qime taxa filter-table error using p-mode and p-exact: "Got unexpected extra arguments"


I would like to filter my feature table to include a handful of taxa that differ across my 2 treatments so I used “p mode exact” and “p include”.

Here is my command (sorry for the long file names):

qiime taxa filter-table
–i-table mesocosms-nonchimeric-w-borderline-Exper.Day14to20-table.qza
–i-taxonomy taxonomy-mesocosms-gg99-nonchimera-w-borderline.qza
–p-mode exact
–p-include “k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter;s__”, “k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Oceanospirillales;f__;g__;s__”, “k__Bacteria;p__Bacteroidetes;c__[Saprospirae];o__[Saprospirales];f__Saprospiraceae;g__;s__”, “k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Microbacteriaceae;g__Candidatus Aquiluna;s__rubra”
–o-filtered-table mesocosms-nonchimeric-w-borderline-Exper.Day14to20-ANCOMdifferingtaxa-table.qza-exact.qza

I got the error message:
" Got unexpected extra arguments (k__Bacteria;p__Proteobacteria;c__Gammap
roteobacteria;o__Oceanospirillales;f__;g__;s__, k__Bacteria;p__Bacteroidetes
;c__[Saprospirae];o__[Saprospirales];f__Saprospiraceae;g__;s__, k__Bacteria;
g__Candidatus Aquiluna;s__rubra)

Would you let me know what I did wrong? Am I not supposed to put commas between the taxa names and have the exact taxa names in quotes?

Thank you!


It looks like you put spaces between the quoted taxon names. There should be no spaces in the comma-separated list.

Let me know if that fixes your problem!

Thanks Nicholas. I removed the spaces between taxon names (but same exact command) and then I got this error message: Plugin error from taxa:

All features were filtered, resulting in an empty table.

This is weird because those taxa that I selected should be in the unfiltered table so why would the command yield an empty table? I will try to figure it out as well…


I read some related stuff on the forum and I found that if I enclosed the taxon names in single quotes instead of regular quotes and placed a space between each taxon level within a string, it worked.