What is the best way to resume braker pipeline if it stops unexpectedly?

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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What is the best way to resume braker pipeline if it stops unexpectedly? #733

Closed jackie-duang closed 9 months ago

jackie-duang commented 10 months ago

The Perl script reported an unexpected error during use, but although the problem was fixed, the whole process had to be restarted from the beginning, which was so depressing. Is there a way to restart the process where it left off instead of starting from scratch?

KatharinaHoff commented 10 months ago

I usually delete the species parameters folder (if --species had been specified) and remove the output of the previous run to start clean from scratch.

JiyangChang commented 7 months ago

Hi Katharina,

I also have the same question about this issue, sometimes in the last few steps (after #AUGUSTUS prediction complete), BRAKER pipeline unexpectedly breaks, I wonder whether it is possible to generate the full command list at the beginning so the users can check how many steps still not finish?