RuntimeError: maximum recursion depth exceeded while calling a Python object

[mlaziz]

I am trying to run scoary on roary output from 3100 samples. I get the following error
RuntimeError: maximum recursion depth exceeded while calling a Python object

I tried both python versions 2.7 and 3.5 but the error remains the same

[AdmiralenOla]

Hi @mlaziz, and sorry for not getting back to you sooner. Thanks for reporting this. 3100 samples is a larger dataset than I ever tested Scoary on, and unfortunately it seems python has some problems with very deep recursions. (As will be happening here since Scoary browses every possible sub-tree in your 3100 sample phylogeny)

I would at some point like to fix this, either by changing the algorithm to a loop structure or by increasing the allowed recursion depth. (Not sure if the latter is recommended).

For now, I think you're better off by sub-sampling your data a little.

[AdmiralenOla]

Same problem as #56

[nickp60]

I have the same issue, with ~1300 samples; will try subsampling...

[AdmiralenOla]

Note: It is also possible to increase the default allowed recursion depth using sys.setrecursionlimit(5000).