Abinitio outputs - Augustus

NBISweden / pipelines-nextflow

A set of workflows written in Nextflow for Genome Annotation.

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Abinitio outputs - Augustus #25

Closed ViriatoII closed 4 years ago

ViriatoII commented 4 years ago

Hi,

Your pipeline is working well. I just don't understand what is the output of the Augustus part that I'm supposed to collect for maker and how. I have a good SNAP .hmm but here's what I see in the Augustus part:

guerrer@hilbert141:$ ll Augustus_training/test_species
test_species_exon_probs.pbl
test_species_igenic_probs.pbl
test_species_intron_probs.pbl
test_species_metapars.cfg
test_species_metapars.cgp.cfg
test_species_metapars.utr.cfg
test_species_parameters.cfg
test_species_weightmatrix.txt

Juke34 commented 4 years ago

test_species folder has to be moved into the augustus_path/config/species/ folder. It is a new hmm profile available among the other species standing in this folder (tomato, fly,etc...). Augustus will refer to it as test_species. If you modify the name, be careful to change the name of the folder and of all the files it contains. This must be consistent.

ViriatoII commented 4 years ago

That's it, thank you so much!

maker_opts.ctl:

#-----Gene Prediction
snaphmm=nextflow_abInitio/Snap_training/test_species.hmm
gmhmm= #GeneMark HMM file
augustus_species=test_species  <--- same name as folder in augustus_path/config/species/