The primary output of Illumina sequencing instruments are per-cycle base call files in BCL format. Bcl2fastq converts BCL files to fastq files used by most downstream software. It also separates reads into individual fastq files based on their barcode (demultiplexing), does adapter masking/trimming and moves unique molecular identifier (UMI) bases from the read to the fastq header. Bcl2fastq operates on Illumina run folders.

bcl2fastq creates a number of files summarizing statistics of the conversion in the InterOp folder of the run folder. They can be examined with the Illumina Sequence Analysis Viewer.

• User guide for v2.20 [PDF]
• User guide for version 2.19 [PDF]

• Module Name: bcl2fastq (see the modules page for more information)

bcl2fastq is a multithreaded application. By default it will run as many threads as there are CPUs for the conversion/demultiplexing plus additional threads for reading/writing data. You must therefore limit the threads to the number of threads allocated to your job or allocate nodes exclusively.

The relevant options for limiting the number of threads are

-r [ --loading-threads ] arg (=4)     number of threads used for loading BCL data
-p [ --processing-threads ] arg       number of threads used for processing demultiplexed data
-w [ --writing-threads ] arg (=4)     number of threads used for writing FASTQ data

Version 2.17 has an additional setting for the numer demultiplexing threads which is not present in later versions:

-d [ --demultiplexing-threads ] arg   number of threads used for demultiplexing

For a job allocated 16 CPUs these options should be set to

bcl2fastq -r 4 -w 4 -p 14 ...

This leads to a nominal overload but according to testing by Illumina this should yield optimal throughput.

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

[user@biowulf]$ sinteractive --cpus-per-task=16
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 bcl2fastq
[user@cn3144 ~]$ bcl2fastq --help
BCL to FASTQ file converter
bcl2fastq v2.20.0.422
Copyright (c) 2007-2017 Illumina, Inc.

Usage:
      bcl2fastq [options]
[...snip...]

[user@cn3144 ~]$ bcl2fastq -r 4 -w 4 -p 14 \
    --runfolder-dir /path/to/your/run/folder/160601_mach1_0023 ...

[user@cn3144 ~]$

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. bcl2fastq.sh), which uses the input file 'bcl2fastq.in'. For example:

#! /bin/bash

module load bcl2fastq/2.20.0 || exit 1
bcl2fastq --runfolder-dir /path/to/your/run/folder/160601_mach1_0023 \
          --output-dir ./160601_mach1_0023 \
          -r 4 -w 4 -p 14 \
          --barcode-mismatches 0

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=16 bcl2fastq.sh

Create a swarmfile (e.g. bcl2fastq.swarm). For example:

bcl2fastq --runfolder-dir /path/to/your/run/folder/160601_mach1_0023 \
          --output-dir ./160601_mach1_0023 \
          -r 4 -w 4 -p 14
bcl2fastq --runfolder-dir /path/to/your/run/folder/160602_mach1_0024 \
          --output-dir ./160602_mach1_0024 \
          -r 4 -w 4 -p 14
bcl2fastq --runfolder-dir /path/to/your/run/folder/160603_mach1_0025 \
          --output-dir ./160603_mach1_0025 \
          -r 4 -w 4 -p 14

Submit this job using the swarm command.

swarm -f bcl2fastq.swarm -t 16 --module bcl2fastq