[maker-devel] BUSCO trained Augustus parameter for MAKER

[Arnab Ghosh]

Hello,

I am trying to annotate genes in a non-model organism. I am using MAKER for
this purpose and have trained SNAP and plan on Genemark and Augustus as
well for the predictions.

After searching the google group on MAKER-devel I understand  BUSCO is a
good choice for training Augustus and decided to give it a shot. From one
of the earlier posts on BUSCO, I read that it is supposed to generate a
species name specific folder in the config directory of Augustus. However I
did not get any. The BUSCO run finished fine with the run_species folder
and all necessary table, hmm folder and other files etc. generated under
the run_species folder.

Following was the command i used to run BUSCO:

python run_BUSCO.py --in mySpecies.fasta  --out my_species --long
--lineage_path /usr/home/aves_odb9 --mode genome

So there was no "my_species" folder generated under the config directory of
augustus.

Did I miss something ? My question is-- what should I pass to the "
*augustus_species"* variable now in the maker control file for the next run
of maker ?

Thanks so much for your time !!
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