diff --git a/amt/run.py b/amt/run.py
index f3993d2..b0bf425 100644
--- a/amt/run.py
+++ b/amt/run.py
@@ -467,13 +467,14 @@ def transcribe(
 
     files_to_process = []
     for audio_path in file_paths:
-        if segments_by_audio_file.get(audio_path, None) is not None:
+        abs_audio_path = os.path.abspath(audio_path)
+        if segments_by_audio_file.get(abs_audio_path, None) is not None:
             file_info = {
-                "path": audio_path,
-                "segments": segments_by_audio_file[audio_path],
+                "path": abs_audio_path,
+                "segments": segments_by_audio_file[abs_audio_path]["segments"],
             }
         else:
-            file_info = {"path": audio_path}
+            file_info = {"path": abs_audio_path}
 
         files_to_process.append(file_info)