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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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Adjust GeneMark max core ceiling? #117

Closed michaelkarlcoleman closed 4 years ago

michaelkarlcoleman commented 4 years ago

Not sure about the history of this, but would it be possible to skip clamping the max core count to 48? We performed a run with 112 cores (with the latest GeneMark), and it seemed to run correctly.

(Warning isn't a problem, but it's mildly inconvenient to have to comment out the actual clamp.)

https://github.com/Gaius-Augustus/BRAKER/blob/036eb3b28fb3591cd58010489898b860332bbd41/scripts/braker.pl#L3742-L3760

KatharinaHoff commented 4 years ago

That's good hear.

We implemented the upper limit after one user reported problems with more than 48 cores. It might depend on the properties of an individual genome. GeneMark itself doesn't really have a limit for 48 cores... just sometimes the genome bins are apparently too small if you split the data into too many bins. I'll consider deleting line 3759 and only issue a warning.

KatharinaHoff commented 4 years ago

I have removed the hard coded upper limit with commit https://github.com/Gaius-Augustus/BRAKER/commit/cf2dd4a1125fd0b1e4f3deb4d41100cab7d9fb91