{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_H17"},{"status":"SUCCEEDED","id":"data_set_H18"},{"status":"SUCCEEDED","id":"data_set_HKA"},{"status":"SUCCEEDED","id":"data_set_M17"},{"status":"SUCCEEDED","id":"data_set_M18"},{"status":"SUCCEEDED","id":"data_set_N"},{"status":"SUCCEEDED","id":"data_set_NKA"},{"status":"SUCCEEDED","id":"data_set_S17"},{"status":"SUCCEEDED","id":"data_set_V"}],"duration":0.114342,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"}],"tasks":[{"simulatorDetails":[{"value":"1000.0","key":"total"},{"value":"rungekutta","key":"meth"},{"value":"0.05","key":"dt"},{"value":"0.0","key":"t0"},{"value":"20","key":"njmp"}],"algorithm":"KISAO_0000032","duration":0.318912,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.526782,"output":"Archive contains 2 SED-ML documents with 2 models, 2 simulations, 2 tasks, 2 reports, and 0 plots:\r\n  XPP/CIPN_HillPax.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 10 data sets\r\n  XPP/DRG.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 18 data sets\r\n\r\nExecuting SED-ML file 1: XPP/CIPN_HillPax.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":"XPP/CIPN_HillPax.sedml"},{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_H17"},{"status":"SUCCEEDED","id":"data_set_H17INF"},{"status":"SUCCEEDED","id":"data_set_H18"},{"status":"SUCCEEDED","id":"data_set_H18INF"},{"status":"SUCCEEDED","id":"data_set_HKA"},{"status":"SUCCEEDED","id":"data_set_HKAINF"},{"status":"SUCCEEDED","id":"data_set_M17"},{"status":"SUCCEEDED","id":"data_set_M17INF"},{"status":"SUCCEEDED","id":"data_set_M18"},{"status":"SUCCEEDED","id":"data_set_M18INF"},{"status":"SUCCEEDED","id":"data_set_N"},{"status":"SUCCEEDED","id":"data_set_NKA"},{"status":"SUCCEEDED","id":"data_set_NKAINF"},{"status":"SUCCEEDED","id":"data_set_NKINF"},{"status":"SUCCEEDED","id":"data_set_S17"},{"status":"SUCCEEDED","id":"data_set_S17INF"},{"status":"SUCCEEDED","id":"data_set_V"}],"duration":0.143741,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"}],"tasks":[{"simulatorDetails":[{"value":"100.0","key":"total"},{"value":"rungekutta","key":"meth"},{"value":"0.05","key":"dt"},{"value":"0.0","key":"t0"},{"value":"2","key":"njmp"}],"algorithm":"KISAO_0000032","duration":0.108779,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.357828,"output":" \u001b[34msucceeded\u001b[0m\r\n\r\n  Executed 1 tasks and 1 outputs:\r\n    Tasks:\r\n      Succeeded: 1\r\n      Skipped: 0\r\n      Failed: 0\r\n    Outputs:\r\n      Succeeded: 1\r\n      Skipped: 0\r\n      Failed: 0\r\nExecuting SED-ML file 2: XPP/DRG.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":"XPP/DRG.sedml"}],"duration":1.293369,"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    483      0 --:--:-- --:--:-- --:--:--   484\n\r100 15892  100 15892    0     0  41380      0 --:--:-- --:--:-- --:--:-- 41380\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 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 (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/MATCONT/DRG.m  \n  inflating: contents/MATCONT/JN_D.m  \n  inflating: contents/MATCONT/DRG_Jacobian.m  \n  inflating: contents/MATCONT/DRG_Steady_Periodic_I.m  \n  inflating: contents/MATCONT/JP_D.m  \n  inflating: contents/MATCONT/J_D.m  \n  inflating: contents/MATCONT/JhKA_D.m  \n  inflating: contents/XPP/CIPN_HillPax.ode  \n  inflating: contents/XPP/DRG.ode    \n  inflating: contents/XPP/CIPN_HillPax.sedml  \n  inflating: contents/XPP/DRG.sedml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 3.0 KiB/50.9 KiB (51.1 KiB/s) with 14 file(s) remaining\rupload: contents/MATCONT/DRG_Jacobian.m to s3://files.biosimulations.org/simulations/621d42c8d8a14a834cbf402e/contents/MATCONT/DRG_Jacobian.m\nCompleted 3.0 KiB/50.9 KiB (51.1 KiB/s) with 13 file(s) remaining\rCompleted 6.7 KiB/50.9 KiB (63.5 KiB/s) with 13 file(s) remaining\rupload: contents/MATCONT/DRG.m to s3://files.biosimulations.org/simulations/621d42c8d8a14a834cbf402e/contents/MATCONT/DRG.m\nCompleted 6.7 KiB/50.9 KiB (63.5 KiB/s) with 12 file(s) remaining\rCompleted 7.1 KiB/50.9 KiB (66.8 KiB/s) with 12 file(s) remaining\rupload: contents/MATCONT/JhKA_D.m to s3://files.biosimulations.org/simulations/621d42c8d8a14a834cbf402e/contents/MATCONT/JhKA_D.m\nCompleted 7.1 KiB/50.9 KiB (66.8 KiB/s) with 11 file(s) remaining\rCompleted 9.1 KiB/50.9 KiB (84.2 KiB/s) with 11 file(s) remaining\rupload: contents/MATCONT/DRG_Steady_Periodic_I.m to s3://files.biosimulations.org/simulations/621d42c8d8a14a834cbf402e/contents/MATCONT/DRG_Steady_Periodic_I.m\nCompleted 9.1 KiB/50.9 KiB (84.2 KiB/s) with 10 file(s) remaining\rCompleted 9.7 KiB/50.9 KiB (85.8 KiB/s) with 10 file(s) remaining\rupload: contents/MATCONT/JN_D.m to s3://files.biosimulations.org/simulations/621d42c8d8a14a834cbf402e/contents/MATCONT/JN_D.m\nCompleted 9.7 KiB/50.9 KiB (85.8 KiB/s) with 9 file(s) remaining\rCompleted 16.1 KiB/50.9 KiB (125.2 KiB/s) with 9 file(s) remaining\rupload: contents/XPP/CIPN_HillPax.sedml to s3://files.biosimulations.org/simulations/621d42c8d8a14a834cbf402e/contents/XPP/CIPN_HillPax.sedml\nCompleted 16.1 KiB/50.9 KiB (125.2 KiB/s) with 8 file(s) remaining\rCompleted 25.5 KiB/50.9 KiB (189.4 KiB/s) with 8 file(s) remaining\rupload: contents/XPP/DRG.sedml to s3://files.biosimulations.org/simulations/621d42c8d8a14a834cbf402e/contents/XPP/DRG.sedml\nCompleted 25.5 KiB/50.9 KiB (189.4 KiB/s) with 7 file(s) remaining\rCompleted 27.8 KiB/50.9 KiB (201.8 KiB/s) with 7 file(s) remaining\rupload: contents/XPP/DRG.ode to s3://files.biosimulations.org/simulations/621d42c8d8a14a834cbf402e/contents/XPP/DRG.ode\nCompleted 27.8 KiB/50.9 KiB (201.8 KiB/s) with 6 file(s) remaining\rCompleted 29.4 KiB/50.9 KiB (203.2 KiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/621d42c8d8a14a834cbf402e/contents/manifest.xml\nCompleted 29.4 KiB/50.9 KiB (203.2 KiB/s) with 5 file(s) remaining\rCompleted 30.6 KiB/50.9 KiB (200.8 KiB/s) with 5 file(s) remaining\rupload: contents/MATCONT/JP_D.m to s3://files.biosimulations.org/simulations/621d42c8d8a14a834cbf402e/contents/MATCONT/JP_D.m\nCompleted 30.6 KiB/50.9 KiB (200.8 KiB/s) with 4 file(s) remaining\rCompleted 33.0 KiB/50.9 KiB (209.3 KiB/s) with 4 file(s) remaining\rupload: contents/XPP/CIPN_HillPax.ode to s3://files.biosimulations.org/simulations/621d42c8d8a14a834cbf402e/contents/XPP/CIPN_HillPax.ode\nCompleted 33.0 KiB/50.9 KiB (209.3 KiB/s) with 3 file(s) remaining\rCompleted 44.2 KiB/50.9 KiB (270.2 KiB/s) with 3 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/621d42c8d8a14a834cbf402e/contents/metadata.rdf\nCompleted 44.2 KiB/50.9 KiB (270.2 KiB/s) with 2 file(s) remaining\rCompleted 49.7 KiB/50.9 KiB (279.3 KiB/s) with 2 file(s) remaining\rupload: contents/MATCONT/J_D.m to s3://files.biosimulations.org/simulations/621d42c8d8a14a834cbf402e/contents/MATCONT/J_D.m\nCompleted 49.7 KiB/50.9 KiB (279.3 KiB/s) with 1 file(s) remaining\rCompleted 50.9 KiB/50.9 KiB (276.4 KiB/s) with 1 file(s) remaining\rupload: contents/Readme.txt to s3://files.biosimulations.org/simulations/621d42c8d8a14a834cbf402e/contents/Readme.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /XPP\ncreating group /XPP/CIPN_HillPax.sedml\ncreating dataset /XPP/CIPN_HillPax.sedml/report, shape: (10, 1001), type: float64\ndataset created, uuid: d-61d2bb34-dbfd57d8-6139-8c36ca-b8f96c, chunk_size: (10, 1001)\ncreating group /XPP/DRG.sedml\ncreating dataset /XPP/DRG.sedml/report, shape: (18, 1001), type: float64\ndataset created, uuid: d-61d2bb34-dbfd57d8-2d46-cfe434-ff91a0, chunk_size: (18, 1001)\ncreating attribute combineArchiveLocation in /XPP\ncreating attribute uri in /XPP\ncreating attribute combineArchiveLocation in /XPP/CIPN_HillPax.sedml\ncreating attribute uri in /XPP/CIPN_HillPax.sedml\ncreating attribute _type in /XPP/CIPN_HillPax.sedml/report\ncreating attribute sedmlDataSetDataTypes in /XPP/CIPN_HillPax.sedml/report\ncreating attribute sedmlDataSetIds in /XPP/CIPN_HillPax.sedml/report\ncreating attribute sedmlDataSetLabels in /XPP/CIPN_HillPax.sedml/report\ncreating attribute sedmlDataSetNames in /XPP/CIPN_HillPax.sedml/report\ncreating attribute sedmlDataSetShapes in /XPP/CIPN_HillPax.sedml/report\ncreating attribute sedmlId in /XPP/CIPN_HillPax.sedml/report\ncreating attribute sedmlName in /XPP/CIPN_HillPax.sedml/report\ncreating attribute uri in /XPP/CIPN_HillPax.sedml/report\ncreating attribute combineArchiveLocation in /XPP/DRG.sedml\ncreating attribute uri in /XPP/DRG.sedml\ncreating attribute _type in /XPP/DRG.sedml/report\ncreating attribute sedmlDataSetDataTypes in /XPP/DRG.sedml/report\ncreating attribute sedmlDataSetIds in /XPP/DRG.sedml/report\ncreating attribute sedmlDataSetLabels in /XPP/DRG.sedml/report\ncreating attribute sedmlDataSetNames in /XPP/DRG.sedml/report\ncreating attribute sedmlDataSetShapes in /XPP/DRG.sedml/report\ncreating attribute sedmlId in /XPP/DRG.sedml/report\ncreating attribute sedmlName in /XPP/DRG.sedml/report\ncreating attribute uri in /XPP/DRG.sedml/report\ncreate_links: /\ngot link: XPP\ncreate_links: /XPP\ngot link: CIPN_HillPax.sedml\ngot link: DRG.sedml\ncreate_links: /XPP/CIPN_HillPax.sedml\ngot link: report\ncreate_links: /XPP/DRG.sedml\ngot link: report\nwrite_dataset src: /XPP/CIPN_HillPax.sedml/report to tgt: /XPP/CIPN_HillPax.sedml/report, shape: (10, 1001), type: float64\niterating over chunks for /XPP/CIPN_HillPax.sedml/report\nwriting dataset data for slice: (slice(0, 10, 1), slice(0, 1001, 1))\ndone with dataload for /XPP/CIPN_HillPax.sedml/report\nwrite_dataset src: /XPP/DRG.sedml/report to tgt: /XPP/DRG.sedml/report, shape: (18, 1001), type: float64\niterating over chunks for /XPP/DRG.sedml/report\nwriting dataset data for slice: (slice(0, 18, 1), slice(0, 1001, 1))\ndone with dataload for /XPP/DRG.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/621d42c8d8a14a834cbf402e\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 78%)\n  adding: outputs/reports.h5 (deflated 58%)\n  adding: rawLog.txt (deflated 81%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 19.8 KiB/28.9 KiB (337.0 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/621d42c8d8a14a834cbf402e/output.zip\nCompleted 19.8 KiB/28.9 KiB (337.0 KiB/s) with 1 file(s) remaining\rCompleted 28.9 KiB/28.9 KiB (325.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/621d42c8d8a14a834cbf402e/rawLog.txt\nCompleted 39.6 KiB/39.6 KiB (553.1 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/621d42c8d8a14a834cbf402e/outputs/reports.h5\nCompleted 4.2 KiB/4.2 KiB (57.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/621d42c8d8a14a834cbf402e/outputs/log.yml\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 SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file 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.\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"}