ValueError: need at least one array to concatenate

[GeorgWa]

When loading an empty or broken file, the following error can appear:

alpharaw: 0.4.7

1 day, 15:47:21.042212 INFO: Creating folder /fs/pool/pool-mann-projects/0_Georg/covalent/processing_cluster/2025_11_05/alphadia_2.0.0/library/quant/CPS_CO_000011_66/figures
1 day, 15:47:21.044844 INFO: Initializing TimingManager
1 day, 15:47:21.046223 INFO: Initializing RawFileManager

0it [00:00, ?it/s]
0it [00:00, ?it/s]
1 day, 15:47:21.265562 �[31;20mERROR: Search for CPS_CO_000011_66 failed with error: need at least one array to concatenate�[0m
Traceback (most recent call last):
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alphadia/search_step.py", line 448, in run
self._process_raw_file(workflow, dia_path, speclib)
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alphadia/search_step.py", line 491, in _process_raw_file
workflow.load(dia_path, speclib)
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alphadia/workflow/peptidecentric/utils.py", line 177, in wrapper
result = func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alphadia/workflow/peptidecentric/peptidecentric.py", line 128, in load
super().load(
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alphadia/workflow/base.py", line 112, in load
self._dia_data = raw_file_manager.get_dia_data_object(dia_data_path)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alphadia/workflow/managers/raw_file_manager.py", line 68, in get_dia_data_object
dia_data = Thermo(
^^^^^^^
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alphadia/raw_data/alpharaw_wrapper.py", line 184, in init
self.load_raw(raw_file_path)
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alpharaw/ms_data_base.py", line 194, in load_raw
self.import_raw(raw_file_path)
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alpharaw/ms_data_base.py", line 183, in import_raw
raw_data_dict = self._import(raw_file_path)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alpharaw/thermo.py", line 199, in _import
_peak_indices = np.concatenate(
^^^^^^^^^^^^^^^
ValueError: need at least one array to concatenate
1 day, 15:47:21.400943 �[31;20mERROR: need at least one array to concatenate�[0m
1 day, 15:47:21.401688 INFO: Finished workflow for CPS_CO_000011_66
1 day, 15:47:21.404495 INFO: Traceback (most recent call last):
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alphadia/cli.py", line 295, in run
SearchPlan(output_directory, user_config, cli_params_config).run_plan()
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alphadia/search_plan.py", line 154, in run_plan
self.run_step(
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alphadia/search_plan.py", line 193, in run_step
step.run()
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alphadia/search_step.py", line 456, in run
raise e
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alphadia/search_step.py", line 448, in run
self._process_raw_file(workflow, dia_path, speclib)
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alphadia/search_step.py", line 491, in _process_raw_file
workflow.load(dia_path, speclib)
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alphadia/workflow/peptidecentric/utils.py", line 177, in wrapper
result = func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alphadia/workflow/peptidecentric/peptidecentric.py", line 128, in load
super().load(
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alphadia/workflow/base.py", line 112, in load
self._dia_data = raw_file_manager.get_dia_data_object(dia_data_path)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alphadia/workflow/managers/raw_file_manager.py", line 68, in get_dia_data_object
dia_data = Thermo(
^^^^^^^
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alphadia/raw_data/alpharaw_wrapper.py", line 184, in init
self.load_raw(raw_file_path)
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alpharaw/ms_data_base.py", line 194, in load_raw
self.import_raw(raw_file_path)
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alpharaw/ms_data_base.py", line 183, in import_raw
raw_data_dict = self._import(raw_file_path)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs/pool/pool-mann-projects/software/alphadia/2.0.0/alphadia-2.0.0/lib/python3.11/site-packages/alpharaw/thermo.py", line 199, in _import
_peak_indices = np.concatenate(
^^^^^^^^^^^^^^^
ValueError: need at least one array to concatenate

1 day, 15:47:21.404630 �[31;20mERROR: need at least one array to concatenate�[0m

[mschwoer]

Hi,
what would be your preference? A custom "CorruptRawFileError"?