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Lesson 4 Practice

The following can be used to practice skills learned in Lesson 4.

Login to Biowulf

If you are already logged in, exit the remote connection and reconnect. Remember, you must be on the NIH network.

Solution 
ssh username@biowulf.nih.gov

Navigate to your working directory. 

cd /data/$USER/Module_1/testscript

Let's run fastqc, a quality control program, on the files we downloaded from the SRA.

Using sbatch

Start a new script, named fastqc.sh in the same directory in which you downloaded data from Lesson (/data/$USER/testscript).

The command you will include in the script is as follows: 

mkdir fastqc
fastqc -o ./fastqc/ -t 4 *.fastq

This command will output the fastqc results to a directory named fastqc inside the current working directory. It will also run using four threads and will run on all fastq files in your working directory.

You need edit this script in order to submit as a job on Biowulf. What is missing?

Solution 
#!/bin/bash
#SBATCH --cpus-per-task=4 

module load fastqc
mkdir fastqc
fastqc -o ./fastqc/ -t 4 *.fastq

Submit the job.

Solution 
sbatch fastqc.sh

How can we check on our job? What is the job's status? How much memory is it using?

Solution 
squeue -u $USER  
sjobs -u $USER

How can we cancel this job?

Solution 

scancel job-id
where job-id is the id of the job. Check the output of squeue -u $USER if you are unsure what the job id is.

Using sinteractive

What if we want to run this same task interactively? How can we access an interactive session to run the same code above?

Solution 
sinteractive --cpus-per-task=4

Additional practice materials from hpc.nih.gov