Hello, I am implementing tests like the following in plinkseq (v0.08)

pseq LOCUS assoc --tests calpha --perm 10000 --phenotype RA --mask loc.group=refseq maf=0.00:0.01

These run fine, and fairly quickly. However, if I change this latter test to:

pseq LOCUS assoc --tests calpha --perm 10000 --phenotype RA --mask loc.group=refseq maf=0.00:0.05

The program runs very slowly. I am not sure if it is hanging or not; a value of 0.03 runs slowly but does eventually complete.

Does anyone know the Big-O notation for this? Or, more empirically, how many variants could I run before I can expect a slowdown. Or am I likely running out of RAM, and if I increased this it would run? Any feedback is welcome.

Thanks.