Python not waiting for MASTER to complete

Hypnotoad:kamphir art$ python kamphir.py MASTER.SIR.py projects/hivepi/scripts/settings.MASTER.json projects/hivepi/data/MASTER.SIR.beta1E-3.gamma03.phi015.N1000.n100.labels.nwk projects/hivepi/data/MASTER.SIR.beta1E-3.gamma03.phi015.N1000.n100.log -driver python
initializing Kamphir with pid 73803
reading in target tree from projects/hivepi/data/MASTER.SIR.beta1E-3.gamma03.phi015.N1000.n100.labels.nwk
read in 274 leaves
Traceback (most recent call last):
  File "MASTER.SIR.py", line 119, in <module>
    for tree in trees:
  File "/Library/Python/2.7/site-packages/Bio/Phylo/_io.py", line 52, in parse
    with File.as_handle(file, 'r') as fp:
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/contextlib.py", line 17, in __enter__
    return self.gen.next()
  File "/Library/Python/2.7/site-packages/Bio/File.py", line 86, in as_handle
    with open(handleish, mode, **kwargs) as fp:
IOError: [Errno 2] No such file or directory: '/tmp/output_73803.nwk'
Traceback (most recent call last):
  File "kamphir.py", line 510, in <module>
    decay=args.toldecay)
  File "kamphir.py", line 349, in abc_mcmc
    cur_score = self.evaluate()
  File "kamphir.py", line 282, in evaluate
    trees = self.simulate()
  File "kamphir.py", line 258, in simulate
    handle = open(self.path_to_output_nwk, 'rU')
IOError: [Errno 2] No such file or directory: '/tmp/output_73803.nwk'
ArtPoon / kamphir

Python not waiting for MASTER to complete #15
