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

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