Hello. I think you should make different tests by varying the parameters below :

--read-mismatches

--read-edit-dist

--read-gap-length

--segment-mismatches

After each test, have a look to the output file "align_summary.txt" and compare the differents results.

You can also decrease --max-intron-length 5000 to 15000 (default is 500000) and maybe --min-intron-length 50 (default is 70)

Usually, people decrease the parameter -g (--max-multihits) to 10 (default is 20)

Thank you David, We will change the parameter and let you know, if  it is working or not.