Skip to content


The Illumina bcl2fastq2 conversion software demultiplexes sequencing data and converts base call (BCL) files into FASTQ files. For every cycle of a sequencing run, the Real-Time Analysis (RTA) software generates a BCL file containing base calls and associated quality scores (Q-scores).

Bcl2fastq2 is available as a module on Apocrita.


To run the default installed version of Bcl2fastq2, simply load the bcl2fastq2 module:

$ module load bcl2fastq2
$ bcl2fastq -h

      bcl2fastq [options]

For usage documentation, run bcl2fastq2 -h.

Example job

Serial job

Threading options

By default, Bcl2fastq2 will run on as many threads as installed CPUs during conversion/demultiplexing, plus additional threads for reading/writing data. Therefore, to prevent overloading a compute node, you must set the number of processing threads to the number of cores requested, or simply use the NSLOTS variable, as shown in the example job below.

The file i/o threads (loading/writing) are typically inactive and consume minimal processing time. By default, each will use 4 threads but we recommend using 1 for reading and 1 for writing unless you need to perform a lot of i/o. If your job is i/o intensive, increasing the loading/writing threads will improve the overall job performance, especially if paired with using your scratch space.

Here is an example job running on 4 cores and 8GB of memory:

#$ -cwd
#$ -j y
#$ -pe smp 4
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G

module load bcl2fastq2

bcl2fastq --runfolder-dir <runfolder_dir> \
          --output-dir <output_dir> \
          --processing-threads ${NSLOTS} \
          --loading-threads 1 \
          --writing-threads 1