In Dapars2_Multi_Sample.py, the line 116 "output_directory = outputdirectory.strip('/') + '' + curr_processing_chr + '/'" will also strip the header "/" in output directory, and caused to create new folder in other path. It should be correct as "output_directory = outputdirectory.rstrip('/') + '' + curr_processing_chr + '/'", rstrip will only strip the tail "/".
It was same issue in DaPars2_Multi_Sample_Multi_Chr.py.
In Dapars2_Multi_Sample.py, the line 116 "output_directory = outputdirectory.strip('/') + '' + curr_processing_chr + '/'" will also strip the header "/" in output directory, and caused to create new folder in other path. It should be correct as "output_directory = outputdirectory.rstrip('/') + '' + curr_processing_chr + '/'", rstrip will only strip the tail "/". It was same issue in DaPars2_Multi_Sample_Multi_Chr.py.