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Kurt-Hetrick / CIDR_SOMATIC_WES_PIPELINES

currently for paired tumor - normal WES samples processed with TWIST UMIs
MIT License
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profile ExtractIlluminaBarcodes and IlluminaBasecallsToSam #3

Open Kurt-Hetrick opened 1 year ago

Kurt-Hetrick commented 1 year ago

currently set up to request an entire server in a limited set of queues, use 15 procs less than max and set java heap space to 50 Gb less than max. Can this be set to a more generalizable set up. need data to test.

Kurt-Hetrick commented 1 year ago

For IlluminaBasecallsToSam, need to profile /tmp as well.

Kurt-Hetrick commented 8 months ago

for novaseqx, it took 7 to 12 hours to demux a lane when using 30 processors and 700 gb of ram. note that I did not profile the ram usage.

Kurt-Hetrick commented 8 months ago

might consider having a normal mode (somewhere around 40 processors, 300ish gb of ram), so that more instances can get on concurrently, versus a fast mode, which only uses the newest nodes and uses around 80 processors and more ram.