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

Failed at optimize_augutus.pl #790

Open kwantn opened 3 months ago

kwantn commented 3 months ago

Dear BRAKER2 people, I was running BRAKER2 with proteins of shorter evolutionary distance. I used GenomeThreader and produced .aln file which I fed into braker.pl. It was running fine and then failed at optimize_augustus.pl with the error below. failed at optimize_augustus pl

When I opened up the "/u/tnkwan/braker/errors/optimize_augustus.stderr" file, the content says: optimize_augustus stderr

I then pursued "/u/tnkwan/braker/tmp_opt_ZM3/curtest" and it was surprisingly empty. I remember seeing the curtest file being populated and time stamped continuously over the few days of running before braker crashed. Upon crash, the curtest file turned empty and interestingly with a Last Modified Date prints of ‘1985-12-26’!

Thank you for helping out and offering understanding (or even questions). Thanks people.

Cheers Kwan

KatharinaHoff commented 3 months ago

I have no idea how to fix it. I have had problems when optimize_augustus.pl temporarily lost writing access to a hard drive. Not sure whether that was the same issue, here.