{"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    464      0 --:--:-- --:--:-- --:--:--   464\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100  594k  100  594k    0     0  1399k      0 --:--:-- --:--:-- --:--:-- 7620k\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  - 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_x_variable_x` may be invalid.\n    - Variable `value_component_x_variable_x` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_y_variable_y` may be invalid.\n    - Variable `value_component_y_variable_y` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_a` may be invalid.\n    - Variable `value_component_model_parameters_variable_a` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_d1` may be invalid.\n    - Variable `value_component_model_parameters_variable_d1` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_r` may be invalid.\n    - Variable `value_component_model_parameters_variable_r` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_d2` may be invalid.\n    - Variable `value_component_model_parameters_variable_d2` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_kappa` may be invalid.\n    - Variable `value_component_model_parameters_variable_kappa` 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  - 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_x_variable_x` may be invalid.\n    - Variable `value_component_x_variable_x` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_y_variable_y` may be invalid.\n    - Variable `value_component_y_variable_y` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_y_variable_d2` may be invalid.\n    - Variable `value_component_y_variable_d2` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_z_variable_z` may be invalid.\n    - Variable `value_component_z_variable_z` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_z_variable_v` may be invalid.\n    - Variable `value_component_z_variable_v` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_a` may be invalid.\n    - Variable `value_component_model_parameters_variable_a` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_d1` may be invalid.\n    - Variable `value_component_model_parameters_variable_d1` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_r` may be invalid.\n    - Variable `value_component_model_parameters_variable_r` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_p` may be invalid.\n    - Variable `value_component_model_parameters_variable_p` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_kappa` may be invalid.\n    - Variable `value_component_model_parameters_variable_kappa` 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_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_x_variable_x` may be invalid.\n    - Variable `value_component_x_variable_x` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_y_variable_y` may be invalid.\n    - Variable `value_component_y_variable_y` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_y_variable_d2` may be invalid.\n    - Variable `value_component_y_variable_d2` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_w_variable_w` may be invalid.\n    - Variable `value_component_w_variable_w` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_w_variable_f` may be invalid.\n    - Variable `value_component_w_variable_f` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_z_variable_z` may be invalid.\n    - Variable `value_component_z_variable_z` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_z_variable_v` may be invalid.\n    - Variable `value_component_z_variable_v` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_a` may be invalid.\n    - Variable `value_component_model_parameters_variable_a` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_d1` may be invalid.\n    - Variable `value_component_model_parameters_variable_d1` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_r` may be invalid.\n    - Variable `value_component_model_parameters_variable_r` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_p` may be invalid.\n    - Variable `value_component_model_parameters_variable_p` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_alpha` may be invalid.\n    - Variable `value_component_model_parameters_variable_alpha` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_mu` may be invalid.\n    - Variable `value_component_model_parameters_variable_mu` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_kappa` may be invalid.\n    - Variable `value_component_model_parameters_variable_kappa` 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    - 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_x_variable_x` may be invalid.\n      - Variable `value_component_x_variable_x` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_y_variable_y` may be invalid.\n      - Variable `value_component_y_variable_y` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_a` may be invalid.\n      - Variable `value_component_model_parameters_variable_a` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_d1` may be invalid.\n      - Variable `value_component_model_parameters_variable_d1` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_r` may be invalid.\n      - Variable `value_component_model_parameters_variable_r` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_d2` may be invalid.\n      - Variable `value_component_model_parameters_variable_d2` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_kappa` may be invalid.\n      - Variable `value_component_model_parameters_variable_kappa` 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 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    - 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_x_variable_x` may be invalid.\n      - Variable `value_component_x_variable_x` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_y_variable_y` may be invalid.\n      - Variable `value_component_y_variable_y` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_y_variable_d2` may be invalid.\n      - Variable `value_component_y_variable_d2` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_z_variable_z` may be invalid.\n      - Variable `value_component_z_variable_z` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_z_variable_v` may be invalid.\n      - Variable `value_component_z_variable_v` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_a` may be invalid.\n      - Variable `value_component_model_parameters_variable_a` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_d1` may be invalid.\n      - Variable `value_component_model_parameters_variable_d1` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_r` may be invalid.\n      - Variable `value_component_model_parameters_variable_r` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_p` may be invalid.\n      - Variable `value_component_model_parameters_variable_p` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_kappa` may be invalid.\n      - Variable `value_component_model_parameters_variable_kappa` 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 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_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_x_variable_x` may be invalid.\n      - Variable `value_component_x_variable_x` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_y_variable_y` may be invalid.\n      - Variable `value_component_y_variable_y` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_y_variable_d2` may be invalid.\n      - Variable `value_component_y_variable_d2` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_w_variable_w` may be invalid.\n      - Variable `value_component_w_variable_w` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_w_variable_f` may be invalid.\n      - Variable `value_component_w_variable_f` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_z_variable_z` may be invalid.\n      - Variable `value_component_z_variable_z` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_z_variable_v` may be invalid.\n      - Variable `value_component_z_variable_v` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_a` may be invalid.\n      - Variable `value_component_model_parameters_variable_a` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_d1` may be invalid.\n      - Variable `value_component_model_parameters_variable_d1` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_r` may be invalid.\n      - Variable `value_component_model_parameters_variable_r` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_p` may be invalid.\n      - Variable `value_component_model_parameters_variable_p` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_alpha` may be invalid.\n      - Variable `value_component_model_parameters_variable_alpha` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_mu` may be invalid.\n      - Variable `value_component_model_parameters_variable_mu` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_kappa` may be invalid.\n      - Variable `value_component_model_parameters_variable_kappa` may be invalid.\n        - XPath could not be validated.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\nArchive contains 3 SED-ML documents with 3 models, 3 simulations, 3 tasks, 3 reports, and 0 plots:\n  simulation_0.sedml:\n    Tasks (1):\n      task\n    Reports (1):\n      report: 8 data sets\n  simulation_1.sedml:\n    Tasks (1):\n      task\n    Reports (1):\n      report: 11 data sets\n  simulation_2.sedml:\n    Tasks (1):\n      task\n    Reports (1):\n      report: 15 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 ...\n\nBundling outputs ...\nCleaning up ...\n\n============= SUMMARY =============\nExecuted 3 SED documents:\n  SED documents (3):\n    Succeeded: 3\n    Skipped: 0\n    Failed: 0\n  Tasks (3):\n    Succeeded: 3\n    Skipped: 0\n    Failed: 0\n  Outputs (3):\n    Succeeded: 3\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 22.2 KiB/22.2 KiB (148.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/rawLog.txt\nCompleted 32.2 KiB/32.2 KiB (178.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/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 91%)\n  adding: rawLog.txt (deflated 92%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 40.1 KiB/40.1 KiB (297.2 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/outputs/reports.h5\nCompleted 8.2 KiB/31.3 KiB (108.7 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/output.zip\nCompleted 8.2 KiB/31.3 KiB (108.7 KiB/s) with 1 file(s) remaining\rCompleted 31.3 KiB/31.3 KiB (158.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/yates_2007b.xul  \n  inflating: contents/yates_stark_klein_antia_callard_2007_a.cellml  \n  inflating: contents/yates_stark_klein_antia_callard_2007_c.session.xml  \n  inflating: contents/yates_stark_klein_antia_callard_2007_a.session.xml  \n  inflating: contents/yates_stark_klein_antia_callard_2007_b.cellml  \n  inflating: contents/yates_2007a.xul  \n  inflating: contents/yates_2007a.svg  \n  inflating: contents/yates_2007b.svg  \n  inflating: contents/yates_2007c.ai  \n  inflating: contents/yates_2007c.svg  \n  inflating: contents/yates_2007b.ai  \n  inflating: contents/yates_stark_klein_antia_callard_2007_c.cellml  \n  inflating: contents/yates_2007c.png  \n  inflating: contents/yates_2007c.xul  \n  inflating: contents/yates_2007b.png  \n  inflating: contents/yates_stark_klein_antia_callard_2007_b.session.xml  \n  inflating: contents/yates_2007a.png  \n  inflating: contents/yates_2007a.ai  \n  inflating: contents/simulation_0.sedml  \n  inflating: contents/simulation_1.sedml  \n  inflating: contents/simulation_2.sedml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 25.4 KiB/992.0 KiB (289.1 KiB/s) with 23 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/metadata.rdf\nCompleted 25.4 KiB/992.0 KiB (289.1 KiB/s) with 22 file(s) remaining\rCompleted 43.5 KiB/992.0 KiB (279.6 KiB/s) with 22 file(s) remaining\rupload: contents/yates_2007a.xul to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/yates_2007a.xul\nCompleted 43.5 KiB/992.0 KiB (279.6 KiB/s) with 21 file(s) remaining\rCompleted 52.5 KiB/992.0 KiB (329.7 KiB/s) with 21 file(s) remaining\rupload: contents/simulation_0.sedml to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/simulation_0.sedml\nCompleted 52.5 KiB/992.0 KiB (329.7 KiB/s) with 20 file(s) remaining\rCompleted 64.1 KiB/992.0 KiB (395.6 KiB/s) with 20 file(s) remaining\rupload: contents/simulation_1.sedml to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/simulation_1.sedml\nCompleted 64.1 KiB/992.0 KiB (395.6 KiB/s) with 19 file(s) remaining\rCompleted 279.8 KiB/992.0 KiB (1.5 MiB/s) with 19 file(s) remaining \rupload: contents/yates_2007b.ai to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/yates_2007b.ai\nCompleted 279.8 KiB/992.0 KiB (1.5 MiB/s) with 18 file(s) remaining\rCompleted 306.4 KiB/992.0 KiB (1.6 MiB/s) with 18 file(s) remaining\rupload: contents/yates_2007b.svg to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/yates_2007b.svg\nCompleted 306.4 KiB/992.0 KiB (1.6 MiB/s) with 17 file(s) remaining\rCompleted 309.1 KiB/992.0 KiB (1.6 MiB/s) with 17 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/manifest.xml\nCompleted 309.1 KiB/992.0 KiB (1.6 MiB/s) with 16 file(s) remaining\rCompleted 524.3 KiB/992.0 KiB (2.6 MiB/s) with 16 file(s) remaining\rupload: contents/yates_2007c.ai to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/yates_2007c.ai\nCompleted 524.3 KiB/992.0 KiB (2.6 MiB/s) with 15 file(s) remaining\rCompleted 534.0 KiB/992.0 KiB (2.5 MiB/s) with 15 file(s) remaining\rupload: contents/yates_2007c.png to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/yates_2007c.png\nCompleted 534.0 KiB/992.0 KiB (2.5 MiB/s) with 14 file(s) remaining\rCompleted 541.8 KiB/992.0 KiB (2.5 MiB/s) with 14 file(s) remaining\rupload: contents/yates_2007b.png to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/yates_2007b.png\nCompleted 541.8 KiB/992.0 KiB (2.5 MiB/s) with 13 file(s) remaining\rCompleted 575.7 KiB/992.0 KiB (2.6 MiB/s) with 13 file(s) remaining\rupload: contents/yates_2007b.xul to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/yates_2007b.xul\nCompleted 575.7 KiB/992.0 KiB (2.6 MiB/s) with 12 file(s) remaining\rCompleted 604.6 KiB/992.0 KiB (2.2 MiB/s) with 12 file(s) remaining\rupload: contents/yates_2007c.svg to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/yates_2007c.svg\nCompleted 604.6 KiB/992.0 KiB (2.2 MiB/s) with 11 file(s) remaining\rCompleted 630.6 KiB/992.0 KiB (2.2 MiB/s) with 11 file(s) remaining\rupload: contents/yates_stark_klein_antia_callard_2007_b.cellml to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/yates_stark_klein_antia_callard_2007_b.cellml\nCompleted 630.6 KiB/992.0 KiB (2.2 MiB/s) with 10 file(s) remaining\rCompleted 641.5 KiB/992.0 KiB (2.2 MiB/s) with 10 file(s) remaining\rCompleted 656.3 KiB/992.0 KiB (2.2 MiB/s) with 10 file(s) remaining\rupload: contents/yates_stark_klein_antia_callard_2007_b.session.xml to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/yates_stark_klein_antia_callard_2007_b.session.xml\nCompleted 656.3 KiB/992.0 KiB (2.2 MiB/s) with 9 file(s) remaining\rCompleted 680.2 KiB/992.0 KiB (2.3 MiB/s) with 9 file(s) remaining\rupload: contents/yates_stark_klein_antia_callard_2007_a.cellml to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/yates_stark_klein_antia_callard_2007_a.cellml\nCompleted 680.2 KiB/992.0 KiB (2.3 MiB/s) with 8 file(s) remaining\rupload: contents/yates_2007a.svg to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/yates_2007a.svg\nCompleted 680.2 KiB/992.0 KiB (2.3 MiB/s) with 7 file(s) remaining\rCompleted 709.1 KiB/992.0 KiB (2.3 MiB/s) with 7 file(s) remaining\rupload: contents/yates_stark_klein_antia_callard_2007_c.cellml to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/yates_stark_klein_antia_callard_2007_c.cellml\nCompleted 709.1 KiB/992.0 KiB (2.3 MiB/s) with 6 file(s) remaining\rCompleted 745.5 KiB/992.0 KiB (2.3 MiB/s) with 6 file(s) remaining\rupload: contents/yates_2007c.xul to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/yates_2007c.xul\nCompleted 745.5 KiB/992.0 KiB (2.3 MiB/s) with 5 file(s) remaining\rCompleted 760.7 KiB/992.0 KiB (2.4 MiB/s) with 5 file(s) remaining\rupload: contents/yates_stark_klein_antia_callard_2007_c.session.xml to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/yates_stark_klein_antia_callard_2007_c.session.xml\nCompleted 760.7 KiB/992.0 KiB (2.4 MiB/s) with 4 file(s) remaining\rCompleted 764.7 KiB/992.0 KiB (2.3 MiB/s) with 4 file(s) remaining\rupload: contents/yates_2007a.png to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/yates_2007a.png\nCompleted 764.7 KiB/992.0 KiB (2.3 MiB/s) with 3 file(s) remaining\rCompleted 780.3 KiB/992.0 KiB (2.1 MiB/s) with 3 file(s) remaining\rupload: contents/simulation_2.sedml to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/simulation_2.sedml\nCompleted 780.3 KiB/992.0 KiB (2.1 MiB/s) with 2 file(s) remaining\rCompleted 793.4 KiB/992.0 KiB (2.1 MiB/s) with 2 file(s) remaining\rupload: contents/yates_stark_klein_antia_callard_2007_a.session.xml to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/yates_stark_klein_antia_callard_2007_a.session.xml\nCompleted 793.4 KiB/992.0 KiB (2.1 MiB/s) with 1 file(s) remaining\rCompleted 992.0 KiB/992.0 KiB (2.4 MiB/s) with 1 file(s) remaining\rupload: contents/yates_2007a.ai to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/contents/yates_2007a.ai\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 31.1 KiB/31.1 KiB (372.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6261791b4679625b32470216/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /simulation_0.sedml\ncreating dataset /simulation_0.sedml/report, shape: (8, 11), type: float64\ndataset created, uuid: d-4e5567b6-0734e024-eae6-bdbd97-e68a1f, chunk_size: (8, 11)\ncreating group /simulation_1.sedml\ncreating dataset /simulation_1.sedml/report, shape: (11, 11), type: float64\ndataset created, uuid: d-4e5567b6-0734e024-abb0-20ef1d-680d16, chunk_size: (11, 11)\ncreating group /simulation_2.sedml\ncreating dataset /simulation_2.sedml/report, shape: (15, 11), type: float64\ndataset created, uuid: d-4e5567b6-0734e024-da03-986d79-4d7dfd, chunk_size: (15, 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\ncreate_links: /\ngot link: simulation_0.sedml\ngot link: simulation_1.sedml\ngot link: simulation_2.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\nwrite_dataset src: /simulation_0.sedml/report to tgt: /simulation_0.sedml/report, shape: (8, 11), type: float64\niterating over chunks for /simulation_0.sedml/report\nwriting dataset data for slice: (slice(0, 8, 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: (11, 11), type: float64\niterating over chunks for /simulation_1.sedml/report\nwriting dataset data for slice: (slice(0, 11, 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: (15, 11), type: float64\niterating over chunks for /simulation_2.sedml/report\nwriting dataset data for slice: (slice(0, 15, 1), slice(0, 11, 1))\ndone with dataload for /simulation_2.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6261791b4679625b32470216\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 SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file 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.\nRetrieve 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":2.325297,"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":0.731556,"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_model_parameters_variable_a` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_y_variable_y` 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_x_variable_x` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_model_parameters_variable_r` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_model_parameters_variable_d2` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_model_parameters_variable_d1` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_model_parameters_variable_kappa` 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":0.617558,"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":0.019901,"dataSets":[{"id":"data_set_value_component_environment_variable_time","status":"SUCCEEDED"},{"id":"data_set_value_component_x_variable_x","status":"SUCCEEDED"},{"id":"data_set_value_component_y_variable_y","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_a","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_d1","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_r","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_d2","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_kappa","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":0.486657,"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_model_parameters_variable_d1` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_model_parameters_variable_p` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_y_variable_d2` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_z_variable_z` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_model_parameters_variable_a` 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_model_parameters_variable_r` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_model_parameters_variable_kappa` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_z_variable_v` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_y_variable_y` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_x_variable_x` may be invalid.\n  - XPath could not be validated.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n","duration":0.368916,"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":0.017567,"dataSets":[{"id":"data_set_value_component_environment_variable_time","status":"SUCCEEDED"},{"id":"data_set_value_component_x_variable_x","status":"SUCCEEDED"},{"id":"data_set_value_component_y_variable_y","status":"SUCCEEDED"},{"id":"data_set_value_component_y_variable_d2","status":"SUCCEEDED"},{"id":"data_set_value_component_z_variable_z","status":"SUCCEEDED"},{"id":"data_set_value_component_z_variable_v","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_a","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_d1","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_r","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_p","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_kappa","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":0.493651,"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_model_parameters_variable_r` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_w_variable_f` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_y_variable_y` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_z_variable_z` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_model_parameters_variable_a` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_model_parameters_variable_kappa` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_x_variable_x` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_w_variable_w` 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_model_parameters_variable_mu` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_model_parameters_variable_p` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_model_parameters_variable_d1` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_y_variable_d2` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_model_parameters_variable_alpha` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_z_variable_v` may be invalid.\n  - XPath could not be validated.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n","duration":0.371738,"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":0.015918,"dataSets":[{"id":"data_set_value_component_environment_variable_time","status":"SUCCEEDED"},{"id":"data_set_value_component_x_variable_x","status":"SUCCEEDED"},{"id":"data_set_value_component_y_variable_y","status":"SUCCEEDED"},{"id":"data_set_value_component_y_variable_d2","status":"SUCCEEDED"},{"id":"data_set_value_component_w_variable_w","status":"SUCCEEDED"},{"id":"data_set_value_component_w_variable_f","status":"SUCCEEDED"},{"id":"data_set_value_component_z_variable_z","status":"SUCCEEDED"},{"id":"data_set_value_component_z_variable_v","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_a","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_d1","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_r","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_p","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_alpha","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_mu","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_kappa","status":"SUCCEEDED"}]}]}]}