[maker-devel] BUSCO trained Augustus parameter for MAKER

[Xabier Vázquez-Campos]

AFAIK, the profile can be the folder
run_my_species/augustus_output/retraining_parameters and the files inside
would look like BUSCO_my_species_[a number]_*.*
Create a folder in the species directory and copy this in there. Note that
the folder and the included files should have the same name prefix e.g.
BUSCO_my_species_[a number], otherwise whenever you call the profile,
Augustus is going to freak out. The prefix will be your augustus_species


On 1 August 2017 at 03:09, Carson Holt <carsonhh at gmail.com> wrote:

> 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
>
> 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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-- 
Xabier Vázquez-Campos, *PhD*
*Research Associate*
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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