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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
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issue with runMACS #119

Open ulitzenburger opened 4 years ago

ulitzenburger commented 4 years ago

Hi, I am running

runMACS(

  • obj=x.sp[which(x.sp@cluster==1),],
  • output.prefix="atac_v1_adult_brain_fresh_5k.1",
  • path.to.snaptools="/Users/ulitzenburger/Desktop/software/snaptools",
  • path.to.macs="/Users/ulitzenburger/Desktop/software/macs2",
  • gsize="mm",
  • buffer.size=500,
  • num.cores=5,
  • macs.options="--nomodel --shift 37 --ext 73 --qval 1e-2 -B --SPMR --call-summits",
  • tmp.folder=tempdir()
  • ); and I am getting the following error: Epoch: checking input parameters ... Error in runMACS(obj = x.sp[which(x.sp@cluster == 1), ], output.prefix = "atac_v1_adult_brain_fresh_5k.1", : path.to.macs does not exist

when I go to the dir in which MACS and snaptools are installed everything seems to work fine:

software ulitzenburger$ macs2 -h usage: macs2 [-h] [--version] {callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak} ...

macs2 -- Model-based Analysis for ChIP-Sequencing ...

and software ulitzenburger$ snaptools usage: snaptools [-h] ...

Program: snaptools (A module for working with snap files in Python) Version: 1.4.8 .....

any idea why? Thanks Ulli