Hi Mike,
Following your tutorial I have made two artifacts, dereplicated sequences and taxa trimmed for 341f and 805r primer sets (ready to be used for training my classifier). Then I've converted them to fasta (the sequence) and tsv (the taxa) files by qiime exporter.
Then I tried to use them as the inputs for the "dada2:::makeTaxonomyFasta_SilvaNR(trimmed-seqs.fasta, full-taxa.txt, output=classifier.gz)". This function uses naiev-bayes method for training. However, reading the taxa.txt file, it kept giving me a format error. Then I tried to compare it with the standard one (full length) from the silva138 website, I realized that the taxa output of qiime has only two columns, Feature ID and Taxon:
it seems compeletely different than the full taxa file I got from silva138 database:
To solve this error, I only used my trimmed (based on the primers) seqs and used the full taxa file instead of the trimmed one. And it ran successfully, but the results I got from this was different than when I used the silva138 full length classifier. Could that be the reason?