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

Technical Support
#1

Hello,

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;
p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Microbacteriaceae;
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!

Lisa

#2

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!

#3

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…

Lisa

#4

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.

Cheers,
Lisa

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