diff --git a/conf/minimal-configuration.json b/conf/minimal-configuration.json
index d4e7cd8..f43436d 100644
--- a/conf/minimal-configuration.json
+++ b/conf/minimal-configuration.json
@@ -51,5 +51,7 @@
   "imputation_out_miss_filename": "don.miss",
   "imputation_out_problem_filename": "don.problem",
   "max_haplotypes_number_in_phase": 100,
+  "imputation_out_path": "output",
+  "pops_count_file": "output/pop_counts_file.txt"
   "imputation_out_path": "output"
 }
diff --git a/grim/run_impute_def.py b/grim/run_impute_def.py
index 3dc9e55..ff1bd68 100644
--- a/grim/run_impute_def.py
+++ b/grim/run_impute_def.py
@@ -33,7 +33,7 @@ def run_impute(
     graph_files_path = json_conf.get("graph_files_path")
     if graph_files_path[-1] != "/":
         graph_files_path += "/"
-    output_dir = json_conf.get("imuptation_out_path", "output")
+    output_dir = json_conf.get("imputation_out_path", "output")
     if output_dir[-1] != "/":
         output_dir += "/"
     config = {
diff --git a/scripts/runfile.py b/scripts/runfile.py
index 557121c..fa99bc6 100755
--- a/scripts/runfile.py
+++ b/scripts/runfile.py
@@ -30,7 +30,7 @@
 
 # read the config file
 output_dir = "output/"
-project_dir = "../"
+project_dir = "./"
 
 # Read configuration file and load properties
 with open(configuration_file) as f: