Common Errors
This page details common errors you might encounter while using lpath.
Discretize
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Extract
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Match
IndexError and DivideByZeroError
- The following tracebacks imply that your states have all accidentally been cleared out by the
expand_shorter_traj()function:: - Traceback(most recent call last):
- File “/home/user/apps/miniconda3/envs/westpa-lpath/bin/lpath”, line 8, in <module>
- sys.exit(entry_point())
- File “/home/user/Documents/lpath/lpath/lpath.py”, line 52, in entry_point
args.func(args)
- File “/home/user/Documents/lpath/lpath/match.py”, line 492, in main
- dist_matrix, weights = gen_dist_matrix(pathways, dictionary, file_name=arguments.dmatrix_save,
- File “/home/atb43/Documents/lpath/lpath/match.py”, line 280, in gen_dist_matrix
- weights.append(nonzero[-1][-1])
~~~~~~~^^^^
IndexError: index -1 is out of bounds for axis 0 with size 0
- Traceback (most recent call last):
- File “/home/atb43/apps/miniconda3/envs/westpa2-ibstates-fix/bin/lpath”, line 8, in <module>
- sys.exit(entry_point())
- File “/home/atb43/Documents/lpath-stride/lpath/lpath.py”, line 52, in entry_point
args.func(args)
- File “/home/atb43/Documents/lpath-stride/lpath/match.py”, line 601, in main
- dist_matrix, weights = gen_dist_matrix(pathways, dictionary, file_name=arguments.dmatrix_save,
- File “/home/atb43/Documents/lpath-stride/lpath/match.py”, line 392, in gen_dist_matrix
- distmat = pairwise_distances(
- File “/home/atb43/apps/miniconda3/envs/westpa2-ibstates-fix/lib/python3.11/site-packages/sklearn/metrics/pairwise.py”, line 2039, in pairwise_distances
- return _parallel_pairwise(X, Y, func, n_jobs, **kwds)
- File “/home/atb43/apps/miniconda3/envs/westpa2-ibstates-fix/lib/python3.11/site-packages/sklearn/metrics/pairwise.py”, line 1579, in _parallel_pairwise
- return func(X, Y, **kwds)
- File “/home/atb43/apps/miniconda3/envs/westpa2-ibstates-fix/lib/python3.11/site-packages/sklearn/metrics/pairwise.py”, line 1623, in _pairwise_callable
- out[i, j] = metric(X[i], Y[j], **kwds)
- File “/home/atb43/Documents/lpath-stride/lpath/match.py”, line 393, in <lambda>
- X=path_strings, metric=lambda x, y: calc_dist(x, y, dictionary)
- File “/home/atb43/Documents/lpath-stride/lpath/match.py”, line 69, in calc_dist
- similarity = (2 * km) / (int(len(seq1_str) + len(seq2_str)))
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ZeroDivisionError: division by zero
- There are two common cause for this problem due to the custom reassign function:
- The most common cause is that you have utilized a custom reassign function but forgot to include an “unknown state” in the dictionary. By LPATH conventions, the last entry in the dictionary is always reserved for this state, represented by
!(orchr(33)). During string comparison, any states assigned “unknown” are removed. Adding the following line into your custom reassign function will typically solve it:: dictionary[len(dictionary)] = ‘!’
- The most common cause is that you have utilized a custom reassign function but forgot to include an “unknown state” in the dictionary. By LPATH conventions, the last entry in the dictionary is always reserved for this state, represented by
- Another potential cause is that you forgot to copy the other columns of data (iteration, seg_id etc.) into the
pathwaysarray during reassignment. Theexpand_shorter_traj()function assumes all segments with iteration 0 are there for padding (i.e., there because the length of the transition is < the longest successful trajectory extracted) and are assigned to the “unknown state”. Include the following line within the secondforloop to copy all columns before reassignment:: - for idx, val2 in enumerate(flipped_val):
pathways[idx,idx2] = val2
- Another potential cause is that you forgot to copy the other columns of data (iteration, seg_id etc.) into the
Plot
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