[WARNING] __init__:0084 >> Not running in a production installation (branch "develop" from source code)
Tracing errors for sample Lipo-100 from sink features_train_CT_0_predict
Located result pickle: /scratch/dspaanderman/tmp/WORC_LIPO_classification_minus/featureconverter_train_predict_CalcFeatures_1_0_CT_0/Lipo-100/__fastr_result__.yaml
===== JOB WORC_LIPO_classification_minus___featureconverter_train_predict_CalcFeatures_1_0_CT_0___Lipo-100 =====
Network: WORC_LIPO_classification_minus
Run: WORC_LIPO_classification_minus_2022-04-01T14-49-29
Node: featureconverter_train_predict_CalcFeatures_1_0_CT_0
Sample index: (0)
Sample id: Lipo-100
Status: JobState.cancelled
Timestamp: 2022-04-01 12:57:00.622826
Job file: /scratch/dspaanderman/tmp/WORC_LIPO_classification_minus/featureconverter_train_predict_CalcFeatures_1_0_CT_0/Lipo-100/__fastr_result__.yaml
----- ERRORS -----
- FastrError: job cancelled by fastr DRMAA plugin (/home/dspaanderman/WORCTutorial/env/lib/python3.6/site-packages/fastr/resources/plugins/executionplugins/drmaaexecution.py:300)
------------------
No process information:
Cannot find process information in Job information, processing probably got killed.
If there are no other errors, this is often a result of too high memory use or
exceeding some other type of resource limit.
Output data:
{}
Status history:
2022-04-01 12:57:00.622843: JobState.created
2022-04-01 13:08:31.203427: JobState.queued
2022-04-01 13:11:35.373959: JobState.cancelled
Located result pickle: /scratch/dspaanderman/tmp/WORC_LIPO_classification_minus/features_train_CT_0_predict/Lipo-100_0/__fastr_result__.yaml
===== JOB WORC_LIPO_classification_minus___features_train_CT_0_predict___Lipo-100___0 =====
Network: WORC_LIPO_classification_minus
Run: WORC_LIPO_classification_minus_2022-04-01T14-49-29
Node: features_train_CT_0_predict
Sample index: (0)
Sample id: Lipo-100
Status: JobState.cancelled
Timestamp: 2022-04-01 12:57:05.028554
Job file: /scratch/dspaanderman/tmp/WORC_LIPO_classification_minus/features_train_CT_0_predict/Lipo-100_0/__fastr_result__.yaml
----- ERRORS -----
- FastrError: job cancelled by fastr DRMAA plugin (/home/dspaanderman/WORCTutorial/env/lib/python3.6/site-packages/fastr/resources/plugins/executionplugins/drmaaexecution.py:300)
------------------
No process information:
Cannot find process information in Job information, processing probably got killed.
If there are no other errors, this is often a result of too high memory use or
exceeding some other type of resource limit.
Output data:
{}
Status history:
2022-04-01 12:57:05.028571: JobState.created
2022-04-01 13:08:36.418976: JobState.queued
2022-04-01 13:11:35.436503: JobState.cancelled
Located result pickle: /scratch/dspaanderman/tmp/WORC_LIPO_classification_minus/calcfeatures_train_predict_CalcFeatures_1_0_CT_0/Lipo-100/__fastr_result__.yaml
===== JOB WORC_LIPO_classification_minus___calcfeatures_train_predict_CalcFeatures_1_0_CT_0___Lipo-100 =====
Network: WORC_LIPO_classification_minus
Run: WORC_LIPO_classification_minus_2022-04-01T14-49-29
Node: calcfeatures_train_predict_CalcFeatures_1_0_CT_0
Sample index: (0)
Sample id: Lipo-100
Status: JobState.execution_failed
Timestamp: 2022-04-01 12:51:50.614785
Job file: /scratch/dspaanderman/tmp/WORC_LIPO_classification_minus/calcfeatures_train_predict_CalcFeatures_1_0_CT_0/Lipo-100/__fastr_result__.yaml
----- ERRORS -----
- FastrOutputValidationError: Output value [HDF5] "vfs://tmp/WORC_LIPO_classification_minus/calcfeatures_train_predict_CalcFeatures_1_0_CT_0/Lipo-100/features_0.hdf5" not valid for datatype "'HDF5'" (/home/dspaanderman/WORCTutorial/env/lib/python3.6/site-packages/fastr/execution/job.py:1151)
- FastrOutputValidationError: The output "features" is invalid! (/home/dspaanderman/WORCTutorial/env/lib/python3.6/site-packages/fastr/execution/job.py:1099)
- FastrErrorInSubprocess: Traceback (most recent call last):
File "/home/dspaanderman/WORCTutorial/env/lib/python3.6/site-packages/WORC/resources/fastr_tools/predict/bin/CalcFeatures_tool.py", line 72, in <module>
main()
File "/home/dspaanderman/WORCTutorial/env/lib/python3.6/site-packages/WORC/resources/fastr_tools/predict/bin/CalcFeatures_tool.py", line 68, in main
semantics_file=args.sem)
File "/home/dspaanderman/WORCTutorial/env/lib/python3.6/site-packages/PREDICT/CalcFeatures.py", line 74, in CalcFeatures
config = config_io.load_config(parameters)
File "/home/dspaanderman/WORCTutorial/env/lib/python3.6/site-packages/PREDICT/IOparser/config_io_CalcFeatures.py", line 94, in load_config
settings['ImageFeatures']['extraction_mode']
File "/cm/shared/apps/python3/3.6.8/lib/python3.6/configparser.py", line 1233, in __getitem__
raise KeyError(key)
KeyError: 'extraction_mode'
(/home/dspaanderman/WORCTutorial/env/lib/python3.6/site-packages/fastr/execution/executionscript.py:111)
- FastrValueError: Output values are not valid! (/home/dspaanderman/WORCTutorial/env/lib/python3.6/site-packages/fastr/execution/job.py:830)
------------------
Command:
List representation: ['python', '/home/dspaanderman/WORCTutorial/env/lib/python3.6/site-packages/WORC/resources/fastr_tools/predict/bin/CalcFeatures_tool.py', '--im', '/scratch/dspaanderman/tmp/WORC_LIPO_classification_minus/preprocessing_train_CT_0/Lipo-100/image_0.nii.gz', '--out', '/scratch/dspaanderman/tmp/WORC_LIPO_classification_minus/calcfeatures_train_predict_CalcFeatures_1_0_CT_0/Lipo-100/features_0.hdf5', '--seg', '/scratch/dspaanderman/tmp/WORC_LIPO_classification_minus/segmentix_train_CT_0/Lipo-100/segmentation_out_0.nii.gz', '--para', '/scratch/dspaanderman/tmp/WORC_LIPO_classification_minus/config_CT_0/id_0/result/config_WORC_LIPO_classification_minus_0.ini']
String representation: python /home/dspaanderman/WORCTutorial/env/lib/python3.6/site-packages/WORC/resources/fastr_tools/predict/bin/CalcFeatures_tool.py --im /scratch/dspaanderman/tmp/WORC_LIPO_classification_minus/preprocessing_train_CT_0/Lipo-100/image_0.nii.gz --out /scratch/dspaanderman/tmp/WORC_LIPO_classification_minus/calcfeatures_train_predict_CalcFeatures_1_0_CT_0/Lipo-100/features_0.hdf5 --seg /scratch/dspaanderman/tmp/WORC_LIPO_classification_minus/segmentix_train_CT_0/Lipo-100/segmentation_out_0.nii.gz --para /scratch/dspaanderman/tmp/WORC_LIPO_classification_minus/config_CT_0/id_0/result/config_WORC_LIPO_classification_minus_0.ini
Output data:
{'features': [<HDF5: 'vfs://tmp/WORC_LIPO_classification_minus/calcfeatures_train_predict_CalcFeatures_1_0_CT_0/Lipo-100/features_0.hdf5'>]}
Status history:
2022-04-01 12:51:50.614800: JobState.created
2022-04-01 13:11:07.530470: JobState.running
2022-04-01 13:11:28.013769: JobState.execution_failed
----- STDOUT -----
------------------
----- STDERR -----
Traceback (most recent call last):
File "/home/dspaanderman/WORCTutorial/env/lib/python3.6/site-packages/WORC/resources/fastr_tools/predict/bin/CalcFeatures_tool.py", line 72, in <module>
main()
File "/home/dspaanderman/WORCTutorial/env/lib/python3.6/site-packages/WORC/resources/fastr_tools/predict/bin/CalcFeatures_tool.py", line 68, in main
semantics_file=args.sem)
File "/home/dspaanderman/WORCTutorial/env/lib/python3.6/site-packages/PREDICT/CalcFeatures.py", line 74, in CalcFeatures
config = config_io.load_config(parameters)
File "/home/dspaanderman/WORCTutorial/env/lib/python3.6/site-packages/PREDICT/IOparser/config_io_CalcFeatures.py", line 94, in load_config
settings['ImageFeatures']['extraction_mode']
File "/cm/shared/apps/python3/3.6.8/lib/python3.6/configparser.py", line 1233, in __getitem__
raise KeyError(key)
KeyError: 'extraction_mode'
------------------
To Reproduce
Fresh Install with the newest version of WORC and PREDICTFastr.
Expected behavior
WORC config file should include extraction_mode in order to determine whether to use 2D, 2.5D or 3D feature extraction.
Thanks for pointing this out, this should be automatically solved by the new WORC 3.6.0 that was just released, which updates the PREDICT dependency to the most recent release.
Describe the bug WORC seems incompatible with PREDICTFastr 3.1.14+ release, due to missing key: extraction_mode introduced in PREDICTFastr 3.1.14.
WORC configuration SimpleWORC config file, here shown only the ImageFeatures:
fastr trace
To Reproduce Fresh Install with the newest version of WORC and PREDICTFastr.
Expected behavior WORC config file should include extraction_mode in order to determine whether to use 2D, 2.5D or 3D feature extraction.
Desktop: