Error while using metadata-based filtering

Hey @kspeer,

If you were to run qiime metadata tabulate on taxonomy_unfiltered.qza do you still see the offending entry? I suspect it will look like this instead: k__Bacteria;p__Bacteroidetes

If I’m remembering correctly, taxa barplot pads out the taxonomy strings to make rendering simpler. In other words k__Bacteria;p__Bacteroidetes;__;__;__;__ is just a side-effect of trying to make the depth match everything else, it’s still really k__Bacteria;p__Bacteroidetes.

However if you saw k__Bacteria;p__Bacteroidetes;c__;o__;f__;g__ (with the prefixes) then that would mean there’s a un-named Greengenes OTU with that taxonomic resolution.

Also, unrelated to what I think is happening, there’s another issue with your command.
If we compare your search string to the list we see that they are not exactly the same:

k__Bacteria;p__Bacteroidetes;__;__;__;__          # Your list
k__Bacteria; p__Bacteroidetes; __; __; __; __     # Your --p-exclude

In particular it looks like your query has spaces in it which the computer considers as different.

If I’m remembering correctly about the behavior of taxa barplot your --p-exclude should look more like:
--p-exclude 'k__Bacteria;p__Bacteroidetes'.

Hope that helps!

1 Like