Question: When running mkfastq I encountered the error "No bcl2fastq found on path. demux requires bcl2fastq v2.17 or greater for RTA version: 3.4.4". How can I fix this?
Answer: This indicates that mkfastq could not find bcl2fastq on your PATH environment variable. To investigate:
# Check if you have bcl2fastq and what version
$bcl2fastq --version
BCL to FASTQ file converter
bcl2fastq v2.19.1.403
Copyright (c) 2007-2017 Illumina, Inc.
If the command above indicates that you do not have bcl2fastq installed, you will need to install it first. (See this article for help on installing bcl2fastq). After installing:
# Find where bcl2fastq is located. Below tells me the directory where bcl2fastq lives
$which bcl2fastq
/usr/local/bin/bcl2fastq
# Check if bcl2fastq is on your PATH.
# Below tells me that /usr/local/bin/ is on my PATH variable where my bcl2fastq lives
$echo $PATH
/mnt/home/user1/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin
# If the path to bcl2fastq is not in PATH variable, you will need to add it.
# You can add it as below.
# A more appropriate way would be to add the path in your .bashrc file
export PATH=$PATH:/use/local/bin