[ensembl-dev] Problem with load_genomedb in compara

[Francesco Lamanna]

Hi all,

I am trying to run the Compara protein-tree pipeline (v91) on a set of two
core ensembl genomes and three custom genomes (stored locally) using a
master database.

when I run beekeeper.pl script load_genomedb fails to find my local genomes
(but it loads correctly the ensembl core genomes), and drops this kind of
error message:

Could not find species_name='petromyzon_marinus',
assembly_name='germline_final' on the servers provided, please investigate
at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/
EnsEMBL/Compara/RunnableDB/LoadOneGenomeDB.pm line 179.

the information regarding the local genomes is stored in a .json file and
loaded in the genome_db table of the master database. The .json file is
invoked in pipeline conf script using:

'curr_file_sources_locs'  => [
'/home/hd/hd_hd/hd_cc141/Vertebrates_project/Ensembl_compara/non_ensembl_species.json'
]

Thank you for your help,
Francesco.
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