qiime taxa filter table - troubleshoot

Hello everyone,

I am trying to get rid of the mitochondria and chloroplast sequences from my dada2-single-end-table.qza using the following command from the tutorial. However, while executing it gives me the following error. I would appreciate any help in this regard.

Thank you,

[email protected] [~/rawdata/16srna/2shi7_learning/fastqs_stitched] % qiime taxa filter-table \

–i-table dada2-single-end-table.qza
–i-taxonomy taxonomy-single-end.qza
–p-include p__
–p-exclude mitochondria,chloroplast
–o-filtered-table table-with-phyla-no-mt-no-chlp.qza
Traceback (most recent call last):
File “/panfs/roc/msisoft/qiime2/2019.10/lib/python3.6/site-packages/q2cli/commands.py”, line 328, in call
results = action(**arguments)
File “</panfs/roc/msisoft/qiime2/2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-139>”, line 2, in filter_table
File “/panfs/roc/msisoft/qiime2/2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
output_types, provenance)
File “/panfs/roc/msisoft/qiime2/2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 383, in callable_executor
output_views = self._callable(**view_args)
File “/panfs/roc/msisoft/qiime2/2019.10/lib/python3.6/site-packages/q2_taxa/_method.py”, line 93, in filter_table
raise ValueError("All features were filtered, resulting in an "
ValueError: All features were filtered, resulting in an empty table.

Plugin error from taxa:

All features were filtered, resulting in an empty table.

See above for debug info.

Hi @Irshad,

Have you checked the taxonomic assignments for the table? How many choloroplast/mitochondrial features do you see?

Have you tried running the command without the p__ include flag?
What database did you use?


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