{"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    457      0 --:--:-- --:--:-- --:--:--   457\n\r100  4524  100  4524    0     0  10683      0 --:--:-- --:--:-- --:--:-- 10683\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\nTraceback (most recent call last):\n  File \"/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py\", line 247, in <module>\n    if not update_paths(args.path, args.scripts_dir, args.clear_args, args.extra_args):\n  File \"/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py\", line 213, in update_paths\n    update_scripts(scripts_dir, new_path, clear_args, extra_args)\n  File \"/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py\", line 125, in update_scripts\n    update_script(os.path.join(bin_dir, fn), new_path, clear_args, extra_args)\n  File \"/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py\", line 118, in update_script\n    with open(script_filename, 'w') as f:\nOSError: [Errno 30] Read-only file system: '/home/opencor/OpenCOR/bin/../python/bin/biosimulators-utils'\n/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mCOMBINE/OMEX archive may be invalid.\n  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\n  - Model `model` may be invalid.\n    - The model file `Boron CO2 expts - original eqns - SS--RO--PH.cellml` may be invalid.\n      - Validation is not available for CellML 1.1 files.\n  - Output `plot1` may be invalid.\n    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n  - Output `plot2` may be invalid.\n    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n  - Output `plot3` may be invalid.\n    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n  - Output `plot4` may be invalid.\n    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n  - Output `plot5` may be invalid.\n    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n  - Output `plot6` may be invalid.\n    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n  - Output `plot7` may be invalid.\n    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\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 `Boron CO2 expts - original eqns - SS--RO--PH.sedml` may be invalid.\n    - Model `model` may be invalid.\n      - The model file `Boron CO2 expts - original eqns - SS--RO--PH.cellml` may be invalid.\n        - Validation is not available for CellML 1.1 files.\n    - Output `plot1` may be invalid.\n      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n    - Output `plot2` may be invalid.\n      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n    - Output `plot3` may be invalid.\n      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n    - Output `plot4` may be invalid.\n      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n    - Output `plot5` may be invalid.\n      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n    - Output `plot6` may be invalid.\n      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n    - Output `plot7` may be invalid.\n      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\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  - Output `plot1` may be invalid.\n    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n  - Output `plot2` may be invalid.\n    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n  - Output `plot3` may be invalid.\n    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n  - Output `plot4` may be invalid.\n    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n  - Output `plot5` may be invalid.\n    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n  - Output `plot6` may be invalid.\n    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n  - Output `plot7` may be invalid.\n    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\nArchive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 0 reports, and 7 plots:\n  Boron CO2 expts - original eqns - SS--RO--PH.sedml:\n    Tasks (2):\n      repeatedTask\n      task1\n    Plots (7):\n      plot1: 2 curves\n      plot2: 2 curves\n      plot3: 2 curves\n      plot4: 1 curves\n      plot5: 1 curves\n      plot6: 1 curves\n      plot7: 1 curves\n\nExecuting SED-ML file 1: Boron CO2 expts - original eqns - SS--RO--PH.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 (2):\n    Succeeded: 2\n    Skipped: 0\n    Failed: 0\n  Outputs (7):\n    Succeeded: 7\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 9.3 KiB/9.3 KiB (61.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/626173424679625b3246dddd/rawLog.txt\nCompleted 16.6 KiB/16.6 KiB (124.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/626173424679625b3246dddd/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 88%)\n  adding: outputs/Boron CO2 expts - original eqns - SS--RO--PH.sedml/ (stored 0%)\n  adding: outputs/Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot3.pdf (deflated 31%)\n  adding: outputs/Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot4.pdf (deflated 32%)\n  adding: outputs/Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot5.pdf (deflated 32%)\n  adding: outputs/Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot7.pdf (deflated 31%)\n  adding: outputs/Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot2.pdf (deflated 31%)\n  adding: outputs/Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot1.pdf (deflated 31%)\n  adding: outputs/Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot6.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 29%)\n  adding: rawLog.txt (deflated 85%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/370.6 KiB (5.4 MiB/s) with 1 file(s) remaining\rCompleted 370.6 KiB/370.6 KiB (2.9 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/626173424679625b3246dddd/outputs/reports.h5\nCompleted 256.0 KiB/436.8 KiB (5.8 MiB/s) with 10 file(s) remaining\rCompleted 266.3 KiB/436.8 KiB (2.1 MiB/s) with 10 file(s) remaining\rupload: outputs/Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot7.pdf to s3://files.biosimulations.org/simulations/626173424679625b3246dddd/outputs/Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot7.pdf\nCompleted 266.3 KiB/436.8 KiB (2.1 MiB/s) with 9 file(s) remaining\rCompleted 325.1 KiB/436.8 KiB (2.2 MiB/s) with 9 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/626173424679625b3246dddd/output.zip\nCompleted 325.1 KiB/436.8 KiB (2.2 MiB/s) with 8 file(s) remaining\rCompleted 333.7 KiB/436.8 KiB (1.7 MiB/s) with 8 file(s) remaining\rupload: outputs/Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot2.pdf to s3://files.biosimulations.org/simulations/626173424679625b3246dddd/outputs/Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot2.pdf\nCompleted 333.7 KiB/436.8 KiB (1.7 MiB/s) with 7 file(s) remaining\rCompleted 343.6 KiB/436.8 KiB (1.7 MiB/s) with 7 file(s) remaining\rupload: outputs/Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot5.pdf to s3://files.biosimulations.org/simulations/626173424679625b3246dddd/outputs/Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot5.pdf\nCompleted 343.6 KiB/436.8 KiB (1.7 MiB/s) with 6 file(s) remaining\rCompleted 352.7 KiB/436.8 KiB (1.7 MiB/s) with 6 file(s) remaining\rupload: outputs/Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot1.pdf to s3://files.biosimulations.org/simulations/626173424679625b3246dddd/outputs/Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot1.pdf\nCompleted 352.7 KiB/436.8 KiB (1.7 MiB/s) with 5 file(s) remaining\rCompleted 397.2 KiB/436.8 KiB (1.9 MiB/s) with 5 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/626173424679625b3246dddd/outputs/plots.zip\nCompleted 397.2 KiB/436.8 KiB (1.9 MiB/s) with 4 file(s) remaining\rCompleted 408.2 KiB/436.8 KiB (1.8 MiB/s) with 4 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/626173424679625b3246dddd/rawLog.txt\nCompleted 408.2 KiB/436.8 KiB (1.8 MiB/s) with 3 file(s) remaining\rCompleted 417.6 KiB/436.8 KiB (1.8 MiB/s) with 3 file(s) remaining\rupload: outputs/Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot6.pdf to s3://files.biosimulations.org/simulations/626173424679625b3246dddd/outputs/Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot6.pdf\nCompleted 417.6 KiB/436.8 KiB (1.8 MiB/s) with 2 file(s) remaining\rCompleted 427.1 KiB/436.8 KiB (1.6 MiB/s) with 2 file(s) remaining\rupload: outputs/Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot3.pdf to s3://files.biosimulations.org/simulations/626173424679625b3246dddd/outputs/Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot3.pdf\nCompleted 427.1 KiB/436.8 KiB (1.6 MiB/s) with 1 file(s) remaining\rCompleted 436.8 KiB/436.8 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: outputs/Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot4.pdf to s3://files.biosimulations.org/simulations/626173424679625b3246dddd/outputs/Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot4.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Boron CO2 expts - original eqns - SS--RO--PH.sedml  \n  inflating: contents/documentation.html  \n  inflating: contents/Boron CO2 expts - original eqns - SS--RO--PH.cellml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 11.9 KiB/29.4 KiB (97.1 KiB/s) with 5 file(s) remaining\rupload: contents/Boron CO2 expts - original eqns - SS--RO--PH.cellml to s3://files.biosimulations.org/simulations/626173424679625b3246dddd/contents/Boron CO2 expts - original eqns - SS--RO--PH.cellml\nCompleted 11.9 KiB/29.4 KiB (97.1 KiB/s) with 4 file(s) remaining\rCompleted 12.2 KiB/29.4 KiB (89.5 KiB/s) with 4 file(s) remaining\rupload: contents/documentation.html to s3://files.biosimulations.org/simulations/626173424679625b3246dddd/contents/documentation.html\nCompleted 12.2 KiB/29.4 KiB (89.5 KiB/s) with 3 file(s) remaining\rCompleted 24.6 KiB/29.4 KiB (170.2 KiB/s) with 3 file(s) remaining\rupload: contents/Boron CO2 expts - original eqns - SS--RO--PH.sedml to s3://files.biosimulations.org/simulations/626173424679625b3246dddd/contents/Boron CO2 expts - original eqns - SS--RO--PH.sedml\nCompleted 24.6 KiB/29.4 KiB (170.2 KiB/s) with 2 file(s) remaining\rCompleted 28.8 KiB/29.4 KiB (194.7 KiB/s) with 2 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/626173424679625b3246dddd/contents/metadata.rdf\nCompleted 28.8 KiB/29.4 KiB (194.7 KiB/s) with 1 file(s) remaining\rCompleted 29.4 KiB/29.4 KiB (145.3 KiB/s) with 1 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/626173424679625b3246dddd/contents/manifest.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 15.9 KiB/15.9 KiB (160.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/626173424679625b3246dddd/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Boron CO2 expts - original eqns - SS--RO--PH.sedml\ncreating dataset /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot1, shape: (4, 1, 1, 5001), type: float64\ndataset created, uuid: d-b97c3017-6466a2d7-1091-d793b9-7547e9, chunk_size: (4, 1, 1, 5001)\ncreating dataset /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot2, shape: (4, 1, 1, 5001), type: float64\ndataset created, uuid: d-b97c3017-6466a2d7-bc9a-2ab39b-bf8459, chunk_size: (4, 1, 1, 5001)\ncreating dataset /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot3, shape: (4, 1, 1, 5001), type: float64\ndataset created, uuid: d-b97c3017-6466a2d7-7c5e-e8efd6-20ed41, chunk_size: (4, 1, 1, 5001)\ncreating dataset /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot4, shape: (2, 1, 1, 5001), type: float64\ndataset created, uuid: d-b97c3017-6466a2d7-eaf6-2bfc5e-6e0068, chunk_size: (2, 1, 1, 5001)\ncreating dataset /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot5, shape: (2, 1, 1, 5001), type: float64\ndataset created, uuid: d-b97c3017-6466a2d7-77a2-b414c5-e632ac, chunk_size: (2, 1, 1, 5001)\ncreating dataset /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot6, shape: (2, 1, 1, 5001), type: float64\ndataset created, uuid: d-b97c3017-6466a2d7-82ae-0ca54a-b440a7, chunk_size: (2, 1, 1, 5001)\ncreating dataset /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot7, shape: (2, 1, 1, 5001), type: float64\ndataset created, uuid: d-b97c3017-6466a2d7-0758-467318-3f1796, chunk_size: (2, 1, 1, 5001)\ncreating attribute combineArchiveLocation in /Boron CO2 expts - original eqns - SS--RO--PH.sedml\ncreating attribute uri in /Boron CO2 expts - original eqns - SS--RO--PH.sedml\ncreating attribute _type in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot1\ncreating attribute sedmlDataSetDataTypes in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot1\ncreating attribute sedmlDataSetIds in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot1\ncreating attribute sedmlDataSetLabels in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot1\ncreating attribute sedmlDataSetNames in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot1\ncreating attribute sedmlDataSetShapes in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot1\ncreating attribute sedmlId in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot1\ncreating attribute uri in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot1\ncreating attribute _type in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot2\ncreating attribute sedmlDataSetDataTypes in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot2\ncreating attribute sedmlDataSetIds in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot2\ncreating attribute sedmlDataSetLabels in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot2\ncreating attribute sedmlDataSetNames in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot2\ncreating attribute sedmlDataSetShapes in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot2\ncreating attribute sedmlId in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot2\ncreating attribute uri in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot2\ncreating attribute _type in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot3\ncreating attribute sedmlDataSetDataTypes in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot3\ncreating attribute sedmlDataSetIds in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot3\ncreating attribute sedmlDataSetLabels in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot3\ncreating attribute sedmlDataSetNames in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot3\ncreating attribute sedmlDataSetShapes in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot3\ncreating attribute sedmlId in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot3\ncreating attribute uri in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot3\ncreating attribute _type in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot4\ncreating attribute sedmlDataSetDataTypes in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot4\ncreating attribute sedmlDataSetIds in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot4\ncreating attribute sedmlDataSetLabels in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot4\ncreating attribute sedmlDataSetNames in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot4\ncreating attribute sedmlDataSetShapes in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot4\ncreating attribute sedmlId in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot4\ncreating attribute uri in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot4\ncreating attribute _type in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot5\ncreating attribute sedmlDataSetDataTypes in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot5\ncreating attribute sedmlDataSetIds in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot5\ncreating attribute sedmlDataSetLabels in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot5\ncreating attribute sedmlDataSetNames in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot5\ncreating attribute sedmlDataSetShapes in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot5\ncreating attribute sedmlId in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot5\ncreating attribute uri in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot5\ncreating attribute _type in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot6\ncreating attribute sedmlDataSetDataTypes in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot6\ncreating attribute sedmlDataSetIds in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot6\ncreating attribute sedmlDataSetLabels in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot6\ncreating attribute sedmlDataSetNames in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot6\ncreating attribute sedmlDataSetShapes in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot6\ncreating attribute sedmlId in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot6\ncreating attribute uri in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot6\ncreating attribute _type in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot7\ncreating attribute sedmlDataSetDataTypes in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot7\ncreating attribute sedmlDataSetIds in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot7\ncreating attribute sedmlDataSetLabels in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot7\ncreating attribute sedmlDataSetNames in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot7\ncreating attribute sedmlDataSetShapes in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot7\ncreating attribute sedmlId in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot7\ncreating attribute uri in /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot7\ncreate_links: /\ngot link: Boron CO2 expts - original eqns - SS--RO--PH.sedml\ncreate_links: /Boron CO2 expts - original eqns - SS--RO--PH.sedml\ngot link: plot1\ngot link: plot2\ngot link: plot3\ngot link: plot4\ngot link: plot5\ngot link: plot6\ngot link: plot7\nwrite_dataset src: /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot1 to tgt: /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot1, shape: (4, 1, 1, 5001), type: float64\niterating over chunks for /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1, 1), slice(0, 1, 1), slice(0, 5001, 1))\ndone with dataload for /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot1\nwrite_dataset src: /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot2 to tgt: /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot2, shape: (4, 1, 1, 5001), type: float64\niterating over chunks for /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot2\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1, 1), slice(0, 1, 1), slice(0, 5001, 1))\ndone with dataload for /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot2\nwrite_dataset src: /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot3 to tgt: /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot3, shape: (4, 1, 1, 5001), type: float64\niterating over chunks for /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot3\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1, 1), slice(0, 1, 1), slice(0, 5001, 1))\ndone with dataload for /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot3\nwrite_dataset src: /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot4 to tgt: /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot4, shape: (2, 1, 1, 5001), type: float64\niterating over chunks for /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot4\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1, 1), slice(0, 1, 1), slice(0, 5001, 1))\ndone with dataload for /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot4\nwrite_dataset src: /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot5 to tgt: /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot5, shape: (2, 1, 1, 5001), type: float64\niterating over chunks for /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot5\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1, 1), slice(0, 1, 1), slice(0, 5001, 1))\ndone with dataload for /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot5\nwrite_dataset src: /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot6 to tgt: /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot6, shape: (2, 1, 1, 5001), type: float64\niterating over chunks for /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot6\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1, 1), slice(0, 1, 1), slice(0, 5001, 1))\ndone with dataload for /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot6\nwrite_dataset src: /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot7 to tgt: /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot7, shape: (2, 1, 1, 5001), type: float64\niterating over chunks for /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot7\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1, 1), slice(0, 1, 1), slice(0, 5001, 1))\ndone with dataload for /Boron CO2 expts - original eqns - SS--RO--PH.sedml/plot7\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/626173424679625b3246dddd\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess the manifest file in the COMBINE archive ... succeeded.\nRead the manifest and post the files to the API ... succeeded.\nCreate thumbnails from the images specified in the manifest ... succeeded.\nPost thumbnails to the API ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":4.903039,"sedDocuments":[{"location":"Boron CO2 expts - original eqns - SS--RO--PH.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"  Found 2 tasks and 7 outputs:\n    Tasks:\n      `repeatedTask`\n      `task1`\n    Outputs:\n      `plot1`\n      `plot2`\n      `plot3`\n      `plot4`\n      `plot5`\n      `plot6`\n      `plot7`\n  Executing task 1: `repeatedTask`\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\n    Generating 7 outputs ...\n      Generating output 1: `plot1` ... \u001b[34msucceeded\u001b[0m\n      Generating output 2: `plot2` ... \u001b[34msucceeded\u001b[0m\n      Generating output 3: `plot3` ... \u001b[34msucceeded\u001b[0m\n      Generating output 4: `plot4` ... \u001b[34msucceeded\u001b[0m\n      Generating output 5: `plot5` ... \u001b[34msucceeded\u001b[0m\n      Generating output 6: `plot6` ... \u001b[34msucceeded\u001b[0m\n      Generating output 7: `plot7` ... \u001b[34msucceeded\u001b[0m\n  Executing task 2: `task1`\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\n    Generating 7 outputs ...\n      Generating output 1: `plot1` ...      Generating output 2: `plot2` ...      Generating output 3: `plot3` ...      Generating output 4: `plot4` ...      Generating output 5: `plot5` ...      Generating output 6: `plot6` ...      Generating output 7: `plot7` .../home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: NoOutputsWarning: \u001b[33mTask task1 does not contribute to any outputs.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n\n  Executed 2 tasks and 7 outputs:\n    Tasks:\n      Succeeded: 2\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 7\n      Skipped: 0\n      Failed: 0\n","duration":4.245796,"tasks":[{"id":"repeatedTask","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 `xVariable7_1` may be invalid.\n  - XPath could not be validated.\n- Variable `yVariable3_2` may be invalid.\n  - XPath could not be validated.\n- Variable `yVariable1_2` may be invalid.\n  - XPath could not be validated.\n- Variable `xVariable2_1` may be invalid.\n  - XPath could not be validated.\n- Variable `yVariable2_2` may be invalid.\n  - XPath could not be validated.\n- Variable `yVariable7_1` may be invalid.\n  - XPath could not be validated.\n- Variable `xVariable6_1` may be invalid.\n  - XPath could not be validated.\n- Variable `yVariable5_1` may be invalid.\n  - XPath could not be validated.\n- Variable `yVariable6_1` may be invalid.\n  - XPath could not be validated.\n- Variable `xVariable3_2` may be invalid.\n  - XPath could not be validated.\n- Variable `yVariable3_1` may be invalid.\n  - XPath could not be validated.\n- Variable `yVariable4_1` may be invalid.\n  - XPath could not be validated.\n- Variable `xVariable2_2` may be invalid.\n  - XPath could not be validated.\n- Variable `xVariable1_2` may be invalid.\n  - XPath could not be validated.\n- Variable `xVariable1_1` may be invalid.\n  - XPath could not be validated.\n- Variable `yVariable2_1` may be invalid.\n  - XPath could not be validated.\n- Variable `yVariable1_1` may be invalid.\n  - XPath could not be validated.\n- Variable `xVariable5_1` may be invalid.\n  - XPath could not be validated.\n- Variable `xVariable4_1` may be invalid.\n  - XPath could not be validated.\n- Variable `xVariable3_1` 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":0.709926,"algorithm":null,"simulatorDetails":null},{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"/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":0.394534,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"OpenCOR.SimulationSupport.Simulation.run"},{"key":"algorithmParameters","value":[{"kisaoID":"KISAO_0000211","value":"9.9999999999999995e-08"},{"kisaoID":"KISAO_0000475","value":"BDF"},{"kisaoID":"KISAO_0000481","value":"true"},{"kisaoID":"KISAO_0000476","value":"Newton"},{"kisaoID":"KISAO_0000477","value":"Dense"},{"kisaoID":"KISAO_0000480","value":"0"},{"kisaoID":"KISAO_0000415","value":"500"},{"kisaoID":"KISAO_0000467","value":"0"},{"kisaoID":"KISAO_0000478","value":"Banded"},{"kisaoID":"KISAO_0000209","value":"9.9999999999999995e-08"},{"kisaoID":"KISAO_0000479","value":"0"}]}]}],"outputs":[{"id":"plot1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\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: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n","duration":0.534008,"curves":[{"id":"curve1_1","status":"SUCCEEDED"},{"id":"curve1_2","status":"SUCCEEDED"}]},{"id":"plot2","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\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: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n","duration":0.499006,"curves":[{"id":"curve2_1","status":"SUCCEEDED"},{"id":"curve2_2","status":"SUCCEEDED"}]},{"id":"plot3","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\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: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n","duration":0.507328,"curves":[{"id":"curve3_1","status":"SUCCEEDED"},{"id":"curve3_2","status":"SUCCEEDED"}]},{"id":"plot4","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.29488,"curves":[{"id":"curve4_1","status":"SUCCEEDED"}]},{"id":"plot5","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.329544,"curves":[{"id":"curve5_1","status":"SUCCEEDED"}]},{"id":"plot6","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.297956,"curves":[{"id":"curve6_1","status":"SUCCEEDED"}]},{"id":"plot7","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.291328,"curves":[{"id":"curve7_1","status":"SUCCEEDED"}]}]}]}