1 files changed, 4 insertions, 3 deletions
diff --git a/src/gemma.cpp b/src/gemma.cpp
index c7f7ab6..f7ebdce 100644
--- a/src/gemma.cpp
+++ b/src/gemma.cpp
@@ -2846,7 +2846,7 @@ void GEMMA::BatchRun(PARAM &cPar) {
             cLmm.mdb_calc_gwa(U, eval, UtW, &UtY_col.vector, W,
                               &Y_col.vector, cPar.setGWASnps);
           }
-          else
+          else {
             if (!cPar.file_bfile.empty()) {
               // PLINK analysis
               if (cPar.file_gxe.empty()) {
@@ -2869,8 +2869,9 @@ void GEMMA::BatchRun(PARAM &cPar) {
                                       &Y_col.vector, env);
               }
             }
-          cLmm.WriteFiles(); // write output files
-          cLmm.CopyToParam(cPar);
+            cLmm.WriteFiles(); // write output files
+            cLmm.CopyToParam(cPar);
+          }
         } else {
           debug_msg("fit mvLMM (multiple phenotypes)");
           MVLMM cMvlmm;