Q: Using MACS2 in ArchR.

[TauHHCC]

Hi

I am using ArchR to analysis scATAC and using MACS2 with ArchR to do peak calling. However, I got this error:

Error in .checkMacs2Options(pathToMacs2) : Macs2 Path (macs2) is out of date (version Traceback (most recent call last): File "/usr/local/bin/macs2", line 23, in from MACS2.Constants import *ModuleNotFoundError: No module named 'MACS2') and does not have --shift option. Please update (https://github.com/taoliu/MACS) and provide new path! In addition: Warning messages: 1: In system2(path, "callpeak -h", stdout = TRUE, stderr = TRUE) : running command ''macs2' callpeak -h 2>&1' had status 1 2: In system2(path, " --version", stdout = TRUE, stderr = TRUE) : running command ''macs2' --version 2>&1' had status 1

I tried pathToMacs2 = pathToMacs2, it can find macs2 and the macs2 in my computer is executable. In the error context, it says update, but I'm not sure if MACS3 fits ArchR.

[taoliu]

@TauHHCC It seems that macs2 has to be installed through commandline into /usr/local/bin. And the installation is either not done yet or not successful.

[TauHHCC]

Hi @taoliu Thank you very much. I uninstalled MACS2 and reinstalled it, it works now.