Better exception handling if query directory is empty or do_run fails

[happykhan]

If do_run fails or input file directory is empty (so do_run does nothing). cluster_matrix throws a big ugly exception that makes no sense to the user.

Should be exception handling/checks if do_run produces no results.

[mscook]

Nouri also wrote some PBS scripts where she managed to delete/overwrite "paralell run". Need to lock a directory as well.