{"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    447      0 --:--:-- --:--:-- --:--:--   448\n\r100  219k  100  219k    0     0   514k      0 --:--:-- --:--:-- --:--:--  514k\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  - 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_x_variable_lamda` may be invalid.\n    - Variable `value_component_x_variable_lamda` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_x_variable_d` may be invalid.\n    - Variable `value_component_x_variable_d` 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_a` may be invalid.\n    - Variable `value_component_y_variable_a` 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_b` may be invalid.\n    - Variable `value_component_z_variable_b` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_v_variable_v` may be invalid.\n    - Variable `value_component_v_variable_v` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_v_variable_k` may be invalid.\n    - Variable `value_component_v_variable_k` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_v_variable_u` may be invalid.\n    - Variable `value_component_v_variable_u` 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_c` may be invalid.\n    - Variable `value_component_w_variable_c` may be invalid.\n      - XPath could not be validated.\n  - Data generator `data_generator_value_component_w_variable_q` may be invalid.\n    - Variable `value_component_w_variable_q` 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_beta` may be invalid.\n    - Variable `value_component_model_parameters_variable_beta` 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    - 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_x_variable_lamda` may be invalid.\n      - Variable `value_component_x_variable_lamda` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_x_variable_d` may be invalid.\n      - Variable `value_component_x_variable_d` 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_a` may be invalid.\n      - Variable `value_component_y_variable_a` 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_b` may be invalid.\n      - Variable `value_component_z_variable_b` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_v_variable_v` may be invalid.\n      - Variable `value_component_v_variable_v` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_v_variable_k` may be invalid.\n      - Variable `value_component_v_variable_k` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_v_variable_u` may be invalid.\n      - Variable `value_component_v_variable_u` 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_c` may be invalid.\n      - Variable `value_component_w_variable_c` may be invalid.\n        - XPath could not be validated.\n    - Data generator `data_generator_value_component_w_variable_q` may be invalid.\n      - Variable `value_component_w_variable_q` 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_beta` may be invalid.\n      - Variable `value_component_model_parameters_variable_beta` 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: 16 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 11.6 KiB/11.6 KiB (92.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/62617797abe612c540c68feb/rawLog.txt\nCompleted 15.0 KiB/15.0 KiB (117.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/62617797abe612c540c68feb/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 83%)\n  adding: rawLog.txt (deflated 86%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 11.6 KiB/11.6 KiB (109.4 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/62617797abe612c540c68feb/outputs/reports.h5\nCompleted 6.0 KiB/18.5 KiB (63.8 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/62617797abe612c540c68feb/output.zip\nCompleted 6.0 KiB/18.5 KiB (63.8 KiB/s) with 1 file(s) remaining\rCompleted 18.5 KiB/18.5 KiB (145.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/62617797abe612c540c68feb/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/revilla_2003.ai  \n  inflating: contents/revilla_2003.xul  \n  inflating: contents/revilla_2003.png  \n  inflating: contents/revilla_garcia-ramos_2003.session.xml  \n  inflating: contents/revilla_2003.svg  \n  inflating: contents/revilla_garcia-ramos_2003.cellml  \n  inflating: contents/simulation_0.sedml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 1.1 KiB/407.8 KiB (15.7 KiB/s) with 9 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/62617797abe612c540c68feb/contents/manifest.xml\nCompleted 1.1 KiB/407.8 KiB (15.7 KiB/s) with 8 file(s) remaining\rCompleted 17.1 KiB/407.8 KiB (128.8 KiB/s) with 8 file(s) remaining\rupload: contents/simulation_0.sedml to s3://files.biosimulations.org/simulations/62617797abe612c540c68feb/contents/simulation_0.sedml\nCompleted 17.1 KiB/407.8 KiB (128.8 KiB/s) with 7 file(s) remaining\rCompleted 32.5 KiB/407.8 KiB (224.1 KiB/s) with 7 file(s) remaining\rupload: contents/revilla_garcia-ramos_2003.session.xml to s3://files.biosimulations.org/simulations/62617797abe612c540c68feb/contents/revilla_garcia-ramos_2003.session.xml\nCompleted 32.5 KiB/407.8 KiB (224.1 KiB/s) with 6 file(s) remaining\rCompleted 46.3 KiB/407.8 KiB (298.2 KiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/62617797abe612c540c68feb/contents/metadata.rdf\nCompleted 46.3 KiB/407.8 KiB (298.2 KiB/s) with 5 file(s) remaining\rCompleted 98.1 KiB/407.8 KiB (596.4 KiB/s) with 5 file(s) remaining\rupload: contents/revilla_2003.svg to s3://files.biosimulations.org/simulations/62617797abe612c540c68feb/contents/revilla_2003.svg\nCompleted 98.1 KiB/407.8 KiB (596.4 KiB/s) with 4 file(s) remaining\rCompleted 157.6 KiB/407.8 KiB (855.6 KiB/s) with 4 file(s) remaining\rupload: contents/revilla_2003.xul to s3://files.biosimulations.org/simulations/62617797abe612c540c68feb/contents/revilla_2003.xul\nCompleted 157.6 KiB/407.8 KiB (855.6 KiB/s) with 3 file(s) remaining\rCompleted 171.8 KiB/407.8 KiB (908.3 KiB/s) with 3 file(s) remaining\rupload: contents/revilla_2003.png to s3://files.biosimulations.org/simulations/62617797abe612c540c68feb/contents/revilla_2003.png\nCompleted 171.8 KiB/407.8 KiB (908.3 KiB/s) with 2 file(s) remaining\rCompleted 193.4 KiB/407.8 KiB (923.9 KiB/s) with 2 file(s) remaining\rupload: contents/revilla_garcia-ramos_2003.cellml to s3://files.biosimulations.org/simulations/62617797abe612c540c68feb/contents/revilla_garcia-ramos_2003.cellml\nCompleted 193.4 KiB/407.8 KiB (923.9 KiB/s) with 1 file(s) remaining\rCompleted 407.8 KiB/407.8 KiB (1.8 MiB/s) with 1 file(s) remaining  \rupload: contents/revilla_2003.ai to s3://files.biosimulations.org/simulations/62617797abe612c540c68feb/contents/revilla_2003.ai\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 15.9 KiB/15.9 KiB (73.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/62617797abe612c540c68feb/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /simulation_0.sedml\ncreating dataset /simulation_0.sedml/report, shape: (16, 11), type: float64\ndataset created, uuid: d-d2f2bff6-f2270eee-e7b6-28f823-05b483, chunk_size: (16, 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: (16, 11), type: float64\niterating over chunks for /simulation_0.sedml/report\nwriting dataset data for slice: (slice(0, 16, 1), slice(0, 11, 1))\ndone with dataload for /simulation_0.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/62617797abe612c540c68feb\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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.38828,"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":0.803539,"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_v_variable_u` 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_x_variable_x` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_model_parameters_variable_beta` 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_d` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_v_variable_k` 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_w_variable_q` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_v_variable_v` 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_b` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_w_variable_c` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_y_variable_a` may be invalid.\n  - XPath could not be validated.\n- Variable `value_component_x_variable_lamda` 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.\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":0.669131,"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":0.036129,"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_x_variable_lamda","status":"SUCCEEDED"},{"id":"data_set_value_component_x_variable_d","status":"SUCCEEDED"},{"id":"data_set_value_component_y_variable_y","status":"SUCCEEDED"},{"id":"data_set_value_component_y_variable_a","status":"SUCCEEDED"},{"id":"data_set_value_component_z_variable_z","status":"SUCCEEDED"},{"id":"data_set_value_component_z_variable_b","status":"SUCCEEDED"},{"id":"data_set_value_component_v_variable_v","status":"SUCCEEDED"},{"id":"data_set_value_component_v_variable_k","status":"SUCCEEDED"},{"id":"data_set_value_component_v_variable_u","status":"SUCCEEDED"},{"id":"data_set_value_component_w_variable_w","status":"SUCCEEDED"},{"id":"data_set_value_component_w_variable_c","status":"SUCCEEDED"},{"id":"data_set_value_component_w_variable_q","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_alpha","status":"SUCCEEDED"},{"id":"data_set_value_component_model_parameters_variable_beta","status":"SUCCEEDED"}]}]}]}