BLAST+

BLAST (basic local alignment search tool) is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences. Using BLAST+ on a CARC cluster involves several steps, including writing a batch script to submit your BLAST jobs to the SLURM scheduler. Below is a short guide on how to use BLAST+.

1 Load the BLAST Module to use it in interactive mode

module purge
module load usc
module load ncbi-blast+

2 or write a SLURM batch script and submit it to the cluster

Create a batch script (blast_job.slurm) that specifies the SLURM directives, the environment, and the execution command.

#!/bin/bash
#SBATCH --job-name=blast_search
#SBATCH --output=blast_%j.out
#SBATCH --error=blast_%j.err
#SBATCH --nodes=1
#SBATCH --ntasks=8
#SBATCH --time=01:00:00
#SBATCH --mem=4G
#SBATCH --partition=main
#SBATCH --account=ttrojan_123

module purge
module load usc
module load ncbi-blast+

# Your BLAST command
blastp -query your_query.fasta -db your_database -out results.out -evalue 0.01 -num_threads $SLURM_NTASKS

Replace your_query.fasta with your query file, your_database with the BLAST database you intend to search against, and adjust other BLAST parameters as needed.

3 Submit Your Job

Use the sbatch command to submit your job to the SLURM scheduler.

sbatch blast_job.slurm

4 Collecting Results

Once the job is completed, the results will be available in the file you specified in the BLAST command (e.g., results.out).