Quick Links Documentation Notes Interactive job Batch job Swarm of jobs

PEPATAC is a robust pipeline for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) built on a loosely coupled modular framework. It may be easily applied to ATAC-seq projects of any size, from one-off experiments to large-scale sequencing projects. It is optimized on unique features of ATAC-seq data to be fast and accurate and provides several unique analytical approaches.

• PEPATAC GitHub page
• PEPATAC Home page
• PEPATAC_tutorial

• Module Name: PEPATAC (see the modules page for more information)
• Unusual environment variables set
  • PEPATAC_HOME  installation directory
  • PEPATAC_BIN       executable directory
  • PEPATAC_SRC       source code directory
  • PEPATAC_DATA  sample data directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=16 --mem=32g --gres=lscratch:10
[user@cn3200 ~]$module load PEPATAC/0.9.16 
[+] Loading bedtools  2.27.1
[+] Loading bowtie  2-2.4.4
[+] Loading preseq  3.1.2
[+] Loading fastqc  0.11.9
[+] Loading samtools 1.12  ...
[+] Loading samblaster  0.1.25
[+] Loading GSL 2.4 for GCC 7.2.0 ...
[+] Loading gcc  7.3.0  ...
[+] Loading openmpi 3.0.2  for GCC 7.3.0
[+] Loading ImageMagick  7.0.8  on cn0852
[+] Loading HDF5  1.10.4
[+] Loading pandoc  2.14.0.2  on cn0852
[+] Loading R 3.5.2
[+] Loading pigz  2.4  on cn0852
[+] Loading pepatac  0.9.16

Described below are the steps to run PEPATAC on the tutorial example:

[user@cn3200 ~]$ mkdir pepatac_tutorial
[user@cn3200 ~]$ export TUTORIAL=$PWD/pepatac_tutorial
[user@cn3200 ~]$ cd pepatac_tutorial
[user@cn3200 ~]$ mkdir data genomes processed templates tools
[user@cn3200 ~]$ cd tools
[user@cn3200 ~]$ git clone https://github.com/databio/pepatac.git

Download tutorial files:

[user@cn3200 ~]$ wget http://big.databio.org/pepatac/tutorial1_r1.fastq.gz
[user@cn3200 ~]$ wget http://big.databio.org/pepatac/tutorial1_r2.fastq.gz
[user@cn3200 ~]$ wget http://big.databio.org/pepatac/tutorial2_r1.fastq.gz
[user@cn3200 ~]$ wget http://big.databio.org/pepatac/tutorial2_r2.fastq.gz

[user@cn3200 ~]$ mv *.fastq.gz pepatac/examples/data/

Configure project files:

[user@cn3200 ~]$ cd ../
[user@cn3200 ~]$ cat >my_file.sh<<'EOF'
adapters:
  CODE: looper.command
  JOBNAME: looper.job_name
  CORES: compute.cores
  LOGFILE: looper.log_file
  TIME: compute.time
  MEM: compute.mem
compute_packages:
  default:
    submission_template: templates/localhost_template.sub
    submission_command: sh
EOF

[user@cn3200 ~]$ export DIVCFG=$TUTORIAL/compute_config.yaml

[user@cn3200 ~]$ cd templates
[user@cn3200 ~]$ cat >localhost_template.sub<<'EOF'
#!/bin/bash
echo 'Compute node:' `hostname`
echo 'Start time:' `date +'%Y-%m-%d %T'`
{
{CODE}
} | tee {LOGFILE} --ignore-interrupts
EOF

Initialize refgenie:

[user@cn3200 ~]$ cd ../tools/pepatac
[user@cn3200 ~]$ refgenie init -c genome_folder/genome_config.yaml
[user@cn3200 ~]$ export REFGENIE=./genome_folder/genome_config.yaml

Run the PEPATAC pipeline using looper:

[user@cn3200 ~]$ looper run examples/tutorial/tutorial.yaml
...
Looper version: 1.3.0
Command: run
/usr/local/apps/PEPATAC/0.9.16/lib/python3.8/site-packages/divvy/compute.py:150: UserWarning: The '_file_path' property is deprecated and will be removed in a future release. Use ComputingConfiguration["__internal"][_file_path] instead.
  os.path.dirname(self._file_path),
/usr/local/apps/PEPATAC/0.9.16/lib/python3.8/site-packages/divvy/compute.py:58: UserWarning: The '_file_path' property is deprecated and will be removed in a future release. Use ComputingConfiguration["__internal"][_file_path] instead.
  self.config_file = self._file_path
## [1 of 2] sample: tutorial1; pipeline: PEPATAC
## [2 of 2] sample: tutorial2; pipeline: PEPATAC
Writing 2 submission scripts for skipped samples
Writing script to $TUTORIAL/processed/submission/PEPATAC_tutorial1.sub
Writing script to $TUTORIAL/processed/submission/PEPATAC_tutorial2.sub

Looper finished
Samples valid for job generation: 2 of 2
Commands submitted: 0 of 2
Jobs submitted: 0

The previous command produces two sbatch scripts.

Finally, submit these scripts to the cluster:

[user@cn3200 ~]$  sbatch $TUTORIAL/processed/submission/PEPATAC_tutorial1.sub
[user@cn3200 ~]$  sbatch $TUTORIAL/processed/submission/PEPATAC_tutorial2.sub

End the interactive session:

[user@cn3200 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$