diff --git a/scripts/ncov-tools.py b/scripts/ncov-tools.py
index 6a33121..1d2ef21 100755
--- a/scripts/ncov-tools.py
+++ b/scripts/ncov-tools.py
@@ -255,7 +255,7 @@ def move(cwd, dest, prefix):
 	#print("Don't forget to update the config.yaml file as needed prior to running ncov-tools.")
 	print("Running ncov-tools using %s cores!" %(snakemake.threads))
 
-	subprocess.run([run_script, '-c', str(snakemake.threads), '-s', str(result_dir), '-n', os.path.join(exec_dir, 'ncov-tools')])
+	subprocess.run([run_script, '-c', str(snakemake.threads), '-s', os.path.basename(result_dir), '-n', os.path.join(exec_dir, 'ncov-tools')])
 	
 	# clean up
 	shutil.rmtree(data_root)