threads default = 1 + handle CalledProcessError by giving error message

Author: LaraFuhrmann

viloca/b2w.py

@@ -588,8 +588,23 @@ def parallel_run_one_window(
             _write_to_file([line], f"coverage_{idx}.txt")
 
 
+import subprocess
 def run_window_wrapper(args):
-    return parallel_run_one_window(*args)
+    try:
+        return parallel_run_one_window(*args)
+    except subprocess.CalledProcessError as e:
+        # Capture critical error details
+        error_msg = f"""
+        Subprocess failed in window {args[3]} (index {args[4]})
+        Command: {e.cmd}
+        Exit code: {e.returncode}
+        Error output: {e.stderr.decode().strip()}
+        """
+        logging.critical(error_msg)
+
+        # Reraise with context for pytest reporting
+        raise RuntimeError(f"Window processing failed: {error_msg}") from e
+
 
 
 def build_windows(alignment_file: str, tiling_strategy: TilingStrategy,

viloca/cli.py

@@ -169,7 +169,7 @@ def main():
                                 default=True, dest="keep_files", help="keep all intermediate files")
 
     parser_shotgun.add_argument("-t", "--threads", metavar='INT', required=False,
-                            type=int, dest="maxthreads", default=0,
+                            type=int, dest="maxthreads", default=1,
                             help="limit maximum number of parallel threads\n(0: CPUs count-1, n: limit to n)")
 
     parser_shotgun.add_argument("-z", "--insert-file", metavar='INSERT_FILE', type=str,