My bad, I forgot to mention the general form of the extract command.
If you want the contribution for the first site, first IMT, first realization, first level the command to use is:
$ oq extract "disagg_by_src?site_id=0&imt_id=0&rlz_id=0&lvl_id=0" <calc_id>
(oq extract "disagg_by_src <calc_id> is a shortcut for that).
If you want the first site, first IMT, first realization and second level:
$ oq extract "disagg_by_src?site_id=0&imt_id=0&rlz_id=0&lvl_id=1" <calc_id>
etc. In this way one can extract a lot of small npz files. The plan is to give a better interface in the future, right now there is only the bare functionality, as you see.