diff --git a/jass/__main__.py b/jass/__main__.py
index 78f40102ef431e7e8fcc862e9a3022ce32f1ac59..27b0e25e5222717725f1ffe346c7efcc140e0e81 100644
--- a/jass/__main__.py
+++ b/jass/__main__.py
@@ -32,32 +32,32 @@ def absolute_path_of_the_file(fileName, output_file = False):
         if (Directory_path_exist == False):
             # Test the path using the Jass data directory
             absoluteFilePath = os.path.normpath(os.path.join(config["DATA_DIR"], fileName))
-            
+
             Directory_path_exist = os.path.exists(os.path.dirname(absoluteFilePath))
-        
+
         if (Directory_path_exist == False):
             Message = "The directory of the file {} does not exist".format(fileName)
             raise NameError(Message)
     else:
         # Test if the file path exist
         File_path_exist = os.path.exists(absoluteFilePath)
-    
+
         if (File_path_exist == False):
             # Test the path using the Jass data directory
             absoluteFilePath = os.path.normpath(os.path.join(config["DATA_DIR"], fileName))
             File_path_exist = os.path.exists(absoluteFilePath)
-        
+
         if (File_path_exist == False):
             Message = "The file {} does not exist".format(fileName)
             raise NameError(Message)
-        
+
         # Test if it is realy a file
         Is_a_file = os.path.isfile(absoluteFilePath)
-        
+
         if (not Is_a_file) :
             Message = "{} is not a file".format(fileName)
             raise NameError(Message)
-            
+
     return absoluteFilePath
 
 
@@ -72,7 +72,7 @@ def w_list_phenotypes(args):
 
 
 def compute_worktable(args):
-    
+
     csv_file_path = args.csv_file_path
     if (csv_file_path is not None):
         csv_file_path = absolute_path_of_the_file(csv_file_path, True)
@@ -82,7 +82,7 @@ def compute_worktable(args):
     remove_nan = not (args.keep_nans)
     significance_treshold = float(args.significance_treshold)
     post_filtering = bool(args.post_filtering)
-    custom_loadings = args.custom_loadings    
+    custom_loadings = args.custom_loadings
     chromosome = args.chromosome_number
     pos_Start = args.start_position
     pos_End = args.end_position
@@ -99,10 +99,10 @@ def compute_worktable(args):
         strategy = args.strategy
 
     create_worktable_file(
-        phenotype_ids = selected_phenotypes, 
-        init_file_path = init_table_path, 
+        phenotype_ids = selected_phenotypes,
+        init_file_path = init_table_path,
         project_hdf_path = worktable_path,
-        remove_nan = remove_nan, 
+        remove_nan = remove_nan,
         stat = strategy,
         optim_na = True,
         csv_file = csv_file_path,
@@ -125,8 +125,8 @@ def w_create_project_data(args):
     manhattan_plot_path = absolute_path_of_the_file(args.manhattan_plot_path, True)
     quadrant_plot_path = absolute_path_of_the_file(args.quadrant_plot_path, True)
     create_global_plot(worktable_path, manhattan_plot_path)
-    create_quadrant_plot(worktable_path, 
-                         quadrant_plot_path, 
+    create_quadrant_plot(worktable_path,
+                         quadrant_plot_path,
                          significance_treshold = float(args.significance_treshold))
 
 
@@ -136,7 +136,7 @@ def w_create_inittable(args):
     regions_map_path = absolute_path_of_the_file(args.regions_map_path)
     description_file_path = absolute_path_of_the_file(args.description_file_path)
     init_table_path = absolute_path_of_the_file(args.init_table_path, True)
-    
+
     create_inittable_file(
         input_data_path,
         regions_map_path,
@@ -155,8 +155,8 @@ def w_plot_quadrant(args):
     worktable_path = absolute_path_of_the_file(args.worktable_path)
     plot_path = absolute_path_of_the_file(args.plot_path)
     significance_treshold = float(args.significance_treshold)
-    create_quadrant_plot(worktable_path, 
-                         plot_path, 
+    create_quadrant_plot(worktable_path,
+                         plot_path,
                          significance_treshold=significance_treshold)
 
 
@@ -197,7 +197,7 @@ def get_parser():
     parser_create_pd.add_argument(
         "--worktable-path", required=True, help="path to the worktable file to generate"
     )
-    parser_create_pd.add_argument("--keep-nans", action="store_true", default=False)
+    parser_create_pd.add_argument("--keep-nans", action="store_true", default=True)
     parser_create_pd.add_argument(
         "--manhattan-plot-path",
         required=True,
@@ -237,7 +237,7 @@ def get_parser():
         required=False,
         help="path to the results file in csv format"
     )
-    
+
     parser_create_pd.add_argument(
         "--chromosome-number",
         required=False,
@@ -255,7 +255,7 @@ def get_parser():
         required=False,
         help="option used only for local analysis: end position of the region studied"
     )
-  
+
     strategies = parser_create_pd.add_mutually_exclusive_group()
     strategies.add_argument("--omnibus", action="store_true", default=True)
     strategies.add_argument("--sumz", action="store_true", default=False)
@@ -336,15 +336,15 @@ def get_parser():
         required=False,
         help="path to the results file in csv format"
     )
-    
+
     parser_create_wt.add_argument(
         "--chunk-size",
         required=False,
         default=50,
         help="Number of region to load in memory at once",
     )
-    
-    parser_create_wt.add_argument("--keep-nans", action="store_true", default=False)
+
+    parser_create_wt.add_argument("--keep-nans", action="store_true", default=True)
 
     parser_create_wt.add_argument(
         "--chromosome-number",
@@ -363,14 +363,14 @@ def get_parser():
         required=False,
         help="option used only for local analysis: end position of the region studied"
     )
-        
+
     strategies = parser_create_wt.add_mutually_exclusive_group()
     strategies.add_argument("--omnibus", action="store_true", default=True)
     strategies.add_argument("--sumz", action="store_true", default=False)
     strategies.add_argument("--fisher_test", action="store_true", default=False)
     strategies.add_argument("--meta_analysis", action="store_true", default=False)
     strategies.add_argument("--strategy")
-    
+
     parser_create_wt.set_defaults(func=w_create_worktable)
 
     # ------- plot-manhattan -------
@@ -385,8 +385,8 @@ def get_parser():
         help="path to the worktable file containing the data",
     )
     parser_create_mp.add_argument(
-        "--plot-path", 
-        required=True, 
+        "--plot-path",
+        required=True,
         help="path to the manhattan plot file to generate"
     )
     parser_create_mp.set_defaults(func=w_plot_manhattan)
@@ -402,8 +402,8 @@ def get_parser():
         help="path to the worktable file containing the data",
     )
     parser_create_mp.add_argument(
-        "--plot-path", 
-        required=True, 
+        "--plot-path",
+        required=True,
         help="path to the quadrant plot file to generate"
     )
     parser_create_mp.add_argument(
@@ -412,7 +412,7 @@ def get_parser():
         help="threshold at which a p-value is considered significant"
     )
     parser_create_mp.set_defaults(func=w_plot_quadrant)
-    
+
     return parser