Any better way for Peak-calling using MACS2 for windows users

[kryptonitecircuit2002]

I am analysing scMultiome data and following Signac's standard workflow, I do peak-calling via MACS2 using a command mentioned in #560 by @npojo (#560 (comment))

I use the following script for working

system('bash -c "/home/name/.local/bin/macs2 callpeak -t /location/atac_fragments_control.tsv.gz -g 1.4e+09 -f BED --nomodel --extsize 200 --shift -100 -n output directory --outdir /location/output directory" ', 
                wait = TRUE,  ignore.stderr = FALSE,  ignore.stdout = FALSE)
peak_path <- "path/_peaks.narrowPeak"
peaks <- rtracklayer::import(peak_path, format = "narrowPeak")
peaks <- keepStandardChromosomes(peaks, pruning.mode = 'coarse')
# quantify counts in each peak
macs_count <- FeatureMatrix(fragments = Fragments(Seurat),
                            features = peaks,
                            cells = colnames(Control))

Seurat[['ATAC']] <- CreateChromatinAssay(
  counts = macs_count,
  sep = c(":", "-"),
  genome = 'GRCz11',
  fragments = fragpath.Control,
  min.cells = 10,
  annotation = annotation
)

However, I see a lot of overlapping cells in ATAC clusters. Is there a better way to do it?