Clustering by contacts fails with varying errors

[Trayder]

I can cluster by RMSD fine. But clustering by contact fails on multiple data sets.
I get all sorts of different errors depending on settings and clustering algorithm.
Anyone know what's going on here?
Thanks,
-Trayder

In the below examples my test.dat file simply reads:
1 2
1 3

Cluster contact -c test.dat -C -1 -s closest hybrid -k 10

Traceback (most recent call last):
File "/vcp2/student/trayder/anaconda/bin/Cluster", line 9, in
load_entry_point('msmbuilder==2.8.2', 'console_scripts', 'Cluster')()
File "/vcp2/student/trayder/anaconda/lib/python2.7/site-packages/msmbuilder-2.8.2-py2.7.egg/msmbuilder/scripts/Cluster.py", line 287, in entry_point
main(args, metric)
File "/vcp2/student/trayder/anaconda/lib/python2.7/site-packages/msmbuilder-2.8.2-py2.7.egg/msmbuilder/scripts/Cluster.py", line 248, in main
raise Exception("something went wrong in loading step (%d v %d)" % (num_frames, len(which)))
Exception: something went wrong in loading step (120 v 1260)`

Cluster contact -c test.dat -C 1 -s closest hybrid -k 10

Traceback (most recent call last):
File "/vcp2/student/trayder/anaconda/bin/Cluster", line 9, in
load_entry_point('msmbuilder==2.8.2', 'console_scripts', 'Cluster')()
File "/vcp2/student/trayder/anaconda/lib/python2.7/site-packages/msmbuilder-2.8.2-py2.7.egg/msmbuilder/scripts/Cluster.py", line 287, in entry_point
main(args, metric)
File "/vcp2/student/trayder/anaconda/lib/python2.7/site-packages/msmbuilder-2.8.2-py2.7.egg/msmbuilder/scripts/Cluster.py", line 242, in main
ptrajs, which = load_prep_trajectories(project, args.stride, atom_indices, metric)
File "/vcp2/student/trayder/anaconda/lib/python2.7/site-packages/msmbuilder-2.8.2-py2.7.egg/msmbuilder/scripts/Cluster.py", line 135, in load_prep_trajectories
ptraj = np.concatenate(ptraj)
ValueError: zero-dimensional arrays cannot be concatenated`

Cluster contact -c test.dat -C -1 -s closest hierarchical -m ward

16:14:07 - Loaded 60 trajs
16:14:07 - Preparing...
16:14:08 - Getting all to all pairwise distance matrix...
Traceback (most recent call last):
File "/vcp2/student/trayder/anaconda/bin/Cluster", line 9, in
load_entry_point('msmbuilder==2.8.2', 'console_scripts', 'Cluster')()
File "/vcp2/student/trayder/anaconda/lib/python2.7/site-packages/msmbuilder-2.8.2-py2.7.egg/msmbuilder/scripts/Cluster.py", line 287, in entry_point
main(args, metric)
File "/vcp2/student/trayder/anaconda/lib/python2.7/site-packages/msmbuilder-2.8.2-py2.7.egg/msmbuilder/scripts/Cluster.py", line 257, in main
clusterer = cluster(metric, trajectories, ptrajs, args, **extra_kwargs)
File "/vcp2/student/trayder/anaconda/lib/python2.7/site-packages/msmbuilder-2.8.2-py2.7.egg/msmbuilder/scripts/Cluster.py", line 189, in cluster
method=args.hierarchical_method)
File "/vcp2/student/trayder/anaconda/lib/python2.7/site-packages/msmbuilder-2.8.2-py2.7.egg/msmbuilder/clustering.py", line 769, in init
dmat = metric.all_pairwise(pflat_trajectory)
File "/vcp2/student/trayder/anaconda/lib/python2.7/site-packages/msmbuilder-2.8.2-py2.7.egg/msmbuilder/metrics/baseclasses.py", line 343, in all_pairwise
V=self.V, VI=self.VI)
File "/vcp2/student/trayder/anaconda/lib/python2.7/site-packages/scipy/spatial/distance.py", line 1178, in pdist
[X] = _copy_arrays_if_base_present([_convert_to_double(X)])
File "/vcp2/student/trayder/anaconda/lib/python2.7/site-packages/scipy/spatial/distance.py", line 113, in _convert_to_double
X = X.astype(np.double)
ValueError: setting an array element with a sequence.`

Cluster contact -c test.dat -C 1 -s closest hierarchical -m ward

16:15:15 - Loaded 60 trajs
16:15:15 - Preparing...
16:15:17 - Getting all to all pairwise distance matrix...
Traceback (most recent call last):
File "/vcp2/student/trayder/anaconda/bin/Cluster", line 9, in
load_entry_point('msmbuilder==2.8.2', 'console_scripts', 'Cluster')()
File "/vcp2/student/trayder/anaconda/lib/python2.7/site-packages/msmbuilder-2.8.2-py2.7.egg/msmbuilder/scripts/Cluster.py", line 287, in entry_point
main(args, metric)
File "/vcp2/student/trayder/anaconda/lib/python2.7/site-packages/msmbuilder-2.8.2-py2.7.egg/msmbuilder/scripts/Cluster.py", line 257, in main
clusterer = cluster(metric, trajectories, ptrajs, args, **extra_kwargs)
File "/vcp2/student/trayder/anaconda/lib/python2.7/site-packages/msmbuilder-2.8.2-py2.7.egg/msmbuilder/scripts/Cluster.py", line 189, in cluster
method=args.hierarchical_method)
File "/vcp2/student/trayder/anaconda/lib/python2.7/site-packages/msmbuilder-2.8.2-py2.7.egg/msmbuilder/clustering.py", line 769, in init
dmat = metric.all_pairwise(pflat_trajectory)
File "/vcp2/student/trayder/anaconda/lib/python2.7/site-packages/msmbuilder-2.8.2-py2.7.egg/msmbuilder/metrics/baseclasses.py", line 343, in all_pairwise
V=self.V, VI=self.VI)
File "/vcp2/student/trayder/anaconda/lib/python2.7/site-packages/scipy/spatial/distance.py", line 1182, in pdist
raise ValueError('A 2-dimensional array must be passed.')
ValueError: A 2-dimensional array must be passed.`