Taxa Filtering issue

Hi QIIME2 Community,

I am having an issue with the qiime taxa filter-table command. I am using qiime2-2019.4 installed on conda. Specifically, my issue is with the --p-exclude parameter. I want to exclude certain taxa from my data set. The taxa filter command completes without throwing any errors; however, when I pop the barplot into Qiime2View, the taxa are still there. Please find the code I ran below.

qiime taxa filter-table --i-table table-NoMorC.qza --i-taxonomy classify/classification.qza --p-exclude “k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;;” --o-filtered-table table-NoE.qza

Any help with this issue would be greatly appreciated.

Thank you,

Ryan

My guess is that there is a subtle typo (maybe whitespace?) in the exclude parameter value. Let’s start by verifying feature counts before and after filtering:

qiime tools inspect-metadata table-NoMorC.qza --tsv | wc -l | awk '{print $1-1}'
qiime tools inspect-metadata table-NoE.qza --tsv | wc -l | awk '{print $1-1}'

:qiime2:

Hi Matthew,
Thanks for your reply. Both tables have 21882 features. I played around with this and found out that when I use --p-exclude “f__Enterobacteriaceae” the number of features is reduced to 13249. However, when I use --p-exclude “f__ Enterobacteriaceae;g__;s__” or --p-exclude “f__ Enterobacteriaceae;;” the number of features is 21882 again.

Thank you,

Ryan