Biowulf High Performance Computing at the NIH
Circleseq on HPC

Circleseq takes sample-specific paired end FASTQ files as input and produces a list of CIRCLE-seq detected off-target cleavage sites as output. The individual pipeline steps are:

1. Merge: Merge read1 an read2 for easier mapping to genome.
2. Read Alignment: Merged paired end reads from the assay are aligned to the reference genome using the BWA-MEM algorithm with default parameters (Li. H, 2009).
3. Cleavage Site Identification: Mapped sites are analyzed to determine which represent high-quality cleavage sites.
4. Visualization of Results: Identified on-target and off-target cleavage sites are rendered as a color-coded alignment map for easy analysis of results.

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 ~]$ cp -rp /usr/local/apps/circleseq/1.0/test /data/$USER/circlese
[user@cn3144 ~]$ cd /data/teacher/circleseq/
[user@cn3144 ~]$ module load circleseq
[user@cn3144 ~]$ python /usr/local/apps/circleseq/1.0/circleseq/circleseq.py all --manifest CIRCLEseq_StandardTest.yaml [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 circleseq
python /usr/local/apps/circleseq/1.0/circleseq/circleseq.py all --manifest CIRCLEseq_StandardTest.yaml

Submit this job using the Slurm sbatch command.

sbatch 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; python /usr/local/apps/circleseq/1.0/circleseq/circleseq.py all --manifest CIRCLEseq_StandardTest.yaml
cd dir2; python /usr/local/apps/circleseq/1.0/circleseq/circleseq.py all --manifest CIRCLEseq_StandardTest.yaml
cd dir3; python /usr/local/apps/circleseq/1.0/circleseq/circleseq.py all --manifest CIRCLEseq_StandardTest.yaml

Submit this job using the swarm command.

swarm -f job.swarm --module circleseq
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module Loads the module for each subjob in the swarm