biosustain / biosustain/pyOpenMS_UmetaFlow
Notebook 4 GNPS export memory error
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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