Biowulf High Performance Computing at the NIH
Htgts on HPC

HTGTS represents High-Throughput Genome-Wide Translocation Sequencing pipeline - provided by theĀ Alt Lab

 

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@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 htgts
[user@cn3144 ~]$ TranslocPreprocess.pl tutorial_metadata.txt preprocess/ results/ --threads $SLURM_CPUS_PER_TASK --read1 pooled_R1.fastq.gz --read2 pooled_R2.fastq.gz

[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 htgts
TranslocPreprocess.pl tutorial_metadata.txt preprocess/ results/ --threads $SLURM_CPUS_PER_TASK --read1 pooled_R1.fastq.gz --read2 pooled_R2.fastq.gz

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 --mem=20g 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. job.swarm). For example:

cd dir1; TranslocPreprocess.pl tutorial_metadata.txt preprocess/ results/ --threads $SLURM_CPUS_PER_TASK --read1 pooled_R1.fastq.gz --read2 pooled_R2.fastq.gz
cd dir2; TranslocPreprocess.pl tutorial_metadata.txt preprocess/ results/ --threads $SLURM_CPUS_PER_TASK --read1 pooled_R1.fastq.gz --read2 pooled_R2.fastq.gz
cd dir3; TranslocPreprocess.pl tutorial_metadata.txt preprocess/ results/ --threads $SLURM_CPUS_PER_TASK --read1 pooled_R1.fastq.gz --read2 pooled_R2.fastq.gz

Submit this job using the swarm command.

swarm -f job.swarm -g 20 -t 4 --module htgts
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 Loads the module for each subjob in the swarm