Biowulf High Performance Computing at the NIH
FastQC on Biowulf

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.

The main functions of FastQC are

- Import of data from BAM, SAM or FastQ files (any variant)
- Providing a quick overview to tell you in which areas there may be problems
- Summary graphs and tables to quickly assess your data
- Export of results to an HTML based permanent report
- Offline operation to allow automated generation of reports without running the interactive application

References:

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 fastqc
[user@cn3144 ~]$ fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file seqfile1 .. seqfileN

[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. fastqc.sh). For example:

#!/bin/bash
set -e
module load fastqc
fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file seqfile1 .. seqfileN

Submit this job using the Slurm sbatch command.

sbatch --mem=10g fastqc.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. fastqc.swarm). For example:

cd dir1;fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file seqfile1 .. seqfileN
cd dir2;fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file seqfile1 .. seqfileN
cd dir3;fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file seqfile1 .. seqfileN
cd dir4;fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file seqfile1 .. seqfileN
cd dir5;fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file seqfile1 .. seqfileN

Submit this job using the swarm command.

swarm -f fastqc.swarm -g 10 --module fastqc
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module fastqc Loads the fastqc module for each subjob in the swarm