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
BCL to FASTQ file converter
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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
# Check if bcl2fastq is on your PATH.
# Below tells me that /usr/local/bin/ is on my PATH variable where my bcl2fastq lives
# 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