genome_masking.sh

#!/bin/bash
#SBATCH --job-name=repeatmasker	                        # Job name
#SBATCH --partition=batch		                            # Partition (queue) name
#SBATCH --ntasks=10			                                # Single task job
#SBATCH --cpus-per-task=6		                            # Number of cores per task - match this to the num_threads used by BLAST
#SBATCH --mem=40gb			                                # Total memory for job
#SBATCH --time=2:00:00  		                            # Time limit hrs:min:sec
#SBATCH --output=/work/gene8940/yl87482/log.%j			    # Location of standard output and error log files (replace cbergman with your myid)
#SBATCH --mail-user=yl87482@uga.edu                    # Where to send mail (replace cbergman with your myid)
#SBATCH --mail-type=END,FAIL                            # Mail events (BEGIN, END, FAIL, ALL)

ml RepeatMasker/4.1.2-p1-foss-2020b

RepeatMasker -xsmall -gff  #-int masks only low complexity