TopHat 2 does not seem to recognize or use the designated output directory

Question

I am trying to set up a data analysis pipeline in TopHat. For some reason, I cannot seem to get the program to use my designated output directory. I have tried the following commands:

--output-dir "/path" \
--output-dir /path \
-o "/path" \
-o /path \

However, all the files keep being written to ./tophat_out

Has anyone encountered a similar problem?

Answer 1

I ran into this problem too, specifying all options before the genome and sequence files solves this however.