The empty .SUBCKT definition for the bipolar may be in the layout netlist as a direct result of there being a DEVICE description in the rule file for the Calibre run. Do you see a DEVICE definition in the rule file for that bipolar?
If there is a DEVICE definition for the bipolar in the rule file then the next thing to check for could the existence of a bad device, or a good seed shape, appropriate pins touching the seed shape, that sort of thing.
Other people might recognize this as a situation they've seen before, maybe relating to pcells? If you don't get any responses along those lines I might be able to offer some debug hints for you to work through the problem using some basic ideas.
Thanks for the reply.
Indeed, the problem was that in the rule file the BJT was not defined at all.
I have replaced it with a correct rule file and everything works fine.
Thanks a lot,