{"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    451      0 --:--:-- --:--:-- --:--:--   451\n\r100 84502  100 84502    0     0   182k      0 --:--:-- --:--:-- --:--:--  182k\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)\nArchive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:\n  action-potential.xml:\n    Tasks (1):\n      task1\n    Plots (1):\n      plot1: 1 curves\n\nExecuting SED-ML file 1: action-potential.xml ...\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 2.7 KiB/2.7 KiB (27.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6261783790c6a195955798bc/rawLog.txt\nCompleted 2.8 KiB/2.8 KiB (27.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6261783790c6a195955798bc/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 66%)\n  adding: outputs/action-potential.xml/ (stored 0%)\n  adding: outputs/action-potential.xml/plot1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 37%)\n  adding: rawLog.txt (deflated 67%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 31.6 KiB/31.6 KiB (410.7 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6261783790c6a195955798bc/outputs/reports.h5\nCompleted 29.5 KiB/49.4 KiB (371.7 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6261783790c6a195955798bc/output.zip\nCompleted 29.5 KiB/49.4 KiB (371.7 KiB/s) with 3 file(s) remaining\rCompleted 35.9 KiB/49.4 KiB (297.9 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6261783790c6a195955798bc/outputs/plots.zip\nCompleted 35.9 KiB/49.4 KiB (297.9 KiB/s) with 2 file(s) remaining\rCompleted 39.6 KiB/49.4 KiB (271.5 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6261783790c6a195955798bc/rawLog.txt\nCompleted 39.6 KiB/49.4 KiB (271.5 KiB/s) with 1 file(s) remaining\rCompleted 49.4 KiB/49.4 KiB (322.5 KiB/s) with 1 file(s) remaining\rupload: outputs/action-potential.xml/plot1.pdf to s3://files.biosimulations.org/simulations/6261783790c6a195955798bc/outputs/action-potential.xml/plot1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/action-potential.png  \n  inflating: contents/Ohara_Rudy_2011.cellml  \n  inflating: contents/index.html     \n  inflating: contents/action-potential.xml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 213.0 KiB/293.9 KiB (2.1 MiB/s) with 6 file(s) remaining\rupload: contents/Ohara_Rudy_2011.cellml to s3://files.biosimulations.org/simulations/6261783790c6a195955798bc/contents/Ohara_Rudy_2011.cellml\nCompleted 213.0 KiB/293.9 KiB (2.1 MiB/s) with 5 file(s) remaining\rCompleted 214.4 KiB/293.9 KiB (1.7 MiB/s) with 5 file(s) remaining\rupload: contents/index.html to s3://files.biosimulations.org/simulations/6261783790c6a195955798bc/contents/index.html\nCompleted 214.4 KiB/293.9 KiB (1.7 MiB/s) with 4 file(s) remaining\rCompleted 220.8 KiB/293.9 KiB (1.6 MiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6261783790c6a195955798bc/contents/metadata.rdf\nCompleted 220.8 KiB/293.9 KiB (1.6 MiB/s) with 3 file(s) remaining\rCompleted 222.4 KiB/293.9 KiB (1.6 MiB/s) with 3 file(s) remaining\rupload: contents/action-potential.xml to s3://files.biosimulations.org/simulations/6261783790c6a195955798bc/contents/action-potential.xml\nCompleted 222.4 KiB/293.9 KiB (1.6 MiB/s) with 2 file(s) remaining\rCompleted 223.1 KiB/293.9 KiB (1.2 MiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6261783790c6a195955798bc/contents/manifest.xml\nCompleted 223.1 KiB/293.9 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 293.9 KiB/293.9 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: contents/action-potential.png to s3://files.biosimulations.org/simulations/6261783790c6a195955798bc/contents/action-potential.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 6.7 KiB/6.7 KiB (55.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6261783790c6a195955798bc/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /action-potential.xml\ncreating dataset /action-potential.xml/plot1, shape: (2, 2501), type: float64\ndataset created, uuid: d-7a473ec9-e0df4edc-ff54-4f28e3-c53715, chunk_size: (2, 2501)\ncreating attribute combineArchiveLocation in /action-potential.xml\ncreating attribute uri in /action-potential.xml\ncreating attribute _type in /action-potential.xml/plot1\ncreating attribute sedmlDataSetDataTypes in /action-potential.xml/plot1\ncreating attribute sedmlDataSetIds in /action-potential.xml/plot1\ncreating attribute sedmlDataSetLabels in /action-potential.xml/plot1\ncreating attribute sedmlDataSetNames in /action-potential.xml/plot1\ncreating attribute sedmlDataSetShapes in /action-potential.xml/plot1\ncreating attribute sedmlId in /action-potential.xml/plot1\ncreating attribute sedmlName in /action-potential.xml/plot1\ncreating attribute uri in /action-potential.xml/plot1\ncreate_links: /\ngot link: action-potential.xml\ncreate_links: /action-potential.xml\ngot link: plot1\nwrite_dataset src: /action-potential.xml/plot1 to tgt: /action-potential.xml/plot1, shape: (2, 2501), type: float64\niterating over chunks for /action-potential.xml/plot1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 2501, 1))\ndone with dataload for /action-potential.xml/plot1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6261783790c6a195955798bc\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 the metadata in the COMBINE archive ... succeeded.\nPost the metadata 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.\nProcess and upload the outputs of the simulation run ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":2.043343,"sedDocuments":[{"location":"action-potential.xml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"  Found 1 tasks and 1 outputs:\n    Tasks:\n      `task1`\n    Outputs:\n      `plot1`\n  Executing task 1: `task1`\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\n    Generating 1 outputs ...\n      Generating output 1: `plot1` ... \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":1.490047,"tasks":[{"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[33m- Variable `t` may be invalid.\n  - XPath could not be validated.\n- Variable `v` 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":1.182511,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"OpenCOR.SimulationSupport.Simulation.run"},{"key":"algorithmParameters","value":[]}]}],"outputs":[{"id":"plot1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.199593,"curves":[{"id":"c1","status":"SUCCEEDED"}]}]}]}