As an update, I have continued to try to address this problem:
- I have checked that ulimit -s is in all run scripts.
- I have increased the memory for the scripts up to 64G, no change.
- I have deleted all the intermediate files and re-run the sector, no change.
A similar problem was brought up here: 2016 emission platform v1 adjust sectors - #6 by eyth.alison , but the solution was not explicitly stated.