Removing sampleID's from table.qza not found in the metadata


I'm very new to qiime2 but I am having trouble removing SampleID's from my table.qza that are not found in my sample-metadata.tsv. I have tried to following command (as an example)

--i-table table.qza
--m-metadata-file sample-metadata.tsv
--p-where "SampleID='90-ITS'" \
--o-filtered-table filtered.qza

I get the following error:
Plugin error from feature-table:

Selection of IDs failed with query:

SELECT "sample-id" FROM metadata WHERE NOT "SampleID" IN (metadata["#SampleID"]) GROUP BY "sample-id" ORDER BY "sample-id";

If one of the metadata column names specified in the where statement is on this list of reserved keywords (SQLite Keywords), please ensure it is quoted appropriately in the where statement.

90-ITS is just an example of something I would want to remove. The table.qza file contains both 16S and ITS barcodes but the metadata only contains 16S data. For downstream applications, I need the ITS data removed...

Any help is appreciated, thanks!

1 Like

Hi @Noah_Weber,

This is a case where you can just pass the metadata file! Skip the --p-where argument and try again with your filtered table.



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