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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
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ln: failed to create symbolic link '/home//braker/traingenes.gtf': File exists #657

Open PallaviShakya opened 1 year ago

PallaviShakya commented 1 year ago

I am running BRAKER3 with singularity.

I always get an error in the Augustus step. This is what the error looks like:

AUGUSTUS_CONFIG_PATH/species (in this case /usr/share/augustus/config//species) is not writeable. BRAKER will try to copy the AUGUSTUS config directory to a writeable location. ln: failed to create symbolic link '/home/pshakya/braker/traingenes.gtf': File exists ERROR in file /opt/BRAKER/scripts/braker.pl at line 5988 failed to execute: ln -s /home/braker/GeneMark-ET/genemark.gtf /home/braker/traingenes.gtf!

I am not familiar with perl script. I could not figure out where this error is coming from.

Could anyone help me figure out?

Thank you!

KatharinaHoff commented 6 months ago

This may be file system specific. On some file systems, creating symbolic links is not allowed.