Biowulf High Performance Computing at the NIH
Cicero on Biowulf

CICERO (Clipped-reads Extended for RNA Optimization) is an assembly-based algorithm to detect diverse classes of driver gene fusions from RNA-seq.

References:

Documentation
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 --mem=10g --gres=lscratch:20 --time=12:00:00 --cpus-per-task=4
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 cicero
[user@cn3144 ~]$ RNApeg.sh -b bamfile -f fasta -r refflat
[user@cn3144 ~]$ Cicero.sh -n $SLURM_CPUS_PER_TASK -b /data/$USER/cicero/demo/MV4_11_RNAseq_1.bam -g GRCh38_no_alt -r /fdb/cicero/reference -o /lscratch/$SLURM_JOBID/outdir 
[user@cn3144 ~]$ cp -rp /lscratch/$SLUCRM_JOBID/{outdir,results} /data/$USER/

[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. batch.sh). For example:

#!/bin/bash
set -e
module load cicero
RNApeg.sh -b bamfile -f fasta -r refflat
Cicero.sh -n $SLURM_CPUS_PER_TASK -b /data/$USER/cicero/demo/MV4_11_RNAseq_1.bam -g GRCh38_no_alt -r /fdb/cicero/reference -o /lscratch/$SLURM_JOBID/outdir
cp -rp /lscratch/$SLUCRM_JOBID/{outdir,results} /data/$USER/

Submit this job using the Slurm sbatch command.

sbatch --gres=lscratch:20 --cpus-per-task=4 --mem=10g batch.sh
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. cicero.swarm). For example:

cd dir1; Cicero.sh -n $SLURM_CPUS_PER_TASK ....
cd dir2; Cicero.sh -n $SLURM_CPUS_PER_TASK ....
....
cd dir10; Cicero.sh -n $SLURM_CPUS_PER_TASK ....

Submit this job using the swarm command.

swarm -f cicero.swarm -g 10 -t 4 --gres=lscratch:20 --module cicero
where
-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 cicero Loads the cicero module for each subjob in the swarm
--gres=lscratch:20 allocate 20g of space which can be used as /lscratch/$SLURM_JOBID in the job