{"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    460      0 --:--:-- --:--:-- --:--:--   461\n\r100 88165  100 88165    0     0   207k      0 --:--:-- --:--:-- --:--:--  207k\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  - 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_H1_variable_H1` may be invalid.\n    - Variable `value_component_H1_variable_H1` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_H2_variable_H2` may be invalid.\n    - Variable `value_component_H2_variable_H2` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_A_variable_A` may be invalid.\n    - Variable `value_component_A_variable_A` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_A_variable_t_on` may be invalid.\n    - Variable `value_component_A_variable_t_on` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_A_variable_t_off` may be invalid.\n    - Variable `value_component_A_variable_t_off` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_A_variable_A_max` may be invalid.\n    - Variable `value_component_A_variable_A_max` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_beta_I` may be invalid.\n    - Variable `value_component_model_parameters_variable_beta_I` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_beta_C` may be invalid.\n    - Variable `value_component_model_parameters_variable_beta_C` 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_lamda` may be invalid.\n    - Variable `value_component_model_parameters_variable_lamda` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_tau_I` may be invalid.\n    - Variable `value_component_model_parameters_variable_tau_I` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_tau_C` may be invalid.\n    - Variable `value_component_model_parameters_variable_tau_C` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_tau_alpha` may be invalid.\n    - Variable `value_component_model_parameters_variable_tau_alpha` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_model_parameters_variable_tau_lamda` may be invalid.\n    - Variable `value_component_model_parameters_variable_tau_lamda` 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    - 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_H1_variable_H1` may be invalid.\n      - Variable `value_component_H1_variable_H1` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_H2_variable_H2` may be invalid.\n      - Variable `value_component_H2_variable_H2` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_A_variable_A` may be invalid.\n      - Variable `value_component_A_variable_A` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_A_variable_t_on` may be invalid.\n      - Variable `value_component_A_variable_t_on` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_A_variable_t_off` may be invalid.\n      - Variable `value_component_A_variable_t_off` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_A_variable_A_max` may be invalid.\n      - Variable `value_component_A_variable_A_max` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_beta_I` may be invalid.\n      - Variable `value_component_model_parameters_variable_beta_I` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_beta_C` may be invalid.\n      - Variable `value_component_model_parameters_variable_beta_C` 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_lamda` may be invalid.\n      - Variable `value_component_model_parameters_variable_lamda` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_tau_I` may be invalid.\n      - Variable `value_component_model_parameters_variable_tau_I` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_tau_C` may be invalid.\n      - Variable `value_component_model_parameters_variable_tau_C` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_tau_alpha` may be invalid.\n      - Variable `value_component_model_parameters_variable_tau_alpha` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_model_parameters_variable_tau_lamda` may be invalid.\n      - Variable `value_component_model_parameters_variable_tau_lamda` 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: 15 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 10.9 KiB/10.9 KiB (104.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/626173e290c6a19595578492/rawLog.txt\nCompleted 14.3 KiB/14.3 KiB (137.5 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/626173e290c6a19595578492/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 89%)\n  adding: outputs/reports.h5 (deflated 88%)\n  adding: rawLog.txt (deflated 86%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 15.3 KiB/15.3 KiB (94.9 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/626173e290c6a19595578492/outputs/reports.h5\nCompleted 5.6 KiB/17.4 KiB (74.3 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/626173e290c6a19595578492/output.zip\nCompleted 5.6 KiB/17.4 KiB (74.3 KiB/s) with 1 file(s) remaining\rCompleted 17.4 KiB/17.4 KiB (139.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/626173e290c6a19595578492/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/brown_1997.ai  \n  inflating: contents/brown_1997.svg  \n  inflating: contents/brown_1997.png  \n  inflating: contents/brown_choe_shanahan_czeisler_1997.cellml  \n  inflating: contents/brown_choe_shanahan_czeisler_1997.session.xml  \n  inflating: contents/brown_1997.xul  \n  inflating: contents/simulation_0.sedml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 58.0 KiB/225.0 KiB (600.0 KiB/s) with 9 file(s) remaining\rupload: contents/brown_1997.ai to s3://files.biosimulations.org/simulations/626173e290c6a19595578492/contents/brown_1997.ai\nCompleted 58.0 KiB/225.0 KiB (600.0 KiB/s) with 8 file(s) remaining\rCompleted 74.9 KiB/225.0 KiB (478.3 KiB/s) with 8 file(s) remaining\rupload: contents/brown_choe_shanahan_czeisler_1997.session.xml to s3://files.biosimulations.org/simulations/626173e290c6a19595578492/contents/brown_choe_shanahan_czeisler_1997.session.xml\nCompleted 74.9 KiB/225.0 KiB (478.3 KiB/s) with 7 file(s) remaining\rCompleted 90.7 KiB/225.0 KiB (556.4 KiB/s) with 7 file(s) remaining\rupload: contents/simulation_0.sedml to s3://files.biosimulations.org/simulations/626173e290c6a19595578492/contents/simulation_0.sedml\nCompleted 90.7 KiB/225.0 KiB (556.4 KiB/s) with 6 file(s) remaining\rCompleted 127.0 KiB/225.0 KiB (763.6 KiB/s) with 6 file(s) remaining\rupload: contents/brown_1997.svg to s3://files.biosimulations.org/simulations/626173e290c6a19595578492/contents/brown_1997.svg\nCompleted 127.0 KiB/225.0 KiB (763.6 KiB/s) with 5 file(s) remaining\rCompleted 171.2 KiB/225.0 KiB (1008.2 KiB/s) with 5 file(s) remaining\rupload: contents/brown_1997.xul to s3://files.biosimulations.org/simulations/626173e290c6a19595578492/contents/brown_1997.xul\nCompleted 171.2 KiB/225.0 KiB (1008.2 KiB/s) with 4 file(s) remaining\rCompleted 185.1 KiB/225.0 KiB (1.0 MiB/s) with 4 file(s) remaining   \rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/626173e290c6a19595578492/contents/metadata.rdf\nCompleted 185.1 KiB/225.0 KiB (1.0 MiB/s) with 3 file(s) remaining\rCompleted 186.2 KiB/225.0 KiB (1.0 MiB/s) with 3 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/626173e290c6a19595578492/contents/manifest.xml\nCompleted 186.2 KiB/225.0 KiB (1.0 MiB/s) with 2 file(s) remaining\rCompleted 200.8 KiB/225.0 KiB (1.1 MiB/s) with 2 file(s) remaining\rupload: contents/brown_1997.png to s3://files.biosimulations.org/simulations/626173e290c6a19595578492/contents/brown_1997.png\nCompleted 200.8 KiB/225.0 KiB (1.1 MiB/s) with 1 file(s) remaining\rCompleted 225.0 KiB/225.0 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: contents/brown_choe_shanahan_czeisler_1997.cellml to s3://files.biosimulations.org/simulations/626173e290c6a19595578492/contents/brown_choe_shanahan_czeisler_1997.cellml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 15.2 KiB/15.2 KiB (141.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/626173e290c6a19595578492/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /simulation_0.sedml\ncreating dataset /simulation_0.sedml/report, shape: (15, 11), type: float64\ndataset created, uuid: d-21d12e69-c9c5dcd6-34f9-e4f644-a02b89, 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\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: (15, 11), type: float64\niterating over chunks for /simulation_0.sedml/report\nwriting dataset data for slice: (slice(0, 15, 1), slice(0, 11, 1))\ndone with dataload for /simulation_0.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/626173e290c6a19595578492\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 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.\nProcess and upload the outputs of the simulation run ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.331505,"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":0.781766,"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_H1_variable_H1` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_model_parameters_variable_beta_C` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_model_parameters_variable_tau_alpha` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_A_variable_t_off` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_model_parameters_variable_tau_I` 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_A_variable_t_on` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_A_variable_A_max` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_H2_variable_H2` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_A_variable_A` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_model_parameters_variable_tau_C` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_model_parameters_variable_lamda` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_model_parameters_variable_tau_lamda` 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_beta_I` 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":0.686005,"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":0.022103,"dataSets":[{"id":"data_set_value_component_environment_variable_time","status":"SUCCEEDED"},{"id":"data_set_value_component_H1_variable_H1","status":"SUCCEEDED"},{"id":"data_set_value_component_H2_variable_H2","status":"SUCCEEDED"},{"id":"data_set_value_component_A_variable_A","status":"SUCCEEDED"},{"id":"data_set_value_component_A_variable_t_on","status":"SUCCEEDED"},{"id":"data_set_value_component_A_variable_t_off","status":"SUCCEEDED"},{"id":"data_set_value_component_A_variable_A_max","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_beta_I","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_beta_C","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_alpha","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_lamda","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_tau_I","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_tau_C","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_tau_alpha","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_tau_lamda","status":"SUCCEEDED"}]}]}]}