diff --git a/tools/ALARAJOYWrapper/README.md b/tools/ALARAJOYWrapper/README.md
index 77c5f30f..74354ac2 100644
--- a/tools/ALARAJOYWrapper/README.md
+++ b/tools/ALARAJOYWrapper/README.md
@@ -33,7 +33,7 @@ To run this preprocessor, the user must first have acquired TENDL files for each
 
 Running ALARAJOYWrapper can be done with one Python command:
 ```
-python preprocess_fendl3.py -f /path/to/fendl3_data_dir/ -d /path/to/eaf_decay_library/ -a
+python preprocess_fendl3.py -f /path/to/fendl3_data_dir/ -d /path/to/eaf_decay_library/ -a -t -r
 ```
 To read in detail about each of these arguments, call this command:
 ```
diff --git a/tools/ALARAJOYWrapper/njoy_tools.py b/tools/ALARAJOYWrapper/njoy_tools.py
index a2163e00..3329aa03 100644
--- a/tools/ALARAJOYWrapper/njoy_tools.py
+++ b/tools/ALARAJOYWrapper/njoy_tools.py
@@ -362,8 +362,10 @@ def run_njoy(element, A, matb, file_capture):
     }
 
     # Run NJOY
-    result = subprocess.run(['njoy'], input=open(INPUT).read(),
-                        text=True, capture_output=True)
+    with open(INPUT, 'r') as f:
+        result = subprocess.run(
+            ['njoy'], stdin=f, text=True, capture_output=True
+        )
 
     fileinfo = file_metadata[file_capture]
     fileinfo['save'] = None
diff --git a/tools/ALARAJOYWrapper/preprocess_fendl3.py b/tools/ALARAJOYWrapper/preprocess_fendl3.py
index c195d657..6f338b20 100644
--- a/tools/ALARAJOYWrapper/preprocess_fendl3.py
+++ b/tools/ALARAJOYWrapper/preprocess_fendl3.py
@@ -5,6 +5,7 @@
 import numpy as np
 import argparse
 import warnings
+import logging
 from pathlib import Path
 from collections import defaultdict
 
@@ -44,8 +45,55 @@ def args():
         # Temperature for NJOY run [Kelvin]
         '--temperature', '-t', required=False, nargs=1, default=[293.16]
     )
+    parser.add_argument(
+        '--redirect_warnings', '-r', action='store_true',
+        help=('''
+            Optional argument to redirect any non-fatal warnings that may
+                arise to a log file.
+        ''')
+    )
     return parser.parse_args()
 
+def configure_logging(redirect_warnings=False):
+    """
+    Configure a logger to redirect output messages away from the terminal.
+
+    Arguments:
+        redirect_warnings (bool, optional): Option to redirect warning
+            messages to a separate 'warnings.log' file to avoid cluttering
+            the terminal with non-fatal warnings.
+
+    Returns:
+        None
+    """
+
+    logger = logging.getLogger()
+    logger.setLevel(logging.INFO)
+
+    formatter = logging.Formatter(
+        '%(asctime)s - %(levelname)s: \n\t%(message)s',
+        datefmt='%Y-%m-%d %H:%M:%S'
+    )
+
+    console_handler = logging.StreamHandler()
+    console_handler.setFormatter(formatter)
+
+    if redirect_warnings:
+        console_handler.setLevel(logging.INFO)
+        console_handler.addFilter(lambda record: record.levelno < logging.WARNING)
+
+        warning_log = Path('warnings.log')
+        warning_log.unlink(missing_ok=True)
+
+        file_handler = logging.FileHandler(warning_log)
+        file_handler.setLevel(logging.WARNING)
+        file_handler.setFormatter(formatter)
+
+        logger.addHandler(file_handler)
+        warnings.simplefilter('always')
+        logging.captureWarnings(True)
+
+    logger.addHandler(console_handler)
 
 def process_pendf(
     njoy_prep_input, material_id, MTs, pKZA, mt_dict, temperature, tendl_path
@@ -160,7 +208,7 @@ def process_gendf(
             diffs = sorted(MTs - gendf_MTs)
             warnings.warn(
                 f'GENDF file missing MTs {diffs} present in the ' \
-                'original TENDL file.'
+                f'original TENDL file for {element}-{A}.'
             )
         if gendf_MTs:
             all_rxns = tp.iterate_MTs(
@@ -322,6 +370,12 @@ def main():
     Main method when run as a command line script.
     """
 
+    warnings.formatwarning = (
+        lambda msg, cat, fname, lineno, file=None, line=None:
+            f"{Path(fname).name}:{lineno}: {cat.__name__}: {msg}\n"
+    )
+    configure_logging(args().redirect_warnings)
+
     TAPE20 = Path('tape20')
 
     dir = njt.set_directory()