Hello @Nick_Jeffery. This thread appears to be discussing a similar issue. Did you use an Illumina iSeq machine, and is it possible you are encountering the same issue? I suspect something similar is happening based on this
"Error rates could not be estimated (this is usually because of very few reads).
Error in getErrors(err, enforce = TRUE) : Error matrix is NULL."
appearing in both your error message and the one in that thread. Thank you.