Biowulf High Performance Computing at the NIH
Minialign on Biowulf

Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining, and SIMD-parallel Smith-Waterman-Gotoh extension.

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 minialign
[user@cn3144 ~]$ minialign -t 4 ref.fa input.fa > out.sam
[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. minialign.sh). For example:

#!/bin/bash
set -e
module load minialign
minialign -t $SLURM_CPUS_PER_TASK ref.fa input.fa > out.sam

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] minialign.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. minialign.swarm). For example:

cd dir1; minialign -t $SLURM_CPUS_PER_TASK ref.fa input.fa > out.sam
cd dir2; minialign -t $SLURM_CPUS_PER_TASK ref.fa input.fa > out.sam
cd dir3; minialign -t $SLURM_CPUS_PER_TASK ref.fa input.fa > out.sam
cd dir4; minialign -t $SLURM_CPUS_PER_TASK ref.fa input.fa > out.sam

Submit this job using the swarm command.

swarm -f minialign.swarm [-g #] [-t #] --module minialign
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 Loads the module for each subjob in the swarm