biosustain / biosustain/pyOpenMS_UmetaFlow

Notebook 4 GNPS export memory error

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Jupyter Notebook
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Description

Hi,

Thank you for these detailed notebooks and workflow.

I managed to get to notebook 4 with my own dataset but in step 3 for MSMS clustering, when I try to run the line:

`spectra_clustering.store(Consensus_file, [s.encode() for s in mzML_files], String(out_file))`

I run into what seems like an error with memory:

```
---------------------------------------------------------------------------
MemoryError Traceback (most recent call last)
Cell In[9], line 1
----> 1 spectra_clustering.store(Consensus_file, [s.encode() for s in mzML_files], String(out_file))

File pyopenms/_pyopenms_1.pyx:3028, in pyopenms._pyopenms_1.GNPSMGFFile.store()

MemoryError: std::bad_alloc
```

However I am very sure my machine is not running out of memory. Happy to provide more information but not sure what to - I'm very puzzled as to why this is happening?

Contributor guide

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Research direction

Start with notebook 4, step 3, and reproduce the call to spectra_clustering.store using the reported Consensus_file, mzML_files, and out_file inputs. Investigate the pyopenms GNPSMGFFile.store traceback and document what causes the std::bad_alloc error; done means the export completes or the required input and memory constraints are clearly identified.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook, python
Domain
data-engineering
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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