Hi,
I tried to follow this [instruction][1] on how to retrain Augustus with BUSCO. I ran BUSCO:

    run_BUSCO.py -i NbV1Ch07.fasta -o augustus_busco -l /assembly/busco-embryophyta_odb9/ -m geno --cpu 1 --long -sp coyote_tobacco --augustus_parameters='--progress=true'

and it created a folder `/augustus/run_augustus_busco/augustus_output/retraining_parameters` with the following content:

    BUSCO_augustus_busco_3750827137_weightmatrix.txt
    BUSCO_augustus_busco_3750827137_parameters.cfg.orig1
    BUSCO_augustus_busco_3750827137_parameters.cfg
    BUSCO_augustus_busco_3750827137_metapars.utr.cfg
    BUSCO_augustus_busco_3750827137_metapars.cgp.cfg
    BUSCO_augustus_busco_3750827137_metapars.cfg
    BUSCO_augustus_busco_3750827137_intron_probs.pbl
    BUSCO_augustus_busco_3750827137_igenic_probs.pbl
    BUSCO_augustus_busco_3750827137_exon_probs.pbl

Which file should I use to run Augustus trained with BUSCO and how the command looks like?

Thank you in advance,
 

  [1]: https://www.biostars.org/p/261203/#295503
You copy the files from `/augustus/run_augustus_busco/augustus_output/retraining_parameters` to your `augustus` installation directory under `/augustus-install-directory/config/species/BUSCO_augustus_busco_3750827137/`

    usage:
    augustus [parameters] --species=BUSCO_augustus_busco_3750827137 queryfilename

    or if you want to output to be redirected to a file (see also outfile parameter):
    augustus [parameters] --species=BUSCO_augustus_busco_3750827137 queryfilename > output.gff
