diff --git a/src/f5c.c b/src/f5c.c
index ad4cabf4..9ac740e1 100644
--- a/src/f5c.c
+++ b/src/f5c.c
@@ -1077,6 +1077,8 @@ void output_db(core_t* core, db_t* db) {
             }
         }
     }
+    fflush(stdout);
+
     //core->read_index = core->read_index + db->n_bam_rec;
     double output_end = realtime();
     core->output_time += (output_end-output_start);
diff --git a/src/meth_main.c b/src/meth_main.c
index 52f26a68..a29b83b0 100644
--- a/src/meth_main.c
+++ b/src/meth_main.c
@@ -807,7 +807,5 @@ int meth_main(int argc, char* argv[], int8_t mode) {
     //free the core data structure
     free_core(core,opt);
 
-    fflush(stdout);
-
     return 0;
 }