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MACS2 CPU and Memory Usage

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taoliu edited this page Apr 11, 2013 · 5 revisions

Version of MACS2

macs2 2.0.10.20130404 (tag:beta)

Test data

human CTCF ChIP-seq, 65 Million reads, subsampled into 50, 40, 30, 20, 10, 5, 2 and 1 million reads.

Hardware

  • CPU: AMD Opteron(tm) Processor 8439 SE 2,813 MHz x 48 cores
  • Total Memory: 512G

Command line

macs2 callpeak -t CTCF_XM.bed.gz -c Ctrl_XM.bed.gz -n XM --call-summit

For each depth, we ran MACS2 with the above command for five times. In the following figure, we drew the average runtime and memory usage together with standard derivation at each point.

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