{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_HK"},{"status":"SUCCEEDED","id":"data_set_HNA"},{"status":"SUCCEEDED","id":"data_set_IK"},{"status":"SUCCEEDED","id":"data_set_MNA"},{"status":"SUCCEEDED","id":"data_set_NI"},{"status":"SUCCEEDED","id":"data_set_NIR"},{"status":"SUCCEEDED","id":"data_set_NK"},{"status":"SUCCEEDED","id":"data_set_RIR"},{"status":"SUCCEEDED","id":"data_set_V"}],"duration":0.162894,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"}],"tasks":[{"simulatorDetails":[{"value":"700.0","key":"total"},{"value":"euler","key":"meth"},{"value":"0.05","key":"dt"},{"value":"0.0","key":"t0"},{"value":"14","key":"njmp"}],"algorithm":"KISAO_0000030","duration":0.203232,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.46429,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n  JTBfig07.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 10 data sets\r\n\r\nExecuting SED-ML file 1: JTBfig07.sedml ...\r\n  Found 1 tasks and 1 outputs:\r\n    Tasks:\r\n      `task`\r\n    Outputs:\r\n      `report`\r\n  Executing task 1: `task`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 1 outputs ...\r\n      Generating output 1: `report` ...","skipReason":null,"exception":null,"status":"SUCCEEDED","location":"JTBfig07.sedml"}],"duration":0.981959,"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    467      0 --:--:-- --:--:-- --:--:--   466\n\r100  168k  100  168k    0     0   411k      0 --:--:-- --:--:-- --:--:--  411k\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 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\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 contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/readme.html    \n  inflating: contents/JTBfig07.ode   \n  inflating: contents/JTBfig07.sedml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/JTBfig07.jpg   \n  inflating: contents/manifest.xml   \nCompleted 100.4 KiB/259.3 KiB (867.9 KiB/s) with 6 file(s) remaining\rupload: contents/JTBfig07.jpg to s3://files.biosimulations.org/simulations/621d42a3d8a14a834cbf3dd6/contents/JTBfig07.jpg\nCompleted 100.4 KiB/259.3 KiB (867.9 KiB/s) with 5 file(s) remaining\rCompleted 106.9 KiB/259.3 KiB (774.0 KiB/s) with 5 file(s) remaining\rupload: contents/JTBfig07.sedml to s3://files.biosimulations.org/simulations/621d42a3d8a14a834cbf3dd6/contents/JTBfig07.sedml\nCompleted 106.9 KiB/259.3 KiB (774.0 KiB/s) with 4 file(s) remaining\rCompleted 107.6 KiB/259.3 KiB (706.3 KiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/621d42a3d8a14a834cbf3dd6/contents/manifest.xml\nCompleted 107.6 KiB/259.3 KiB (706.3 KiB/s) with 3 file(s) remaining\rCompleted 109.8 KiB/259.3 KiB (708.9 KiB/s) with 3 file(s) remaining\rupload: contents/readme.html to s3://files.biosimulations.org/simulations/621d42a3d8a14a834cbf3dd6/contents/readme.html\nCompleted 109.8 KiB/259.3 KiB (708.9 KiB/s) with 2 file(s) remaining\rCompleted 257.1 KiB/259.3 KiB (1.3 MiB/s) with 2 file(s) remaining  \rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/621d42a3d8a14a834cbf3dd6/contents/metadata.rdf\nCompleted 257.1 KiB/259.3 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 259.3 KiB/259.3 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: contents/JTBfig07.ode to s3://files.biosimulations.org/simulations/621d42a3d8a14a834cbf3dd6/contents/JTBfig07.ode\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /JTBfig07.sedml\ncreating dataset /JTBfig07.sedml/report, shape: (10, 1001), type: float64\ndataset created, uuid: d-c0338a0b-ff9b67a2-a1ad-9814b4-c2f99a, chunk_size: (10, 1001)\ncreating attribute combineArchiveLocation in /JTBfig07.sedml\ncreating attribute uri in /JTBfig07.sedml\ncreating attribute _type in /JTBfig07.sedml/report\ncreating attribute sedmlDataSetDataTypes in /JTBfig07.sedml/report\ncreating attribute sedmlDataSetIds in /JTBfig07.sedml/report\ncreating attribute sedmlDataSetLabels in /JTBfig07.sedml/report\ncreating attribute sedmlDataSetNames in /JTBfig07.sedml/report\ncreating attribute sedmlDataSetShapes in /JTBfig07.sedml/report\ncreating attribute sedmlId in /JTBfig07.sedml/report\ncreating attribute sedmlName in /JTBfig07.sedml/report\ncreating attribute uri in /JTBfig07.sedml/report\ncreate_links: /\ngot link: JTBfig07.sedml\ncreate_links: /JTBfig07.sedml\ngot link: report\nwrite_dataset src: /JTBfig07.sedml/report to tgt: /JTBfig07.sedml/report, shape: (10, 1001), type: float64\niterating over chunks for /JTBfig07.sedml/report\nwriting dataset data for slice: (slice(0, 10, 1), slice(0, 1001, 1))\ndone with dataload for /JTBfig07.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/621d42a3d8a14a834cbf3dd6\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 65%)\n  adding: outputs/reports.h5 (deflated 15%)\n  adding: rawLog.txt (deflated 75%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 70.4 KiB/75.7 KiB (756.0 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/621d42a3d8a14a834cbf3dd6/output.zip\nCompleted 70.4 KiB/75.7 KiB (756.0 KiB/s) with 1 file(s) remaining\rCompleted 75.7 KiB/75.7 KiB (597.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/621d42a3d8a14a834cbf3dd6/rawLog.txt\nCompleted 79.7 KiB/79.7 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/621d42a3d8a14a834cbf3dd6/outputs/reports.h5\nCompleted 2.0 KiB/2.0 KiB (37.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/621d42a3d8a14a834cbf3dd6/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 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.\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","skipReason":null,"exception":null,"status":"SUCCEEDED"}