I have to annotate novel diplonema genome. So that I chose to use braker.

I have run command prothint to generate and prothint_augustus.gff used to run braker in next step.

Along with bam file obtained from Star aligner using --twopassMode Basic

1.) prothint.py dj.fa protein_homo_database.fasta

2.) braker.pl --genome=genome.masked.fa --species=species_name --hints=prothint_augustus.gff --bam genomestaralign.bam --etpmode --softmasking –AUGUSTUS_ab_initio

genemark.gtf is present, However, Augustus.gff file is missing and species folder is also empty.

Could anybody please suggest, where I am making mistake or it is fine ? Any suggestion, how can I improve the pipeline ? Thank you very much in advance :)