diff --git a/pyprophet/cli/util.py b/pyprophet/cli/util.py
index 41a49003..7c11822a 100644
--- a/pyprophet/cli/util.py
+++ b/pyprophet/cli/util.py
@@ -93,8 +93,13 @@ class GlobalLogLevelGroup(click.Group):
 
     def invoke(self, ctx):
         log_level = ctx.params.get("log_level", "INFO").upper()
-        header = setup_logger(log_level=log_level)
-        ctx.obj = {"LOG_LEVEL": log_level, "LOG_HEADER": header}
+        log_colorize = ctx.params.get("log_colorize", True)
+        header = setup_logger(log_level=log_level, log_colorize=log_colorize)
+        ctx.obj = {
+            "LOG_LEVEL": log_level,
+            "LOG_HEADER": header,
+            "LOG_COLORIZE": log_colorize,
+        }
         return super().invoke(ctx)
 
 
@@ -274,9 +279,9 @@ def get_execution_context():
     return " ".join([sys.executable] + sys.argv)
 
 
-def setup_logger(log_level):
+def setup_logger(log_level, log_colorize):
     def formatter(record):
-        if log_level != "info":
+        if log_level.lower() != "info":
             # Format with module, function, and line number
             mod_func_line = f"{record['name']}::{record['function']}:{record['line']}"
             return (
@@ -319,7 +324,7 @@ def formatter(record):
 
     # Main console logger
     # logger.remove()  # Remove default logger
-    logger.add(sys.stdout, colorize=True, format=formatter, level=log_level)
+    logger.add(sys.stdout, colorize=log_colorize, format=formatter, level=log_level)
 
     _LOGGER_INITIALIZED = True
 
diff --git a/pyprophet/io/ipf/osw.py b/pyprophet/io/ipf/osw.py
index 1cb2bd83..41bae28a 100644
--- a/pyprophet/io/ipf/osw.py
+++ b/pyprophet/io/ipf/osw.py
@@ -307,25 +307,49 @@ def _fetch_alignment_features_duckdb(self, con):
                 f"Perform feature alignment using ARYCAL, and apply scoring to alignment-level data before running IPF.\nTable Info:\n{self._fetch_tables_duckdb(con)}"
             )
 
-        subquery = """
-    SELECT 
-        FEATURE_ID,
-        MIN(PEP) AS pep
-    FROM osw.SCORE_ALIGNMENT
-    GROUP BY FEATURE_ID
-        """
         query = f"""
-            SELECT
-                DENSE_RANK() OVER (ORDER BY fma.PRECURSOR_ID, fma.ALIGNMENT_ID) AS ALIGNMENT_GROUP_ID,
-                fma.ALIGNED_FEATURE_ID      AS FEATURE_ID
-            FROM osw.FEATURE_MS2_ALIGNMENT AS fma
-            JOIN (
-                {subquery}
+            SELECT 
+                DENSE_RANK() OVER (ORDER BY merged.PRECURSOR_ID, merged.ALIGNMENT_ID) AS ALIGNMENT_GROUP_ID,
+                merged.ALIGNMENT_ID,
+                merged.FEATURE_ID,
+                merged.PRECURSOR_ID,
+                merged.FEATURE_TYPE
+            FROM (
+                SELECT DISTINCT
+                    fma.ALIGNMENT_ID,
+                    fma.REFERENCE_FEATURE_ID AS FEATURE_ID,
+                    fma.PRECURSOR_ID,
+                    'REFERENCE' AS FEATURE_TYPE
+                FROM osw.FEATURE_MS2_ALIGNMENT AS fma
+                WHERE fma.LABEL = 1
+                AND fma.REFERENCE_FEATURE_ID != fma.ALIGNED_FEATURE_ID
+
+                UNION
+
+                SELECT DISTINCT
+                    fma.ALIGNMENT_ID,
+                    fma.ALIGNED_FEATURE_ID AS FEATURE_ID,
+                    fma.PRECURSOR_ID,
+                    'QUERY' AS FEATURE_TYPE
+                FROM osw.FEATURE_MS2_ALIGNMENT AS fma
+                WHERE fma.LABEL = 1
+                AND fma.REFERENCE_FEATURE_ID != fma.ALIGNED_FEATURE_ID
+            ) AS merged
+            LEFT JOIN (
+                SELECT 
+                    FEATURE_ID,
+                    MIN(PEP) AS pep
+                FROM osw.SCORE_ALIGNMENT
+                WHERE PEP <= {pep_threshold}
+                GROUP BY FEATURE_ID
             ) AS sa
-            ON sa.FEATURE_ID = fma.ALIGNED_FEATURE_ID
-            WHERE fma.LABEL = 1
-            AND sa.pep < {pep_threshold}
-            ORDER BY ALIGNMENT_GROUP_ID
+            ON merged.FEATURE_ID = sa.FEATURE_ID
+            ORDER BY 
+                ALIGNMENT_GROUP_ID,
+                CASE merged.FEATURE_TYPE 
+                    WHEN 'REFERENCE' THEN 0 
+                    WHEN 'QUERY' THEN 1 
+                END;
         """
 
         df = con.execute(query).fetchdf()
diff --git a/pyprophet/main.py b/pyprophet/main.py
index 8a6105ab..bf9c2c93 100644
--- a/pyprophet/main.py
+++ b/pyprophet/main.py
@@ -55,8 +55,13 @@ def profile(fun):
     ),
     help="Set global logging level.",
 )
+@click.option(
+    "--log-colorize/--no-log-colorize",
+    default=True,
+    help="Turn on/off colorized logging output.",
+)
 @click.pass_context
-def cli(ctx, log_level):
+def cli(ctx, log_level, log_colorize):
     """
     PyProphet: Semi-supervised learning and scoring of OpenSWATH results.