diff --git a/.gitignore b/.gitignore
index 4696f44..353c69e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,5 @@
 /tests/test_data
 *.pyc
 *.DS_Store
-*__pycache__*
\ No newline at end of file
+*__pycache__*
+*.egg-info
diff --git a/pcpostprocess/scripts/run_herg_qc.py b/pcpostprocess/scripts/run_herg_qc.py
index 7bb7979..d2c10db 100644
--- a/pcpostprocess/scripts/run_herg_qc.py
+++ b/pcpostprocess/scripts/run_herg_qc.py
@@ -87,6 +87,18 @@ def main():
 
     else:
         wells = args.wells
+        # this warning addresses the error that occurs if a user inputs wrong data into args.wells
+        wrongWellNames = [well for well in wells if well not in all_wells]
+        if len(wrongWellNames) > 0:
+            if len(wrongWellNames) == len(wells):
+                logging.error("Specified well names are not in the list of available wells.")
+                return
+            else:
+                logging.warning(f"Specified well names {wrongWellNames} are not in the list of available wells."
+                                f"Removing them from the list of wells to be processed.")
+                wells = [well for well in wells if well not in wrongWellNames]
+                # other functions read args.wells later on, so we need to update it
+                args.wells = wells
 
     # Import and exec config file
     global export_config
@@ -160,6 +172,11 @@ def main():
             times_list.append([times[1], times[3]])
             readnames.append(protocol)
 
+    # this error is raised if the user has not specified the dictionary of protocols in the export_config.py file
+    if not readnames:
+        logging.error("No compatible protocols found in export config file.")
+        return
+
     with multiprocessing.Pool(min(args.no_cpus, len(readnames)),
                               **pool_kws) as pool: