Question: When running mkfastq I encountered the error "No bcl2fastq found on path. mkfastq requires bcl2fastq v2.17 or greater for RTA version: 2.11.3". 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
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
# 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
You can also check if Cell Ranger can find and use bcl2fastq without error. For Cell Ranger version 4.0+, you can check bcl2fastq by running:
cellranger pass which bcl2fastq #check which bcl2fastq installation is used by Cell Ranger
cellranger pass bcl2fastq --help #print bcl2fastq help message
For Cell Ranger versions prior to 4.0, you can check bcl2fastq by running:
cellranger which bcl2fastq #check which bcl2fastq installation is used by Cell Ranger
cellranger bcl2fastq --help #print bcl2fastq help message
If the installed bcl2fastq can be found by Cell Ranger, the help message of bcl2fastq should be printed out. If you do not see bcl2fastq help message, please try re-installing bcl2fastq.