[ensembl-dev] empty SpeciesFactory in FASTA pipeline

Lel Eory lel.eory at roslin.ed.ac.uk
Thu Dec 18 10:30:46 GMT 2014

Hello Developers,

I try to run the FASTA pipeline per the document 
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 
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 Eory, PhD
The Roslin Institute
University of Edinburgh Easter Bush Campus
Midlothian EH25 9RG
Scotland UK
Phone: +44 131 6519212

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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