<OUTDIR>/evidence/hints/merged.hints.gff- extrinsic hints file from all evidences. It is always generated when you run the pipeline and its primary output.
<OUTDIR/annotation/augustus/augustus.merged.out.gff- output as generated by Augustus. It includes the annotated gene models, the extrinsic hints used, the protein sequences and the accuracy of each predicted model.
<OUTDIR>/annotation/augustus/augustus.proteins.fa- protein sequences of the predicted models.
You can also see the output of each intermediate step, which is saved in specific folders inside the output directory. Of special interest are:
<OUTDIR>/evidence/- each separate type of evidence and resulting hints file.
<OUTDIR>/pipeline_info/- reports on pipeline performance.
