search

superphy / prairiedog

next-gen pangenome graphs for predictive genomics
Other
0 stars 0 forks source link

RecursionError: maximum recursion depth exceeded #77

Open kevinkle opened 5 years ago

kevinkle commented 5 years ago 
2019-06-21 14:11:37 panther prairiedog[32057] INFO Edge along >SRR3664820.fasta|NODE_2_length_725620_cov_53.3023_ID_3462 in SRR3664820.fasta has len 248877
  File "/home/kevin/prairiedog/venv/lib/python3.7/site-packages/LemonGraph-0.10.0-py3.7-linux-x86_64.egg/LemonGraph/__init__.py", line 919, in iterlinks
    if self.srcID != self.tgtID:
  File "/home/kevin/prairiedog/venv/lib/python3.7/site-packages/LemonGraph-0.10.0-py3.7-linux-x86_64.egg/LemonGraph/__init__.py", line 902, in srcID
    return self.src.ID
  File "/home/kevin/prairiedog/venv/lib/python3.7/site-packages/LemonGraph-0.10.0-py3.7-linux-x86_64.egg/LemonGraph/__init__.py", line 894, in src
    return self.txn.node(ID=self._data.src, beforeID=self.beforeID)
  File "/home/kevin/prairiedog/venv/lib/python3.7/site-packages/LemonGraph-0.10.0-py3.7-linux-x86_64.egg/LemonGraph/__init__.py", line 421, in node
    return self._node_edge_property(Node, **kwargs)
  File "/home/kevin/prairiedog/venv/lib/python3.7/site-packages/LemonGraph-0.10.0-py3.7-linux-x86_64.egg/LemonGraph/__init__.py", line 417, in _node_edge_property
    return constructor(self, **kwargs)
  File "/home/kevin/prairiedog/venv/lib/python3.7/site-packages/LemonGraph-0.10.0-py3.7-linux-x86_64.egg/LemonGraph/__init__.py", line 603, in ByID
    beforeID = txn.b4ID(beforeID)
  File "/home/kevin/prairiedog/venv/lib/python3.7/site-packages/LemonGraph-0.10.0-py3.7-linux-x86_64.egg/LemonGraph/__init__.py", line 219, in b4ID
    ret = next(x for x in args if x is not None)
RecursionError: maximum recursion depth exceeded
kevinkle commented 5 years ago

Tried overriding the max recursive depth on long paths, but it still returns chain of len 0

kevinkle commented 5 years ago

Bypassing nodes of length > recursiondepth works for now