Question: Advice to RIPSeeker users to improve RAM and CPU use
gravatar for Davis, Wade
5.0 years ago by
Davis, Wade350
Davis, Wade350 wrote:
I strongly recommend those using the RIPSeeker library to take advantage of the parameters minBinSize and maxBinSize when using the RIPSeek function. For one pair of bam files (RIP and control), I didn't set any limits on minBinSize and maxBinSize, and it used more than 300GB of RAM. CPU time : 147356.28 sec. Max Memory : 314981 MB Max Swap : 315400 MB After observing that all of the optimal bin sizes (estimated for each chromosome) were between 200 and 250 bp, I re-ran the code using minBinSize=200 and maxBinSize=250. The CPU time was cut by 40% and the RAM usage was reduced >90% (<20GB). CPU time : 91439.59 sec. Max Memory : 19365 MB Max Swap : 19785 MB Just thought I would pass this along. Wade Davis [[alternative HTML version deleted]]
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