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bcl2fastq
Overview
BCL2FastQ is a program to convert and demultiplex BCL files to FastQ format.
Version 2.20.0.422 is installed on the CSF.
Restrictions on use
The software and materials are proprietary to Illumina, Inc., and are intended solely for the use of its customers and for no other purpose than use with Illumina’s products or services. The downloadable materials and their contents shall not be used or distributed for any other purpose or otherwise communicated, disclosed, or reproduced in any way without the prior written consent of Illumina, Inc.
Set up procedure
To access the software you must first load the modulefile:
module load apps/gcc/bcl2fastq/2.20
Running the application
Please do not run bcl2fastq on the login node. Jobs should be submitted to the compute nodes via batch.
Serial batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings # Note that the executable is called 'bcl2fastq'. # Force use of just one thread overriding the defaults. bcl2fastq --input-dir BaseCalls_dir --output-dir BaseCalls_dir \ --loading-threads 1 --writing-threads 1 \ --demultiplexing-threads 1 --processing-threads 1
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Parallel batch job submission
The software will use a default number of threads for various operations (read, write, demultiplexing and processing). To ensure you use no more threads than were reserved by the jobscript your jobscript should specify the number of threads to use using the four threads flags on the the command-line (see example below). Please also see P25 of the online documentation (link at end of this page).
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings #$ -pe smp.pe 16 # Job will use 16 cores for the 'make' task # Note that the executable is called 'bcl2fastq'. # The default number of threads for file read/write is 4. Reduce if PE line above requests fewer. bcl2fastq --input-dir BaseCalls_dir --output-dir BaseCalls_dir \ --loading-threads 4 --writing-threads 4 \ --demultiplexing-threads $NSLOTS --processing-threads $NSLOTS
Further info
Updates
None.