Running BLAST on HPC

Overview

Teaching: 0 min
Exercises: 20 min

Questions

Objectives

• Run a real-world bioinformatics application on HPC

Goal

In this exercise, you’re going to download BLAST reference sequences to Setonix, make a BLAST database, and run queries in series (one at a time).

The demo directory exercises/sequential contains two scripts. One script is to download the fasta files, and the other is to perform the BLAST query.

Before you start, cd into the appropriate directory:

cd $MYSCRATCH/Intro2HPC/exercises/sequential

Run a BLAST query using sbatch scripting

To set your job script running

sbatch blast.sh

Let’s look at the contents of blast.sh with cat blast.sh. Can you answer:

1. How long was the job time limit set for?
2. How many BLAST comparisons were run in this script?
3. This script will launch both the download script and perform the BLAST query. How did it manage that?

Solution

1. 5 minutes (#SBATCH --time=00:05:00
2. 4 comparisons (see the 4 lines under # Run Blast comparisons)
3. The blast.sh script executes the download.sh script using bash download.sh. This is run within the existing job, and saves you the hassle of launching two job scripts.

How can you check the status of your job(s) and view the job ID while they’re running?

Solution

squeue -u $USER

The final results are stored in result1.txt to result4.txt:

less result1.txt

Query= sp|Q4LEZ3|AARD_HUMAN Alanine and arginine-rich domain-containing
protein OS=Homo sapiens OX=9606 GN=AARD PE=1 SV=1

Length=155
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

XP_003200692.1 protein FAM167A-like [Danio rerio]                     47.0    6e-07
NP_001020721.1 protein FAM167A [Danio rerio]                          38.1    0.003
XP_005160526.1 protein FAM167A isoform X1 [Danio rerio]               38.1    0.003
XP_005160525.1 protein FAM167A isoform X1 [Danio rerio]               38.1    0.003
XP_021328850.1 protein FAM167B [Danio rerio]                          32.0    0.25 
XP_001923404.1 protein FAM167B [Danio rerio]                          32.0    0.25 
NP_001116846.1 serine hydroxymethyltransferase, mitochondrial [Da...  32.0    0.42 
NP_001017854.1 autophagy-related protein 16-1 [Danio rerio]           30.0    1.8  
NP_998623.1 SH3 domain-binding protein 5b [Danio rerio]               28.9    4.7  
NP_001076492.1 uncharacterized protein LOC100009654 [Danio rerio]     28.5    6.3  
NP_998042.1 serpin peptidase inhibitor, clade B (ovalbumin), memb...  28.1    6.5  
NP_001038588.1 sodium channel, voltage gated, type V-like, alpha ...  28.1    8.3 
[..]

When you’re done, quit the view by hitting the q button.

Well done, you’ve just BLASTed some sequences!

Key Points

• Submit jobs to the queue using a job script

• The #SBATCH flags allow you to change resource allocations, jobs names and other aspects of your job