Hi - This workflow is over 5 years old (from 2014) and most of the tools included now have newer versions and should be updated in the workflow before use. In particular, the BWA for Illumia tool has been deprecated and can produce unexpected results/errors. It seems like you are not getting any hits.
Either BWA or BWA-MEM are a better choices for mapping. If you do not get hits again, you’ll need to check your inputs and tool settings.