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mmzdouc / FERMO

Dashboard for analysis of liquid chromatography (tandem) mass spectrometry data.
https://fermo.bioinformatics.nl/example
MIT License
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Callback error updating ..store_processing.data...processed_data_FERMO.data.. #7

Closed mariannaiorio closed 1 year ago

mariannaiorio commented 1 year ago

Hi Mitjia! During the processing of my data the following error occurred:

Traceback (most recent call last): File "C:\Users\Marianna\anaconda3\envs\FERMO\lib\site-packages\flask\app.py", line 1820, in full_dispatch_request rv = self.dispatch_request() File "C:\Users\Marianna\anaconda3\envs\FERMO\lib\site-packages\flask\app.py", line 1796, in dispatch_request return self.ensure_sync(self.view_functions[rule.endpoint])(*view_args) File "C:\Users\Marianna\anaconda3\envs\FERMO\lib\site-packages\dash\dash.py", line 1274, in dispatch ctx.run( File "C:\Users\Marianna\anaconda3\envs\FERMO\lib\site-packages\dash_callback.py", line 422, in add_context raise LongCallbackError( dash.exceptions.LongCallbackError: An error occurred inside a long callback: 'NoneType' object has no attribute 'peaks' Traceback (most recent call last): File "C:\Users\Marianna\anaconda3\envs\FERMO\lib\site-packages\dash\long_callback\managers\diskcache_manager.py", line 175, in run user_callback_output = fn(maybe_progress, user_callback_args) File "C:\Users\Marianna\Downloads\FERMO\FERMO-main\FERMO-main\src\fermo\app.py", line 364, in app_peaktable_processing FERMO_data = peaktable_processing(uploaded_files, dict_params,) File "C:\Users\Marianna\anaconda3\envs\FERMO\lib\site-packages\fermo\app_utils\FERMO_peaktable_processing.py", line 280, in peaktable_processing feature_dicts = library_search( File "C:\Users\Marianna\anaconda3\envs\FERMO\lib\site-packages\fermo\processing\library_search.py", line 79, in library_search scores = matchms.calculate_scores( File "C:\Users\Marianna\anaconda3\envs\FERMO\lib\site-packages\matchms\calculate_scores.py", line 62, in calculate_scores return Scores(references=references, queries=queries, File "C:\Users\Marianna\anaconda3\envs\FERMO\lib\site-packages\deprecated\classic.py", line 285, in wrapperfunction return wrapped(args, **kwargs) File "C:\Users\Marianna\anaconda3\envs\FERMO\lib\site-packages\matchms\Scores.py", line 125, in calculate self._scores = self.similarity_function.matrix(self.references, File "C:\Users\Marianna\anaconda3\envs\FERMO\lib\site-packages\matchms\similarity\BaseSimilarity.py", line 67, in matrix scores[i_ref][i_query] = self.pair(reference, query) File "C:\Users\Marianna\anaconda3\envs\FERMO\lib\site-packages\matchms\similarity\ModifiedCosine.py", line 131, in pair spec1 = reference.peaks.to_numpy AttributeError: 'NoneType' object has no attribute 'peaks'

mmzdouc commented 1 year ago

Hi Marianna!

Thanks for reporting the error!

It looks like there is a problem with the spectral library searching module (library_search.py).

Is your spectral library file in the correct (.mgf) format? You can also open your spectral library in a text editor and compare it to the example file in our Spectral library preparation tutorial to check if the format is correct.

If that does not help you to solve the error, you can send me your library file to mitja.zdouc (a) wur.nl and I will give it a look!

Kind regards,

Mitja

mariannaiorio commented 1 year ago

Hi Mitjia, you were right! I had "PrecursorMz" instead of "PEPMASS" in my library. By replacing all it perfectly worked! Thank you, Marianna