Mapping Issue

[Former user]

I'm having the following issue running ROSE, after the BAM file passes QC and the GFF regions are stitched properly. The mapping just hangs without the timer counting but simply "WAITING FOR MAPPING TO COMPLETE' with 0 min elapsed.

Any idea what the issue might be?

TypeError  File "ROSE_bamToGFF.py", line 238, in main
: float() argument must be a string or a number
    newGFF = mapBamToGFF(bamFile,gffFile,options.sense,int(options.extension),options.floor,options.rpm,options.matrix)
  File "ROSE_bamToGFF.py", line 40, in mapBamToGFF
    MMR= round(float(bam.getTotalReads('mapped'))/1000000,4)

[Bryan Matthews]

OP here, just wanted to add that I get the same error when working with the example data as well. Thanks!

[Andrew Hoss]

I had this same error and it was because samtools wasnt loaded properly.