I am imputing on few candidate regions of 1.5Mb using Mach and 1000 genome phase 1 as reference dataset. I am following a two step approach for imputation. The run time for my first step is 3 hours, the command line for which was:
mach1 –p chr1.ped –d chr1.dat –h chr1ref.hap –s chr1ref.snp --greedy --rounds 50 --states 200 --compact --autoFlip --prefix step1_chr1
For second step of imputation, the command line was:
mach1 –p chr1.ped –d chr1.dat –h chr1ref.hap -s chr1ref.snps --errormap step1chr1.erate --cross step1chr1.rec --greedy --mle --mldetails --compact --autoFlip --mask 0.02 --prefix step2_chr1
It has been more than 48 hours and the programme is still running.According to the information available on Mach the second step is comparatively faster than the first step. Should it take this long? Can anyone tell me what went wrong??