Updated 2023-02-07

Run Bedtools on the Cluster


  • Bedtools contains a multitude of tools used for genomic analysis and allows for functionality such as shuffling, merging, and intersecting genomic intervals.
  • Use module avail bedtools to see all the available versions of bedtools on the cluster
  • To load bedtools in your SLURM script:
    • Load its dependent module first with module load gcc/4.9.0
    • Load bedtools with module load bedtools/2.25. Replace the version number with any version you prefer that is available on the cluster (found with module avail)
  • To run bedtools:
    • In your SLURM script, put all lines executing bedtools after the module load lines that load SLURMbedtools
    • Example: using the intersect tool, the line bedtools intersect -a <filename>.bed -b genes.bed would go in the SLURM script after the lines that load the correct modules for bedtools.

Example SLURM Script

#SBATCH -J bedtoolsTest
#SBATCH -A [Account] 
#SBATCH -N 2 --ntasks-per-node=4
#SBATCH -t 20
#SBATCH -p inferno
#SBATCH -o bedtoolsResult.out

module load gcc/4.9.0
module load bedtools/2.30.0
bedtools intersect -a reads.bed -b genes.bed
  • The SLURM directives are standard, requesting 20 min of walltime and 2 nodes with 4 cores per node.


If using $SLURM_SUBMIT_DIR,the .bed files, as well as any other files required for the job, must be stored in the same folder as the SBATCH script

  • $SLURM_SUBMIT_DIR is simply a variable that represents the directory you submit the SLURM script from. Make sure the .bed files, and any other files you need are in the same directory you put the SLURM script in. This line tells the cluster to enter this directory where you have stored the SBATCH script, and look for all the files for the job. If you use $SLURM_SUBMIT_DIR, you need to have all your files in the same folder as your SBATCH script otherwise the cluster won't be able to find the files it needs.
  • Output Files: Any files generated by the job will also show up in the same directory as the SLURM script.
  • The module load lines load bedtools and its dsbatchependent module
  • The bedtools intersect line is just a general example showing how bedtools might be executed. The line is from the bedtools documentation which includes much more information on the capabilities of bedtools. The point is to show that the execution lines must be included after:
    • Entering the correct folder with all the files and SLURM script, in this case achieved with cd $SLURM_SUBMIT_DIR
    • bedtools is loaded with the module load lines

Submit Job and Check Status

  • Make sure you're in the directory that contains the SLURM script, the sequence files, and any other files you need.
  • Submit with sbatch <SLURM script name>. In this case sbatch bedtools.SLURM or whatever you called the SLURM script. You can name the SLURM scripts whatever you want, just keep the .SLURM at the end
  • Check job status with squeue -u username3 -n, replacing "username3" with your gt username
  • You can delete the job with scancel 22182721, replacing the number with the jobid returned after running sbatch
  • Depending on the resources requested and queue the job is run on, it may take varying amounts of time for the job to start. To estimate the time until the job executes, run showstart 22182721, replacing the number with the jobid returned after running sbatch. More helpful commands can be found in this guide

Collecting Results

  • All files created will be in the same folder where your SLURM script is (same directory you ran sbatch from)
  • The .out file will be found here as well. It contains the results of the job, as well as diagnostics and a report of resources used during the job. If the job fails or doesn't produce the result your were hoping for, the .out file is a great debugging tool.
  • You can transfer the resulting files off the cluster using scp or a file transfer service