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ArtPoon / kamphir

Phylogenetic inference using a tree-shape kernel in an Approximate Bayesian Computation framework
BSD 3-Clause "New" or "Revised" License
6 stars 2 forks source link

Time-out tree simulation if MASTER takes too long to simulate trees. #17

Closed ArtPoon closed 9 years ago

ArtPoon commented 9 years ago 
^CTraceback (most recent call last):
  File "MASTER.SIR.py", line 115, in <module>
    p.wait()
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1357, in wait
    pid, sts = _eintr_retry_call(os.waitpid, self.pid, 0)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 478, in _eintr_retry_call
    return func(*args)
KeyboardInterrupt
WARNING: none of the trees managed to coalesce in simulation time - returning 0.
31  0.88448 0.00000 758.86876   0.00211 0.1789  1.0 0.27    28.77443
ArtPoon commented 9 years ago

This is caused by N declining to low values, it becomes too difficult to generate a tree with the minimum required number of leaves. Set minimum to 750 and reduce sigma to 100.

ArtPoon commented 9 years ago

Should probably add some time-out on the Python level to prevent MASTER from hanging the process indefinitely.