Dear Kelly,
Millions thanks for your help.
According to your suggestions, I tried different parameter settings and used the unfiltered hapmap data. If only change the preferred haplotype size to 2000 and min sites to test match to 500 without changing other parameters, it was still not working. Then I set the preferred haplotype size to 1000 and min sites to test match to 200. It worked. One more question, why there is still a lot of missing values after imputation? The proportions of not missing before and after imputation are nearly the same. Any solutions for that.
Many thanks and regards,
Shanshan