{"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    488      0 --:--:-- --:--:-- --:--:--   489\n\r100  990k  100  990k    0     0  2260k      0 --:--:-- --:--:-- --:--:-- 2260k\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  - 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.\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 `goldbeter_guilmot_1995_Fig2.sedml` may be invalid.\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.\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 1 plots:\n  goldbeter_guilmot_1995_Fig2.sedml:\n    Tasks (2):\n      repeatedTask\n      task1\n    Plots (1):\n      plot1: 3 curves\n\nExecuting SED-ML file 1: goldbeter_guilmot_1995_Fig2.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 (1):\n    Succeeded: 1\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 3.8 KiB/3.8 KiB (40.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6261738b90c6a195955782e2/rawLog.txt\nCompleted 6.6 KiB/6.6 KiB (56.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6261738b90c6a195955782e2/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 78%)\n  adding: outputs/goldbeter_guilmot_1995_Fig2.sedml/ (stored 0%)\n  adding: outputs/goldbeter_guilmot_1995_Fig2.sedml/plot1.pdf (deflated 20%)\n  adding: outputs/reports.h5 (deflated 40%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 33.5 KiB/33.5 KiB (214.9 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6261738b90c6a195955782e2/outputs/reports.h5\nCompleted 35.1 KiB/65.2 KiB (400.8 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6261738b90c6a195955782e2/output.zip\nCompleted 35.1 KiB/65.2 KiB (400.8 KiB/s) with 3 file(s) remaining\rCompleted 40.0 KiB/65.2 KiB (291.1 KiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6261738b90c6a195955782e2/rawLog.txt\nCompleted 40.0 KiB/65.2 KiB (291.1 KiB/s) with 2 file(s) remaining\rCompleted 51.1 KiB/65.2 KiB (310.1 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6261738b90c6a195955782e2/outputs/plots.zip\nCompleted 51.1 KiB/65.2 KiB (310.1 KiB/s) with 1 file(s) remaining\rCompleted 65.2 KiB/65.2 KiB (344.8 KiB/s) with 1 file(s) remaining\rupload: outputs/goldbeter_guilmot_1995_Fig2.sedml/plot1.pdf to s3://files.biosimulations.org/simulations/6261738b90c6a195955782e2/outputs/goldbeter_guilmot_1995_Fig2.sedml/plot1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/goldbeter_guilmot_1995.cellml  \n  inflating: contents/goldbeter_guilmot_1995.svg  \n  inflating: contents/goldbeter_guilmot_1995.xul  \n  inflating: contents/goldbeter_guilmot_1995.session.xml  \n  inflating: contents/goldbeter_guilmot_1995_Fig2.sedml  \n  inflating: contents/goldbeter_guilmot_1995.png  \n  inflating: contents/goldbeter_guilmot_1995.ai  \n  inflating: contents/goldbeter_guilmot_1995.html  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 13.4 KiB/1.1 MiB (147.9 KiB/s) with 10 file(s) remaining\rupload: contents/goldbeter_guilmot_1995.cellml to s3://files.biosimulations.org/simulations/6261738b90c6a195955782e2/contents/goldbeter_guilmot_1995.cellml\nCompleted 13.4 KiB/1.1 MiB (147.9 KiB/s) with 9 file(s) remaining\rCompleted 269.4 KiB/1.1 MiB (2.3 MiB/s) with 9 file(s) remaining \rCompleted 525.4 KiB/1.1 MiB (4.1 MiB/s) with 9 file(s) remaining \rCompleted 781.4 KiB/1.1 MiB (6.1 MiB/s) with 9 file(s) remaining \rCompleted 1.0 MiB/1.1 MiB (8.0 MiB/s) with 9 file(s) remaining   \rCompleted 1.0 MiB/1.1 MiB (7.8 MiB/s) with 9 file(s) remaining   \rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6261738b90c6a195955782e2/contents/manifest.xml\nCompleted 1.0 MiB/1.1 MiB (7.8 MiB/s) with 8 file(s) remaining\rCompleted 1.0 MiB/1.1 MiB (6.9 MiB/s) with 8 file(s) remaining\rupload: contents/goldbeter_guilmot_1995.html to s3://files.biosimulations.org/simulations/6261738b90c6a195955782e2/contents/goldbeter_guilmot_1995.html\nCompleted 1.0 MiB/1.1 MiB (6.9 MiB/s) with 7 file(s) remaining\rCompleted 1.0 MiB/1.1 MiB (6.8 MiB/s) with 7 file(s) remaining\rupload: contents/goldbeter_guilmot_1995.xul to s3://files.biosimulations.org/simulations/6261738b90c6a195955782e2/contents/goldbeter_guilmot_1995.xul\nCompleted 1.0 MiB/1.1 MiB (6.8 MiB/s) with 6 file(s) remaining\rCompleted 1.1 MiB/1.1 MiB (6.0 MiB/s) with 6 file(s) remaining\rupload: contents/goldbeter_guilmot_1995.png to s3://files.biosimulations.org/simulations/6261738b90c6a195955782e2/contents/goldbeter_guilmot_1995.png\nCompleted 1.1 MiB/1.1 MiB (6.0 MiB/s) with 5 file(s) remaining\rCompleted 1.1 MiB/1.1 MiB (5.9 MiB/s) with 5 file(s) remaining\rupload: contents/goldbeter_guilmot_1995.session.xml to s3://files.biosimulations.org/simulations/6261738b90c6a195955782e2/contents/goldbeter_guilmot_1995.session.xml\nCompleted 1.1 MiB/1.1 MiB (5.9 MiB/s) with 4 file(s) remaining\rCompleted 1.1 MiB/1.1 MiB (5.0 MiB/s) with 4 file(s) remaining\rupload: contents/goldbeter_guilmot_1995_Fig2.sedml to s3://files.biosimulations.org/simulations/6261738b90c6a195955782e2/contents/goldbeter_guilmot_1995_Fig2.sedml\nCompleted 1.1 MiB/1.1 MiB (5.0 MiB/s) with 3 file(s) remaining\rCompleted 1.1 MiB/1.1 MiB (4.9 MiB/s) with 3 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6261738b90c6a195955782e2/contents/metadata.rdf\nCompleted 1.1 MiB/1.1 MiB (4.9 MiB/s) with 2 file(s) remaining\rCompleted 1.1 MiB/1.1 MiB (4.9 MiB/s) with 2 file(s) remaining\rupload: contents/goldbeter_guilmot_1995.svg to s3://files.biosimulations.org/simulations/6261738b90c6a195955782e2/contents/goldbeter_guilmot_1995.svg\nCompleted 1.1 MiB/1.1 MiB (4.9 MiB/s) with 1 file(s) remaining\rCompleted 1.1 MiB/1.1 MiB (4.0 MiB/s) with 1 file(s) remaining\rupload: contents/goldbeter_guilmot_1995.ai to s3://files.biosimulations.org/simulations/6261738b90c6a195955782e2/contents/goldbeter_guilmot_1995.ai\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.5 KiB/9.5 KiB (77.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6261738b90c6a195955782e2/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /goldbeter_guilmot_1995_Fig2.sedml\ncreating dataset /goldbeter_guilmot_1995_Fig2.sedml/plot1, shape: (6, 1, 1, 801), type: float64\ndataset created, uuid: d-0b0b2971-3b31bcfe-3d29-f36cbf-a69684, chunk_size: (6, 1, 1, 801)\ncreating attribute combineArchiveLocation in /goldbeter_guilmot_1995_Fig2.sedml\ncreating attribute uri in /goldbeter_guilmot_1995_Fig2.sedml\ncreating attribute _type in /goldbeter_guilmot_1995_Fig2.sedml/plot1\ncreating attribute sedmlDataSetDataTypes in /goldbeter_guilmot_1995_Fig2.sedml/plot1\ncreating attribute sedmlDataSetIds in /goldbeter_guilmot_1995_Fig2.sedml/plot1\ncreating attribute sedmlDataSetLabels in /goldbeter_guilmot_1995_Fig2.sedml/plot1\ncreating attribute sedmlDataSetNames in /goldbeter_guilmot_1995_Fig2.sedml/plot1\ncreating attribute sedmlDataSetShapes in /goldbeter_guilmot_1995_Fig2.sedml/plot1\ncreating attribute sedmlId in /goldbeter_guilmot_1995_Fig2.sedml/plot1\ncreating attribute uri in /goldbeter_guilmot_1995_Fig2.sedml/plot1\ncreate_links: /\ngot link: goldbeter_guilmot_1995_Fig2.sedml\ncreate_links: /goldbeter_guilmot_1995_Fig2.sedml\ngot link: plot1\nwrite_dataset src: /goldbeter_guilmot_1995_Fig2.sedml/plot1 to tgt: /goldbeter_guilmot_1995_Fig2.sedml/plot1, shape: (6, 1, 1, 801), type: float64\niterating over chunks for /goldbeter_guilmot_1995_Fig2.sedml/plot1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1, 1), slice(0, 1, 1), slice(0, 801, 1))\ndone with dataload for /goldbeter_guilmot_1995_Fig2.sedml/plot1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6261738b90c6a195955782e2\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... succeeded.\nProcess 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.89401,"sedDocuments":[{"location":"goldbeter_guilmot_1995_Fig2.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"  Found 2 tasks and 1 outputs:\n    Tasks:\n      `repeatedTask`\n      `task1`\n    Outputs:\n      `plot1`\n  Executing task 1: `repeatedTask`\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\n    Generating 1 outputs ...\n      Generating output 1: `plot1` ... \u001b[34msucceeded\u001b[0m\n  Executing task 2: `task1`\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\n    Generating 1 outputs ...\n      Generating output 1: `plot1` .../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 1 outputs:\n    Tasks:\n      Succeeded: 2\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n","duration":1.392622,"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 `yVariable1_3` may be invalid.\n  - XPath could not be validated.\n- Variable `xVariable1_1` may be invalid.\n  - XPath could not be validated.\n- Variable `yVariable1_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 `yVariable1_1` may be invalid.\n  - XPath could not be validated.\n- Variable `xVariable1_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":0.656264,"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":0.380503,"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":"0"},{"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":"/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":0.246906,"curves":[{"id":"curve1_1","status":"SUCCEEDED"},{"id":"curve1_2","status":"SUCCEEDED"},{"id":"curve1_3","status":"SUCCEEDED"}]}]}]}