Biowulf High Performance Computing at the NIH
Arriba on Biowulf

Arriba is a command-line tool for detecting gene fusions in RNA-Seq data. It can also detect other clinically-relevant structural variations such as exon duplications or truncations of genes (i.e., breakpoints in introns and intergenic regions).


A dedicated publication about Arriba has not been released yet. Until then, please refer to Arriba in your methods section as follows (or similar): We used Arriba ( to detect gene fusions from RNA-Seq data.
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load arriba
[+] Loading arriba  1.2.0  on cn3113
[+] Loading singularity  3.5.3  on cn3113
[user@cn3144 ~]$
Usage: STAR_genomeDir/ annotation.gtf assembly.fa blacklist.tsv read1.fastq.gz read2.fastq.gz threads
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. For example:

set -e
module load arriba  > arriba.out

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#]
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. Arriba.swarm). For example:  > Arriba_1.out  > Arriba_2.out  > Arriba_3.out  > Arriba_4.out

Submit this job using the swarm command.

swarm -f Arriba.swarm [-g #] [-t #] --module arriba
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module arriba Loads the arriba module for each subjob in the swarm