Can Shake track the number of threads used by build commands that are themselves parallel?

Question

Shake builds things in parallel whenever possible, but what happens if an individual assembly step is itself parallelizable? For example, I execute BLAST commands. Each team compares the genomes of two species. Several comparisons can be performed in parallel, but there is also a flag to divide the comparison into N pieces and run them in parallel. Do I need to choose one of the ways to separate tasks and stick to it, or can I say Shake "Use N threads in general, and by the way, each of these specific tasks takes N threads on its own"?

(This occurs when comparing many small bacterial genomes and several larger eukaryotic ones)

EDIT: The question can be simplified to "How to determine how many Thread Shake threads are currently running / queued from Shake?"