Thanks a lot, it works!
Please allow me to upload my protocol:
First of all, upgrade to qiime2-2018.4
Download the latest Silva 132 qiime compatible full-length classifier.
Please download at: Silva 132 classifiers
(Silva 132 99% OTUs (full-length, seven-level taxonomy) )
Using the command:
qiime feature-classifier classify-sklearn --i-classifier silva-132-99-nb-classifier.qza --i-reads YourRepSeqsFromDada2.qza --o-classification taxonomy.qza
Next step is to exclude sequences that your primer does not target, e.g., for archaea specific primers, you should exclude mitochondria, chloroplast, bacteria. Use the command:
qiime taxa filter-table --i-table YourTableFromDada2.qza --i-taxonomy taxonomy.qza --p-exclude bacteria,chloroplast,mitochondria,eukaryota --o-filtered-table table-filtered.qza,
final step, visualize it: (please note that metadata file MUST be in TSV format)
qiime taxa barplot --i-table table-filtered.qza --i-taxonomy taxonomy.qza --o-visualization filterred-txonomy.qzv --m-metadata-file YourMetadataFile.tsv