[ensembl-dev] empty SpeciesFactory in FASTA pipeline

[Lel Eory]

Hello Developers,

I try to run the FASTA pipeline per the document 
https://github.com/Ensembl/ensembl-production/blob/release/78/docs/fasta.textile
My registry file is set-up as suggested.
I run init_pipeline either with -run_all or with -species defined, but 
then beekeeper skips the analyses as no species defined for the pipeline.

 From beekeeper:
Scheduler : Discarded 17 analyses because they do not need any Workers.

....
Worker 1 [ UNSPECIALIZED ] specializing to ScheduleSpecies(1)

-------------------- WARNING ----------------------
MSG: acanthisitta_chloris is not a valid species name (check DB and API 
version)
FILE: Bio/EnsEMBL/Registry.pm LINE: 1200
CALLED BY: Production/Pipeline/SpeciesFactory.pm  LINE: 85
Date (localtime)    = Thu Dec 18 10:25:53 2014
Ensembl API version = 78
---------------------------------------------------

The problem is most likely related to my production database, as I can 
list all the core databases using my registry file and these are present 
for release 78. Can someone suggest a way to check what is wrong and why 
SpeciesFactory does not generate the list of species beekeeper needs?

Thank you.

Best wishes,
Lel



---------------------------------------------
Lel Eory, PhD
The Roslin Institute
University of Edinburgh Easter Bush Campus
Midlothian EH25 9RG
Scotland UK
Phone: +44 131 6519212


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