why otu table show many levels in taxonomy level

[SoilRotifer (Mike Robeson)]

Hi @Fatemeh_Abedini,

There are several forum threads that address this, but I think you'll find this helpful:

Why all taxonomic levels on BarPlot have 'D' letter?

I can likely provide some insight here as I am one of the contributors that helped to format SILVA database for QIIME. The D_X__ convention was chosen to be as much of a unique and "safe" text string as possible, considering many of the bizarre taxonomy text annotations within the SILVA reference database. That is, it was meant as a quick fix to be able to search and parse these taxonomy strings. The 'D' was a way of annotating the "taxonomic Depth". At the time some of the code was written, th…

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.

-Cheers!
-Mike