Biowulf High Performance Computing at the NIH
atactk on Biowulf

A toolkit for working with ATAC-seq data. Includes three programs useful for processing ATAC-seq data:

  • trim_adapters
  • make_cut_matrix
  • plot_aggregate_matrix.R
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 --mem=8g --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]$  trim_adapters forward.fastq.gz reverse.fastq.gz
[user@cn3144]$  # align trimmed reads
[user@cn3144]$  make_cut_matrix -d -b '(36-149 150-324 325-400 1)' -p $SLURM_CPUS_PER_TASK \
                      input.bam CTCF.bed.gz \
                   | gzip -c > CTCF.discrete.matrix.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. atactk.sh), which uses the input file 'atactk.in'. For example:

#!/bin/bash
module load atactk/0.1.6 || exit 1
make_cut_matrix -d -b '(36-149 150-324 325-400 1)' -p $SLURM_CPUS_PER_TASK \
  input.bam CTCF.bed.gz | \
  gzip -c > CTCF.discrete.matrix.gz

Submit this job using the Slurm sbatch command.

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

trim_adapters sample1_fw.fastq.gz sample1_rev.fastq.gz
trim_adapters sample2_fw.fastq.gz sample2_rev.fastq.gz
trim_adapters sample3_fw.fastq.gz sample3_rev.fastq.gz

Submit this job using the swarm command.

swarm -f atactk.swarm [-g #] [-t #] --module atactk
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 atactk Loads the atactk module for each subjob in the swarm