diff --git a/suite2p/run_s2p.py b/suite2p/run_s2p.py
index ff22e7bd..be775caf 100644
--- a/suite2p/run_s2p.py
+++ b/suite2p/run_s2p.py
@@ -344,7 +344,7 @@ def run_s2p(ops={}, db={}, server={}):
     print(db)
     if 'save_path0' not in ops or len(ops['save_path0'])==0:
         if ops.get('h5py'):
-            ops['save_path0'] = os.path.split(ops['h5py'])[0]
+            ops['save_path0'] = os.path.split(ops['h5py'][0])[0] # Use first element in h5py key to find save_path
         elif ops.get('nwb_file'):
             ops['save_path0'] = os.path.split(ops['nwb_file'])[0]
         else:
@@ -378,6 +378,9 @@ def run_s2p(ops={}, db={}, server={}):
     else:
         if len(ops['h5py']):
             ops['input_format'] = 'h5'
+            # Overwrite data_path with path provided by h5py. 
+            # Use the directory containing the first h5 file
+            ops['data_path'] = [os.path.split(ops['h5py'][0])[0]]
         elif len(ops['nwb_file']):
             ops['input_format'] = 'nwb'
         elif ops.get('mesoscan'):