Hi @futoncrawler ,
This error indicates that your sequences and/or taxonomy do not match the weights. Either (1) you are using different versions of the SILVA database or much more likely (2) when you use extract-reads it is dropping sequences that fail to trim due to mismatch with the primers. In the case of #2, the solution is to filter your taxonomy to match the sequences — this can be done using RESCRIPt, which has a filter-taxa action (you should be able to pass the sequences artifact as --m-ids-to-keep-file) — and filter the class weights to drop taxa that are missing from the taxonomy (this could probably be done with qiime feature-table filter-features but I have never tried).
If that does not work the best option will be to just re-create the class weights following the tutorial.
Good luck!