search

Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
Other
334 stars 80 forks source link

Braker via Singularity, fails to execute Augustus #805

Closed emgiles closed 2 months ago

emgiles commented 2 months ago

Hi again I am running Braker via Singularity which has worked for me in the past. However, now, there is an issue with Augustus. All of the files in the errors/ subdirectory are empty. Do you have any idea how to fix this? Here is my error:

[Wed Apr 17 17:10:22 2024] ProtHint finished. ERROR in file /opt/BRAKER/scripts/braker.pl at line 6288 Failed to execute: /opt/Augustus/bin//etraining --species=Scurria.viridula --AUGUSTUS_CONFIG_PATH=/home/pablo/.augustus /home/pablo/braker_18apr2023/train.f.gb 1> /home/pablo/braker_18apr2023/gbFilterEtraining.stdout 2>/home/pablo/braker_18apr2023/errors/gbFilterEtraining.stderr

emgiles commented 2 months ago

I have now seen this: https://github.com/Gaius-Augustus/BRAKER/issues/609#issuecomment-1571506735

Which as mostly solved my issue. Copying from within the braker3.sif did not work.

KatharinaHoff commented 2 months ago

If it solved, I will close here.