diff --git a/chrombpnet/CHROMBPNET.py b/chrombpnet/CHROMBPNET.py
index a9de3c71..f0062e7f 100644
--- a/chrombpnet/CHROMBPNET.py
+++ b/chrombpnet/CHROMBPNET.py
@@ -38,8 +38,8 @@ def main():
 			pipelines.train_bias_pipeline(args)
 		
 		elif args.cmd_bias == "qc":
-			os.makedirs(os.path.join(args.output_dir,"auxiliary"), exist_ok=False)
-			os.makedirs(os.path.join(args.output_dir,"evaluation"), exist_ok=False)
+			os.makedirs(os.path.join(args.output_dir,"auxiliary"), exist_ok=True)
+			os.makedirs(os.path.join(args.output_dir,"evaluation"), exist_ok=True)
 			
 			pipelines.bias_model_qc(args)
 			
diff --git a/chrombpnet/pipelines.py b/chrombpnet/pipelines.py
index 5b1e9d7c..c1de0b48 100644
--- a/chrombpnet/pipelines.py
+++ b/chrombpnet/pipelines.py
@@ -418,7 +418,7 @@ def load_model_wrapper(model_hdf5):
 	else:
 		sub_peaks = peaks
 	sub_peaks.to_csv(os.path.join(args_copy.output_dir,"auxiliary/{}30K_subsample_peaks.bed".format(fpx)),sep="\t", header=False, index=False)
-	os.makedirs(os.path.join(args.output_dir,"auxiliary/interpret_subsample/"), exist_ok=False)
+	os.makedirs(os.path.join(args.output_dir,"auxiliary/interpret_subsample/"), exist_ok=True)
 
 	args_copy = copy.deepcopy(args)
 	args_copy.profile_or_counts = ["counts", "profile"]