[maker-devel] BUSCO trained Augustus parameter for MAKER

[Carson Holt]

Hello Arnab,

Perhaps someone on the list will chime in with an answer for you, but you may also want to post to direct to BUSCO since your question is entirely related to BUSCO and you are more likely to get a quick response there.

—> https://gitlab.com/ezlab/busco/issues <https://gitlab.com/ezlab/busco/issues>

Thanks,
Carson




> On Jul 19, 2017, at 2:24 PM, Arnab Ghosh <leo1985.arnab at gmail.com> wrote:
> 
> 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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