{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_BBS"},{"status":"SUCCEEDED","id":"data_set_CA"},{"status":"SUCCEEDED","id":"data_set_CCS"},{"status":"SUCCEEDED","id":"data_set_HHS"},{"status":"SUCCEEDED","id":"data_set_NNS"},{"status":"SUCCEEDED","id":"data_set_QQS"},{"status":"SUCCEEDED","id":"data_set_RRS"},{"status":"SUCCEEDED","id":"data_set_VVS"},{"status":"SUCCEEDED","id":"data_set_ZZS"}],"duration":0.126764,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"},{"curves":[{"status":"SUCCEEDED","id":"curve_1"}],"duration":0.180554,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"plot"}],"tasks":[{"simulatorDetails":[{"value":"500.0","key":"total"},{"value":"10","key":"njmp"},{"value":"0.0","key":"t0"},{"value":"0.0","key":"trans"},{"value":"rungekutta","key":"meth"},{"value":"0.05","key":"dt"}],"algorithm":"KISAO_0000032","duration":0.177199,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.612556,"output":"Archive contains 2 SED-ML documents with 2 models, 2 simulations, 2 tasks, 2 reports, and 2 plots:\r\n  nca.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 10 data sets\r\n    Plots (1):\r\n      plot: 1 curves\r\n  zca.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 6 data sets\r\n    Plots (1):\r\n      plot: 1 curves\r\n\r\nExecuting SED-ML file 1: nca.sedml ...\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":"nca.sedml"},{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_BBS"},{"status":"SUCCEEDED","id":"data_set_HHS"},{"status":"SUCCEEDED","id":"data_set_NNS"},{"status":"SUCCEEDED","id":"data_set_VVS"},{"status":"SUCCEEDED","id":"data_set_ZZS"}],"duration":0.095241,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"},{"curves":[{"status":"SUCCEEDED","id":"curve_1"}],"duration":0.15244,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"plot"}],"tasks":[{"simulatorDetails":[{"value":"500.0","key":"total"},{"value":"10","key":"njmp"},{"value":"0.0","key":"t0"},{"value":"0.0","key":"trans"},{"value":"rungekutta","key":"meth"},{"value":"0.05","key":"dt"}],"algorithm":"KISAO_0000032","duration":0.132576,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.510352,"output":" \u001b[34msucceeded\u001b[0m\r\n\r\n  Executed 1 tasks and 2 outputs:\r\n    Tasks:\r\n      Succeeded: 1\r\n      Skipped: 0\r\n      Failed: 0\r\n    Outputs:\r\n      Succeeded: 2\r\n      Skipped: 0\r\n      Failed: 0\r\nExecuting SED-ML file 2: zca.sedml ...\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":"zca.sedml"}],"duration":1.604827,"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    476      0 --:--:-- --:--:-- --:--:--   476\n\r100  209k  100  209k    0     0   500k      0 --:--:-- --:--:-- --:--:--  500k\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 \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 2 SED documents:\n  SED documents (2):\n    Succeeded: 2\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 contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/zca.ode        \n  inflating: contents/casup.pdf      \n  inflating: contents/nca.ode        \n  inflating: contents/README.HTML    \n  inflating: contents/nca.sedml      \n  inflating: contents/zca.sedml      \n  inflating: contents/metadata.rdf   \n  inflating: contents/ncaScreenShot.jpg  \n  inflating: contents/zcaScreenShot.jpg  \n  inflating: contents/manifest.xml   \nCompleted 957 Bytes/327.3 KiB (8.1 KiB/s) with 10 file(s) remaining\rupload: contents/README.HTML to s3://files.biosimulations.org/simulations/621d429ed8a14a834cbf3db7/contents/README.HTML\nCompleted 957 Bytes/327.3 KiB (8.1 KiB/s) with 9 file(s) remaining\rCompleted 3.0 KiB/327.3 KiB (17.2 KiB/s) with 9 file(s) remaining \rupload: contents/nca.ode to s3://files.biosimulations.org/simulations/621d429ed8a14a834cbf3db7/contents/nca.ode\nCompleted 3.0 KiB/327.3 KiB (17.2 KiB/s) with 8 file(s) remaining\rCompleted 4.6 KiB/327.3 KiB (25.6 KiB/s) with 8 file(s) remaining\rupload: contents/zca.ode to s3://files.biosimulations.org/simulations/621d429ed8a14a834cbf3db7/contents/zca.ode\nCompleted 4.6 KiB/327.3 KiB (25.6 KiB/s) with 7 file(s) remaining\rCompleted 5.6 KiB/327.3 KiB (30.4 KiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/621d429ed8a14a834cbf3db7/contents/manifest.xml\nCompleted 5.6 KiB/327.3 KiB (30.4 KiB/s) with 6 file(s) remaining\rCompleted 64.8 KiB/327.3 KiB (337.7 KiB/s) with 6 file(s) remaining\rupload: contents/ncaScreenShot.jpg to s3://files.biosimulations.org/simulations/621d429ed8a14a834cbf3db7/contents/ncaScreenShot.jpg\nCompleted 64.8 KiB/327.3 KiB (337.7 KiB/s) with 5 file(s) remaining\rCompleted 85.9 KiB/327.3 KiB (434.4 KiB/s) with 5 file(s) remaining\rupload: contents/casup.pdf to s3://files.biosimulations.org/simulations/621d429ed8a14a834cbf3db7/contents/casup.pdf\nCompleted 85.9 KiB/327.3 KiB (434.4 KiB/s) with 4 file(s) remaining\rCompleted 90.7 KiB/327.3 KiB (453.7 KiB/s) with 4 file(s) remaining\rupload: contents/zca.sedml to s3://files.biosimulations.org/simulations/621d429ed8a14a834cbf3db7/contents/zca.sedml\nCompleted 90.7 KiB/327.3 KiB (453.7 KiB/s) with 3 file(s) remaining\rCompleted 150.4 KiB/327.3 KiB (690.8 KiB/s) with 3 file(s) remaining\rupload: contents/zcaScreenShot.jpg to s3://files.biosimulations.org/simulations/621d429ed8a14a834cbf3db7/contents/zcaScreenShot.jpg\nCompleted 150.4 KiB/327.3 KiB (690.8 KiB/s) with 2 file(s) remaining\rCompleted 320.2 KiB/327.3 KiB (1.3 MiB/s) with 2 file(s) remaining  \rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/621d429ed8a14a834cbf3db7/contents/metadata.rdf\nCompleted 320.2 KiB/327.3 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 327.3 KiB/327.3 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: contents/nca.sedml to s3://files.biosimulations.org/simulations/621d429ed8a14a834cbf3db7/contents/nca.sedml\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /nca.sedml\ncreating dataset /nca.sedml/plot, shape: (2, 1001), type: float64\ndataset created, uuid: d-2d108bd5-8288df3c-6b4d-253432-d25b56, chunk_size: (2, 1001)\ncreating dataset /nca.sedml/report, shape: (10, 1001), type: float64\ndataset created, uuid: d-2d108bd5-8288df3c-272a-e743b8-98dfc0, chunk_size: (10, 1001)\ncreating group /zca.sedml\ncreating dataset /zca.sedml/plot, shape: (2, 1001), type: float64\ndataset created, uuid: d-2d108bd5-8288df3c-5210-5f5f68-7964e7, chunk_size: (2, 1001)\ncreating dataset /zca.sedml/report, shape: (6, 1001), type: float64\ndataset created, uuid: d-2d108bd5-8288df3c-957a-bf5719-f24d6a, chunk_size: (6, 1001)\ncreating attribute combineArchiveLocation in /nca.sedml\ncreating attribute uri in /nca.sedml\ncreating attribute _type in /nca.sedml/plot\ncreating attribute sedmlDataSetDataTypes in /nca.sedml/plot\ncreating attribute sedmlDataSetIds in /nca.sedml/plot\ncreating attribute sedmlDataSetLabels in /nca.sedml/plot\ncreating attribute sedmlDataSetNames in /nca.sedml/plot\ncreating attribute sedmlDataSetShapes in /nca.sedml/plot\ncreating attribute sedmlId in /nca.sedml/plot\ncreating attribute uri in /nca.sedml/plot\ncreating attribute _type in /nca.sedml/report\ncreating attribute sedmlDataSetDataTypes in /nca.sedml/report\ncreating attribute sedmlDataSetIds in /nca.sedml/report\ncreating attribute sedmlDataSetLabels in /nca.sedml/report\ncreating attribute sedmlDataSetNames in /nca.sedml/report\ncreating attribute sedmlDataSetShapes in /nca.sedml/report\ncreating attribute sedmlId in /nca.sedml/report\ncreating attribute sedmlName in /nca.sedml/report\ncreating attribute uri in /nca.sedml/report\ncreating attribute combineArchiveLocation in /zca.sedml\ncreating attribute uri in /zca.sedml\ncreating attribute _type in /zca.sedml/plot\ncreating attribute sedmlDataSetDataTypes in /zca.sedml/plot\ncreating attribute sedmlDataSetIds in /zca.sedml/plot\ncreating attribute sedmlDataSetLabels in /zca.sedml/plot\ncreating attribute sedmlDataSetNames in /zca.sedml/plot\ncreating attribute sedmlDataSetShapes in /zca.sedml/plot\ncreating attribute sedmlId in /zca.sedml/plot\ncreating attribute uri in /zca.sedml/plot\ncreating attribute _type in /zca.sedml/report\ncreating attribute sedmlDataSetDataTypes in /zca.sedml/report\ncreating attribute sedmlDataSetIds in /zca.sedml/report\ncreating attribute sedmlDataSetLabels in /zca.sedml/report\ncreating attribute sedmlDataSetNames in /zca.sedml/report\ncreating attribute sedmlDataSetShapes in /zca.sedml/report\ncreating attribute sedmlId in /zca.sedml/report\ncreating attribute sedmlName in /zca.sedml/report\ncreating attribute uri in /zca.sedml/report\ncreate_links: /\ngot link: nca.sedml\ngot link: zca.sedml\ncreate_links: /nca.sedml\ngot link: plot\ngot link: report\ncreate_links: /zca.sedml\ngot link: plot\ngot link: report\nwrite_dataset src: /nca.sedml/plot to tgt: /nca.sedml/plot, shape: (2, 1001), type: float64\niterating over chunks for /nca.sedml/plot\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /nca.sedml/plot\nwrite_dataset src: /nca.sedml/report to tgt: /nca.sedml/report, shape: (10, 1001), type: float64\niterating over chunks for /nca.sedml/report\nwriting dataset data for slice: (slice(0, 10, 1), slice(0, 1001, 1))\ndone with dataload for /nca.sedml/report\nwrite_dataset src: /zca.sedml/plot to tgt: /zca.sedml/plot, shape: (2, 1001), type: float64\niterating over chunks for /zca.sedml/plot\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /zca.sedml/plot\nwrite_dataset src: /zca.sedml/report to tgt: /zca.sedml/report, shape: (6, 1001), type: float64\niterating over chunks for /zca.sedml/report\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1001, 1))\ndone with dataload for /zca.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/621d429ed8a14a834cbf3db7\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 78%)\n  adding: outputs/nca.sedml/ (stored 0%)\n  adding: outputs/nca.sedml/plot.pdf (deflated 27%)\n  adding: outputs/zca.sedml/ (stored 0%)\n  adding: outputs/zca.sedml/plot.pdf (deflated 25%)\n  adding: outputs/reports.h5 (deflated 25%)\n  adding: rawLog.txt (deflated 81%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 141.5 KiB/182.3 KiB (1.8 MiB/s) with 5 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/621d429ed8a14a834cbf3db7/output.zip\nCompleted 141.5 KiB/182.3 KiB (1.8 MiB/s) with 4 file(s) remaining\rCompleted 154.8 KiB/182.3 KiB (1.5 MiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/621d429ed8a14a834cbf3db7/outputs/plots.zip\nCompleted 154.8 KiB/182.3 KiB (1.5 MiB/s) with 3 file(s) remaining\rCompleted 163.7 KiB/182.3 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: outputs/nca.sedml/plot.pdf to s3://files.biosimulations.org/simulations/621d429ed8a14a834cbf3db7/outputs/nca.sedml/plot.pdf\nCompleted 163.7 KiB/182.3 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 173.2 KiB/182.3 KiB (1.6 MiB/s) with 2 file(s) remaining\rupload: outputs/zca.sedml/plot.pdf to s3://files.biosimulations.org/simulations/621d429ed8a14a834cbf3db7/outputs/zca.sedml/plot.pdf\nCompleted 173.2 KiB/182.3 KiB (1.6 MiB/s) with 1 file(s) remaining\rCompleted 182.3 KiB/182.3 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/621d429ed8a14a834cbf3db7/rawLog.txt\nCompleted 165.6 KiB/165.6 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/621d429ed8a14a834cbf3db7/outputs/reports.h5\nCompleted 4.2 KiB/4.2 KiB (75.8 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/621d429ed8a14a834cbf3db7/outputs/log.yml\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 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata 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"}