SCIMITAR
Input saved to /scratch/irc/personal/robrechtc/tmp//RtmpfAj4j5/input:
expression.csv
params.json
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.6085
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5174
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.534
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5439
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5954
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.737
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8644
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.6058
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5698
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5563
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5114
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.6148
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5973
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5391
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5308
Specified shrinkage intensity lambda (correlation matrix): 0.05
Initializing
Iteration 0
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.6368
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5518
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5032
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5595
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5377
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5468
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.7671
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8705
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.7676
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.6835
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.6599
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.6406
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5783
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.3922
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5677
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5943
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.6241
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5754
Specified shrinkage intensity lambda (correlation matrix): 0.05
R: 0.7992869035807436
Iteration 1
Estimating optimal shrinkage intensity lambda.var (variance vector): 1
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.637
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5288
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5555
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5617
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.7704
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.6431
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.6249
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.7179
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.7765
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.841
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8565
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8016
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8278
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.6029
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.9497
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.7101
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.7343
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.6525
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.6587
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.6032
Specified shrinkage intensity lambda (correlation matrix): 0.05
R: 0.9605999543283588
Converged!
Final R: 0.9605999543283588output saved in /scratch/irc/personal/robrechtc/tmp//RtmpfAj4j5/output:
pseudotime.csv
timings.json
Input saved to /scratch/irc/personal/robrechtc/tmp//Rtmpt9s5xg/input:
expression.csv
params.json
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.9086
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.9495
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8099
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.7962
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.9078
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 1
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 1
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.9142
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8328
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.9067
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.9386
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.913
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8713
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.7316
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.651
Specified shrinkage intensity lambda (correlation matrix): 0.05
Initializing
Iteration 0
Estimating optimal shrinkage intensity lambda.var (variance vector): 1
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 1
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.9537
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.9743
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 1
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8987
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8536
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.9562
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8034
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.816
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8826
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8468
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8538
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8376
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.9008
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8838
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.7187
Specified shrinkage intensity lambda (correlation matrix): 0.05
R: 0.9329528845828017
Converged!
Final R: 0.9329528845828017output saved in /scratch/irc/personal/robrechtc/tmp//Rtmpt9s5xg/output:
pseudotime.csv
timings.json
Input saved to /scratch/irc/personal/robrechtc/tmp//Rtmp6wzLIg/input:
expression.csv
params.json
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.2947
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.207
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.1727
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.1677
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.1834
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.2015
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.2117
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.2233
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.2059
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.1957
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.1872
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.2072
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.2608
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.3812
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.6832
Specified shrinkage intensity lambda (correlation matrix): 0.05
Traceback (most recent call last):
File "/code/run.py", line 35, in
cov_reg=p["cov_reg"]
File "/usr/local/lib/python2.7/site-packages/scimitar/morphing_mixture.py", line 396, in morphing_gaussian_from_embedding
pseudotimes, cov_estimator=cov_estimator, **kwargs)
File "/usr/local/lib/python2.7/site-packages/scimitar/morphing_mixture.py", line 325, in morphing_mixture_from_pseudotime
timepoints=timepoints)
File "/usr/local/lib/python2.7/site-packages/scimitar/morphing_mixture.py", line 202, in state_interpolation
sorted_chols = np.array([np.linalg.cholesky(c).tolist() for c in sorted_covariances])
MemoryError
Input saved to /scratch/irc/personal/robrechtc/tmp//Rtmpb0Ywdh/input:
expression.csv
params.json
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.1231
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.0838
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.0725
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.0836
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.119
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.1746
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.2042
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.1851
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.1182
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.0731
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.0561
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.0469
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.0415
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.0591
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.0904
Specified shrinkage intensity lambda (correlation matrix): 0.05
Traceback (most recent call last):
File "/code/run.py", line 35, in
cov_reg=p["cov_reg"]
File "/usr/local/lib/python2.7/site-packages/scimitar/morphing_mixture.py", line 396, in morphing_gaussian_from_embedding
pseudotimes, cov_estimator=cov_estimator, **kwargs)
File "/usr/local/lib/python2.7/site-packages/scimitar/morphing_mixture.py", line 325, in morphing_mixture_from_pseudotime
timepoints=timepoints)
File "/usr/local/lib/python2.7/site-packages/scimitar/morphing_mixture.py", line 202, in state_interpolation
sorted_chols = np.array([np.linalg.cholesky(c).tolist() for c in sorted_covariances])
MemoryError
Input saved to /scratch/irc/personal/robrechtc/tmp//Rtmppgy6Jg/input:
expression.csv
params.json
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8067
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8188
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8445
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.6723
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.6414
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.6714
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.7542
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8634
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8565
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.9302
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.911
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.7972
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.6284
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5525
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.563
Specified shrinkage intensity lambda (correlation matrix): 0.05
Initializing
Iteration 0
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.7852
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.7683
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.713
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.688
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.6135
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.7513
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.9281
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 1
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.9017
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8858
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.8288
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.754
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.7735
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5876
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.5619
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.694
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.7957
Specified shrinkage intensity lambda (correlation matrix): 0.05
Estimating optimal shrinkage intensity lambda.var (variance vector): 0.7849
Specified shrinkage intensity lambda (correlation matrix): 0.05
R: 0.918348633805256
Converged!
Final R: 0.918348633805256output saved in /scratch/irc/personal/robrechtc/tmp//Rtmppgy6Jg/output:
pseudotime.csv
timings.json
Part of 