Thanks heaps for putting up this tutorial! I have been keen to set taxonomic weights for my own projects. This is super helpful. I understand this is a work in progress, but I am a bit confused by some of the components.
First in ‘Assembling Weights’, in the
fit-classifier-naive-bayes command, the input reference reads are ref-seqs-v4.qza, but the previous command outputs ref-seqs-150-v4.qza. I changed the fit-classifier to this and it worked. However, the same thing happens under ‘Retrain the Classifier’, where the
fit-classifier-naive-bayes has the same input ref-seqs-v4.qza, which as far as I can tell was not created anywhere. In this section, I assumed to use the ref-seqs-120-v4.qza, however then got this error: Number of priors must match number of classes.
My guess is that the ref-seqs used should match the one used to create the uniform-classifier, and thus the weights, else the taxa included will be different and hence the above error. If this is right then I am not sure why the tutorial has a second
extract-reads command for 120, as the weights were derived from 150 bp extract.
I apologize if I missed something and got it totally wrong. I have been very happy with Qiime2, and using Naive-Bayes, even without bespoke weights, has improved my results.