I am trying to run prepDE (found here http://ccb.jhu.edu/software/stringtie/dl/prepDE.py) however I am getting an error that does not give me a lot of information on what exactly the issue is or where to look on where to solve it. I googled but didn't find much. 

C:\Python27\python.exe prepDE.py -i C:\sample_lst.txt
0 1683-bulk
1 1680-bulk
Traceback (most recent call last):
  File "C:\prepDE.py", line 269, in <module>
    geneDict.setdefault(geneIDs[i], {})  # gene_id
KeyError: 'MSTRG.23895.4'

I tried printing the values to get a sense of the issue but it is taking a long time to complete. Has anyone seen this error, how did you resolve it? 

I don’t maintain this software or script. You’ll have better luck with the maintainers.