Biowulf High Performance Computing at the NIH
Bsmap on HPC

BSMAP is a short reads mapping software for bisulfite sequencing reads. Bisulfite treatment converts unmethylated Cytosines into Uracils (sequenced as Thymine) and leave methylated Cytosines unchanged, hence provides a way to study DNA cytosine methylation at single nucleotide resolution. BSMAP aligns the Ts in the reads to both Cs and Ts in the reference.

RRBSMAP is a specifically designed version of BSMAP for reduced representation bisulfite sequencing (RRBS), it indexes the genome only on the enzyme digestion sites and therefore guarantees all reads were mapped to digestion sites, and greatly reduces the CPU/memory usage. Since BSMAP-2.0, RRBSMAP has been merged into BSMAP.

References:

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@biowulf]$ sinteractive --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 bsmap
[user@cn3144 ~]$ bsmap -a infile -d ref.fa -o out.bam -p $SLURM_CPUS_PER_TASK

[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. batch.sh). For example:

#!/bin/bash
set -e
module load bsmap
bsmap -a infile -d ref.fa -o out.bam -p $SLURM_CPUS_PER_TASK

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 batch.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. job.swarm). For example:

cd dir1; bsmap -a infile -d ref.fa -o out.bam -p $SLURM_CPUS_PER_TASK
cd dir2; bsmap -a infile -d ref.fa -o out.bam -p $SLURM_CPUS_PER_TASK
cd dir3; bsmap -a infile -d ref.fa -o out.bam -p $SLURM_CPUS_PER_TASK

Submit this job using the swarm command.

swarm -f job.swarm -t 4 --module bsmap
where
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module Loads the module for each subjob in the swarm