{"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    485      0 --:--:-- --:--:-- --:--:--   484\n\r100  125k  100  125k    0     0   299k      0 --:--:-- --:--:-- --:--:--  299k\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 `model1` may be invalid.\n    - The model file `sin_approximations_import.xml` may be invalid.\n      - Validation is not available for CellML 1.1 files.\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 `sin_approximations_sedml.xml` may be invalid.\n    - Model `model1` may be invalid.\n      - The model file `sin_approximations_import.xml` may be invalid.\n        - Validation is not available for CellML 1.1 files.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\nArchive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\n  sin_approximations_sedml.xml:\n    Tasks (1):\n      task1\n    Reports (1):\n      report: 4 data sets\n\nExecuting SED-ML file 1: sin_approximations_sedml.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 3.7 KiB/3.7 KiB (48.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/626177e5abe612c540c691da/rawLog.txt\nCompleted 4.0 KiB/4.0 KiB (50.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/626177e5abe612c540c691da/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 73%)\n  adding: outputs/reports.h5 (deflated 90%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 13.4 KiB/13.4 KiB (80.7 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/626177e5abe612c540c691da/outputs/reports.h5\nCompleted 4.2 KiB/8.9 KiB (46.3 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/626177e5abe612c540c691da/output.zip\nCompleted 4.2 KiB/8.9 KiB (46.3 KiB/s) with 1 file(s) remaining\rCompleted 8.9 KiB/8.9 KiB (65.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/626177e5abe612c540c691da/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/sin.xml        \n  inflating: contents/SED-ML web tools screenshot.png  \n  inflating: contents/sin_approximations_import.xml  \n  inflating: contents/documentation.html  \n  inflating: contents/documentation-sedml.html  \n  inflating: contents/documentation-csim.html  \n  inflating: contents/sin_approximations_sedml.xml  \n  inflating: contents/OpenCell-results.png  \n  inflating: contents/parabolic_approx_sin.xml  \n  inflating: contents/sin_approximations.xml  \n  inflating: contents/deriv_approx_sin.xml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 47.6 KiB/162.7 KiB (442.9 KiB/s) with 13 file(s) remaining\rupload: contents/OpenCell-results.png to s3://files.biosimulations.org/simulations/626177e5abe612c540c691da/contents/OpenCell-results.png\nCompleted 47.6 KiB/162.7 KiB (442.9 KiB/s) with 12 file(s) remaining\rCompleted 50.2 KiB/162.7 KiB (358.4 KiB/s) with 12 file(s) remaining\rupload: contents/deriv_approx_sin.xml to s3://files.biosimulations.org/simulations/626177e5abe612c540c691da/contents/deriv_approx_sin.xml\nCompleted 50.2 KiB/162.7 KiB (358.4 KiB/s) with 11 file(s) remaining\rCompleted 57.4 KiB/162.7 KiB (385.8 KiB/s) with 11 file(s) remaining\rupload: contents/parabolic_approx_sin.xml to s3://files.biosimulations.org/simulations/626177e5abe612c540c691da/contents/parabolic_approx_sin.xml\nCompleted 57.4 KiB/162.7 KiB (385.8 KiB/s) with 10 file(s) remaining\rCompleted 66.6 KiB/162.7 KiB (427.7 KiB/s) with 10 file(s) remaining\rupload: contents/sin_approximations.xml to s3://files.biosimulations.org/simulations/626177e5abe612c540c691da/contents/sin_approximations.xml\nCompleted 66.6 KiB/162.7 KiB (427.7 KiB/s) with 9 file(s) remaining\rCompleted 67.3 KiB/162.7 KiB (410.9 KiB/s) with 9 file(s) remaining\rupload: contents/documentation-csim.html to s3://files.biosimulations.org/simulations/626177e5abe612c540c691da/contents/documentation-csim.html\nCompleted 67.3 KiB/162.7 KiB (410.9 KiB/s) with 8 file(s) remaining\rCompleted 74.6 KiB/162.7 KiB (418.1 KiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/626177e5abe612c540c691da/contents/metadata.rdf\nCompleted 74.6 KiB/162.7 KiB (418.1 KiB/s) with 7 file(s) remaining\rCompleted 76.2 KiB/162.7 KiB (421.5 KiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/626177e5abe612c540c691da/contents/manifest.xml\nCompleted 76.2 KiB/162.7 KiB (421.5 KiB/s) with 6 file(s) remaining\rCompleted 78.5 KiB/162.7 KiB (398.9 KiB/s) with 6 file(s) remaining\rupload: contents/sin.xml to s3://files.biosimulations.org/simulations/626177e5abe612c540c691da/contents/sin.xml\nCompleted 78.5 KiB/162.7 KiB (398.9 KiB/s) with 5 file(s) remaining\rCompleted 83.1 KiB/162.7 KiB (374.2 KiB/s) with 5 file(s) remaining\rupload: contents/sin_approximations_import.xml to s3://files.biosimulations.org/simulations/626177e5abe612c540c691da/contents/sin_approximations_import.xml\nCompleted 83.1 KiB/162.7 KiB (374.2 KiB/s) with 4 file(s) remaining\rCompleted 157.4 KiB/162.7 KiB (659.5 KiB/s) with 4 file(s) remaining\rupload: contents/SED-ML web tools screenshot.png to s3://files.biosimulations.org/simulations/626177e5abe612c540c691da/contents/SED-ML web tools screenshot.png\nCompleted 157.4 KiB/162.7 KiB (659.5 KiB/s) with 3 file(s) remaining\rCompleted 158.2 KiB/162.7 KiB (656.3 KiB/s) with 3 file(s) remaining\rupload: contents/documentation-sedml.html to s3://files.biosimulations.org/simulations/626177e5abe612c540c691da/contents/documentation-sedml.html\nCompleted 158.2 KiB/162.7 KiB (656.3 KiB/s) with 2 file(s) remaining\rCompleted 159.9 KiB/162.7 KiB (649.0 KiB/s) with 2 file(s) remaining\rupload: contents/documentation.html to s3://files.biosimulations.org/simulations/626177e5abe612c540c691da/contents/documentation.html\nCompleted 159.9 KiB/162.7 KiB (649.0 KiB/s) with 1 file(s) remaining\rCompleted 162.7 KiB/162.7 KiB (535.3 KiB/s) with 1 file(s) remaining\rupload: contents/sin_approximations_sedml.xml to s3://files.biosimulations.org/simulations/626177e5abe612c540c691da/contents/sin_approximations_sedml.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.3 KiB/9.3 KiB (120.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/626177e5abe612c540c691da/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /sin_approximations_sedml.xml\ncreating dataset /sin_approximations_sedml.xml/report, shape: (4, 16), type: float64\ndataset created, uuid: d-976f22ac-2bc59b26-a985-f37aad-34888e, chunk_size: (4, 16)\ncreating attribute combineArchiveLocation in /sin_approximations_sedml.xml\ncreating attribute uri in /sin_approximations_sedml.xml\ncreating attribute _type in /sin_approximations_sedml.xml/report\ncreating attribute sedmlDataSetDataTypes in /sin_approximations_sedml.xml/report\ncreating attribute sedmlDataSetIds in /sin_approximations_sedml.xml/report\ncreating attribute sedmlDataSetLabels in /sin_approximations_sedml.xml/report\ncreating attribute sedmlDataSetNames in /sin_approximations_sedml.xml/report\ncreating attribute sedmlDataSetShapes in /sin_approximations_sedml.xml/report\ncreating attribute sedmlId in /sin_approximations_sedml.xml/report\ncreating attribute sedmlName in /sin_approximations_sedml.xml/report\ncreating attribute uri in /sin_approximations_sedml.xml/report\ncreate_links: /\ngot link: sin_approximations_sedml.xml\ncreate_links: /sin_approximations_sedml.xml\ngot link: report\nwrite_dataset src: /sin_approximations_sedml.xml/report to tgt: /sin_approximations_sedml.xml/report, shape: (4, 16), type: float64\niterating over chunks for /sin_approximations_sedml.xml/report\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 16, 1))\ndone with dataload for /sin_approximations_sedml.xml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/626177e5abe612c540c691da\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 and upload the outputs of the simulation run ... succeeded.\nProcess the manifest file in the COMBINE archive ... succeeded.\nRead the manifest and post the files to the API ... succeeded.\nCreate thumbnails from the images specified in the manifest ... succeeded.\nPost thumbnails to the API ... succeeded.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.225587,"sedDocuments":[{"location":"sin_approximations_sedml.xml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"  Found 1 tasks and 1 outputs:\n    Tasks:\n      `task1`\n    Outputs:\n      `report`\n  Executing task 1: `task1`\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\n    Generating 1 outputs ...\n      Generating output 1: `report` ... \u001b[34msucceeded\u001b[0m\n\n  Executed 1 tasks and 1 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n","duration":0.749649,"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 `sin3` may be invalid.\n  - XPath could not be validated.\n- Variable `sin2` may be invalid.\n  - XPath could not be validated.\n- Variable `sin1` may be invalid.\n  - XPath could not be validated.\n- Variable `x` 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":0.679082,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"OpenCOR.SimulationSupport.Simulation.run"},{"key":"algorithmParameters","value":[]}]}],"outputs":[{"id":"report","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.026261,"dataSets":[{"id":"col_1","status":"SUCCEEDED"},{"id":"col_2","status":"SUCCEEDED"},{"id":"col_3","status":"SUCCEEDED"},{"id":"col_4","status":"SUCCEEDED"}]}]}]}