bwa-mem2 on Biowulf
Quick Links
Documentation
Notes
Interactive job
Batch job
Swarm of jobs

Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.

Reference
Vasimuddin Md, Sanchit Misra, Heng Li, Srinivas Aluru. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IEEE Parallel and Distributed Processing Symposium (IPDPS), 2019.

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --mem=100g --cpus-per-task=4
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load bwa-mem2

[user@cn3144 ~]$ bwa-mem2 mem -t $SLURM_CPUS_PER_TASK /fdb/bwa-mem2/hg38/genome.fa f1.fastq.gz f2.fastq.gz > /data/$USER/Ourfile

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. bwa-mem2.sh). For example:

#!/bin/bash
set -e
module load bwa-mem2
cd /data/$USER
bwa-mem2 mem -t $SLURM_CPUS_PER_TASK /fdb/bwa-mem2/hg38/genome.fa f1.fastq.gz f2.fastq.gz > /data/$USER/Ourfile

Submit this job using the Slurm sbatch command.

sbatch --mem=50g --cpus-per-task=4 bwa-mem2.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. bwa-mem2.swarm). For example:

cd dir1; bwa-mem2 mem -t $SLURM_CPUS_PER_TASK /fdb/bwa-mem2/hg38/genome.fa f1.fastq.gz f2.fastq.gz > /data/$USER/Ourfile
cd dir2; bwa-mem2 mem -t $SLURM_CPUS_PER_TASK /fdb/bwa-mem2/hg38/genome.fa f1.fastq.gz f2.fastq.gz > /data/$USER/Ourfileq
...
cd dir10; bwa-mem2 mem -t $SLURM_CPUS_PER_TASK /fdb/bwa-mem2/hg38/genome.fa f1.fastq.gz f2.fastq.gz > /data/$USER/Ourfileq

Submit this job using the swarm command.

swarm -f bwa-mem2.swarm -g 50 -t 4 --module bwa-mem2
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module bwa-mem2 Loads the bwa-mem2 module for each subjob in the swarm