Hi @Lu_Yang! The first command is failing because your rep-seqs.qza have Feature IDs, but you are using your Sample IDs to filter with. You will need to filter your feature tables based on the sample IDs, then grab the Feature IDs from a feature-table summarize visualization, then use those IDs to filter the rep seqs. Please see this forum post for more detailed step-by-step instructions.
This workflow is a pain right now --- we have an open issue to streamline this a bit. Let me know if you get stuck! 