I used Silva and some of my taxonomy looks like this:
D_0__Bacteria;D_1__Cyanobacteria;D_2__Melainabacteria;D_3__Obscuribacterales;D_4__uncultured Firmicutes bacterium ;D_5__;D_6__;D_7__;D_8__;D_9__;D_10__;D_11__;D_12__;D_13__;D_14__;D_15__;D_16__
I want to know what is “D_5__;D_6__;D_7__;D_8__;D_9__;D_10__;D_11__;D_12__;D_13__;D_14__;D_15__;D_16_” ?
There are several forum threads that address this, but I think you’ll find this helpful:
That being said, I’d suggest that you upgrade to the cleaner taxonomy formatted SILVA v138 Database, which has GreenGenes-like taxonomic rank prefixes. The some pre-made classifiers are here, and the files used to make them are here (should you like to train the classifiers yourself for a different version of QIIME 2). Finally, if you’d like to download and process the SILVA database yourself, you can install the RESCRIPt plugin, and use / modify the procedure here.
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