MACS2 CPU and Memory Usage

Version of MACS2

macs2 2.0.10.20130404 (tag:beta)

Test data

human CTCF ChIP-seq, we subsampled 65, 50, 40, 30, 20, 10, 5, 2 and 1 million reads for both ChIP and Control.

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 (X), 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.