Hi,
I asked you to troubleshoot using R_2016_09_21_11_26_19_user_S5-00580-8-Medexome, but you used R_2016_09_21_14_01_15_user_S5-00580-8-Medexome
Regardless. In the input file the line that detonates the working directory does not match with what you actually have in your system.
input file:
IonXpress_007 MEV21
IonXpress_008 MEV22
IonXpress_009 MEV23
R_2016_09_21_14_01_15_user_S5-00580-9-Medexome
The script is designed to jump any directory that can not open or it doesn't exist.
