arcasHLA on HPC

arcasHLA: high resolution HLA typing from RNA seq. arcasHLA performs high resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples.


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@biowulf]$ sinteractive --mem=5g --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 arcashla
[user@cn3144 ~]$ cd /data/$USER/
[user@cn3144 ~]$ cp -r /usr/local/apps/arcashla/0.5.0/test .
[user@cn3144 ~]$ arcasHLA extract test/test.bam -o test/output -t $SLURM_CPUS_PER_TASK
[user@cn3144 ~]$ arcasHLA genotype test/output/test.extracted.1.fq.gz test/output/test.extracted.2.fq.gz -g A,B,C,DPB1,DQB1,DQA1,DRB1 -o test/output -t $SLURM_CPUS_PER_TASK
[user@cn3144 ~]$ 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 arcashla
cd /data/$USER/test
arcasHLA extract test.bam -o output -t $SLURM_CPUS_PER_TASK
arcasHLA genotype output/test.extracted.1.fq.gz output/test.extracted.2.fq.gz -g A,B,C,DPB1,DQB1,DQA1,DRB1 -o output -t $SLURM_CPUS_PER_TASK

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] [--cpus-per-task=#]
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. job.swarm). For example:

cd dir1; arcasHLA extract test.bam -o output -t $SLURM_CPUS_PER_TASK
cd dir2; arcasHLA extract test.bam -o output -t $SLURM_CPUS_PER_TASK
cd dir3; arcasHLA extract test.bam -o output -t $SLURM_CPUS_PER_TASK

Submit this job using the swarm command.

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