The logging output of sort_RUM_by_location is making it into the mapping stats file. I believe the stdout from that script is supposed to be the chromosome counts, which are used to create the mapping_stats.txt file. Under some logging configurations, the logging output goes to stdout. I think I'm going to change it so that it accepts an option for the chromosome counts so that stdout output won't accidentally make it into the mapping stats file.
The logging output of sort_RUM_by_location is making it into the mapping stats file. I believe the stdout from that script is supposed to be the chromosome counts, which are used to create the mapping_stats.txt file. Under some logging configurations, the logging output goes to stdout. I think I'm going to change it so that it accepts an option for the chromosome counts so that stdout output won't accidentally make it into the mapping stats file.