One more question, would it be possible to ask the pipeline to stop at a certain step, for example, stop after assembly? I know that I can put '--skip_XXX' flags but was wondering if there is any better way

No, we don't have anything like that. But

--skip_binning

should stop after assembly

Thanks! How about using pre-proceeded reads directly for SPAdes? (can steps before assemblers being skipped)

thank you!