diff --git a/internal/tests/pytests/util/run_util/test_run_util.py b/internal/tests/pytests/util/run_util/test_run_util.py
index 661d106c56..6815e0b9d2 100644
--- a/internal/tests/pytests/util/run_util/test_run_util.py
+++ b/internal/tests/pytests/util/run_util/test_run_util.py
@@ -48,6 +48,8 @@
     'METPLUS_BASE',
     'PARM_BASE',
     'METPLUS_VERSION',
+    'ALLOW_MISSING_INPUTS',
+    'INPUT_THRESH',
 ]
 
 
diff --git a/metplus/wrappers/extract_tiles_wrapper.py b/metplus/wrappers/extract_tiles_wrapper.py
index 141cb225f7..641bbcfc14 100755
--- a/metplus/wrappers/extract_tiles_wrapper.py
+++ b/metplus/wrappers/extract_tiles_wrapper.py
@@ -212,6 +212,7 @@ def run_at_time_once(self, time_info):
         location_input = self.c_dict.get('LOCATION_INPUT')
         input_path = self.get_location_input_file(time_info, location_input)
         if not input_path:
+            self.missing_input_count += 1
             return
 
         # get unique storm ids or object cats from the input file
diff --git a/metplus/wrappers/pcp_combine_wrapper.py b/metplus/wrappers/pcp_combine_wrapper.py
index 77b5b0b823..8fce625291 100755
--- a/metplus/wrappers/pcp_combine_wrapper.py
+++ b/metplus/wrappers/pcp_combine_wrapper.py
@@ -537,6 +537,7 @@ def setup_derive_method(self, time_info, lookback, data_src):
                                          data_type=data_src,
                                          return_list=True)
             if not input_files:
+                self.missing_input_count += 1
                 return None
 
             files_found = []
diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index d4673c3712..ef40128fc5 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -38,6 +38,8 @@ class RuntimeFreqWrapper(CommandBuilder):
 
     def __init__(self, config, instance=None):
         super().__init__(config, instance=instance)
+        self.run_count = 0
+        self.missing_input_count = 0
 
     def create_c_dict(self):
         c_dict = super().create_c_dict()
@@ -59,6 +61,13 @@ def create_c_dict(self):
         )
         self.validate_runtime_freq(c_dict)
 
+        # check if missing inputs are allowed and threshold of missing inputs
+        name = 'ALLOW_MISSING_INPUTS'
+        c_dict[name] = self.get_wrapper_or_generic_config(name, 'bool')
+        if c_dict[name]:
+            name = 'INPUT_THRESH'
+            c_dict[name] = self.get_wrapper_or_generic_config(name, 'float')
+
         return c_dict
 
     def validate_runtime_freq(self, c_dict):
@@ -195,6 +204,7 @@ def run_once(self, custom):
             return None
 
         self.clear()
+        self.run_count += 1
         return self.run_at_time_once(time_info)
 
     def run_once_per_init_or_valid(self, custom):
@@ -222,6 +232,7 @@ def run_once_per_init_or_valid(self, custom):
             self.c_dict['ALL_FILES'] = self.get_all_files_from_leads(time_info)
 
             self.clear()
+            self.run_count += 1
             if not self.run_at_time_once(time_info):
                 success = False
 
@@ -253,6 +264,7 @@ def run_once_per_lead(self, custom):
             self.c_dict['ALL_FILES'] = self.get_all_files_for_lead(time_info)
 
             self.clear()
+            self.run_count += 1
             if not self.run_at_time_once(time_info):
                 success = False
 
@@ -307,6 +319,7 @@ def run_at_time(self, input_dict):
 
             # Run for given init/valid time and forecast lead combination
             self.clear()
+            self.run_count += 1
             if not self.run_at_time_once(time_info):
                 success = False
 
diff --git a/parm/metplus_config/defaults.conf b/parm/metplus_config/defaults.conf
index ba67ccd233..4d27e017a9 100644
--- a/parm/metplus_config/defaults.conf
+++ b/parm/metplus_config/defaults.conf
@@ -65,6 +65,10 @@ GFDL_TRACKER_EXEC = /path/to/standalone_gfdl-vortextracker_v3.9a/trk_exec
 #     that value will be used instead of the value set in this file.          #
 #   * SCRUB_STAGING_DIR removes intermediate files generated by a METplus run #
 #     Set to False to preserve these files                                    #
+#   * ALLOW_MISSING_INPUTS determines if an error should be reported if input #
+#     files are not found, or if a warning should be reported instead         #
+#   * INPUT_THRESH specifies the percentage (0-1) of inputs that must be      #
+#     found to prevent an error (only used if ALLOW_MISSING_INPUTS=True)      #
 ###############################################################################
 
 PROCESS_LIST = Usage
@@ -73,6 +77,9 @@ OMP_NUM_THREADS = 1
 
 SCRUB_STAGING_DIR = True
 
+ALLOW_MISSING_INPUTS = False
+INPUT_THRESH = 0.0
+
 
 ###############################################################################
 # Log File Information (Where to write logs files)                            #