{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_M"},{"status":"SUCCEEDED","id":"data_set_V"},{"status":"SUCCEEDED","id":"data_set_W"},{"status":"SUCCEEDED","id":"data_set_Z"}],"duration":0.08337,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"},{"curves":[{"status":"SUCCEEDED","id":"curve_1"}],"duration":0.174592,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"plot"}],"tasks":[{"simulatorDetails":[{"value":"10000.0","key":"total"},{"value":"euler","key":"meth"},{"value":"0.05","key":"dt"},{"value":"0.0","key":"t0"},{"value":"200","key":"njmp"}],"algorithm":"KISAO_0000030","duration":0.192402,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.537466,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n  eLIFE_model.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 5 data sets\r\n    Plots (1):\r\n      plot: 1 curves\r\n\r\nExecuting SED-ML file 1: eLIFE_model.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":"eLIFE_model.sedml"}],"duration":0.829825,"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    426      0 --:--:-- --:--:-- --:--:--   427\n\r100  566k  100  566k    0     0  1251k      0 --:--:-- --:--:-- --:--:-- 1251k\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 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/readme.txt     \n  inflating: contents/eLIFE_model.ode  \n  inflating: contents/eLIFE_model.sedml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/article-figures/PMC3970756/elife02370f001.jpg  \n  inflating: contents/article-figures/PMC3970756/elife02370fs001.jpg  \n  inflating: contents/article-figures/PMC3970756/elife02370f002.jpg  \n  inflating: contents/article-figures/PMC3970756/elife02370f003.jpg  \n  inflating: contents/article-figures/PMC3970756/elife02370f004.jpg  \n  inflating: contents/article-figures/PMC3970756/elife02370f005.jpg  \n  inflating: contents/manifest.xml   \nCompleted 99.5 KiB/707.9 KiB (1.2 MiB/s) with 11 file(s) remaining\rupload: contents/article-figures/PMC3970756/elife02370f001.jpg to s3://files.biosimulations.org/simulations/621d42c287550e369891bbf3/contents/article-figures/PMC3970756/elife02370f001.jpg\nCompleted 99.5 KiB/707.9 KiB (1.2 MiB/s) with 10 file(s) remaining\rCompleted 100.9 KiB/707.9 KiB (807.1 KiB/s) with 10 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/621d42c287550e369891bbf3/contents/manifest.xml\nCompleted 100.9 KiB/707.9 KiB (807.1 KiB/s) with 9 file(s) remaining\rCompleted 227.6 KiB/707.9 KiB (1.7 MiB/s) with 9 file(s) remaining  \rupload: contents/article-figures/PMC3970756/elife02370f003.jpg to s3://files.biosimulations.org/simulations/621d42c287550e369891bbf3/contents/article-figures/PMC3970756/elife02370f003.jpg\nCompleted 227.6 KiB/707.9 KiB (1.7 MiB/s) with 8 file(s) remaining\rCompleted 232.3 KiB/707.9 KiB (1.7 MiB/s) with 8 file(s) remaining\rupload: contents/eLIFE_model.sedml to s3://files.biosimulations.org/simulations/621d42c287550e369891bbf3/contents/eLIFE_model.sedml\nCompleted 232.3 KiB/707.9 KiB (1.7 MiB/s) with 7 file(s) remaining\rCompleted 233.6 KiB/707.9 KiB (1.7 MiB/s) with 7 file(s) remaining\rupload: contents/eLIFE_model.ode to s3://files.biosimulations.org/simulations/621d42c287550e369891bbf3/contents/eLIFE_model.ode\nCompleted 233.6 KiB/707.9 KiB (1.7 MiB/s) with 6 file(s) remaining\rCompleted 244.6 KiB/707.9 KiB (1.7 MiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/621d42c287550e369891bbf3/contents/metadata.rdf\nCompleted 244.6 KiB/707.9 KiB (1.7 MiB/s) with 5 file(s) remaining\rCompleted 324.5 KiB/707.9 KiB (2.3 MiB/s) with 5 file(s) remaining\rupload: contents/article-figures/PMC3970756/elife02370f004.jpg to s3://files.biosimulations.org/simulations/621d42c287550e369891bbf3/contents/article-figures/PMC3970756/elife02370f004.jpg\nCompleted 324.5 KiB/707.9 KiB (2.3 MiB/s) with 4 file(s) remaining\rCompleted 324.9 KiB/707.9 KiB (2.2 MiB/s) with 4 file(s) remaining\rupload: contents/readme.txt to s3://files.biosimulations.org/simulations/621d42c287550e369891bbf3/contents/readme.txt\nCompleted 324.9 KiB/707.9 KiB (2.2 MiB/s) with 3 file(s) remaining\rCompleted 444.4 KiB/707.9 KiB (2.8 MiB/s) with 3 file(s) remaining\rupload: contents/article-figures/PMC3970756/elife02370f005.jpg to s3://files.biosimulations.org/simulations/621d42c287550e369891bbf3/contents/article-figures/PMC3970756/elife02370f005.jpg\nCompleted 444.4 KiB/707.9 KiB (2.8 MiB/s) with 2 file(s) remaining\rCompleted 592.0 KiB/707.9 KiB (3.6 MiB/s) with 2 file(s) remaining\rupload: contents/article-figures/PMC3970756/elife02370f002.jpg to s3://files.biosimulations.org/simulations/621d42c287550e369891bbf3/contents/article-figures/PMC3970756/elife02370f002.jpg\nCompleted 592.0 KiB/707.9 KiB (3.6 MiB/s) with 1 file(s) remaining\rCompleted 707.9 KiB/707.9 KiB (3.9 MiB/s) with 1 file(s) remaining\rupload: contents/article-figures/PMC3970756/elife02370fs001.jpg to s3://files.biosimulations.org/simulations/621d42c287550e369891bbf3/contents/article-figures/PMC3970756/elife02370fs001.jpg\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /eLIFE_model.sedml\ncreating dataset /eLIFE_model.sedml/plot, shape: (2, 1001), type: float64\ndataset created, uuid: d-b1cb8a3b-a2794dbe-e7a3-9ec79b-f216fa, chunk_size: (2, 1001)\ncreating dataset /eLIFE_model.sedml/report, shape: (5, 1001), type: float64\ndataset created, uuid: d-b1cb8a3b-a2794dbe-5949-b07abe-5ba410, chunk_size: (5, 1001)\ncreating attribute combineArchiveLocation in /eLIFE_model.sedml\ncreating attribute uri in /eLIFE_model.sedml\ncreating attribute _type in /eLIFE_model.sedml/plot\ncreating attribute sedmlDataSetDataTypes in /eLIFE_model.sedml/plot\ncreating attribute sedmlDataSetIds in /eLIFE_model.sedml/plot\ncreating attribute sedmlDataSetLabels in /eLIFE_model.sedml/plot\ncreating attribute sedmlDataSetNames in /eLIFE_model.sedml/plot\ncreating attribute sedmlDataSetShapes in /eLIFE_model.sedml/plot\ncreating attribute sedmlId in /eLIFE_model.sedml/plot\ncreating attribute uri in /eLIFE_model.sedml/plot\ncreating attribute _type in /eLIFE_model.sedml/report\ncreating attribute sedmlDataSetDataTypes in /eLIFE_model.sedml/report\ncreating attribute sedmlDataSetIds in /eLIFE_model.sedml/report\ncreating attribute sedmlDataSetLabels in /eLIFE_model.sedml/report\ncreating attribute sedmlDataSetNames in /eLIFE_model.sedml/report\ncreating attribute sedmlDataSetShapes in /eLIFE_model.sedml/report\ncreating attribute sedmlId in /eLIFE_model.sedml/report\ncreating attribute sedmlName in /eLIFE_model.sedml/report\ncreating attribute uri in /eLIFE_model.sedml/report\ncreate_links: /\ngot link: eLIFE_model.sedml\ncreate_links: /eLIFE_model.sedml\ngot link: plot\ngot link: report\nwrite_dataset src: /eLIFE_model.sedml/plot to tgt: /eLIFE_model.sedml/plot, shape: (2, 1001), type: float64\niterating over chunks for /eLIFE_model.sedml/plot\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /eLIFE_model.sedml/plot\nwrite_dataset src: /eLIFE_model.sedml/report to tgt: /eLIFE_model.sedml/report, shape: (5, 1001), type: float64\niterating over chunks for /eLIFE_model.sedml/report\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 1001, 1))\ndone with dataload for /eLIFE_model.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/621d42c287550e369891bbf3\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 65%)\n  adding: outputs/eLIFE_model.sedml/ (stored 0%)\n  adding: outputs/eLIFE_model.sedml/plot.pdf (deflated 35%)\n  adding: outputs/reports.h5 (deflated 77%)\n  adding: rawLog.txt (deflated 81%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 14.4 KiB/35.2 KiB (226.3 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/621d42c287550e369891bbf3/output.zip\nCompleted 14.4 KiB/35.2 KiB (226.3 KiB/s) with 3 file(s) remaining\rCompleted 19.2 KiB/35.2 KiB (219.3 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/621d42c287550e369891bbf3/outputs/plots.zip\nCompleted 19.2 KiB/35.2 KiB (219.3 KiB/s) with 2 file(s) remaining\rCompleted 27.5 KiB/35.2 KiB (264.5 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/621d42c287550e369891bbf3/rawLog.txt\nCompleted 27.5 KiB/35.2 KiB (264.5 KiB/s) with 1 file(s) remaining\rCompleted 35.2 KiB/35.2 KiB (289.5 KiB/s) with 1 file(s) remaining\rupload: outputs/eLIFE_model.sedml/plot.pdf to s3://files.biosimulations.org/simulations/621d42c287550e369891bbf3/outputs/eLIFE_model.sedml/plot.pdf\nCompleted 26.8 KiB/26.8 KiB (425.9 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/621d42c287550e369891bbf3/outputs/reports.h5\nCompleted 2.1 KiB/2.1 KiB (36.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/621d42c287550e369891bbf3/outputs/log.yml\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mRetrieve 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 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.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file 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"}