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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

Priors don't work #47

Closed rmcclosk closed 9 years ago

rmcclosk commented 9 years ago

Tried this:

python kamphir.py PANGEA settings/pangea.json /home/rmcclosk/pangea/data/February2015/Regional/hyphy/root2tip/150129_PANGEAsim_Regional_FirstObj_scA_SIMULATED_all.nwk scA.log -delimiter _ -ncores 20 -nthreads 20 -nreps 5 -tscale 0.142857 -tol0 0.03 -mintol 0.01 -prior

got this:

Traceback (most recent call last):
  File "kamphir.py", line 768, in <module>
    decay=args.toldecay)
  File "kamphir.py", line 482, in abc_mcmc
    cur_score, _ = self.evaluate()
  File "kamphir.py", line 440, in evaluate
    for tree in trees]
  File "kamphir.py", line 32, in apply_async
    return pool.apply_async(run_dill_encoded, (dill.dumps((fun, args)),))
...
  File "/usr/local/lib/python2.7/pickle.py", line 405, in save_reduce
    self.memoize(obj)
  File "/usr/local/lib/python2.7/pickle.py", line 244, in memoize
    assert id(obj) not in self.memo
AssertionError