Hi @yanxianl! Thanks so much for your input files, that was really helpful!
Did you happen to run feature-table summarize on blank-library-sequences.qza? If you did, you would see that that table has zero samples and zero features! The reason is because your feature-table filter-samples command is filtering out all of your samples! If you revise the --p-where parameter to: "SampleType='Blank-library'", then you will wind up with three samples in blank-library-sequences.qza!
The moral of the story is that the SQL where clauses are case-sensitive --- in your metadata.tsv file you have the values listed as Blank-library, not blank-library.
Reading on to your later commands --- the feature-table filter-features in the last step will not work, because you cannot use a feature table as metadata. Please check out this forum post for details on how to create a feature metadata file from your feature table that you can use here. There is an open issue to streamline this step so that you don't have to do this extra work presented in the post, but for now that is the best option.
Hope that helps! 