{"status":"SUCCEEDED","exception":null,"skipReason":null,"output":"\u001b[0;36mThank you for using runBioSimulations!\u001b[0m\n\n\u001b[0;36m================================================ Loading Singularity ================================================\u001b[0m\n\n\u001b[0;36m=================================================== Set up storage ==================================================\u001b[0m\n\n\u001b[0;36m========================================== Downloading COMBINE/OMEX archive =========================================\u001b[0m\n  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\n                                 Dload  Upload   Total   Spent    Left  Speed\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    466      0 --:--:-- --:--:-- --:--:--   468\n\r100 40933  100 40933    0     0  99154      0 --:--:-- --:--:-- --:--:-- 99154\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\nTraceback (most recent call last):\n  File \"/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py\", line 247, in <module>\n    if not update_paths(args.path, args.scripts_dir, args.clear_args, args.extra_args):\n  File \"/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py\", line 213, in update_paths\n    update_scripts(scripts_dir, new_path, clear_args, extra_args)\n  File \"/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py\", line 125, in update_scripts\n    update_script(os.path.join(bin_dir, fn), new_path, clear_args, extra_args)\n  File \"/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py\", line 118, in update_script\n    with open(script_filename, 'w') as f:\nOSError: [Errno 30] Read-only file system: '/home/opencor/OpenCOR/bin/../python/bin/biosimulators-utils'\n/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mCOMBINE/OMEX archive may be invalid.\n  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\n  - Model `model` may be invalid.\n    - The model file `moussa.cellml` may be invalid.\n      - Validation is not available for CellML 1.1 files.\n    - The changes of the model may be invalid.\n      - Change 1 may be invalid.\n        - XPath could not be validated.\n      - Change 2 may be invalid.\n        - XPath could not be validated.\n      - Change 3 may be invalid.\n        - XPath could not be validated.\n      - Change 4 may be invalid.\n        - XPath could not be validated.\n      - Change 5 may be invalid.\n        - XPath could not be validated.\n      - Change 6 may be invalid.\n        - XPath could not be validated.\n      - Change 7 may be invalid.\n        - XPath could not be validated.\n      - Change 8 may be invalid.\n        - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_k2` may be invalid.\n    - Variable `value_component_moussa_variable_k2` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_k1` may be invalid.\n    - Variable `value_component_moussa_variable_k1` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_X1` may be invalid.\n    - Variable `value_component_moussa_variable_X1` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_X2` may be invalid.\n    - Variable `value_component_moussa_variable_X2` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_time` may be invalid.\n    - Variable `value_component_moussa_variable_time` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_A` may be invalid.\n    - Variable `value_component_moussa_variable_A` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_D` may be invalid.\n    - Variable `value_component_moussa_variable_D` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_R` may be invalid.\n    - Variable `value_component_moussa_variable_R` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_E1` may be invalid.\n    - Variable `value_component_moussa_variable_E1` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_E2` may be invalid.\n    - Variable `value_component_moussa_variable_E2` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_A1` may be invalid.\n    - Variable `value_component_moussa_variable_A1` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_A2` may be invalid.\n    - Variable `value_component_moussa_variable_A2` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_T` may be invalid.\n    - Variable `value_component_moussa_variable_T` may be invalid.\n      - XPath could not be validated.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\n  - Model `model` may be invalid.\n    - The model file `jung-10-lesion.cellml` may be invalid.\n      - Validation is not available for CellML 1.1 files.\n    - The changes of the model may be invalid.\n      - Change 1 may be invalid.\n        - XPath could not be validated.\n      - Change 2 may be invalid.\n        - XPath could not be validated.\n      - Change 3 may be invalid.\n        - XPath could not be validated.\n      - Change 4 may be invalid.\n        - XPath could not be validated.\n      - Change 5 may be invalid.\n        - XPath could not be validated.\n      - Change 6 may be invalid.\n        - XPath could not be validated.\n      - Change 7 may be invalid.\n        - XPath could not be validated.\n      - Change 8 may be invalid.\n        - XPath could not be validated.\n      - Change 9 may be invalid.\n        - XPath could not be validated.\n      - Change 10 may be invalid.\n        - XPath could not be validated.\n      - Change 11 may be invalid.\n        - XPath could not be validated.\n      - Change 12 may be invalid.\n        - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_p` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_p` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_c` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_c` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_P0` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_P0` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_P1` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_P1` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_P2` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_P2` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_P3` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_P3` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_P4` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_P4` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_P5` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_P5` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_P6` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_P6` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_P7` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_P7` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_P8` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_P8` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_P9` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_P9` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_time` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_time` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_A` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_A` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_D` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_D` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_S` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_S` may be invalid.\n      - XPath could not be validated.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\n  - Model `model` may be invalid.\n    - The model file `oneill_cell_death_fast.cellml` may be invalid.\n      - Validation is not available for CellML 1.1 files.\n    - The changes of the model may be invalid.\n      - Change 1 may be invalid.\n        - XPath could not be validated.\n      - Change 2 may be invalid.\n        - XPath could not be validated.\n      - Change 3 may be invalid.\n        - XPath could not be validated.\n      - Change 4 may be invalid.\n        - XPath could not be validated.\n      - Change 5 may be invalid.\n        - XPath could not be validated.\n      - Change 6 may be invalid.\n        - XPath could not be validated.\n  - Data generator `data_generator_value_component_equation_1_variable_A` may be invalid.\n    - Variable `value_component_equation_1_variable_A` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_equation_1_variable_D` may be invalid.\n    - Variable `value_component_equation_1_variable_D` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_equation_1_variable_kf` may be invalid.\n    - Variable `value_component_equation_1_variable_kf` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_equation_1_variable_kb` may be invalid.\n    - Variable `value_component_equation_1_variable_kb` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_equation_1_variable_time` may be invalid.\n    - Variable `value_component_equation_1_variable_time` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_equation_1_variable_kf_` may be invalid.\n    - Variable `value_component_equation_1_variable_kf_` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_equation_1_variable_Tk` may be invalid.\n    - Variable `value_component_equation_1_variable_Tk` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_equation_1_variable_T` may be invalid.\n    - Variable `value_component_equation_1_variable_T` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_equation_1_variable_V` may be invalid.\n    - Variable `value_component_equation_1_variable_V` may be invalid.\n      - XPath could not be validated.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\n  - Model `model` may be invalid.\n    - The model file `arrhenius-cell-death.cellml` may be invalid.\n      - Validation is not available for CellML 1.1 files.\n    - The changes of the model may be invalid.\n      - Change 1 may be invalid.\n        - XPath could not be validated.\n      - Change 2 may be invalid.\n        - XPath could not be validated.\n      - Change 3 may be invalid.\n        - XPath could not be validated.\n      - Change 4 may be invalid.\n        - XPath could not be validated.\n      - Change 5 may be invalid.\n        - XPath could not be validated.\n      - Change 6 may be invalid.\n        - XPath could not be validated.\n  - Data generator `data_generator_value_component_rate_kinetics_variable_k` may be invalid.\n    - Variable `value_component_rate_kinetics_variable_k` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_rate_kinetics_variable_E` may be invalid.\n    - Variable `value_component_rate_kinetics_variable_E` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_rate_kinetics_variable_R` may be invalid.\n    - Variable `value_component_rate_kinetics_variable_R` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_rate_kinetics_variable_T` may be invalid.\n    - Variable `value_component_rate_kinetics_variable_T` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_rate_kinetics_variable_A` may be invalid.\n    - Variable `value_component_rate_kinetics_variable_A` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_rate_kinetics_variable_time` may be invalid.\n    - Variable `value_component_rate_kinetics_variable_time` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_rate_kinetics_variable_C` may be invalid.\n    - Variable `value_component_rate_kinetics_variable_C` may be invalid.\n      - XPath could not be validated.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\n  - The SED-ML file at location `simulation_0.sedml` may be invalid.\n    - Model `model` may be invalid.\n      - The model file `moussa.cellml` may be invalid.\n        - Validation is not available for CellML 1.1 files.\n      - The changes of the model may be invalid.\n        - Change 1 may be invalid.\n          - XPath could not be validated.\n        - Change 2 may be invalid.\n          - XPath could not be validated.\n        - Change 3 may be invalid.\n          - XPath could not be validated.\n        - Change 4 may be invalid.\n          - XPath could not be validated.\n        - Change 5 may be invalid.\n          - XPath could not be validated.\n        - Change 6 may be invalid.\n          - XPath could not be validated.\n        - Change 7 may be invalid.\n          - XPath could not be validated.\n        - Change 8 may be invalid.\n          - XPath could not be validated.\n    - Data generator `data_generator_value_component_moussa_variable_k2` may be invalid.\n      - Variable `value_component_moussa_variable_k2` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_moussa_variable_k1` may be invalid.\n      - Variable `value_component_moussa_variable_k1` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_moussa_variable_X1` may be invalid.\n      - Variable `value_component_moussa_variable_X1` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_moussa_variable_X2` may be invalid.\n      - Variable `value_component_moussa_variable_X2` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_moussa_variable_time` may be invalid.\n      - Variable `value_component_moussa_variable_time` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_moussa_variable_A` may be invalid.\n      - Variable `value_component_moussa_variable_A` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_moussa_variable_D` may be invalid.\n      - Variable `value_component_moussa_variable_D` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_moussa_variable_R` may be invalid.\n      - Variable `value_component_moussa_variable_R` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_moussa_variable_E1` may be invalid.\n      - Variable `value_component_moussa_variable_E1` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_moussa_variable_E2` may be invalid.\n      - Variable `value_component_moussa_variable_E2` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_moussa_variable_A1` may be invalid.\n      - Variable `value_component_moussa_variable_A1` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_moussa_variable_A2` may be invalid.\n      - Variable `value_component_moussa_variable_A2` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_moussa_variable_T` may be invalid.\n      - Variable `value_component_moussa_variable_T` may be invalid.\n        - XPath could not be validated.\n  - The SED-ML file at location `simulation_1.sedml` may be invalid.\n    - Model `model` may be invalid.\n      - The model file `jung-10-lesion.cellml` may be invalid.\n        - Validation is not available for CellML 1.1 files.\n      - The changes of the model may be invalid.\n        - Change 1 may be invalid.\n          - XPath could not be validated.\n        - Change 2 may be invalid.\n          - XPath could not be validated.\n        - Change 3 may be invalid.\n          - XPath could not be validated.\n        - Change 4 may be invalid.\n          - XPath could not be validated.\n        - Change 5 may be invalid.\n          - XPath could not be validated.\n        - Change 6 may be invalid.\n          - XPath could not be validated.\n        - Change 7 may be invalid.\n          - XPath could not be validated.\n        - Change 8 may be invalid.\n          - XPath could not be validated.\n        - Change 9 may be invalid.\n          - XPath could not be validated.\n        - Change 10 may be invalid.\n          - XPath could not be validated.\n        - Change 11 may be invalid.\n          - XPath could not be validated.\n        - Change 12 may be invalid.\n          - XPath could not be validated.\n    - Data generator `data_generator_value_component_jung_10_lesions_variable_p` may be invalid.\n      - Variable `value_component_jung_10_lesions_variable_p` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_jung_10_lesions_variable_c` may be invalid.\n      - Variable `value_component_jung_10_lesions_variable_c` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_jung_10_lesions_variable_P0` may be invalid.\n      - Variable `value_component_jung_10_lesions_variable_P0` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_jung_10_lesions_variable_P1` may be invalid.\n      - Variable `value_component_jung_10_lesions_variable_P1` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_jung_10_lesions_variable_P2` may be invalid.\n      - Variable `value_component_jung_10_lesions_variable_P2` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_jung_10_lesions_variable_P3` may be invalid.\n      - Variable `value_component_jung_10_lesions_variable_P3` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_jung_10_lesions_variable_P4` may be invalid.\n      - Variable `value_component_jung_10_lesions_variable_P4` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_jung_10_lesions_variable_P5` may be invalid.\n      - Variable `value_component_jung_10_lesions_variable_P5` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_jung_10_lesions_variable_P6` may be invalid.\n      - Variable `value_component_jung_10_lesions_variable_P6` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_jung_10_lesions_variable_P7` may be invalid.\n      - Variable `value_component_jung_10_lesions_variable_P7` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_jung_10_lesions_variable_P8` may be invalid.\n      - Variable `value_component_jung_10_lesions_variable_P8` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_jung_10_lesions_variable_P9` may be invalid.\n      - Variable `value_component_jung_10_lesions_variable_P9` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_jung_10_lesions_variable_time` may be invalid.\n      - Variable `value_component_jung_10_lesions_variable_time` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_jung_10_lesions_variable_A` may be invalid.\n      - Variable `value_component_jung_10_lesions_variable_A` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_jung_10_lesions_variable_D` may be invalid.\n      - Variable `value_component_jung_10_lesions_variable_D` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_jung_10_lesions_variable_S` may be invalid.\n      - Variable `value_component_jung_10_lesions_variable_S` may be invalid.\n        - XPath could not be validated.\n  - The SED-ML file at location `simulation_2.sedml` may be invalid.\n    - Model `model` may be invalid.\n      - The model file `oneill_cell_death_fast.cellml` may be invalid.\n        - Validation is not available for CellML 1.1 files.\n      - The changes of the model may be invalid.\n        - Change 1 may be invalid.\n          - XPath could not be validated.\n        - Change 2 may be invalid.\n          - XPath could not be validated.\n        - Change 3 may be invalid.\n          - XPath could not be validated.\n        - Change 4 may be invalid.\n          - XPath could not be validated.\n        - Change 5 may be invalid.\n          - XPath could not be validated.\n        - Change 6 may be invalid.\n          - XPath could not be validated.\n    - Data generator `data_generator_value_component_equation_1_variable_A` may be invalid.\n      - Variable `value_component_equation_1_variable_A` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_equation_1_variable_D` may be invalid.\n      - Variable `value_component_equation_1_variable_D` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_equation_1_variable_kf` may be invalid.\n      - Variable `value_component_equation_1_variable_kf` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_equation_1_variable_kb` may be invalid.\n      - Variable `value_component_equation_1_variable_kb` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_equation_1_variable_time` may be invalid.\n      - Variable `value_component_equation_1_variable_time` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_equation_1_variable_kf_` may be invalid.\n      - Variable `value_component_equation_1_variable_kf_` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_equation_1_variable_Tk` may be invalid.\n      - Variable `value_component_equation_1_variable_Tk` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_equation_1_variable_T` may be invalid.\n      - Variable `value_component_equation_1_variable_T` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_equation_1_variable_V` may be invalid.\n      - Variable `value_component_equation_1_variable_V` may be invalid.\n        - XPath could not be validated.\n  - The SED-ML file at location `simulation_3.sedml` may be invalid.\n    - Model `model` may be invalid.\n      - The model file `arrhenius-cell-death.cellml` may be invalid.\n        - Validation is not available for CellML 1.1 files.\n      - The changes of the model may be invalid.\n        - Change 1 may be invalid.\n          - XPath could not be validated.\n        - Change 2 may be invalid.\n          - XPath could not be validated.\n        - Change 3 may be invalid.\n          - XPath could not be validated.\n        - Change 4 may be invalid.\n          - XPath could not be validated.\n        - Change 5 may be invalid.\n          - XPath could not be validated.\n        - Change 6 may be invalid.\n          - XPath could not be validated.\n    - Data generator `data_generator_value_component_rate_kinetics_variable_k` may be invalid.\n      - Variable `value_component_rate_kinetics_variable_k` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_rate_kinetics_variable_E` may be invalid.\n      - Variable `value_component_rate_kinetics_variable_E` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_rate_kinetics_variable_R` may be invalid.\n      - Variable `value_component_rate_kinetics_variable_R` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_rate_kinetics_variable_T` may be invalid.\n      - Variable `value_component_rate_kinetics_variable_T` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_rate_kinetics_variable_A` may be invalid.\n      - Variable `value_component_rate_kinetics_variable_A` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_rate_kinetics_variable_time` may be invalid.\n      - Variable `value_component_rate_kinetics_variable_time` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_rate_kinetics_variable_C` may be invalid.\n      - Variable `value_component_rate_kinetics_variable_C` may be invalid.\n        - XPath could not be validated.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\n  - Model `model` may be invalid.\n    - The changes of the model may be invalid.\n      - Change 1 may be invalid.\n        - XPath could not be validated.\n      - Change 2 may be invalid.\n        - XPath could not be validated.\n      - Change 3 may be invalid.\n        - XPath could not be validated.\n      - Change 4 may be invalid.\n        - XPath could not be validated.\n      - Change 5 may be invalid.\n        - XPath could not be validated.\n      - Change 6 may be invalid.\n        - XPath could not be validated.\n      - Change 7 may be invalid.\n        - XPath could not be validated.\n      - Change 8 may be invalid.\n        - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_k2` may be invalid.\n    - Variable `value_component_moussa_variable_k2` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_k1` may be invalid.\n    - Variable `value_component_moussa_variable_k1` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_X1` may be invalid.\n    - Variable `value_component_moussa_variable_X1` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_X2` may be invalid.\n    - Variable `value_component_moussa_variable_X2` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_time` may be invalid.\n    - Variable `value_component_moussa_variable_time` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_A` may be invalid.\n    - Variable `value_component_moussa_variable_A` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_D` may be invalid.\n    - Variable `value_component_moussa_variable_D` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_R` may be invalid.\n    - Variable `value_component_moussa_variable_R` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_E1` may be invalid.\n    - Variable `value_component_moussa_variable_E1` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_E2` may be invalid.\n    - Variable `value_component_moussa_variable_E2` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_A1` may be invalid.\n    - Variable `value_component_moussa_variable_A1` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_A2` may be invalid.\n    - Variable `value_component_moussa_variable_A2` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_moussa_variable_T` may be invalid.\n    - Variable `value_component_moussa_variable_T` may be invalid.\n      - XPath could not be validated.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\n  - Model `model` may be invalid.\n    - The changes of the model may be invalid.\n      - Change 1 may be invalid.\n        - XPath could not be validated.\n      - Change 2 may be invalid.\n        - XPath could not be validated.\n      - Change 3 may be invalid.\n        - XPath could not be validated.\n      - Change 4 may be invalid.\n        - XPath could not be validated.\n      - Change 5 may be invalid.\n        - XPath could not be validated.\n      - Change 6 may be invalid.\n        - XPath could not be validated.\n      - Change 7 may be invalid.\n        - XPath could not be validated.\n      - Change 8 may be invalid.\n        - XPath could not be validated.\n      - Change 9 may be invalid.\n        - XPath could not be validated.\n      - Change 10 may be invalid.\n        - XPath could not be validated.\n      - Change 11 may be invalid.\n        - XPath could not be validated.\n      - Change 12 may be invalid.\n        - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_p` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_p` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_c` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_c` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_P0` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_P0` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_P1` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_P1` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_P2` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_P2` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_P3` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_P3` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_P4` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_P4` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_P5` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_P5` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_P6` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_P6` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_P7` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_P7` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_P8` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_P8` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_P9` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_P9` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_time` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_time` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_A` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_A` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_D` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_D` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_jung_10_lesions_variable_S` may be invalid.\n    - Variable `value_component_jung_10_lesions_variable_S` may be invalid.\n      - XPath could not be validated.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\n  - Model `model` may be invalid.\n    - The changes of the model may be invalid.\n      - Change 1 may be invalid.\n        - XPath could not be validated.\n      - Change 2 may be invalid.\n        - XPath could not be validated.\n      - Change 3 may be invalid.\n        - XPath could not be validated.\n      - Change 4 may be invalid.\n        - XPath could not be validated.\n      - Change 5 may be invalid.\n        - XPath could not be validated.\n      - Change 6 may be invalid.\n        - XPath could not be validated.\n  - Data generator `data_generator_value_component_equation_1_variable_A` may be invalid.\n    - Variable `value_component_equation_1_variable_A` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_equation_1_variable_D` may be invalid.\n    - Variable `value_component_equation_1_variable_D` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_equation_1_variable_kf` may be invalid.\n    - Variable `value_component_equation_1_variable_kf` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_equation_1_variable_kb` may be invalid.\n    - Variable `value_component_equation_1_variable_kb` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_equation_1_variable_time` may be invalid.\n    - Variable `value_component_equation_1_variable_time` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_equation_1_variable_kf_` may be invalid.\n    - Variable `value_component_equation_1_variable_kf_` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_equation_1_variable_Tk` may be invalid.\n    - Variable `value_component_equation_1_variable_Tk` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_equation_1_variable_T` may be invalid.\n    - Variable `value_component_equation_1_variable_T` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_equation_1_variable_V` may be invalid.\n    - Variable `value_component_equation_1_variable_V` may be invalid.\n      - XPath could not be validated.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\n  - Model `model` may be invalid.\n    - The changes of the model may be invalid.\n      - Change 1 may be invalid.\n        - XPath could not be validated.\n      - Change 2 may be invalid.\n        - XPath could not be validated.\n      - Change 3 may be invalid.\n        - XPath could not be validated.\n      - Change 4 may be invalid.\n        - XPath could not be validated.\n      - Change 5 may be invalid.\n        - XPath could not be validated.\n      - Change 6 may be invalid.\n        - XPath could not be validated.\n  - Data generator `data_generator_value_component_rate_kinetics_variable_k` may be invalid.\n    - Variable `value_component_rate_kinetics_variable_k` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_rate_kinetics_variable_E` may be invalid.\n    - Variable `value_component_rate_kinetics_variable_E` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_rate_kinetics_variable_R` may be invalid.\n    - Variable `value_component_rate_kinetics_variable_R` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_rate_kinetics_variable_T` may be invalid.\n    - Variable `value_component_rate_kinetics_variable_T` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_rate_kinetics_variable_A` may be invalid.\n    - Variable `value_component_rate_kinetics_variable_A` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_rate_kinetics_variable_time` may be invalid.\n    - Variable `value_component_rate_kinetics_variable_time` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_rate_kinetics_variable_C` may be invalid.\n    - Variable `value_component_rate_kinetics_variable_C` may be invalid.\n      - XPath could not be validated.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\nArchive contains 4 SED-ML documents with 4 models, 4 simulations, 4 tasks, 4 reports, and 0 plots:\n  simulation_0.sedml:\n    Tasks (1):\n      task\n    Reports (1):\n      report: 13 data sets\n  simulation_1.sedml:\n    Tasks (1):\n      task\n    Reports (1):\n      report: 16 data sets\n  simulation_2.sedml:\n    Tasks (1):\n      task\n    Reports (1):\n      report: 9 data sets\n  simulation_3.sedml:\n    Tasks (1):\n      task\n    Reports (1):\n      report: 7 data sets\n\nExecuting SED-ML file 1: simulation_0.sedml ...\nExecuting SED-ML file 2: simulation_1.sedml ...\nExecuting SED-ML file 3: simulation_2.sedml ...\nExecuting SED-ML file 4: simulation_3.sedml ...\n\nBundling outputs ...\nCleaning up ...\n\n============= SUMMARY =============\nExecuted 4 SED documents:\n  SED documents (4):\n    Succeeded: 4\n    Skipped: 0\n    Failed: 0\n  Tasks (4):\n    Succeeded: 4\n    Skipped: 0\n    Failed: 0\n  Outputs (4):\n    Succeeded: 4\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 41.5 KiB/41.5 KiB (456.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/rawLog.txt\nCompleted 56.4 KiB/56.4 KiB (611.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 94%)\n  adding: outputs/reports.h5 (deflated 90%)\n  adding: rawLog.txt (deflated 94%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nsrun: Job 4484002 step creation temporarily disabled, retrying\nsrun: Step created for job 4484002\nCompleted 59.1 KiB/59.1 KiB (635.3 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/outputs/reports.h5\nCompleted 12.1 KiB/54.6 KiB (144.3 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/output.zip\nCompleted 12.1 KiB/54.6 KiB (144.3 KiB/s) with 1 file(s) remaining\rCompleted 54.6 KiB/54.6 KiB (385.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/moussa.cellml  \n  inflating: contents/index.html     \n  inflating: contents/jung-10-lesion.cellml  \n  inflating: contents/oneill-2011-documentation.html  \n  inflating: contents/cell-death-schem.png  \n  inflating: contents/cell-death-schem.svg  \n  inflating: contents/moussa-documentation.html  \n  inflating: contents/jung-10-lesion-documentation.html  \n  inflating: contents/arrhenius-cell-death-documentation.html  \n  inflating: contents/oneill_cell_death_fast.cellml  \n  inflating: contents/oneill-fig.png  \n  inflating: contents/arrhenius-cell-death.cellml  \n  inflating: contents/simulation_0.sedml  \n  inflating: contents/simulation_1.sedml  \n  inflating: contents/simulation_2.sedml  \n  inflating: contents/simulation_3.sedml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 2.2 KiB/125.9 KiB (23.2 KiB/s) with 18 file(s) remaining\rupload: contents/arrhenius-cell-death-documentation.html to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/contents/arrhenius-cell-death-documentation.html\nCompleted 2.2 KiB/125.9 KiB (23.2 KiB/s) with 17 file(s) remaining\rCompleted 4.3 KiB/125.9 KiB (31.8 KiB/s) with 17 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/contents/manifest.xml\nCompleted 4.3 KiB/125.9 KiB (31.8 KiB/s) with 16 file(s) remaining\rCompleted 7.3 KiB/125.9 KiB (47.2 KiB/s) with 16 file(s) remaining\rupload: contents/moussa.cellml to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/contents/moussa.cellml\nCompleted 7.3 KiB/125.9 KiB (47.2 KiB/s) with 15 file(s) remaining\rCompleted 28.8 KiB/125.9 KiB (183.5 KiB/s) with 15 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/contents/metadata.rdf\nCompleted 28.8 KiB/125.9 KiB (183.5 KiB/s) with 14 file(s) remaining\rCompleted 31.7 KiB/125.9 KiB (196.8 KiB/s) with 14 file(s) remaining\rCompleted 44.5 KiB/125.9 KiB (263.9 KiB/s) with 14 file(s) remaining\rupload: contents/simulation_0.sedml to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/contents/simulation_0.sedml\nCompleted 44.5 KiB/125.9 KiB (263.9 KiB/s) with 13 file(s) remaining\rupload: contents/oneill-2011-documentation.html to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/contents/oneill-2011-documentation.html\nCompleted 44.5 KiB/125.9 KiB (263.9 KiB/s) with 12 file(s) remaining\rCompleted 58.2 KiB/125.9 KiB (314.4 KiB/s) with 12 file(s) remaining\rupload: contents/cell-death-schem.png to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/contents/cell-death-schem.png\nCompleted 58.2 KiB/125.9 KiB (314.4 KiB/s) with 11 file(s) remaining\rCompleted 69.0 KiB/125.9 KiB (341.4 KiB/s) with 11 file(s) remaining\rupload: contents/cell-death-schem.svg to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/contents/cell-death-schem.svg\nCompleted 69.0 KiB/125.9 KiB (341.4 KiB/s) with 10 file(s) remaining\rCompleted 86.4 KiB/125.9 KiB (409.6 KiB/s) with 10 file(s) remaining\rupload: contents/simulation_1.sedml to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/contents/simulation_1.sedml\nCompleted 86.4 KiB/125.9 KiB (409.6 KiB/s) with 9 file(s) remaining\rCompleted 92.1 KiB/125.9 KiB (430.2 KiB/s) with 9 file(s) remaining\rupload: contents/oneill-fig.png to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/contents/oneill-fig.png\nCompleted 92.1 KiB/125.9 KiB (430.2 KiB/s) with 8 file(s) remaining\rCompleted 93.9 KiB/125.9 KiB (393.9 KiB/s) with 8 file(s) remaining\rupload: contents/moussa-documentation.html to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/contents/moussa-documentation.html\nCompleted 93.9 KiB/125.9 KiB (393.9 KiB/s) with 7 file(s) remaining\rCompleted 96.6 KiB/125.9 KiB (400.2 KiB/s) with 7 file(s) remaining\rupload: contents/oneill_cell_death_fast.cellml to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/contents/oneill_cell_death_fast.cellml\nCompleted 96.6 KiB/125.9 KiB (400.2 KiB/s) with 6 file(s) remaining\rCompleted 106.2 KiB/125.9 KiB (418.6 KiB/s) with 6 file(s) remaining\rupload: contents/simulation_2.sedml to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/contents/simulation_2.sedml\nCompleted 106.2 KiB/125.9 KiB (418.6 KiB/s) with 5 file(s) remaining\rCompleted 107.5 KiB/125.9 KiB (419.0 KiB/s) with 5 file(s) remaining\rupload: contents/arrhenius-cell-death.cellml to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/contents/arrhenius-cell-death.cellml\nCompleted 107.5 KiB/125.9 KiB (419.0 KiB/s) with 4 file(s) remaining\rCompleted 115.6 KiB/125.9 KiB (427.8 KiB/s) with 4 file(s) remaining\rupload: contents/simulation_3.sedml to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/contents/simulation_3.sedml\nCompleted 115.6 KiB/125.9 KiB (427.8 KiB/s) with 3 file(s) remaining\rCompleted 120.7 KiB/125.9 KiB (435.3 KiB/s) with 3 file(s) remaining\rupload: contents/jung-10-lesion.cellml to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/contents/jung-10-lesion.cellml\nCompleted 120.7 KiB/125.9 KiB (435.3 KiB/s) with 2 file(s) remaining\rCompleted 122.6 KiB/125.9 KiB (413.6 KiB/s) with 2 file(s) remaining\rupload: contents/index.html to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/contents/index.html\nCompleted 122.6 KiB/125.9 KiB (413.6 KiB/s) with 1 file(s) remaining\rCompleted 125.9 KiB/125.9 KiB (389.3 KiB/s) with 1 file(s) remaining\rupload: contents/jung-10-lesion-documentation.html to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/contents/jung-10-lesion-documentation.html\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 48.8 KiB/48.8 KiB (360.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/62617429abe612c540c67bc3/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /simulation_0.sedml\ncreating dataset /simulation_0.sedml/report, shape: (13, 11), type: float64\ndataset created, uuid: d-d7ab1b20-02837ff9-b1ee-896c63-6a800a, chunk_size: (13, 11)\ncreating group /simulation_1.sedml\ncreating dataset /simulation_1.sedml/report, shape: (16, 11), type: float64\ndataset created, uuid: d-d7ab1b20-02837ff9-c52c-0fcf3f-ba40a3, chunk_size: (16, 11)\ncreating group /simulation_2.sedml\ncreating dataset /simulation_2.sedml/report, shape: (9, 11), type: float64\ndataset created, uuid: d-d7ab1b20-02837ff9-b846-0d858c-1d1571, chunk_size: (9, 11)\ncreating group /simulation_3.sedml\ncreating dataset /simulation_3.sedml/report, shape: (7, 11), type: float64\ndataset created, uuid: d-d7ab1b20-02837ff9-a6ac-fd16d4-798e84, chunk_size: (7, 11)\ncreating attribute combineArchiveLocation in /simulation_0.sedml\ncreating attribute uri in /simulation_0.sedml\ncreating attribute _type in /simulation_0.sedml/report\ncreating attribute sedmlDataSetDataTypes in /simulation_0.sedml/report\ncreating attribute sedmlDataSetIds in /simulation_0.sedml/report\ncreating attribute sedmlDataSetLabels in /simulation_0.sedml/report\ncreating attribute sedmlDataSetNames in /simulation_0.sedml/report\ncreating attribute sedmlDataSetShapes in /simulation_0.sedml/report\ncreating attribute sedmlId in /simulation_0.sedml/report\ncreating attribute uri in /simulation_0.sedml/report\ncreating attribute combineArchiveLocation in /simulation_1.sedml\ncreating attribute uri in /simulation_1.sedml\ncreating attribute _type in /simulation_1.sedml/report\ncreating attribute sedmlDataSetDataTypes in /simulation_1.sedml/report\ncreating attribute sedmlDataSetIds in /simulation_1.sedml/report\ncreating attribute sedmlDataSetLabels in /simulation_1.sedml/report\ncreating attribute sedmlDataSetNames in /simulation_1.sedml/report\ncreating attribute sedmlDataSetShapes in /simulation_1.sedml/report\ncreating attribute sedmlId in /simulation_1.sedml/report\ncreating attribute uri in /simulation_1.sedml/report\ncreating attribute combineArchiveLocation in /simulation_2.sedml\ncreating attribute uri in /simulation_2.sedml\ncreating attribute _type in /simulation_2.sedml/report\ncreating attribute sedmlDataSetDataTypes in /simulation_2.sedml/report\ncreating attribute sedmlDataSetIds in /simulation_2.sedml/report\ncreating attribute sedmlDataSetLabels in /simulation_2.sedml/report\ncreating attribute sedmlDataSetNames in /simulation_2.sedml/report\ncreating attribute sedmlDataSetShapes in /simulation_2.sedml/report\ncreating attribute sedmlId in /simulation_2.sedml/report\ncreating attribute uri in /simulation_2.sedml/report\ncreating attribute combineArchiveLocation in /simulation_3.sedml\ncreating attribute uri in /simulation_3.sedml\ncreating attribute _type in /simulation_3.sedml/report\ncreating attribute sedmlDataSetDataTypes in /simulation_3.sedml/report\ncreating attribute sedmlDataSetIds in /simulation_3.sedml/report\ncreating attribute sedmlDataSetLabels in /simulation_3.sedml/report\ncreating attribute sedmlDataSetNames in /simulation_3.sedml/report\ncreating attribute sedmlDataSetShapes in /simulation_3.sedml/report\ncreating attribute sedmlId in /simulation_3.sedml/report\ncreating attribute uri in /simulation_3.sedml/report\ncreate_links: /\ngot link: simulation_0.sedml\ngot link: simulation_1.sedml\ngot link: simulation_2.sedml\ngot link: simulation_3.sedml\ncreate_links: /simulation_0.sedml\ngot link: report\ncreate_links: /simulation_1.sedml\ngot link: report\ncreate_links: /simulation_2.sedml\ngot link: report\ncreate_links: /simulation_3.sedml\ngot link: report\nwrite_dataset src: /simulation_0.sedml/report to tgt: /simulation_0.sedml/report, shape: (13, 11), type: float64\niterating over chunks for /simulation_0.sedml/report\nwriting dataset data for slice: (slice(0, 13, 1), slice(0, 11, 1))\ndone with dataload for /simulation_0.sedml/report\nwrite_dataset src: /simulation_1.sedml/report to tgt: /simulation_1.sedml/report, shape: (16, 11), type: float64\niterating over chunks for /simulation_1.sedml/report\nwriting dataset data for slice: (slice(0, 16, 1), slice(0, 11, 1))\ndone with dataload for /simulation_1.sedml/report\nwrite_dataset src: /simulation_2.sedml/report to tgt: /simulation_2.sedml/report, shape: (9, 11), type: float64\niterating over chunks for /simulation_2.sedml/report\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 11, 1))\ndone with dataload for /simulation_2.sedml/report\nwrite_dataset src: /simulation_3.sedml/report to tgt: /simulation_3.sedml/report, shape: (7, 11), type: float64\niterating over chunks for /simulation_3.sedml/report\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 11, 1))\ndone with dataload for /simulation_3.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/62617429abe612c540c67bc3\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... succeeded.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess the manifest file in the COMBINE archive ... succeeded.\nRead the manifest and post the files to the API ... succeeded.\nCreate thumbnails from the images specified in the manifest ... succeeded.\nPost thumbnails to the API ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":3.105679,"sedDocuments":[{"location":"simulation_0.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"  Found 1 tasks and 1 outputs:\n    Tasks:\n      `task`\n    Outputs:\n      `report`\n  Executing task 1: `task`\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\n    Generating 1 outputs ...\n      Generating output 1: `report` ... \u001b[34msucceeded\u001b[0m\n\n  Executed 1 tasks and 1 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n","duration":0.806411,"tasks":[{"id":"task","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `value_component_moussa_variable_k1` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_moussa_variable_R` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_moussa_variable_A1` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_moussa_variable_time` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_moussa_variable_A2` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_moussa_variable_D` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_moussa_variable_E2` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_moussa_variable_X1` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_moussa_variable_k2` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_moussa_variable_T` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_moussa_variable_X2` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_moussa_variable_A` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_moussa_variable_E1` may be invalid.\n  - XPath could not be validated.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\n  - The following tasks do not contribute to outputs:\n    - `repeatedTask`\n    - `task1`\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n","duration":0.673818,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"OpenCOR.SimulationSupport.Simulation.run"},{"key":"algorithmParameters","value":[]}]}],"outputs":[{"id":"report","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.028956,"dataSets":[{"id":"data_set_value_component_moussa_variable_k2","status":"SUCCEEDED"},{"id":"data_set_value_component_moussa_variable_k1","status":"SUCCEEDED"},{"id":"data_set_value_component_moussa_variable_X1","status":"SUCCEEDED"},{"id":"data_set_value_component_moussa_variable_X2","status":"SUCCEEDED"},{"id":"data_set_value_component_moussa_variable_time","status":"SUCCEEDED"},{"id":"data_set_value_component_moussa_variable_A","status":"SUCCEEDED"},{"id":"data_set_value_component_moussa_variable_D","status":"SUCCEEDED"},{"id":"data_set_value_component_moussa_variable_R","status":"SUCCEEDED"},{"id":"data_set_value_component_moussa_variable_E1","status":"SUCCEEDED"},{"id":"data_set_value_component_moussa_variable_E2","status":"SUCCEEDED"},{"id":"data_set_value_component_moussa_variable_A1","status":"SUCCEEDED"},{"id":"data_set_value_component_moussa_variable_A2","status":"SUCCEEDED"},{"id":"data_set_value_component_moussa_variable_T","status":"SUCCEEDED"}]}]},{"location":"simulation_1.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"  Found 1 tasks and 1 outputs:\n    Tasks:\n      `task`\n    Outputs:\n      `report`\n  Executing task 1: `task`\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\n    Generating 1 outputs ...\n      Generating output 1: `report` ... \u001b[34msucceeded\u001b[0m\n\n  Executed 1 tasks and 1 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n","duration":0.511952,"tasks":[{"id":"task","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `value_component_jung_10_lesions_variable_p` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_jung_10_lesions_variable_P5` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_jung_10_lesions_variable_P1` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_jung_10_lesions_variable_D` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_jung_10_lesions_variable_c` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_jung_10_lesions_variable_A` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_jung_10_lesions_variable_time` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_jung_10_lesions_variable_P9` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_jung_10_lesions_variable_S` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_jung_10_lesions_variable_P7` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_jung_10_lesions_variable_P3` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_jung_10_lesions_variable_P8` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_jung_10_lesions_variable_P4` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_jung_10_lesions_variable_P6` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_jung_10_lesions_variable_P2` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_jung_10_lesions_variable_P0` may be invalid.\n  - XPath could not be validated.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n","duration":0.37391,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"OpenCOR.SimulationSupport.Simulation.run"},{"key":"algorithmParameters","value":[]}]}],"outputs":[{"id":"report","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.024798,"dataSets":[{"id":"data_set_value_component_jung_10_lesions_variable_p","status":"SUCCEEDED"},{"id":"data_set_value_component_jung_10_lesions_variable_c","status":"SUCCEEDED"},{"id":"data_set_value_component_jung_10_lesions_variable_P0","status":"SUCCEEDED"},{"id":"data_set_value_component_jung_10_lesions_variable_P1","status":"SUCCEEDED"},{"id":"data_set_value_component_jung_10_lesions_variable_P2","status":"SUCCEEDED"},{"id":"data_set_value_component_jung_10_lesions_variable_P3","status":"SUCCEEDED"},{"id":"data_set_value_component_jung_10_lesions_variable_P4","status":"SUCCEEDED"},{"id":"data_set_value_component_jung_10_lesions_variable_P5","status":"SUCCEEDED"},{"id":"data_set_value_component_jung_10_lesions_variable_P6","status":"SUCCEEDED"},{"id":"data_set_value_component_jung_10_lesions_variable_P7","status":"SUCCEEDED"},{"id":"data_set_value_component_jung_10_lesions_variable_P8","status":"SUCCEEDED"},{"id":"data_set_value_component_jung_10_lesions_variable_P9","status":"SUCCEEDED"},{"id":"data_set_value_component_jung_10_lesions_variable_time","status":"SUCCEEDED"},{"id":"data_set_value_component_jung_10_lesions_variable_A","status":"SUCCEEDED"},{"id":"data_set_value_component_jung_10_lesions_variable_D","status":"SUCCEEDED"},{"id":"data_set_value_component_jung_10_lesions_variable_S","status":"SUCCEEDED"}]}]},{"location":"simulation_2.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"  Found 1 tasks and 1 outputs:\n    Tasks:\n      `task`\n    Outputs:\n      `report`\n  Executing task 1: `task`\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\n    Generating 1 outputs ...\n      Generating output 1: `report` ... \u001b[34msucceeded\u001b[0m\n\n  Executed 1 tasks and 1 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n","duration":0.49396,"tasks":[{"id":"task","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `value_component_equation_1_variable_kf_` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_equation_1_variable_D` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_equation_1_variable_V` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_equation_1_variable_kf` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_equation_1_variable_time` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_equation_1_variable_kb` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_equation_1_variable_A` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_equation_1_variable_Tk` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_equation_1_variable_T` may be invalid.\n  - XPath could not be validated.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n","duration":0.36264,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"OpenCOR.SimulationSupport.Simulation.run"},{"key":"algorithmParameters","value":[]}]}],"outputs":[{"id":"report","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.01526,"dataSets":[{"id":"data_set_value_component_equation_1_variable_A","status":"SUCCEEDED"},{"id":"data_set_value_component_equation_1_variable_D","status":"SUCCEEDED"},{"id":"data_set_value_component_equation_1_variable_kf","status":"SUCCEEDED"},{"id":"data_set_value_component_equation_1_variable_kb","status":"SUCCEEDED"},{"id":"data_set_value_component_equation_1_variable_time","status":"SUCCEEDED"},{"id":"data_set_value_component_equation_1_variable_kf_","status":"SUCCEEDED"},{"id":"data_set_value_component_equation_1_variable_Tk","status":"SUCCEEDED"},{"id":"data_set_value_component_equation_1_variable_T","status":"SUCCEEDED"},{"id":"data_set_value_component_equation_1_variable_V","status":"SUCCEEDED"}]}]},{"location":"simulation_3.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"  Found 1 tasks and 1 outputs:\n    Tasks:\n      `task`\n    Outputs:\n      `report`\n  Executing task 1: `task`\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\n    Generating 1 outputs ...\n      Generating output 1: `report` ... \u001b[34msucceeded\u001b[0m\n\n  Executed 1 tasks and 1 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n","duration":0.526686,"tasks":[{"id":"task","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `value_component_rate_kinetics_variable_k` may be invalid.\n  - 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