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Thank you for explanation what is going on. I called matplotlibs drawing function to include 49308 dots and corresponding legend items with their colors. That's all I can say. I am not a native English speaker so I don't know what 'rogue extension modules' means.
Do you think it is a matplotlib or numpy issue which were in the stacktrace? Or a memory module error?
I am running analyses which take weeks. Will python give me a clear warning/error when the object counter overflows?
So what should I do now? I am clue-less right now.