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Genome annotation pipeline

MAKER Homepage

Available Modules

module load MAKER/2.31.9-gimkl-2020a

Local Customisations

Since the MAKER control file maker_exe.ctl is just an annoyance in an environment module based system we have patched MAKER to make that optional. If it is absent then the defaults will be used directly. 


MAKER can be used with MPI, though due to a complicated interaction between Infiniband libraries and MAKER's use of forking it can't be used across multiple nodes. So we recommend running large MAKER jobs with up to 36 tasks on one node (ie: one full regular node), eg:

#SBATCH --nodes=1
#SBATCH --ntasks-per-node=36
#SBATCH --mem-per-cpu=1500

module load MAKER/2.31.9-gimkl-2020a
srun maker -q


MAKER creates many files in its output, sometimes hundreds of thousands.  There is a risk that you exhaust your quota of inodes, so:

  • Don't run too many MAKER jobs simultaneously.
  • Delete unneeded output files promptly after MAKER finishes.  You can use nn_archive_files or tar to archive them first.