Reference Based Motion Correction: automatically deal with duplicated particles

I have been running numerous RBMC jobs recently and have observed that the ‘remove duplicated particles’ job does not consistently handle all duplicated particles identified by the RBMC job. I tried 50, 70, 120, and 150 Å distance for removal. Is it feasible to incorporate an automatic process within the RBMC job to manage duplicated particles? This issue has already caused my job to halt on three occasions.

 [CPU:   25.0 MB  Avail: 250.57 GB]

====== Job process terminated abnormally.
[CPU:  212.0 MB  Avail: 250.46 GB]

DIE: particle pairwise distance matrix is singular, check for duplicate particles (sgetrf failed)

It would allow smooth runs overnight,
Best,
Dawid