Cluster.split taxonomy file issues


I am new to mothur and am quite confused about the taxonomy option in cluster.split while using splitmethod=classify.

The cluster.slit command page requires that we use a taxonomy file without any probabilities (classify.seqs with probs=f). However, I was following Miseq SOP and this does not appear to be the case in its classify.seqs followed by cluster.split protocol.

Why should taxonomy file without probabilities be used while using cluster.split? Are any errors expected if a file with probabilities is used?


cluster.split is able to handle taxonomy files with the confidence scores