How to speed the running

[aaannaw]

Dear author,
I am running the REforge but it is too slow. I have 226,746 CNEs and downloaded the 879 motif matrix of vertebrata from JASPAR. I chose to run by submitting the task in slurm. I split alljobs_226746cne.scores_simulationfile of 226,746 lines into 100 tasks with 2500 lines per task. However, 5,272 CNEs was completed. Could you give me any suggestions?
Best wishes,
Na Wan

[MichaelHiller]

I think this takes time, if it continues to run and generate results, I would leave it running.