Exercise

Convert existing script to a batch script and run it using the sbatch command from Slurm

Set up

  1. Locate the file generate_bad_reads_summary.sh (which was created in the Loops and Automation lesson)

    Hint: This file is likely in your badreads directory.

    cd ~/unix_lesson/badreads
  2. Duplicate this file and call the duplicate file sbatch_generate_bad_reads_summary.sh. (Hint: use the cp command) 
    cp generate_bad_reads_summary.sh sbatch_generate_bad_reads_summary.sh
  3. Create a new directory inside the badreads directory called sbatch_output. 
    mkdir sbatch_output

Update the new shell script

Using vim open up the file sbatch_generate_bad_reads_summary.sh to make some edits. Once inside the file, do the following:

Hint: Remember to change to insert mode in vim before beginning to edit!

  1. Update these two lines of code below, such that the grep output in both cases is redirected to the ~/unix_lesson/badreads/sbatch_output/ directory. Do not change the names of the output files. 
           grep -B1 -A2 NNNNNNNNNN $filename > ~/unix_lesson/badreads/${samplename}_badreads.fq
          
       grep -cH NNNNNNNNNN $filename >> ~/unix_lesson/badreads/badreads.count.summary
  2. Add SLURM/sbatch directives at the top of the script requesting the following resources:
    • Use partition priority (-p)
    • Request 5 minutes (-t)
    • Request 100MB of memory (--mem)
    • Request a single core (-c)
    • Specify the output file name (-o)
    • Specify the error file name (-e)
  3. Save the file and exit vim.

Run the new shell script to start a new job on O2

  1. Run the new script using the sbatch command

Check the job/run

  1. Use sacct to check the status of your job submission
  2. Check the contents of your current directory -
    • Are there any new files with names ending in .out and .err?
    • What are the contents of these two files?
  3. Check the contents of ~/unix_lesson/badreads/sbatch_output/, are the expected files there?

This lesson has been developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC). These are open access materials distributed under the terms of the Creative Commons Attribution license (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.