Thank you for the high praise! We do try our best. 
Correct, often low-quality data will make some of these parameters too restrictive. Especially, if you are using the incorrect primer sequence(s) and/or orientation, as outlined in this thread. This is also why I also append the following commands (often only the first one is required, but I use both just because):
--p-match-adapter-wildcards \
--p-match-read-wildcards \
You're welcome!
-Mike