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.

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.

• https://github.com/bwa-mem2/bwa-mem2/tree/master

• Module Name: bwa-mem2 (see the modules page for more information)
• Multi-threaded using '-t' flag
• Index files in /fdb/bwa-mem2

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 ~]$

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

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