emmaxCMC is super slow

[Syed M. Ijlal Haider]

Dear Prof Dr. Kang,

I am extremely sorry for bothering you, Actually I am working with panel sequencing data and running gene burden test on 61000 targeted  sequencing data.

I have successfully generated the kinships file and  annotated the vcf and have generated the groups with epacts. But emmaxCMC is super slow. Its been 22 days the script is stuck at SVD step. Although I have 200 gb memory and 30 cores for this job but its not helping at all. I have looked into my job on cluster its running but it is consuming only 1 cpu (100% and memory consumption is static at 170gb). So basically the parallel runs works only till “Makefile” but pEmmax is not able to parallel jobs.

I have even tried playing with --unit increasing it to 10000-500000 still no success. I would be very grateful if you can kindly assist in this regard? Is there a way to speedup the process? Even with 18000 samples previously epacts took 7 days to generate results. Whereas our colleagues are able to do it in 8-10 hours. I do not understand why the performance of epacts on our cluster is so slow. Do you have idea what could possibly be wrong here?  And I apologies again for bothering you.

Looking forward to hearing from you. Thanking you in advance

Ps. I am using the latest release of Epacts updated in 2019..

Kind Regards
Haider