::EnsEMBL::Compara::MethodLinkSpeciesSet found for
   <ENSEMBL_ORTHOLOGUES> and Arabidopsis thaliana(TAIR9), Rattus 
norvegicus(RGSC3.4)
FILE: Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm LINE: 669
CALLED BY: orthologs.pl  LINE: 96
---------------------------------------------------

-------------------- EXCEPTION --------------------
MSG: method_link_species_set arg is required

STACK 
Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::fetch_all_by_MethodLinkSpeciesSet 
/ebi/microarray/sw/dw/src/genomes-5/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/HomologyAdaptor.pm:325
STACK toplevel orthologs.pl:97
---------------------------------------------------


Is there a reason why these two species are not used in the compara 
pipeline to find orthologs?

I found these two species orthologs are present in the branch-ensembl-59 
api but I can't use it since I require orthologs from other species such 
as plants, fungi and bacteria....unless I call separately this api but 
prefer not if there is a good reason. Anyway, I only require orthologs 
pairs from these species combinations:
anopheles gambiae
arabidopsis thaliana
bacillus subtilis
bos taurus
caenorhabditis elegans
danio rerio
drosophila melanogaster
gallus gallus
homo sapiens
mus musculus
rattus norvegicus
saccharomyces cerevisiae
schizosaccharomyces pombe


I'm happy to listen to any help to improve performance or do this an 
alternative way..thanks :)

Best,
Niran
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