RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program.

• RepeatMasker Main Site
• RepeatMasker Documentation

• Module Name: repeatmasker (see the modules page for more information)
• By default, RepeatMasker will start 2 threads for every CPU in the node resulting in badly overloaded jobs. Users must prevent this behavior by setting -pa N where N is equal to the number of allocated CPUs divided by 2. In -pa N, "N" must always be greater than or equal to 2; -pa 1 causes RepeatMasker to run as though the -pa option was not specified and to start 2 threads for each CPU. See the examples below for details.
• RepeatMasker uses the Repbase libraries. Users should be aware of the Repbase academic license agreement before using RepeatMasker on the NIH HPC Systems.
• On Biowulf, RepeatMasker has been configured to have HMMER as the default search engine. RMBlast can be used instead by passing -engine rmblast to the RepeatMasker command.
• Setting a species/clade: RepeatMasker in v4.1.1 has switched to the FamDB format for the Dfam database. You may notice RepeatMasker being more strict with regards to what is acceptable for the -species flag. To check for valid names, you can query the database using famdb.py. See famdb.py --help for usage information and below for an example using our copy of the database:

  famdb.py -i /fdb/dfam/Dfam.h5 names mammal

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
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 repeatmasker
[user@cn3144 ~]$ RepeatMasker -pa 2 sequence.fasta # for any sequence file sequence.fasta
RepeatMasker version open-4.0.7
Search Engine: HMMER [ 3.1b2 (February 2015) ]
Master RepeatMasker Database: /usr/local/apps/repeatmasker/4.0.7/Libraries/Dfam.hmm ( Complete Database: Dfam_2.0 )


analyzing file sequence.fasta
identifying Simple Repeats in batch 1 of 1
identifying full-length ALUs in batch 1 of 1
identifying full-length interspersed repeats in batch 1 of 1
identifying remaining ALUs in batch 1 of 1
identifying most interspersed repeats in batch 1 of 1
identifying Simple Repeats in batch 1 of 1
processing output: 
cycle 1 
cycle 2 
cycle 3 
cycle 4 
cycle 5 
cycle 6 
cycle 7 
cycle 8 
cycle 9 
cycle 10 
Generating output... 
masking
done
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. repeatmasker.sh). For example:

#!/bin/sh
set -e
module load repeatmasker
RepeatMasker -engine rmblast -pa 2 sample.fasta

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] repeatmasker.sh

Create a swarmfile (e.g. repeatmasker.swarm). For example:

RepeatMasker -pa 2 sample1.fasta
RepeatMasker -pa 2 sample2.fasta
RepeatMasker -pa 2 sample3.fasta
RepeatMasker -pa 2 sample4.fasta

Submit this job using the swarm command.

swarm -f repeatmasker.swarm [-g #] [-t #] --module repeatmasker