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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.


To run the default installed version of RepeatModeler, simply load the repeatmodeler module:

$ module load repeatmodeler
$ RepeatModeler --help
    RepeatModeler - Model repetitive DNA

      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:

#$ -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:

#$ -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

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.