"Feature IDs found in the table are missing from the taxonomy" but are actually present


I am trying to create a taxa barplot with the following command:

Create taxa barplot

qiime taxa barplot
--i-table feature_tables/WoL_table.qza
--i-taxonomy taxonomy/WoL_taxonomy.qza
--m-metadata-file metadata/shotgun_metadata_q2.txt
--o-visualization taxonomy/taxa-bar-plots.qzv

But I get a value error saying that my taxonomies in the feature table and taxonomy.qza don't match. So I checked a few that were in my table to see if I could find them in my taxonomy thinking there may be a formatting issue but I found the 'missing' taxonomies were actually present. What could be causing Q2 to think they are missing?

I have attached my error log, table, and taxonomy files.

qiime2-q2cli-err-x3bev2vg.txt (697.2 KB) WoL_table.qza (2.4 MB) WoL_table.qzv (820.7 KB) WoL_taxonomy.qza (190.6 KB) WoL_taxonomy.qzv (1.7 MB)

Hi @Zach_Burcham

Your feature table has the taxonomic classifications as IDs (i.e. k__Archaea;p__Crenarchaeota;c__Thermoprotei;o__Sulfolobales;f__Sulfolobaceae;g__Sulfolobus;s__Sulfolobus acidocaldarius;t__) while the taxonomy has what I assume are the gOTU IDs (i.e. G000005825). I believe qiime taxa barplot requires the column names of the feature table to map to the row names of the taxonomy.

Did you convert the feature table feature IDs to their taxonomy beforehand? I think your command will work if you change the columns of your feature table back to the corresponding gOTU IDs.


Hi @gibsramen,

Thank you for the response! That makes perfect sense. I did not change my feature IDs they were already assigned as the taxonomy name after using ShoGun, but I can convert them to the gOTU ID. Thank you!



This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.