instability example: TypeError when running fit-ghmm

[gkiss]

Description:

• This error occurs on occasion.

• When I run it again, things are fine.

  head -n 1 hmms.jsonlines
  /g/g90/kiss2/mixtape-master/scripts/hmsm fit-ghmm --featurizer features_rmsd.dat -k 2 3 4 5 6 7 8 -l 100 --dir ../Trajectories --ext lh5 --top ../2g2z_TetInt_TIP3P_300Wat.pdb

Traceback (most recent call last):
File "/g/g90/kiss2/mixtape-master/scripts/hmsm", line 8, in
app.start()
File "/g/g90/kiss2/Progs/Python2.7/lib/python2.7/site-packages/mixtape-0.1-py2.7-linux-x86_64.egg/mixtape/cmdline.py", line 219, in start
instance.start()
File "/g/g90/kiss2/Progs/Python2.7/lib/python2.7/site-packages/mixtape-0.1-py2.7-linux-x86_64.egg/mixtape/commands/fitghmm.py", line 129, in start
self.fit(subsampled, subsampled, n_states, lag_time, 0, args, outfile)
File "/g/g90/kiss2/Progs/Python2.7/lib/python2.7/site-packages/mixtape-0.1-py2.7-linux-x86_64.egg/mixtape/commands/fitghmm.py", line 173, in fit
json.dump(result, outfile)
File "/g/g90/kiss2/Progs/Python2.7/lib/python2.7/json/init.py", line 181, in dump
for chunk in iterable:
File "/g/g90/kiss2/Progs/Python2.7/lib/python2.7/json/encoder.py", line 428, in _iterencode
for chunk in _iterencode_dict(o, _current_indent_level):
File "/g/g90/kiss2/Progs/Python2.7/lib/python2.7/json/encoder.py", line 402, in _iterencode_dict
for chunk in chunks:
File "/g/g90/kiss2/Progs/Python2.7/lib/python2.7/json/encoder.py", line 326, in _iterencode_list
for chunk in chunks:
File "/g/g90/kiss2/Progs/Python2.7/lib/python2.7/json/encoder.py", line 436, in _iterencode
o = _default(o)
File "/g/g90/kiss2/Progs/Python2.7/lib/python2.7/json/encoder.py", line 178, in default
raise TypeError(repr(o) + " is not JSON serializable")
TypeError: (31.019121170043945+0j) is not JSON serializable

[gkiss]

Update:
Additional poking around suggests that the issue is not with mixtape, but with the imaging protocol going from Anton's Desmond trajectories to the water-stripped input that I'm throwing at mixtape.
Let's put this issue on hold until I have ruled out any ambiguity.

[rmcgibbo]

Fixed this particular symptom, with d1af022