I've executed exonerate with a dataset, but it isn't producing any output despite the fact I set --showvulgar yes. I've seen a previous thread on this Problems with Exonerate output. However, this doesn't solve my problem as a file is printed that simply repeats the commands I've used and nothing more. Another thread on a different site had the answer of "exonerate -h". Sadly, the exonerate "help" and manual do not indicate on option for creating an output, other than telling the program what kind of output you want.
How do I get my results?!?!?!