{"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    458      0 --:--:-- --:--:-- --:--:--   460\n\r100  377k  100  377k    0     0   837k      0 --:--:-- --:--:-- --:--:--  837k\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 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      - Change 13 may be invalid.\n        - XPath could not be validated.\n      - Change 14 may be invalid.\n        - XPath could not be validated.\n      - Change 15 may be invalid.\n        - XPath could not be validated.\n      - Change 16 may be invalid.\n        - XPath could not be validated.\n      - Change 17 may be invalid.\n        - XPath could not be validated.\n      - Change 18 may be invalid.\n        - XPath could not be validated.\n      - Change 19 may be invalid.\n        - XPath could not be validated.\n      - Change 20 may be invalid.\n        - XPath could not be validated.\n      - Change 21 may be invalid.\n        - XPath could not be validated.\n      - Change 22 may be invalid.\n        - XPath could not be validated.\n      - Change 23 may be invalid.\n        - XPath could not be validated.\n      - Change 24 may be invalid.\n        - XPath could not be validated.\n      - Change 25 may be invalid.\n        - XPath could not be validated.\n      - Change 26 may be invalid.\n        - XPath could not be validated.\n      - Change 27 may be invalid.\n        - XPath could not be validated.\n      - Change 28 may be invalid.\n        - XPath could not be validated.\n      - Change 29 may be invalid.\n        - XPath could not be validated.\n      - Change 30 may be invalid.\n        - XPath could not be validated.\n      - Change 31 may be invalid.\n        - XPath could not be validated.\n      - Change 32 may be invalid.\n        - XPath could not be validated.\n  - Data generator `data_generator_value_component_environment_variable_time` may be invalid.\n    - Variable `value_component_environment_variable_time` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_k_0` may be invalid.\n    - Variable `value_component_Constants_variable_k_0` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_k_1` may be invalid.\n    - Variable `value_component_Constants_variable_k_1` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_k_2` may be invalid.\n    - Variable `value_component_Constants_variable_k_2` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_k_3` may be invalid.\n    - Variable `value_component_Constants_variable_k_3` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_k_4` may be invalid.\n    - Variable `value_component_Constants_variable_k_4` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_k_5` may be invalid.\n    - Variable `value_component_Constants_variable_k_5` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_k_6` may be invalid.\n    - Variable `value_component_Constants_variable_k_6` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_k_7` may be invalid.\n    - Variable `value_component_Constants_variable_k_7` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_k_8` may be invalid.\n    - Variable `value_component_Constants_variable_k_8` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_k_9` may be invalid.\n    - Variable `value_component_Constants_variable_k_9` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_k_10` may be invalid.\n    - Variable `value_component_Constants_variable_k_10` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_k_11` may be invalid.\n    - Variable `value_component_Constants_variable_k_11` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_C_PLC_T` may be invalid.\n    - Variable `value_component_Constants_variable_C_PLC_T` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_K_D` may be invalid.\n    - Variable `value_component_Constants_variable_K_D` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_K_P` may be invalid.\n    - Variable `value_component_Constants_variable_K_P` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_K_R` may be invalid.\n    - Variable `value_component_Constants_variable_K_R` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_K_G` may be invalid.\n    - Variable `value_component_Constants_variable_K_G` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_K_S` may be invalid.\n    - Variable `value_component_Constants_variable_K_S` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_K_ER` may be invalid.\n    - Variable `value_component_Constants_variable_K_ER` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_K_C1` may be invalid.\n    - Variable `value_component_Constants_variable_K_C1` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_K_C2` may be invalid.\n    - Variable `value_component_Constants_variable_K_C2` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_beta` may be invalid.\n    - Variable `value_component_Constants_variable_beta` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_lambda` may be invalid.\n    - Variable `value_component_Constants_variable_lambda` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_rho` may be invalid.\n    - Variable `value_component_Constants_variable_rho` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_n` may be invalid.\n    - Variable `value_component_Constants_variable_n` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_m` may be invalid.\n    - Variable `value_component_Constants_variable_m` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_Constants_variable_w` may be invalid.\n    - Variable `value_component_Constants_variable_w` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_R_values_variable_R_APLC` may be invalid.\n    - Variable `value_component_R_values_variable_R_APLC` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_R_values_variable_R_PKC` may be invalid.\n    - Variable `value_component_R_values_variable_R_PKC` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_R_values_variable_R_G` may be invalid.\n    - Variable `value_component_R_values_variable_R_G` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_R_values_variable_R_DG` may be invalid.\n    - Variable `value_component_R_values_variable_R_DG` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_R_values_variable_R_IP_3` may be invalid.\n    - Variable `value_component_R_values_variable_R_IP_3` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_R_values_variable_R_Cyt1` may be invalid.\n    - Variable `value_component_R_values_variable_R_Cyt1` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_R_values_variable_R_Cyt2` may be invalid.\n    - Variable `value_component_R_values_variable_R_Cyt2` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_R_values_variable_R_ER` may be invalid.\n    - Variable `value_component_R_values_variable_R_ER` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_G_GTP_variable_G` may be invalid.\n    - Variable `value_component_G_GTP_variable_G` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_APLC_variable_APLC` may be invalid.\n    - Variable `value_component_APLC_variable_APLC` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_APLC_variable_PLC` may be invalid.\n    - Variable `value_component_APLC_variable_PLC` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_IP_3_variable_IP_3` may be invalid.\n    - Variable `value_component_IP_3_variable_IP_3` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_DG_variable_DG` may be invalid.\n    - Variable `value_component_DG_variable_DG` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_C_cyt_variable_C_cyt` may be invalid.\n    - Variable `value_component_C_cyt_variable_C_cyt` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_C_ER_variable_C_ER` may be invalid.\n    - Variable `value_component_C_ER_variable_C_ER` 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 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        - Change 13 may be invalid.\n          - XPath could not be validated.\n        - Change 14 may be invalid.\n          - XPath could not be validated.\n        - Change 15 may be invalid.\n          - XPath could not be validated.\n        - Change 16 may be invalid.\n          - XPath could not be validated.\n        - Change 17 may be invalid.\n          - XPath could not be validated.\n        - Change 18 may be invalid.\n          - XPath could not be validated.\n        - Change 19 may be invalid.\n          - XPath could not be validated.\n        - Change 20 may be invalid.\n          - XPath could not be validated.\n        - Change 21 may be invalid.\n          - XPath could not be validated.\n        - Change 22 may be invalid.\n          - XPath could not be validated.\n        - Change 23 may be invalid.\n          - XPath could not be validated.\n        - Change 24 may be invalid.\n          - XPath could not be validated.\n        - Change 25 may be invalid.\n          - XPath could not be validated.\n        - Change 26 may be invalid.\n          - XPath could not be validated.\n        - Change 27 may be invalid.\n          - XPath could not be validated.\n        - Change 28 may be invalid.\n          - XPath could not be validated.\n        - Change 29 may be invalid.\n          - XPath could not be validated.\n        - Change 30 may be invalid.\n          - XPath could not be validated.\n        - Change 31 may be invalid.\n          - XPath could not be validated.\n        - Change 32 may be invalid.\n          - XPath could not be validated.\n    - Data generator `data_generator_value_component_environment_variable_time` may be invalid.\n      - Variable `value_component_environment_variable_time` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_k_0` may be invalid.\n      - Variable `value_component_Constants_variable_k_0` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_k_1` may be invalid.\n      - Variable `value_component_Constants_variable_k_1` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_k_2` may be invalid.\n      - Variable `value_component_Constants_variable_k_2` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_k_3` may be invalid.\n      - Variable `value_component_Constants_variable_k_3` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_k_4` may be invalid.\n      - Variable `value_component_Constants_variable_k_4` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_k_5` may be invalid.\n      - Variable `value_component_Constants_variable_k_5` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_k_6` may be invalid.\n      - Variable `value_component_Constants_variable_k_6` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_k_7` may be invalid.\n      - Variable `value_component_Constants_variable_k_7` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_k_8` may be invalid.\n      - Variable `value_component_Constants_variable_k_8` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_k_9` may be invalid.\n      - Variable `value_component_Constants_variable_k_9` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_k_10` may be invalid.\n      - Variable `value_component_Constants_variable_k_10` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_k_11` may be invalid.\n      - Variable `value_component_Constants_variable_k_11` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_C_PLC_T` may be invalid.\n      - Variable `value_component_Constants_variable_C_PLC_T` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_K_D` may be invalid.\n      - Variable `value_component_Constants_variable_K_D` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_K_P` may be invalid.\n      - Variable `value_component_Constants_variable_K_P` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_K_R` may be invalid.\n      - Variable `value_component_Constants_variable_K_R` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_K_G` may be invalid.\n      - Variable `value_component_Constants_variable_K_G` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_K_S` may be invalid.\n      - Variable `value_component_Constants_variable_K_S` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_K_ER` may be invalid.\n      - Variable `value_component_Constants_variable_K_ER` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_K_C1` may be invalid.\n      - Variable `value_component_Constants_variable_K_C1` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_K_C2` may be invalid.\n      - Variable `value_component_Constants_variable_K_C2` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_beta` may be invalid.\n      - Variable `value_component_Constants_variable_beta` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_lambda` may be invalid.\n      - Variable `value_component_Constants_variable_lambda` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_rho` may be invalid.\n      - Variable `value_component_Constants_variable_rho` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_n` may be invalid.\n      - Variable `value_component_Constants_variable_n` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_m` may be invalid.\n      - Variable `value_component_Constants_variable_m` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_Constants_variable_w` may be invalid.\n      - Variable `value_component_Constants_variable_w` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_R_values_variable_R_APLC` may be invalid.\n      - Variable `value_component_R_values_variable_R_APLC` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_R_values_variable_R_PKC` may be invalid.\n      - Variable `value_component_R_values_variable_R_PKC` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_R_values_variable_R_G` may be invalid.\n      - Variable `value_component_R_values_variable_R_G` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_R_values_variable_R_DG` may be invalid.\n      - Variable `value_component_R_values_variable_R_DG` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_R_values_variable_R_IP_3` may be invalid.\n      - Variable `value_component_R_values_variable_R_IP_3` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_R_values_variable_R_Cyt1` may be invalid.\n      - Variable `value_component_R_values_variable_R_Cyt1` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_R_values_variable_R_Cyt2` may be invalid.\n      - Variable `value_component_R_values_variable_R_Cyt2` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_R_values_variable_R_ER` may be invalid.\n      - Variable `value_component_R_values_variable_R_ER` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_G_GTP_variable_G` may be invalid.\n      - Variable `value_component_G_GTP_variable_G` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_APLC_variable_APLC` may be invalid.\n      - Variable `value_component_APLC_variable_APLC` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_APLC_variable_PLC` may be invalid.\n      - Variable `value_component_APLC_variable_PLC` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_IP_3_variable_IP_3` may be invalid.\n      - Variable `value_component_IP_3_variable_IP_3` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_DG_variable_DG` may be invalid.\n      - Variable `value_component_DG_variable_DG` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_C_cyt_variable_C_cyt` may be invalid.\n      - Variable `value_component_C_cyt_variable_C_cyt` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_C_ER_variable_C_ER` may be invalid.\n      - Variable `value_component_C_ER_variable_C_ER` may be invalid.\n        - XPath could not be validated.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\nArchive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\n  simulation_0.sedml:\n    Tasks (1):\n      task\n    Reports (1):\n      report: 43 data sets\n\nExecuting SED-ML file 1: simulation_0.sedml ...\n\nBundling outputs ...\nCleaning up ...\n\n============= SUMMARY =============\nExecuted 1 SED documents:\n  SED documents (1):\n    Succeeded: 1\n    Skipped: 0\n    Failed: 0\n  Tasks (1):\n    Succeeded: 1\n    Skipped: 0\n    Failed: 0\n  Outputs (1):\n    Succeeded: 1\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 25.3 KiB/25.3 KiB (289.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/626178874679625b3246fefb/rawLog.txt\nCompleted 34.9 KiB/34.9 KiB (420.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/626178874679625b3246fefb/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 92%)\n  adding: outputs/reports.h5 (deflated 83%)\n  adding: rawLog.txt (deflated 91%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 24.3 KiB/24.3 KiB (256.4 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/626178874679625b3246fefb/outputs/reports.h5\nCompleted 9.6 KiB/35.8 KiB (68.0 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/626178874679625b3246fefb/output.zip\nCompleted 9.6 KiB/35.8 KiB (68.0 KiB/s) with 1 file(s) remaining\rCompleted 35.8 KiB/35.8 KiB (194.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/626178874679625b3246fefb/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/wang_2006.session.xml  \n  inflating: contents/wang_2006.ai   \n  inflating: contents/wang_2006.png  \n  inflating: contents/wang_2006.xul  \n  inflating: contents/wang_2006.svg  \n  inflating: contents/wang_2006.cellml  \n  inflating: contents/simulation_0.sedml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 1.0 KiB/911.0 KiB (8.1 KiB/s) with 9 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/626178874679625b3246fefb/contents/manifest.xml\nCompleted 1.0 KiB/911.0 KiB (8.1 KiB/s) with 8 file(s) remaining\rCompleted 228.3 KiB/911.0 KiB (1.4 MiB/s) with 8 file(s) remaining\rupload: contents/wang_2006.svg to s3://files.biosimulations.org/simulations/626178874679625b3246fefb/contents/wang_2006.svg\nCompleted 228.3 KiB/911.0 KiB (1.4 MiB/s) with 7 file(s) remaining\rCompleted 271.4 KiB/911.0 KiB (1.7 MiB/s) with 7 file(s) remaining\rupload: contents/simulation_0.sedml to s3://files.biosimulations.org/simulations/626178874679625b3246fefb/contents/simulation_0.sedml\nCompleted 271.4 KiB/911.0 KiB (1.7 MiB/s) with 6 file(s) remaining\rCompleted 506.6 KiB/911.0 KiB (3.0 MiB/s) with 6 file(s) remaining\rupload: contents/wang_2006.xul to s3://files.biosimulations.org/simulations/626178874679625b3246fefb/contents/wang_2006.xul\nCompleted 506.6 KiB/911.0 KiB (3.0 MiB/s) with 5 file(s) remaining\rCompleted 669.4 KiB/911.0 KiB (3.6 MiB/s) with 5 file(s) remaining\rupload: contents/wang_2006.png to s3://files.biosimulations.org/simulations/626178874679625b3246fefb/contents/wang_2006.png\nCompleted 669.4 KiB/911.0 KiB (3.6 MiB/s) with 4 file(s) remaining\rCompleted 851.5 KiB/911.0 KiB (4.5 MiB/s) with 4 file(s) remaining\rupload: contents/wang_2006.ai to s3://files.biosimulations.org/simulations/626178874679625b3246fefb/contents/wang_2006.ai\nCompleted 851.5 KiB/911.0 KiB (4.5 MiB/s) with 3 file(s) remaining\rCompleted 868.4 KiB/911.0 KiB (4.5 MiB/s) with 3 file(s) remaining\rupload: contents/wang_2006.session.xml to s3://files.biosimulations.org/simulations/626178874679625b3246fefb/contents/wang_2006.session.xml\nCompleted 868.4 KiB/911.0 KiB (4.5 MiB/s) with 2 file(s) remaining\rCompleted 899.3 KiB/911.0 KiB (4.4 MiB/s) with 2 file(s) remaining\rupload: contents/wang_2006.cellml to s3://files.biosimulations.org/simulations/626178874679625b3246fefb/contents/wang_2006.cellml\nCompleted 899.3 KiB/911.0 KiB (4.4 MiB/s) with 1 file(s) remaining\rCompleted 911.0 KiB/911.0 KiB (3.6 MiB/s) with 1 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/626178874679625b3246fefb/contents/metadata.rdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 29.4 KiB/29.4 KiB (305.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/626178874679625b3246fefb/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /simulation_0.sedml\ncreating dataset /simulation_0.sedml/report, shape: (43, 11), type: float64\ndataset created, uuid: d-e1398375-fbe158a9-9b08-3f6783-f51caa, chunk_size: (43, 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\ncreate_links: /\ngot link: simulation_0.sedml\ncreate_links: /simulation_0.sedml\ngot link: report\nwrite_dataset src: /simulation_0.sedml/report to tgt: /simulation_0.sedml/report, shape: (43, 11), type: float64\niterating over chunks for /simulation_0.sedml/report\nwriting dataset data for slice: (slice(0, 43, 1), slice(0, 11, 1))\ndone with dataload for /simulation_0.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/626178874679625b3246fefb\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.434472,"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":0.852149,"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_Constants_variable_K_C1` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_R_values_variable_R_G` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_k_7` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_lambda` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_K_C2` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_k_9` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_R_values_variable_R_PKC` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_R_values_variable_R_Cyt2` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_k_10` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_R_values_variable_R_DG` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_IP_3_variable_IP_3` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_APLC_variable_APLC` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_k_1` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_rho` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_K_S` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_K_P` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_R_values_variable_R_IP_3` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_k_3` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_APLC_variable_PLC` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_K_G` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_R_values_variable_R_Cyt1` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_DG_variable_DG` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_environment_variable_time` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_R_values_variable_R_APLC` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_C_PLC_T` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_n` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_k_6` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_C_cyt_variable_C_cyt` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_C_ER_variable_C_ER` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_R_values_variable_R_ER` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_k_11` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_k_2` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_m` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_K_D` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_K_ER` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_w` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_k_5` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_k_8` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_beta` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_k_0` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_G_GTP_variable_G` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_k_4` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_Constants_variable_K_R` 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":0.696902,"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":0.033925,"dataSets":[{"id":"data_set_value_component_environment_variable_time","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_k_0","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_k_1","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_k_2","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_k_3","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_k_4","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_k_5","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_k_6","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_k_7","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_k_8","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_k_9","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_k_10","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_k_11","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_C_PLC_T","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_K_D","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_K_P","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_K_R","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_K_G","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_K_S","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_K_ER","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_K_C1","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_K_C2","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_beta","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_lambda","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_rho","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_n","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_m","status":"SUCCEEDED"},{"id":"data_set_value_component_Constants_variable_w","status":"SUCCEEDED"},{"id":"data_set_value_component_R_values_variable_R_APLC","status":"SUCCEEDED"},{"id":"data_set_value_component_R_values_variable_R_PKC","status":"SUCCEEDED"},{"id":"data_set_value_component_R_values_variable_R_G","status":"SUCCEEDED"},{"id":"data_set_value_component_R_values_variable_R_DG","status":"SUCCEEDED"},{"id":"data_set_value_component_R_values_variable_R_IP_3","status":"SUCCEEDED"},{"id":"data_set_value_component_R_values_variable_R_Cyt1","status":"SUCCEEDED"},{"id":"data_set_value_component_R_values_variable_R_Cyt2","status":"SUCCEEDED"},{"id":"data_set_value_component_R_values_variable_R_ER","status":"SUCCEEDED"},{"id":"data_set_value_component_G_GTP_variable_G","status":"SUCCEEDED"},{"id":"data_set_value_component_APLC_variable_APLC","status":"SUCCEEDED"},{"id":"data_set_value_component_APLC_variable_PLC","status":"SUCCEEDED"},{"id":"data_set_value_component_IP_3_variable_IP_3","status":"SUCCEEDED"},{"id":"data_set_value_component_DG_variable_DG","status":"SUCCEEDED"},{"id":"data_set_value_component_C_cyt_variable_C_cyt","status":"SUCCEEDED"},{"id":"data_set_value_component_C_ER_variable_C_ER","status":"SUCCEEDED"}]}]}]}