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Dear Steve and Anderson, randomise_parallel script has been modified for my specific server environment. It has been nothing pitfalls previously by output all the outputs I need( In this case I didnot use --glm_output option). However, it didnot generate a GLM file when I use --glmoutput=GLM. I am confused. I saw randomise_parallel script again, but I had no idea which line or stage generating the glmoutput. I need your help. Thanks.Any reply will be highly appreciated. All the best. 2013-12-13 Rujing Zha