Filter OTUs using OTU ID failed


I am trying to use OTUs ID to filter out OTUs from the feature-table. I’ve checked and followed this post [Filter OTUs from features table using OTU IDs?], but only some OTUs were removed from the list.

I am using QIIME2.2019.1
Here is what I ran:
qiime feature-table filter-samples
–i-table feature-table.qza
–m-metadata-file OTUs_ID.tsv
–o-filtered-table Filtered-feature-table.qza \

My OTUs_ID file is like


I have around 267 OTUs to remove, and output only removed 85 OTUs. Is the OTUs read number matter? There are some OTUs have high read number. If the read number doesn’t matter, is there a way to troubleshoot this? Or any other suggestion?

Thank you.

Interesting puzzle, @SY_Yang!
Are you trying to filter out the samples that contain those OTUs, or actually trying to filter out the features themselves?

You may want to look at the qiime feature-table filter-features command instead of filter-samples.

Good luck!

Dear @ChrisKeefe,

Thank you!!! It works perfectly!!! All the features has been removed!

About the 85 OTUs that has been filtered first, those are the OTUs only in one sample that I removed earlier. I think they just got removed when I ran the filter-samples with OTUs ID, and their values were zero.

Have a great day!

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