CPG Training in CAT

[fbemm]

CAT is currently calling the Augustus CPG training like this:

cmd = ['augustus',
'--species={}'.format(args.species),
'--treefile={}'.format(tree_path),
'--alnfile={}'.format(cat_maf),
'--dbaccess={}'.format(hints_db),
'--speciesfilenames={}'.format(genome_fofn),
'--refSpecies={}'.format(args.ref_genome),
'--referenceFile={}'.format(gtf),
'--param_outfile={}'.format(params)]

Looking at the --paramlist at least refSpecies, referenceFile and referenceFile are not allowed in Augustus 3.2.3 (compiled COMPGENEPRED = true).

Any idea why I don't see these parameter?

[Mario]

Yes, this older release did not work with Ian Fiddes' Comparative Annotation Pipeline yet.
Please check out the current one: augustus3.3

Mario