Running and Verifying GEMMA

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following command to go to the installation directory of the executable file:

   cd /path/to/GEMMA/GEMMA-0.98.1/bin

3. Run the following command to run the test case:

   ./gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt -gk -o mouse_hs1940

   After the command is run, the following information is displayed:

   GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
   Reading Files ...
   ## number of total individuals = 1940
   ## number of analyzed individuals = 1410
   ## number of covariates = 1
   ## number of phenotypes = 1
   ## number of total SNPs/var        =    12226
   ## number of analyzed SNPs         =    10768
   Calculating Relatedness Matrix ...
   ================================================== 100%
   **** INFO: Done.