ASV table and Taxonomy table have different formats with greengenes2

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Dear Qiime2 community,

With the l advent if greengenes 2, I thought I'd reanalyse my data with the new database. However, when I exported my data from Qiime2 to R, I ran into a predicament. My ASV table had the normal "4f9070b5d72c4cada7a60e06269fc149" format of classification. However, my taxonomy table was totally different with formats such as "MJ006-1-barcode41-umi149015bins-ubs-3" or "JN873915".

I think this disparity between the two tables is what's causing my phyloseq object error:
Error in validObject(.Object) : invalid class “phyloseq” object:
Component taxa/OTU names do not match.
Taxa indices are critical to analysis.
Try taxa_names()

I have attached screenshots of the tables below, please let me know if you have any advice!

Kind regards,

Johann

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2

Hi @Johanndb,

How did you process your data against Greengenes2?

Best,
Daniel

3

Hi @wasade,

I think my problem was that I tried to use both the Greengenes2 package and qiime2 in tandem to train my own classifier. When I just used Qiime2 to classify my sequences, all went well.

Kind regards,

Johann

4

Hi @Johanndb,

Okay :slight_smile: glad it's working. Just to verify, were you successful in using Greengenes2 2022.10 specifically or are you still having an issue that you would like help with?

Best,
Daniel