RepeatMasker (Module)¶
RepeatMasker screens DNA sequences for interspersed repeats and low complexity DNA sequences.
RepeatMasker 4.0.7 is available as a module on Apocrita.
To run newer versions of RepeatMasker, we recommend installing it by following the Anaconda installation instructions.
Usage¶
To run the default installed version of RepeatMasker, simply load the
repeatmasker module:
module load repeatmasker
For usage documentation, run RepeatMasker with no arguments:
$ RepeatMasker
RepeatMasker version X.Y.Z
No query sequence file indicated
NAME
RepeatMasker - Mask repetitive DNA
SYNOPSIS
RepeatMasker [-options] <seqfiles(s) in fasta format>
A more detailed help document can be viewed by running RepeatMasker -help.
Example jobs¶
Serial jobs¶
Here is an example job running on 1 core and 1GB of 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 of 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.