Usage

The default shared Genome Database location is /data/reference/gmap. If you are a part of a group that's using a large Genome Database you're welcome to put the shared data into the shared Genome Database location. This is, of course, not necessary for custom databases that can be passed to the gmap with "-D" and "-d" command line switches.

If you are using an older gmap module the reference directory path could be wrong in which case you can specify the path with the '-D' argument.

Make sure to request two additional processors by increasing the "ppn" in the job script accordingly when running with the "-t X" argument to enable multi-threaded execution. When "-t" is used Gmap will create two more processes than the number of threads set with "-t", which will interfere with other people's jobs on the server gmap is running on and could result in the offending user's account being disabled.