{"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    486      0 --:--:-- --:--:-- --:--:--   486\r100   139  100   139    0     0    480      0 --:--:-- --:--:-- --:--:--   479\n\r100  175k  100  175k    0     0   422k      0 --:--:-- --:--:-- --:--:--  422k\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 `BG_cAMP.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.\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 `BG_cAMP.sedml` may be invalid.\n    - Model `model` may be invalid.\n      - The model file `BG_cAMP.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.\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.\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 4 plots:\n  BG_cAMP.sedml:\n    Tasks (2):\n      repeatedTask\n      task1\n    Plots (4):\n      plot1: 1 curves\n      plot2: 1 curves\n      plot3: 8 curves\n      plot4: 3 curves\n\nExecuting SED-ML file 1: BG_cAMP.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 (4):\n    Succeeded: 4\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 6.8 KiB/6.8 KiB (69.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/rawLog.txt\nCompleted 13.8 KiB/13.8 KiB (89.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 86%)\n  adding: outputs/BG_cAMP.sedml/ (stored 0%)\n  adding: outputs/BG_cAMP.sedml/plot3.pdf (deflated 33%)\n  adding: outputs/BG_cAMP.sedml/plot4.pdf (deflated 33%)\n  adding: outputs/BG_cAMP.sedml/plot2.pdf (deflated 34%)\n  adding: outputs/BG_cAMP.sedml/plot1.pdf (deflated 34%)\n  adding: outputs/reports.h5 (deflated 1%)\n  adding: rawLog.txt (deflated 81%)\n\n\u001b[0;36m=================================================== Saving outputs 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s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/output.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BG_cAMP.sedml  \n  inflating: contents/BG_cAMP.cellml  \n  inflating: contents/parameter_finder/find_BG_parameters.py  \n  inflating: contents/parameter_finder/find_BG_parameters.m  \n  inflating: contents/parameter_finder/kinetic_parameters.m  \n  inflating: contents/parameter_finder/TEMP.cellml.txt  \n  inflating: contents/parameter_finder/kinetic_parameters_cAMP.py  \n  inflating: contents/parameter_finder/data/rxnID.txt  \n  inflating: contents/parameter_finder/data/Kname.txt  \n  inflating: contents/parameter_finder/data/all_forward_matrix.txt  \n  inflating: contents/parameter_finder/data/all_reverse_matrix.txt  \n  inflating: contents/parameter_finder/data/stoichiometric_matrix.xlsx  \n  inflating: contents/parameter_finder/data/~$stoichiometric_matrix.xlsx  \n  inflating: contents/parameter_finder/output/all_parameters_out.json  \n  inflating: contents/parameter_finder/output/all_params.mat  \n  inflating: contents/units_and_constants/constants_BG.cellml  \n  inflating: contents/units_and_constants/units_BG.cellml  \n  inflating: contents/exposure/exposure_frontpage.rst  \n  inflating: contents/exposure/drawing.svg  \n  inflating: contents/exposure/BG_cAMP_network.png  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 63.0 KiB/417.0 KiB (829.4 KiB/s) with 22 file(s) remaining\rupload: contents/BG_cAMP.cellml to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/contents/BG_cAMP.cellml\nCompleted 63.0 KiB/417.0 KiB (829.4 KiB/s) with 21 file(s) remaining\rCompleted 69.4 KiB/417.0 KiB (466.6 KiB/s) with 21 file(s) remaining\rupload: contents/parameter_finder/find_BG_parameters.m to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/contents/parameter_finder/find_BG_parameters.m\nCompleted 69.4 KiB/417.0 KiB (466.6 KiB/s) with 20 file(s) remaining\rCompleted 215.1 KiB/417.0 KiB (1.4 MiB/s) with 20 file(s) remaining \rupload: contents/exposure/BG_cAMP_network.png to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/contents/exposure/BG_cAMP_network.png\nCompleted 215.1 KiB/417.0 KiB (1.4 MiB/s) with 19 file(s) remaining\rCompleted 321.2 KiB/417.0 KiB (2.0 MiB/s) with 19 file(s) remaining\rupload: contents/exposure/drawing.svg to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/contents/exposure/drawing.svg\nCompleted 321.2 KiB/417.0 KiB (2.0 MiB/s) with 18 file(s) remaining\rCompleted 324.1 KiB/417.0 KiB (2.0 MiB/s) with 18 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/contents/manifest.xml\nCompleted 324.1 KiB/417.0 KiB (2.0 MiB/s) with 17 file(s) remaining\rCompleted 358.3 KiB/417.0 KiB (2.1 MiB/s) with 17 file(s) remaining\rupload: contents/BG_cAMP.sedml to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/contents/BG_cAMP.sedml\nCompleted 358.3 KiB/417.0 KiB (2.1 MiB/s) with 16 file(s) remaining\rCompleted 372.4 KiB/417.0 KiB (2.1 MiB/s) with 16 file(s) remaining\rupload: contents/parameter_finder/data/stoichiometric_matrix.xlsx to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/contents/parameter_finder/data/stoichiometric_matrix.xlsx\nCompleted 372.4 KiB/417.0 KiB (2.1 MiB/s) with 15 file(s) remaining\rCompleted 372.6 KiB/417.0 KiB (2.1 MiB/s) with 15 file(s) remaining\rCompleted 372.6 KiB/417.0 KiB (2.1 MiB/s) with 15 file(s) remaining\rupload: contents/parameter_finder/data/rxnID.txt to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/contents/parameter_finder/data/rxnID.txt\nCompleted 372.6 KiB/417.0 KiB (2.1 MiB/s) with 14 file(s) remaining\rupload: contents/parameter_finder/data/~$stoichiometric_matrix.xlsx to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/contents/parameter_finder/data/~$stoichiometric_matrix.xlsx\nCompleted 372.6 KiB/417.0 KiB (2.1 MiB/s) with 13 file(s) remaining\rCompleted 375.8 KiB/417.0 KiB (1.8 MiB/s) with 13 file(s) remaining\rupload: contents/exposure/exposure_frontpage.rst to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/contents/exposure/exposure_frontpage.rst\nCompleted 375.8 KiB/417.0 KiB (1.8 MiB/s) with 12 file(s) remaining\rCompleted 378.9 KiB/417.0 KiB (1.5 MiB/s) with 12 file(s) remaining\rupload: contents/parameter_finder/kinetic_parameters_cAMP.py to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/contents/parameter_finder/kinetic_parameters_cAMP.py\nCompleted 378.9 KiB/417.0 KiB (1.5 MiB/s) with 11 file(s) remaining\rCompleted 388.7 KiB/417.0 KiB (1.5 MiB/s) with 11 file(s) remaining\rupload: contents/parameter_finder/find_BG_parameters.py to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/contents/parameter_finder/find_BG_parameters.py\nCompleted 388.7 KiB/417.0 KiB (1.5 MiB/s) with 10 file(s) remaining\rCompleted 391.7 KiB/417.0 KiB (1.5 MiB/s) with 10 file(s) remaining\rupload: contents/parameter_finder/kinetic_parameters.m to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/contents/parameter_finder/kinetic_parameters.m\nCompleted 391.7 KiB/417.0 KiB (1.5 MiB/s) with 9 file(s) remaining\rCompleted 398.5 KiB/417.0 KiB (1.5 MiB/s) with 9 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/contents/metadata.rdf\nCompleted 398.5 KiB/417.0 KiB (1.5 MiB/s) with 8 file(s) remaining\rCompleted 399.0 KiB/417.0 KiB (1.5 MiB/s) with 8 file(s) remaining\rupload: contents/units_and_constants/constants_BG.cellml to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/contents/units_and_constants/constants_BG.cellml\nCompleted 399.0 KiB/417.0 KiB (1.5 MiB/s) with 7 file(s) remaining\rCompleted 399.9 KiB/417.0 KiB (1.5 MiB/s) with 7 file(s) remaining\rupload: contents/parameter_finder/output/all_parameters_out.json to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/contents/parameter_finder/output/all_parameters_out.json\nCompleted 399.9 KiB/417.0 KiB (1.5 MiB/s) with 6 file(s) remaining\rCompleted 400.4 KiB/417.0 KiB (1.5 MiB/s) with 6 file(s) remaining\rupload: contents/parameter_finder/data/all_reverse_matrix.txt to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/contents/parameter_finder/data/all_reverse_matrix.txt\nCompleted 400.4 KiB/417.0 KiB (1.5 MiB/s) with 5 file(s) remaining\rCompleted 401.5 KiB/417.0 KiB (1.4 MiB/s) with 5 file(s) remaining\rupload: contents/parameter_finder/output/all_params.mat to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/contents/parameter_finder/output/all_params.mat\nCompleted 401.5 KiB/417.0 KiB (1.4 MiB/s) with 4 file(s) remaining\rCompleted 414.2 KiB/417.0 KiB (1.3 MiB/s) with 4 file(s) remaining\rupload: contents/parameter_finder/TEMP.cellml.txt to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/contents/parameter_finder/TEMP.cellml.txt\nCompleted 414.2 KiB/417.0 KiB (1.3 MiB/s) with 3 file(s) remaining\rCompleted 416.5 KiB/417.0 KiB (1.2 MiB/s) with 3 file(s) remaining\rupload: contents/units_and_constants/units_BG.cellml to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/contents/units_and_constants/units_BG.cellml\nCompleted 416.5 KiB/417.0 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 416.6 KiB/417.0 KiB (1.2 MiB/s) with 2 file(s) remaining\rupload: contents/parameter_finder/data/Kname.txt to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/contents/parameter_finder/data/Kname.txt\nCompleted 416.6 KiB/417.0 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 417.0 KiB/417.0 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: contents/parameter_finder/data/all_forward_matrix.txt to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/contents/parameter_finder/data/all_forward_matrix.txt\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 22.4 KiB/22.4 KiB (207.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/626173dd90c6a19595578482/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BG_cAMP.sedml\ncreating dataset /BG_cAMP.sedml/plot1, shape: (2, 1, 1, 100001), type: float64\ndataset created, uuid: d-150a65fa-3e24d317-00ff-3aaa6c-89aa98, chunk_size: (2, 1, 1, 100001)\ncreating dataset /BG_cAMP.sedml/plot2, shape: (2, 1, 1, 100001), type: float64\ndataset created, uuid: d-150a65fa-3e24d317-08d7-331f3b-a5de6e, chunk_size: (2, 1, 1, 100001)\ncreating dataset /BG_cAMP.sedml/plot3, shape: (16, 1, 1, 100001), type: float64\ndataset created, uuid: d-150a65fa-3e24d317-04a4-e6eda4-d97fe6, chunk_size: (4, 1, 1, 50008)\ncreating dataset /BG_cAMP.sedml/plot4, shape: (6, 1, 1, 100001), type: float64\ndataset created, uuid: d-150a65fa-3e24d317-ec88-df30d5-724ad2, chunk_size: (6, 1, 1, 25008)\ncreating attribute combineArchiveLocation in /BG_cAMP.sedml\ncreating attribute uri in /BG_cAMP.sedml\ncreating attribute _type in /BG_cAMP.sedml/plot1\ncreating attribute sedmlDataSetDataTypes in /BG_cAMP.sedml/plot1\ncreating attribute sedmlDataSetIds in /BG_cAMP.sedml/plot1\ncreating attribute sedmlDataSetLabels in /BG_cAMP.sedml/plot1\ncreating attribute sedmlDataSetNames in /BG_cAMP.sedml/plot1\ncreating attribute sedmlDataSetShapes in /BG_cAMP.sedml/plot1\ncreating attribute sedmlId in /BG_cAMP.sedml/plot1\ncreating attribute uri in /BG_cAMP.sedml/plot1\ncreating attribute _type in /BG_cAMP.sedml/plot2\ncreating attribute sedmlDataSetDataTypes in /BG_cAMP.sedml/plot2\ncreating attribute sedmlDataSetIds in /BG_cAMP.sedml/plot2\ncreating attribute sedmlDataSetLabels in /BG_cAMP.sedml/plot2\ncreating attribute sedmlDataSetNames in /BG_cAMP.sedml/plot2\ncreating attribute sedmlDataSetShapes in /BG_cAMP.sedml/plot2\ncreating attribute sedmlId in /BG_cAMP.sedml/plot2\ncreating attribute uri in /BG_cAMP.sedml/plot2\ncreating attribute _type in /BG_cAMP.sedml/plot3\ncreating attribute sedmlDataSetDataTypes in /BG_cAMP.sedml/plot3\ncreating attribute sedmlDataSetIds in /BG_cAMP.sedml/plot3\ncreating attribute sedmlDataSetLabels in /BG_cAMP.sedml/plot3\ncreating attribute sedmlDataSetNames in /BG_cAMP.sedml/plot3\ncreating attribute sedmlDataSetShapes in /BG_cAMP.sedml/plot3\ncreating attribute sedmlId in /BG_cAMP.sedml/plot3\ncreating attribute uri in /BG_cAMP.sedml/plot3\ncreating attribute _type in /BG_cAMP.sedml/plot4\ncreating attribute sedmlDataSetDataTypes in /BG_cAMP.sedml/plot4\ncreating attribute sedmlDataSetIds in /BG_cAMP.sedml/plot4\ncreating attribute sedmlDataSetLabels in /BG_cAMP.sedml/plot4\ncreating attribute sedmlDataSetNames in /BG_cAMP.sedml/plot4\ncreating attribute sedmlDataSetShapes in /BG_cAMP.sedml/plot4\ncreating attribute sedmlId in /BG_cAMP.sedml/plot4\ncreating attribute uri in /BG_cAMP.sedml/plot4\ncreate_links: /\ngot link: BG_cAMP.sedml\ncreate_links: /BG_cAMP.sedml\ngot link: plot1\ngot link: plot2\ngot link: plot3\ngot link: plot4\nwrite_dataset src: /BG_cAMP.sedml/plot1 to tgt: /BG_cAMP.sedml/plot1, shape: (2, 1, 1, 100001), type: float64\niterating over chunks for /BG_cAMP.sedml/plot1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1, 1), slice(0, 1, 1), slice(0, 100001, 1))\ndone with dataload for /BG_cAMP.sedml/plot1\nwrite_dataset src: /BG_cAMP.sedml/plot2 to tgt: /BG_cAMP.sedml/plot2, shape: (2, 1, 1, 100001), type: float64\niterating over chunks for /BG_cAMP.sedml/plot2\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1, 1), slice(0, 1, 1), slice(0, 100001, 1))\ndone with dataload for /BG_cAMP.sedml/plot2\nwrite_dataset src: /BG_cAMP.sedml/plot3 to tgt: /BG_cAMP.sedml/plot3, shape: (16, 1, 1, 100001), type: float64\niterating over chunks for /BG_cAMP.sedml/plot3\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1, 1), slice(0, 1, 1), slice(0, 50008, 1))\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1, 1), slice(0, 1, 1), slice(50008, 100001, 1))\nwriting dataset data for slice: (slice(4, 8, 1), slice(0, 1, 1), slice(0, 1, 1), slice(0, 50008, 1))\nwriting dataset data for slice: (slice(4, 8, 1), slice(0, 1, 1), slice(0, 1, 1), slice(50008, 100001, 1))\nwriting dataset data for slice: (slice(8, 12, 1), slice(0, 1, 1), slice(0, 1, 1), slice(0, 50008, 1))\nwriting dataset data for slice: (slice(8, 12, 1), slice(0, 1, 1), slice(0, 1, 1), slice(50008, 100001, 1))\nwriting dataset data for slice: (slice(12, 16, 1), slice(0, 1, 1), slice(0, 1, 1), slice(0, 50008, 1))\nwriting dataset data for slice: (slice(12, 16, 1), slice(0, 1, 1), slice(0, 1, 1), slice(50008, 100001, 1))\ndone with dataload for /BG_cAMP.sedml/plot3\nwrite_dataset src: /BG_cAMP.sedml/plot4 to tgt: /BG_cAMP.sedml/plot4, shape: (6, 1, 1, 100001), type: float64\niterating over chunks for /BG_cAMP.sedml/plot4\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1, 1), slice(0, 1, 1), slice(0, 25008, 1))\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1, 1), slice(0, 1, 1), slice(25008, 50016, 1))\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1, 1), slice(0, 1, 1), slice(50016, 75024, 1))\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1, 1), slice(0, 1, 1), slice(75024, 100001, 1))\ndone with dataload for /BG_cAMP.sedml/plot4\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/626173dd90c6a19595578482\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... succeeded.\nProcess the 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 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":41.37723,"sedDocuments":[{"location":"BG_cAMP.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"  Found 2 tasks and 4 outputs:\n    Tasks:\n      `repeatedTask`\n      `task1`\n    Outputs:\n      `plot1`\n      `plot2`\n      `plot3`\n      `plot4`\n  Executing task 1: `repeatedTask`\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\n    Generating 4 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  Executing task 2: `task1`\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\n    Generating 4 outputs ...\n      Generating output 1: `plot1` ...      Generating output 2: `plot2` ...      Generating output 3: `plot3` ...      Generating output 4: `plot4` .../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 4 outputs:\n    Tasks:\n      Succeeded: 2\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 4\n      Skipped: 0\n      Failed: 0\n","duration":40.756977,"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 `yVariable3_5` may be invalid.\n  - XPath could not be validated.\n- Variable `yVariable3_2` 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_7` may be invalid.\n  - XPath could not be validated.\n- Variable `yVariable4_1` may be invalid.\n  - XPath could not be validated.\n- Variable `xVariable3_8` may be invalid.\n  - XPath could not be validated.\n- Variable `xVariable2_1` may be invalid.\n  - XPath could not be validated.\n- Variable `yVariable3_4` may be invalid.\n  - XPath could not be validated.\n- Variable `xVariable3_5` may be invalid.\n  - XPath could not be validated.\n- Variable `xVariable3_1` may be invalid.\n  - XPath could not be validated.\n- Variable `xVariable1_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 `yVariable1_1` may be invalid.\n  - XPath could not be validated.\n- Variable `yVariable3_6` may be invalid.\n  - XPath could not be validated.\n- Variable `yVariable3_3` may be invalid.\n  - XPath could not be validated.\n- Variable `yVariable3_8` may be invalid.\n  - XPath could not be validated.\n- Variable `xVariable4_3` may be invalid.\n  - XPath could not be validated.\n- Variable `xVariable3_6` may be invalid.\n  - XPath could not be validated.\n- Variable `xVariable3_3` may be invalid.\n  - XPath could not be validated.\n- Variable `yVariable3_1` may be invalid.\n  - XPath could not be validated.\n- Variable `xVariable4_2` may be invalid.\n  - XPath could not be validated.\n- Variable `xVariable3_4` may be invalid.\n  - XPath could not be validated.\n- Variable `yVariable2_1` may be invalid.\n  - XPath could not be validated.\n- Variable `yVariable3_7` may be invalid.\n  - XPath could not be validated.\n- Variable `yVariable4_2` may be invalid.\n  - XPath could not be validated.\n- Variable `yVariable4_3` 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":1.36104,"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":0.851373,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"OpenCOR.SimulationSupport.Simulation.run"},{"key":"algorithmParameters","value":[{"kisaoID":"KISAO_0000211","value":1e-7},{"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":1e-7},{"kisaoID":"KISAO_0000478","value":"Banded"},{"kisaoID":"KISAO_0000209","value":1e-7},{"kisaoID":"KISAO_0000479","value":"0"}]}]}],"outputs":[{"id":"plot1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":3.745685,"curves":[{"id":"curve1_1","status":"SUCCEEDED"}]},{"id":"plot2","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":3.81427,"curves":[{"id":"curve2_1","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/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/viz/io.py:101: UserWarning: Creating legend with loc=\"best\" can be slow with large amounts of data.\n  figure.savefig(os.path.join(base_path, rel_path + '.' + format.value))\n","duration":22.596581,"curves":[{"id":"curve3_1","status":"SUCCEEDED"},{"id":"curve3_2","status":"SUCCEEDED"},{"id":"curve3_3","status":"SUCCEEDED"},{"id":"curve3_4","status":"SUCCEEDED"},{"id":"curve3_5","status":"SUCCEEDED"},{"id":"curve3_6","status":"SUCCEEDED"},{"id":"curve3_7","status":"SUCCEEDED"},{"id":"curve3_8","status":"SUCCEEDED"}]},{"id":"plot4","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/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/viz/io.py:101: UserWarning: Creating legend with loc=\"best\" can be slow with large amounts of data.\n  figure.savefig(os.path.join(base_path, rel_path + '.' + format.value))\n","duration":8.166786,"curves":[{"id":"curve4_1","status":"SUCCEEDED"},{"id":"curve4_2","status":"SUCCEEDED"},{"id":"curve4_3","status":"SUCCEEDED"}]}]}]}