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rafalab / bumphunter

bumphunter
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Stall after [bumphunterEngine] Smoothing coefficients. #24

Closed rrydbirk closed 3 years ago

rrydbirk commented 5 years ago

I'm running bumphunter as integrated in ChAMP (champ.Block) with 20 cores, 100 GB mem. It's stalling at

[bumphunterEngine] Smoothing coefficients.

Input is 224 clusters, and I'm smoothing with loessByCluster. I don't know if 224 clusters is a lot, does that explain why the process stalls? How long should I expect this step to take?

rrydbirk commented 5 years ago

I've had it running overnight with even more cores, this is where I got to after 18 hours:

[===========================] [<<<< ChAMP.Block START >>>>]

Running with 80cores. Loading required package: IlluminaHumanMethylationEPICanno.ilm10b4.hg19 << Load Annotation Successfully >> << Get Clusters by cgi-info Successfully >> << Calculate Average Beta Value Successfully >> << Generate Block Position Successfully >> << 224 clusters are generated for blocks >> << Generate information for New Clusters >> [bumphunterEngine] Parallelizing using 80 workers/cores (backend: doParallelMC, version: 1.0.14). [bumphunterEngine] Computing coefficients. [bumphunterEngine] Smoothing coefficients.

rrydbirk commented 3 years ago

Closed due to inactivity