unable to reproduce test run

[qianyang8]

Hi Eszter @elakatos,

First of all, thank you for developing this tool predicting neoantigens. We would really like to use your tool for our analysis. However, after setting it up following the README file, I am struggling to reproduce what you have shown with the test data.

I pulled your github repository and configured usr_paths.ini. Then ran test data with

python ./NeoPredPipe.py -I Example/input_vcfs/ -H Example/HLAtypes/hlatypes.txt -o ./example_test/ -c 1 2 -E 8 9 10 -m -a

and received below matrix of 0 in "AllSamples.neoantigens.summarytable.txt"
Sample Total Total_WB Total_SB Total_Region_0 Total_Region_1 Total_WB_Region_0 Total_WB_Region_1 Total_SB_Region_0 Total_SB_Region_1 Clonal Subclonal Shared Clonal_WB Clonal_SB Subclonal_WB Subclonal_SB Shared_WB Shared_SB
test1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
test2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

session info
biopython 1.76
Python-2.7.18
OS: linux

would love to get your help on this, thank you.