Open mijhamilt opened 3 years ago
I am getting a permission denied error with MACS2 when running snapATAC. I can run macs2 in the terminal just fine, but not from R. Here is the code:
runMACS( obj=x.sp[which(x.sp@cluster==1),], output.prefix="atac_060_ASCP", path.to.snaptools="/usr/local/bin/snaptools", path.to.macs="/home/michael/anaconda2/lib/python2.7/site-packages/MACS2", gsize="mm", buffer.size=500, num.cores=30, macs.options="--nomodel --shift 37 --ext 73 --qval 1e-2 -B --SPMR --call-summits", tmp.folder=tempdir() )
Epoch: checking input parameters ... Epoch: extracting fragments from each snap files ... sh: 1: /home/michael/anaconda2/lib/python2.7/site-packages/MACS2: Permission denied Error in runMACS(obj = x.sp[which(x.sp@cluster == 1), ], output.prefix = "atac_060_ASCP", : 'MACS' call failed
thank you, Michael
I am getting a permission denied error with MACS2 when running snapATAC. I can run macs2 in the terminal just fine, but not from R. Here is the code:
runMACS( obj=x.sp[which(x.sp@cluster==1),], output.prefix="atac_060_ASCP", path.to.snaptools="/usr/local/bin/snaptools", path.to.macs="/home/michael/anaconda2/lib/python2.7/site-packages/MACS2", gsize="mm", buffer.size=500, num.cores=30, macs.options="--nomodel --shift 37 --ext 73 --qval 1e-2 -B --SPMR --call-summits", tmp.folder=tempdir() )
Epoch: checking input parameters ... Epoch: extracting fragments from each snap files ... sh: 1: /home/michael/anaconda2/lib/python2.7/site-packages/MACS2: Permission denied Error in runMACS(obj = x.sp[which(x.sp@cluster == 1), ], output.prefix = "atac_060_ASCP", : 'MACS' call failed
thank you, Michael