converting .tsv file to .qza artifact and filtering taxa

Hi everyone,

I was recently given a .tsv feature table file, a screenshot of a portion of the file is displayed below:

My goal is to filter taxa with the Eukaryota and Archaea domains using qiime2-2020.11. I first converted the .tsv file to .biom file using the following code:

biom convert -i featuretable.tsv -o featuretable.biom --table-type "Table" --to-hdf5

I then converted the .biom file to .qza artifact:

qiime tools import
--input-path featuretable.biom
--type FeatureTable[Frequency]
--output-path featuretable.qza

I then used the featuretable.qza file as input for my filtering step

qiime taxa filter-table
--i-table featuretable.qza
--i-taxonomy taxonomy.qza
--p-mode contains
--p-exclude "D_0__Eukaryota","D_0__Archaea"
--o-filtered-table filteredtable.qza

When I perform this step, I get the following error: All features ids must be present in taxonomy, but the following ids are not: C4, C18, C22, C42, ...; the error then lists every sample I have in my dataset. When I convert my featuretable.qza to a visualization file, I see that the ASV ids and the sample ids are transposed (please note - the ASVs in this screenshot are in alphabetical order;t the ASVs in the previous screenshot are not):

I tried using qiime feature-table transpose to transpose the artifact. When I re-run my qiime taxa filter-table with the transposed feature table, I get the same error except the ASVs are in-place of the sample IDs.

What am I doing wrong? I've used the same taxonomy file throughout my project and have had no issues with it so far.

Thank you for your help.


If you are receiving this error (in second case):

But this time with list of ASVs instead of sample IDs, that’s meant that your taxonomy file do not contain ASVs form your new feature table.
As I understood, it is a new file:

So i am wondering, if your taxonomy file was produced based on other dataset:

Did you create a taxonomy file based on ASV sequences that are present in your new dataset, or you created it earlier?

If I am correct, you need to create a new taxonomy artifact using representative sequences with ASVs from your new feature table.


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Hi Timur,

Thanks for your response. The taxonomy file I am using in this project was not created using the new ASV file I received. I think I will need to create a new taxonomy artifact using the new sequences I received. Thanks again!


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