Using prothint output in augustus
ShakunthalaNatarajan opened this issue · 1 comments
I have obtained the prothint_augustus.gff file from prothint. I used it for gene prediction with augustus. But an error shows up as:
Unknown hint feature 'P'. Ignoring it. For a list of 17 allowed features see, /config/extrinsic.cfg. The command I used to run augustus was:
augustus --hintsfile=prothint_augustus.gff --extrinsicCfgfile=extrinsic.cfg --species=species_name genome.fasta > output.gff
Is augustus ignoring my protein hints? Should I call this feature type in any other manner? Please help!
Augustus/config/extrinsic/extrinsic.cfg has by default only hints of types M=manual and RM=repeatmasking.
You could use instead extrinsic.MP.cfg or another one with P.
The reason that there is not one configuration for all sources of hints is that the absence of hints is taken as evidence against a gene structure when one has searched for the evidence.