diff --git a/amt/inference/transcribe.py b/amt/inference/transcribe.py
index 85b32d3..e78f717 100644
--- a/amt/inference/transcribe.py
+++ b/amt/inference/transcribe.py
@@ -783,17 +783,17 @@ def get_save_path(
     file_path: str,
     input_dir: str | None,
     save_dir: str,
-    idx: int | str = "",
+    idx_str: int | str = "",
 ):
     if input_dir is None:
         save_path = os.path.join(
             save_dir,
-            os.path.splitext(os.path.basename(file_path))[0] + f"{idx}.mid",
+            os.path.splitext(os.path.basename(file_path))[0] + f"{idx_str}.mid",
         )
     else:
         input_rel_path = os.path.relpath(file_path, input_dir)
         save_path = os.path.join(
-            save_dir, os.path.splitext(input_rel_path)[0] + f"{idx}.mid"
+            save_dir, os.path.splitext(input_rel_path)[0] + f"{idx_str}.mid"
         )
         if not os.path.isdir(os.path.dirname(save_path)):
             os.makedirs(os.path.dirname(save_path), exist_ok=True)
@@ -810,7 +810,7 @@ def process_file(
     save_dir: str,
     input_dir: str,
     logger: logging.Logger,
-    segments: List[Tuple[int, int]] | None = None,
+    segments: List[Tuple[int, Tuple[int, int]]] | None = None,
 ):
     def _save_seq(_seq: List, _save_path: str):
         if os.path.exists(_save_path):
@@ -852,12 +852,17 @@ def remove_failures_from_queue_(_queue: Queue, _pid: int):
 
     pid = threading.get_ident()
     if segments is None:
-        segments = [None]
+        # process_file and get_wav_segments will interpret segment=None as
+        # processing the entire file
+        segments = [(None, None)]
 
     if len(segments) == 0:
         logger.info(f"No segments to transcribe, skipping file: {file_path}")
 
-    for idx, segment in enumerate(segments):
+    for idx, segment in segments:
+        idx_str = f"_{idx}" if idx is not None else ""
+        save_path = get_save_path(file_path, input_dir, save_dir, idx_str)
+
         try:
             seq = transcribe_file(
                 file_path,
@@ -876,15 +881,17 @@ def remove_failures_from_queue_(_queue: Queue, _pid: int):
             logger.info(f"Removed {res_rmv_cnt} from result queue")
             continue
 
-        logger.info(f"Finished file: {file_path} (segment: {idx})")
+        logger.info(
+            f"Finished file: {file_path} (segment: {idx if idx is not None else 'full'})"
+        )
         if len(seq) < 500:
-            logger.info(f"Skipping seq - too short (segment {idx})")
+            logger.info(
+                f"Skipping seq - too short (segment {idx if idx is not None else 'full'})"
+            )
         else:
             logger.debug(
-                f"Saving seq of length {len(seq)} from file: {file_path} (segment: {idx})"
+                f"Saving seq of length {len(seq)} from file: {file_path} (segment: {idx if idx is not None else 'full'})"
             )
-            idx = f"_{idx}" if segment is not None else ""
-            save_path = get_save_path(file_path, input_dir, save_dir, idx)
             _save_seq(seq, save_path)
 
     logger.info(f"{file_queue.qsize()} file(s) remaining in queue")
@@ -997,20 +1004,28 @@ def batch_transcribe(
         files_to_process, key=lambda x: os.path.getsize(x["path"]), reverse=True
     )
     for file_to_process in files_to_process:
-        # Only add to file_queue if transcription MIDI file doesn't exist
-        if (
-            os.path.isfile(
+        if "segments" in file_to_process:
+            # Process files with segments
+            unsaved_segments = []
+            for idx, segment in enumerate(file_to_process["segments"]):
+                segment_save_path = get_save_path(
+                    file_to_process["path"],
+                    input_dir,
+                    save_dir,
+                    idx_str=f"_{idx}",
+                )
+                if not os.path.isfile(segment_save_path):
+                    unsaved_segments.append((idx, segment))
+
+            if unsaved_segments:
+                file_to_process["segments"] = unsaved_segments
+                file_queue.put(file_to_process)
+        else:
+            # Process files without segments (whole file)
+            if not os.path.isfile(
                 get_save_path(file_to_process["path"], input_dir, save_dir)
-            )
-            is False
-        ) and os.path.isfile(
-            get_save_path(
-                file_to_process["path"], input_dir, save_dir, idx="_0"
-            )
-        ) is False:
-            file_queue.put(file_to_process)
-        elif len(files_to_process) == 1:
-            file_queue.put(file_to_process)
+            ):
+                file_queue.put(file_to_process)
 
     logger.info(
         f"Files to process: {file_queue.qsize()}/{len(files_to_process)}"
@@ -1026,7 +1041,7 @@ def batch_transcribe(
             file_queue.qsize(),
         )
     num_processes_per_worker = min(
-        3 * (batch_size // num_workers), file_queue.qsize() // num_workers
+        5 * (batch_size // num_workers), file_queue.qsize() // num_workers
     )
 
     mp_manager = Manager()