FORKS
File: /home/rcannood/Workspace/dynverse/dynbenchmark//derived/04-method_characterisation/method_testing/suite/forks/r2gridengine/20180803_183259_forks_HN1lCuNxvy/log/log.1.e.txt
Error: dataset$cell_ids not equal to model$cell_ids.
Lengths differ: 92 is not 72
Execution halted
File: /home/rcannood/Workspace/dynverse/dynbenchmark//derived/04-method_characterisation/method_testing/suite/forks/r2gridengine/20180803_183259_forks_HN1lCuNxvy/log/log.2.e.txt
Error: dataset$cell_ids not equal to model$cell_ids.
Lengths differ: 94 is not 78
Execution halted
Input saved to /scratch/irc/personal/robrechtc/tmp//RtmpKT6USx/input:
counts.csv
params.json
/usr/local/lib/python3.6/site-packages/sklearn/decomposition/kernel_pca.py:264: RuntimeWarning: invalid value encountered in sqrt
X_transformed = self.alphas_ * np.sqrt(self.lambdas_)
/tmp
data shape before discarding (238,4480)
threshold for detected genes is 964
here
data shape after discarding (231,4480)
Isomap: 1.5 sec
2 231,171
Traceback (most recent call last):
File "/code/run.py", line 119, in
kmeans = KMeans(n_clusters=M, random_state=0).fit(X_reduced)
File "/usr/local/lib/python3.6/site-packages/sklearn/cluster/k_means_.py", line 887, in fit
X = self._check_fit_data(X)
File "/usr/local/lib/python3.6/site-packages/sklearn/cluster/k_means_.py", line 858, in _check_fit_data
X = check_array(X, accept_sparse='csr', dtype=[np.float64, np.float32])
File "/usr/local/lib/python3.6/site-packages/sklearn/utils/validation.py", line 453, in check_array
_assert_all_finite(array)
File "/usr/local/lib/python3.6/site-packages/sklearn/utils/validation.py", line 44, in _assert_all_finite
" or a value too large for %r." % X.dtype)
ValueError: Input contains NaN, infinity or a value too large for dtype('float64').
File: /home/rcannood/Workspace/dynverse/dynbenchmark//derived/04-method_characterisation/method_testing/suite/forks/r2gridengine/20180803_183259_forks_HN1lCuNxvy/log/log.4.e.txt
Error: dataset$cell_ids not equal to model$cell_ids.
Lengths differ: 355 is not 335
Execution halted
File: /home/rcannood/Workspace/dynverse/dynbenchmark//derived/04-method_characterisation/method_testing/suite/forks/r2gridengine/20180803_183259_forks_HN1lCuNxvy/log/log.5.e.txt
Error: dataset$cell_ids not equal to model$cell_ids.
Lengths differ: 84 is not 73
Execution halted
Part of 