RepeatModeler (Module)¶
RepeatModeler is a de-novo transposable element family identification and modelling package.
RepeatModeler 2.0.1 is available as a module which wraps an Apptainer container on Apocrita.
To run newer versions of RepeatModeler, we recommend installing it by following the Anaconda installation instructions.
Usage¶
To run the default installed version of RepeatModeler, simply load the
repeatmodeler module:
module load repeatmodeler
For usage documentation, run RepeatModeler -help:
$ RepeatModeler -help
No database indicated
NAME
RepeatModeler - Model repetitive DNA
SYNOPSIS
RepeatModeler [-options] -database <XDF Database>
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.