- edited description
DefineClones fails to execute with "bygroup --model aa"
Issue #18
resolved
Traceback (most recent call last):
File "/usr/lib64/python2.7/multiprocessing/process.py", line 258, in _bootstrap
PID 30107: Error in sibling process detected. Cleaning up.
PID 30108: Error in sibling process detected. Cleaning up.
self.run()
File "/usr/lib64/python2.7/multiprocessing/process.py", line 114, in run
self._target(*self._args, **self._kwargs)
File "/home/jason/workspace/igpipeline/changeo_v0.4/DefineClones.py", line 496, in processQueue
clones = clone_func(records, **clone_args) if data else None
File "/home/jason/workspace/igpipeline/changeo_v0.4/DefineClones.py", line 241, in distanceClones
dists = squareform(dists)
File "/usr/lib64/python2.7/site-packages/scipy/spatial/distance.py", line 1481, in squareform
is_valid_dm(X, throw=True, name='X')
File "/usr/lib64/python2.7/site-packages/scipy/spatial/distance.py", line 1570, in is_valid_dm
'be zero.') % name)
ValueError: Distance matrix 'X' diagonal must be zero.
Comments (4)
-
reporter -
- changed status to resolved
X scoring was mistakenly 0, is now 1 so all amino acids are considered matches
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- changed status to open
Still experiencing the issue in the 3/13/15 version
Command used: DefineClones.py bygroup -d <file> --model aa --dist 10
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- changed status to resolved
Issue was that score of X with itself was non-zero. Fixed by not calculating distance between junction and itself anymore, so diagonal of distance matrix asserted to be zero.
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