Hi,
some users are currently experiencing a but that causes the fragment picker to seg-fault before the 9mer fragments are written. So after running the fragpicker you'll find the file with 3mer fragments but not the 9mers.
This is really annoying as the crash happens during dumping of the results to the 9mer frag-file, after all the hard-work of picking is done. I am partly finished with removing this bug and will make available a new release version when finished. Sorry for the inconvenience that may cause to you.
Best,
Oliver