jklustor does not export the molecule ID in the input, this has not been a high priority item to fix for quite some time now. There is some workarounds, such as https://www.chemaxon.com/forum/ftopic8475.html, however, if someone who prefers to use the command line jklustor, instead of API to carry out the task, it probably means the user prefers not to program.
The problem becomes more noticeable as I am trying to do "-c bm" using:
jklustor t.sdf -o wrmols:sdf:t_m.sdf -o wrclus:sdf:t_c.sdf -lfin -c bm
The compound ID in the input t.sdf file is lost in the output t_m.sdf file in this case, so even the workaround no longer works. Now one has to do pair-wise exact structure matching in order to get meaningful results, that seems a lots of work to use jklustor.
If we could keep the either the input molecule ID, or simply the order number in input (ID1, ID2, et.), jklustor could have been much more user friendly for people who choose this command version over API.