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RepeatMasker

RepeatMasker screens DNA sequences for interspersed repeats and low complexity DNA sequences.

RepeatMasker is available as a module on Apocrita.

Usage

To run the default installed version of RepeatMasker, simply load the repeatmasker module:

module load repeatmasker

For usage documentation, run RepeatMasker -h. A more detailed help document can be viewed by running RepeatMasker --help.

Example jobs

Serial jobs

Here is an example job running on a single core and 1GB total memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load repeatmasker

RepeatMasker [-options] seqfiles.fa

Here is an example job running on 4 cores and 4GB total memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 4
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load repeatmasker

# By default, RepeatMasker will start 2 threads for every slot requested,
# resulting in badly overloaded jobs. To avoid this, set a variable half of
# the allocated slots
REPCORES=$((NSLOTS / 2))

RepeatMasker [-options] -pa ${REPCORES} seqfiles.fa

To request a different number of slots, simply change the core request (smp X value), no additional changes are required. One should request an even number of slots to ensure the REPCORES variable is set correctly.

References