Issues with ArchR calling MACS2 from WSL in Windows Environment

[joeyQX]

escription:
I'm trying to run ArchR's peak calling functionality on Windows using MACS2 installed in WSL. While MACS2 is successfully installed and running in WSL (confirmed with macs2 --version), ArchR fails to locate and execute it from the R/RStudio environment.

Current Setup:

• Windows 10/11
• R/RStudio running on Windows
• MACS2 installed in WSL (Ubuntu)
• ArchR project loaded with peakSet = NULL

What I've tried:

1. Setting MACS2 path in R:
   pathToMacs2 <- "wsl macs2"
   pathToMacs2 <- "/usr/local/bin/macs2"
   pathToMacs2 <- "wsl.exe macs2"
   #return all not found

Confirming MACS2 installation in WSL:
bash:
which macs2 # returns /usr/local/bin/macs2
macs2 --version # works correctly

[rcorces]

Hi @joeyQX! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other
responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire
a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know!
In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15.
Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.

[joeyQX]

Hi @joeyQX! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know! In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15. Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.

Thanks, hope your future reply!

[immanuelazn]

Hi joey, pretty sure this is a nuanced question on how $PATH is set, and where it happens with respect to when you execute your wsl command from windows.
Have you tried this as a test from R?
system("wsl /usr/local/bin/macs2")

[immanuelazn]

Hi joey, are you still having issues with ArchR?

[joeyQX]

Hi joey, are you still having issues with ArchR?

it seems MACS2 can run but with a new question:

proj <- addReproduciblePeakSet(

• ArchRProj = proj,

• groupBy = "ATAC_clusters",

• pathToMacs2 = pathToMacs2,

• force = TRUE

• )
  ArchR logging to : ArchRLogs\ArchR-addReproduciblePeakSet-5ca06a5724e1-Date-2024-11-29_Time-10-48-27.55436.log
  If there is an issue, please report to github with logFile!
  2024-11-29 10:48:27.631469 : Peak Calling Parameters!, 0.001 mins elapsed.
  Group nCells nCellsUsed nReplicates nMin nMax maxPeaks
  C1 C1 4976 540 2 40 500 150000
  C2 C2 2189 540 2 40 500 150000
  C3 C3 2450 540 2 40 500 150000
  C4 C4 2115 540 2 40 500 150000
  C5 C5 526 526 2 224 302 150000
  C6 C6 4053 1000 2 500 500 150000
  C7 C7 527 527 2 40 487 150000
  C8 C8 1060 558 2 58 500 150000
  C9 C9 1101 959 2 459 500 150000
  C10 C10 1640 540 2 40 500 150000
  C11 C11 262 262 2 40 222 131000
  C12 C12 298 298 2 127 171 149000
  C13 C13 1087 784 2 284 500 150000
  C14 C14 517 517 2 87 430 150000
  C15 C15 360 360 2 115 245 150000
  C16 C16 1004 651 2 151 500 150000
  C17 C17 1103 700 2 200 500 150000
  2024-11-29 10:48:27.637425 : Batching Peak Calls!, 0.001 mins elapsed.
  2024-11-29 10:48:27.642742 : Batch Execution w/ safelapply!, 0 mins elapsed.
  2024-11-29 10:48:27.643881 : Group 1 of 34, Calling Peaks with MACS2!, 0 mins elapsed.
  错误于data.table::fread(summitsFile, select = c(1, 2, 3, 5)):
  文件 'E:\molecular_data\scENDO_scOVAR_2020-1.0.1\scATAC-seq_Processing_Scripts\HGSOC_Cohort\Proj_BeforeIntegration/PeakCalls/InsertionBeds/C1._.Rep1-1_summits.bed' 不存在, 或不可读. getwd()=='E:/molecular_data/scENDO_scOVAR_2020-1.0.1/scATAC-seq_Processing_Scripts/HGSOC_Cohort'

  The same with "Error in peak calling with MACS2 #239", but i can't solve it even i tried the solutions mentioned before such as reinstalled the numpy.

[immanuelazn]

Hi Joey, thanks again for trying to use ArchR. It seems like this is a separate issue, so please create an issue describing how I can reproduce this. Thanks!