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
- Module Name: minialign (see the modules page for more information)
- Multithreaded
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 minialignwhere
-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 |