Biowulf High Performance Computing at the NIH
Muscle on Biowulf

MUSCLE is a popular multiple alignment program with good performance and accuracy. It can align hundreds of sequences quickly and has a simple command line interface with few options. ?Compared to previous versions, Muscle v5 is much more accurate, is often faster, and scales to much larger datasets. At the time of writing (late 2021), Muscle v5 has the highest scores on multiple alignment benchmarks including Balibase, Bralibase, Prefab and Balifam. It can align tens of thousands of sequences with high accuracy on a low-cost commodity computer (say, an 8-core Intel CPU with 32 Gb RAM). On large datasets, Muscle v5 is 20-30% more accurate than MAFFT and Clustal-Omega.


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=16
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 muscle
[+] Loading muscle  5.0.1428

[user@cn3144 ~]$ cp /usr/local/apps/muscle/sample_data/globins13.fa .

[user@cn3144 ~]$ muscle -threads $SLURM_CPUS_PER_TASK -align globins25.fa -output globins25.muscle.out

muscle 5.0.1428_linux64  396Gb RAM, 72 cores
(C) Copyright 2004-2021 Robert C. Edgar.

00:00 24Mb   CPU has 72 cores, defaulting to 20 threads

WARNING: Max OMP threads 16

02:00 1.6Gb   100.0% Calc posteriors
05:44 2.6Gb   100.0% Consistency (1/2)
09:30 2.6Gb   100.0% Consistency (2/2)
09:30 2.6Gb   100.0% UPGMA5
10:01 2.6Gb   100.0% Refining

[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. For example:

set -e
module load muscle
cd /data/$USER/somedir
muscle -threads $SLURM_CPUS_PER_TASK -align inputseqs.fa -output muscle_output

Submit this job using the Slurm sbatch command.

sbatch  [--mem=#] --cpus-per-task=20
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. Muscle.swarm). For example:

muscle -threads $SLURM_CPUS_PER_TASK -align file1.fa -output file1.out
muscle -threads $SLURM_CPUS_PER_TASK -align file2.fa -output file2.out

Submit this job using the swarm command.

swarm -f Muscle.swarm [-g #] -t 16 --module muscle
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t 16Number of CPUs to use for a single muscle command
--module Muscle Loads the Muscle module for each subjob in the swarm

Benchmarks were run with input sequence file globins630.fa (available in /usr/local/apps/muscle/sample_data on Biowulf, and from the Hmmer tutorial) on Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz ('x6140' nodes on Biowulf norm partition). This job requires about 2 GB memory.

Based on the benchmarks below, it is appropriate to submit to 20 or 24 CPUs for this muscle alignment. Increasing the allocated CPUs beyond 24 results in very little performance improvement, and is therefore inefficient.