RepeatModeler¶
RepeatModeler is a de-novo transposable element family identification and modelling package.
RepeatModeler is available as a module which wraps an Apptainer container on Apocrita.
Usage¶
To run the default installed version of RepeatModeler, simply load the
repeatmodeler module:
$ module load repeatmodeler
$ RepeatModeler --help
NAME
RepeatModeler - Model repetitive DNA
SYNOPSIS
RepeatModeler [-options] -database <XDF Database>
For usage documentation, run RepeatModeler --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 repeatmodeler
# create a database for RepeatModeler
BuildDatabase -name DB_NAME INPUT.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 repeatmodeler
# By default, RepeatModeler 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))
RepeatModeler -database DB_NAME -pa ${REPCORES}
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.