Error: ProtHint/ACAB/prothint_augustus.gff not found !

[CongLiu37]

Hello!

I am trying to run ProtHint with hard masked genome. Here is my command:
prothint.py --workdir ProtHint/ACAB/ --threads 64 Mask_genome/ACAB_nonHymenopteraArthropoda_dt_400bp_5x.fna.masked.masked reference_genomes/All.faa

And here is the error:

error: ProtHint exited due to an error in command: Softwares/ProtHint/bin/../dependencies/GeneMarkES/gmes_petap.pl --verbose --cores 64 --ES --seq Mask_genome/ACAB_nonHymenopteraArthropoda_dt_400bp_5x.fna.masked.masked --soft auto
Error: hints file ProtHint/ACAB/prothint_augustus.gff not found!

Also, I'd like to confirm if the output prothint_augustus.gff should be provided as --trainingset or --hints for AUGUSTUS training.

Many thanks.

Cong

[tomasbruna]

Hi Cong,

Also, I'd like to confirm if the output prothint_augustus.gff should be provided as --trainingset or --hints for AUGUSTUS training.

it's best to use BRAKER2 for training and running AUGUSTUS (details in #40). However, if you need to run AUGUSTUS separately, prothint_augustus.gff serves as the "hints" file.

Regarding the actual error, what happens when you call GeneMar-ES directly, like this:

Softwares/ProtHint/bin/../dependencies/GeneMarkES/gmes_petap.pl --verbose --cores 64 --ES --seq Mask_genome/ACAB_nonHymenopteraArthropoda_dt_400bp_5x.fna.masked.masked --soft auto

Best,
Tomas