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 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.