pecanpie was called with this command to generate this directory:
 /usr/local/bin/pecanpie -o /home/srlab/Documents/DNR_PECAN_Run_1_20170303_Output -b /home/srlab/Documents/DNR_PECAN_Run_1_20170303/Combined-gigas-QC.txt -n DNR_PECAN_Run_1_20170303_SpLibrary -s gigas --isolationSchemeType BOARDER --pecanMemRequest 35 /home/srlab/Documents/DNR_PECAN_Run_1_20170303/2017-03-03-mzML-file-path-list.txt /home/srlab/Documents/DNR_PECAN_Run_1_20170303/2017-03-03-background-peptides-path-list.txt /home/srlab/Documents/DNR_PECAN_Run_1_20170303/2017-03-03-isolation-windows.csv