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joerivstrien / process_maxquant

code process maxquant output (protein-groups.txt)
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Maximum recursion error during clustering step #6

Closed joerivstrien closed 3 years ago

joerivstrien commented 3 years ago

When running the tool on a protein_groups file with 6 samples, (each having 60 slices) an error occurs during the clustering step.

The GUI displays the following error: An exception occurred while applying clustering on a sample Maximum recursion depth exceeded in comparison.

relevant lines in log file before error occurs: INFO:root:Step 4, cluster the fractions per sample using hierarchical clustering. INFO:root:Start hierarchical clustering for sample T5

(not sure why it starts clustering T5? maybe something went wrong with parsing the other samples? Samples are T1 - T6)

joerivstrien commented 3 years ago

Turns out T5 is also the first sample in the output (the order of samples in the output is random I guess?), so thats why it started with T5. In the end clustering worked for 2 out of 6 samples, for all the other samples maximum recursion depth error occurred.

Nice that the program continues anyway and produces an output with those that succeeded!

I can look into why the clustering code produces this error?

ArielKomen commented 3 years ago

Using google I found out that the implementation of hierarchical clustering of scipy is mainly used for dendogram visualizations and thus isn't able to compute large dendograms. I found this implementation and applied in the code, tested it and the clustering step has become faster and can cluster more proteins than before. So, this issue has been solved.