{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_C1"},{"status":"SUCCEEDED","id":"data_set_C2"},{"status":"SUCCEEDED","id":"data_set_C3"},{"status":"SUCCEEDED","id":"data_set_C4"},{"status":"SUCCEEDED","id":"data_set_C5"},{"status":"SUCCEEDED","id":"data_set_I1"},{"status":"SUCCEEDED","id":"data_set_I2"},{"status":"SUCCEEDED","id":"data_set_I3"},{"status":"SUCCEEDED","id":"data_set_I4"},{"status":"SUCCEEDED","id":"data_set_I5"},{"status":"SUCCEEDED","id":"data_set_I6"},{"status":"SUCCEEDED","id":"data_set_INA"},{"status":"SUCCEEDED","id":"data_set_O"},{"status":"SUCCEEDED","id":"data_set_OB"},{"status":"SUCCEEDED","id":"data_set_V"}],"duration":0.214655,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"},{"curves":[{"status":"SUCCEEDED","id":"curve_1"}],"duration":0.272999,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"plot"}],"tasks":[{"simulatorDetails":[{"value":"euler","key":"meth"},{"value":"80.0","key":"total"},{"value":"8000","key":"njmp"},{"value":0.00001,"key":"dt"},{"value":"0.0","key":"t0"}],"algorithm":"KISAO_0000030","duration":34.620357,"output":"/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mModel `model` may be invalid.\r\n  - The model file `/tmp/tmpkr65h1h6/RB-INa-Molecules.ode` has warnings.\r\n    - The XPP file may be not be formulated correctly\r\n      - V is a duplicate name\r\n      - INA is a duplicate name\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":35.24511,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n  RB-INa-Molecules.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 16 data sets\r\n    Plots (1):\r\n      plot: 1 curves\r\n\r\nExecuting SED-ML file 1: RB-INa-Molecules.sedml ...\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n  - Model `model` has warnings.\r\n    - The model file `RB-INa-Molecules.ode` has warnings.\r\n      - The XPP file may be not be formulated correctly\r\n        - V is a duplicate name\r\n        - INA is a duplicate name\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task`\r\n    Outputs:\r\n      `plot`\r\n      `report`\r\n  Executing task 1: `task`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `report` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `plot` ...","skipReason":null,"exception":null,"status":"SUCCEEDED","location":"RB-INa-Molecules.sedml"}],"duration":35.832493,"output":"\u001b[0;36mThank you for using runBioSimulations!\u001b[0m\n\n\u001b[0;36m================================================ Loading Singularity ================================================\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    473      0 --:--:-- --:--:-- --:--:--   474\n\r100 3928k  100 3928k    0     0  9226k      0 --:--:-- --:--:-- --:--:-- 9226k\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mCOMBINE/OMEX archive has warnings.\r\n  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n  - Model `model` has warnings.\r\n    - The model file `RB-INa-Molecules.ode` has warnings.\r\n      - The XPP file may be not be formulated correctly\r\n        - V is a duplicate name\r\n        - INA is a duplicate name\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n  - The SED-ML file at location `RB-INa-Molecules.sedml` has warnings.\r\n    - Model `model` has warnings.\r\n      - The model file `RB-INa-Molecules.ode` has warnings.\r\n        - The XPP file may be not be formulated correctly\r\n          - V is a duplicate name\r\n          - INA is a duplicate name\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n \u001b[34msucceeded\u001b[0m\n\n  Executed 1 tasks and 2 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 2\n      Skipped: 0\n      Failed: 0\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 (2):\n    Succeeded: 2\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/molecules-25-03062-Sesamin.pdf  \n  inflating: contents/Readme.html    \n  inflating: contents/RB-INa-Molecules.ode  \n  inflating: contents/Readme-sesamin.docx  \n  inflating: contents/RB-INa-Molecules.sedml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/article-figures/PMC7411736/molecules-25-03062-g001.jpg  \n  inflating: contents/article-figures/PMC7411736/molecules-25-03062-g002.jpg  \n  inflating: contents/article-figures/PMC7411736/molecules-25-03062-g003.jpg  \n  inflating: contents/article-figures/PMC7411736/molecules-25-03062-g004.jpg  \n  inflating: contents/article-figures/PMC7411736/molecules-25-03062-g005.jpg  \n  inflating: contents/article-figures/PMC7411736/molecules-25-03062-g006.jpg  \n  inflating: contents/article-figures/PMC7411736/molecules-25-03062-g007.jpg  \n  inflating: contents/article-figures/PMC7411736/molecules-25-03062-g008.jpg  \n  inflating: contents/article-figures/PMC7411736/molecules-25-03062-g009.jpg  \n  inflating: contents/article-figures/PMC7411736/molecules-25-03062-sch001.jpg  \n  inflating: contents/Diagram.jpg    \n  inflating: contents/Readme_html_5448d781b1de6a46.png  \n  inflating: contents/Readme_html_9ada485dbba73b72.png  \n  inflating: contents/Result-9B.jpg  \n  inflating: contents/manifest.xml   \nCompleted 71.6 KiB/4.2 MiB (977.7 KiB/s) with 21 file(s) remaining\rupload: contents/Diagram.jpg to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/contents/Diagram.jpg\nCompleted 71.6 KiB/4.2 MiB (977.7 KiB/s) with 20 file(s) remaining\rCompleted 73.8 KiB/4.2 MiB (701.2 KiB/s) with 20 file(s) remaining\rupload: contents/RB-INa-Molecules.ode to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/contents/RB-INa-Molecules.ode\nCompleted 73.8 KiB/4.2 MiB (701.2 KiB/s) with 19 file(s) remaining\rCompleted 82.8 KiB/4.2 MiB (630.4 KiB/s) with 19 file(s) remaining\rupload: contents/RB-INa-Molecules.sedml to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/contents/RB-INa-Molecules.sedml\nCompleted 82.8 KiB/4.2 MiB (630.4 KiB/s) with 18 file(s) remaining\rCompleted 89.8 KiB/4.2 MiB (673.3 KiB/s) with 18 file(s) remaining\rupload: contents/Readme.html to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/contents/Readme.html\nCompleted 89.8 KiB/4.2 MiB (673.3 KiB/s) with 17 file(s) remaining\rCompleted 253.4 KiB/4.2 MiB (1.8 MiB/s) with 17 file(s) remaining \rupload: contents/Result-9B.jpg to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/contents/Result-9B.jpg\nCompleted 253.4 KiB/4.2 MiB (1.8 MiB/s) with 16 file(s) remaining\rCompleted 335.8 KiB/4.2 MiB (2.4 MiB/s) with 16 file(s) remaining\rupload: contents/article-figures/PMC7411736/molecules-25-03062-g006.jpg to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/contents/article-figures/PMC7411736/molecules-25-03062-g006.jpg\nCompleted 335.8 KiB/4.2 MiB (2.4 MiB/s) with 15 file(s) remaining\rCompleted 413.6 KiB/4.2 MiB (2.6 MiB/s) with 15 file(s) remaining\rupload: contents/Readme_html_5448d781b1de6a46.png to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/contents/Readme_html_5448d781b1de6a46.png\nCompleted 413.6 KiB/4.2 MiB (2.6 MiB/s) with 14 file(s) remaining\rCompleted 446.8 KiB/4.2 MiB (2.6 MiB/s) with 14 file(s) remaining\rupload: contents/Readme_html_9ada485dbba73b72.png to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/contents/Readme_html_9ada485dbba73b72.png\nCompleted 446.8 KiB/4.2 MiB (2.6 MiB/s) with 13 file(s) remaining\rCompleted 449.6 KiB/4.2 MiB (2.4 MiB/s) with 13 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/contents/manifest.xml\nCompleted 449.6 KiB/4.2 MiB (2.4 MiB/s) with 12 file(s) remaining\rCompleted 555.6 KiB/4.2 MiB (3.0 MiB/s) with 12 file(s) remaining\rupload: contents/article-figures/PMC7411736/molecules-25-03062-g008.jpg to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/contents/article-figures/PMC7411736/molecules-25-03062-g008.jpg\nCompleted 555.6 KiB/4.2 MiB (3.0 MiB/s) with 11 file(s) remaining\rCompleted 566.3 KiB/4.2 MiB (3.0 MiB/s) with 11 file(s) remaining\rupload: contents/article-figures/PMC7411736/molecules-25-03062-sch001.jpg to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/contents/article-figures/PMC7411736/molecules-25-03062-sch001.jpg\nCompleted 566.3 KiB/4.2 MiB (3.0 MiB/s) with 10 file(s) remaining\rCompleted 643.3 KiB/4.2 MiB (3.3 MiB/s) with 10 file(s) remaining\rupload: contents/article-figures/PMC7411736/molecules-25-03062-g004.jpg to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/contents/article-figures/PMC7411736/molecules-25-03062-g004.jpg\nCompleted 643.3 KiB/4.2 MiB (3.3 MiB/s) with 9 file(s) remaining\rCompleted 899.3 KiB/4.2 MiB (4.6 MiB/s) with 9 file(s) remaining\rCompleted 1.1 MiB/4.2 MiB (5.7 MiB/s) with 9 file(s) remaining  \rCompleted 1.4 MiB/4.2 MiB (6.9 MiB/s) with 9 file(s) remaining  \rCompleted 1.6 MiB/4.2 MiB (8.0 MiB/s) with 9 file(s) remaining  \rCompleted 1.7 MiB/4.2 MiB (8.3 MiB/s) with 9 file(s) remaining  \rupload: contents/article-figures/PMC7411736/molecules-25-03062-g009.jpg to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/contents/article-figures/PMC7411736/molecules-25-03062-g009.jpg\nCompleted 1.7 MiB/4.2 MiB (8.3 MiB/s) with 8 file(s) remaining\rCompleted 2.0 MiB/4.2 MiB (9.4 MiB/s) with 8 file(s) remaining\rCompleted 2.2 MiB/4.2 MiB (10.5 MiB/s) with 8 file(s) remaining\rCompleted 2.4 MiB/4.2 MiB (11.1 MiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/contents/metadata.rdf\nCompleted 2.4 MiB/4.2 MiB (11.1 MiB/s) with 7 file(s) remaining\rCompleted 2.4 MiB/4.2 MiB (11.4 MiB/s) with 7 file(s) remaining\rupload: contents/article-figures/PMC7411736/molecules-25-03062-g007.jpg to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/contents/article-figures/PMC7411736/molecules-25-03062-g007.jpg\nCompleted 2.4 MiB/4.2 MiB (11.4 MiB/s) with 6 file(s) remaining\rCompleted 2.7 MiB/4.2 MiB (12.5 MiB/s) with 6 file(s) remaining\rCompleted 2.9 MiB/4.2 MiB (13.5 MiB/s) with 6 file(s) remaining\rCompleted 3.0 MiB/4.2 MiB (13.7 MiB/s) with 6 file(s) remaining\rupload: contents/article-figures/PMC7411736/molecules-25-03062-g005.jpg to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/contents/article-figures/PMC7411736/molecules-25-03062-g005.jpg\nCompleted 3.0 MiB/4.2 MiB (13.7 MiB/s) with 5 file(s) remaining\rCompleted 3.3 MiB/4.2 MiB (14.7 MiB/s) with 5 file(s) remaining\rCompleted 3.5 MiB/4.2 MiB (15.8 MiB/s) with 5 file(s) remaining\rCompleted 3.8 MiB/4.2 MiB (16.8 MiB/s) with 5 file(s) remaining\rCompleted 3.8 MiB/4.2 MiB (16.5 MiB/s) with 5 file(s) remaining\rupload: contents/article-figures/PMC7411736/molecules-25-03062-g003.jpg to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/contents/article-figures/PMC7411736/molecules-25-03062-g003.jpg\nCompleted 3.8 MiB/4.2 MiB (16.5 MiB/s) with 4 file(s) remaining\rCompleted 3.9 MiB/4.2 MiB (16.2 MiB/s) with 4 file(s) remaining\rupload: contents/article-figures/PMC7411736/molecules-25-03062-g002.jpg to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/contents/article-figures/PMC7411736/molecules-25-03062-g002.jpg\nCompleted 3.9 MiB/4.2 MiB (16.2 MiB/s) with 3 file(s) remaining\rCompleted 4.0 MiB/4.2 MiB (15.9 MiB/s) with 3 file(s) remaining\rupload: contents/article-figures/PMC7411736/molecules-25-03062-g001.jpg to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/contents/article-figures/PMC7411736/molecules-25-03062-g001.jpg\nCompleted 4.0 MiB/4.2 MiB (15.9 MiB/s) with 2 file(s) remaining\rCompleted 4.1 MiB/4.2 MiB (16.3 MiB/s) with 2 file(s) remaining\rupload: contents/Readme-sesamin.docx to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/contents/Readme-sesamin.docx\nCompleted 4.1 MiB/4.2 MiB (16.3 MiB/s) with 1 file(s) remaining\rCompleted 4.2 MiB/4.2 MiB (12.5 MiB/s) with 1 file(s) remaining\rupload: contents/molecules-25-03062-Sesamin.pdf to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/contents/molecules-25-03062-Sesamin.pdf\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /RB-INa-Molecules.sedml\ncreating dataset /RB-INa-Molecules.sedml/plot, shape: (2, 1001), type: float64\ndataset created, uuid: d-d53c1fd3-440dcefc-47d3-aae210-ac2df9, chunk_size: (2, 1001)\ncreating dataset /RB-INa-Molecules.sedml/report, shape: (16, 1001), type: float64\ndataset created, uuid: d-d53c1fd3-440dcefc-6e1f-89567f-852b7a, chunk_size: (16, 1001)\ncreating attribute combineArchiveLocation in /RB-INa-Molecules.sedml\ncreating attribute uri in /RB-INa-Molecules.sedml\ncreating attribute _type in /RB-INa-Molecules.sedml/plot\ncreating attribute sedmlDataSetDataTypes in /RB-INa-Molecules.sedml/plot\ncreating attribute sedmlDataSetIds in /RB-INa-Molecules.sedml/plot\ncreating attribute sedmlDataSetLabels in /RB-INa-Molecules.sedml/plot\ncreating attribute sedmlDataSetNames in /RB-INa-Molecules.sedml/plot\ncreating attribute sedmlDataSetShapes in /RB-INa-Molecules.sedml/plot\ncreating attribute sedmlId in /RB-INa-Molecules.sedml/plot\ncreating attribute uri in /RB-INa-Molecules.sedml/plot\ncreating attribute _type in /RB-INa-Molecules.sedml/report\ncreating attribute sedmlDataSetDataTypes in /RB-INa-Molecules.sedml/report\ncreating attribute sedmlDataSetIds in /RB-INa-Molecules.sedml/report\ncreating attribute sedmlDataSetLabels in /RB-INa-Molecules.sedml/report\ncreating attribute sedmlDataSetNames in /RB-INa-Molecules.sedml/report\ncreating attribute sedmlDataSetShapes in /RB-INa-Molecules.sedml/report\ncreating attribute sedmlId in /RB-INa-Molecules.sedml/report\ncreating attribute sedmlName in /RB-INa-Molecules.sedml/report\ncreating attribute uri in /RB-INa-Molecules.sedml/report\ncreate_links: /\ngot link: RB-INa-Molecules.sedml\ncreate_links: /RB-INa-Molecules.sedml\ngot link: plot\ngot link: report\nwrite_dataset src: /RB-INa-Molecules.sedml/plot to tgt: /RB-INa-Molecules.sedml/plot, shape: (2, 1001), type: float64\niterating over chunks for /RB-INa-Molecules.sedml/plot\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /RB-INa-Molecules.sedml/plot\nwrite_dataset src: /RB-INa-Molecules.sedml/report to tgt: /RB-INa-Molecules.sedml/report, shape: (16, 1001), type: float64\niterating over chunks for /RB-INa-Molecules.sedml/report\nwriting dataset data for slice: (slice(0, 16, 1), slice(0, 1001, 1))\ndone with dataload for /RB-INa-Molecules.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/621d42c9d8a14a834cbf404d\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 77%)\n  adding: outputs/RB-INa-Molecules.sedml/ (stored 0%)\n  adding: outputs/RB-INa-Molecules.sedml/plot.pdf (deflated 33%)\n  adding: outputs/reports.h5 (deflated 14%)\n  adding: rawLog.txt (deflated 84%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 125.2 KiB/152.5 KiB (1.3 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/output.zip\nCompleted 125.2 KiB/152.5 KiB (1.3 MiB/s) with 3 file(s) remaining\rCompleted 130.5 KiB/152.5 KiB (1.3 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/outputs/plots.zip\nCompleted 130.5 KiB/152.5 KiB (1.3 MiB/s) with 2 file(s) remaining\rCompleted 144.3 KiB/152.5 KiB (1.1 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/rawLog.txt\nCompleted 144.3 KiB/152.5 KiB (1.1 MiB/s) with 1 file(s) remaining\rCompleted 152.5 KiB/152.5 KiB (1.0 MiB/s) with 1 file(s) remaining\rupload: outputs/RB-INa-Molecules.sedml/plot.pdf to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/outputs/RB-INa-Molecules.sedml/plot.pdf\nCompleted 135.2 KiB/135.2 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/outputs/reports.h5\nCompleted 4.6 KiB/4.6 KiB (77.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/621d42c9d8a14a834cbf404d/outputs/log.yml\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 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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","skipReason":null,"exception":null,"status":"SUCCEEDED"}