{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_H"},{"status":"SUCCEEDED","id":"data_set_N"},{"status":"SUCCEEDED","id":"data_set_V"}],"duration":0.082695,"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":0.144347,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.316631,"output":"Archive contains 2 SED-ML documents with 2 models, 2 simulations, 2 tasks, 2 reports, and 0 plots:\r\n  One_full_cell_fixed_Ko_and_Nai.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 4 data sets\r\n  One_full_cell_with_dyn_ion_conc.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 6 data sets\r\n\r\nExecuting SED-ML file 1: One_full_cell_fixed_Ko_and_Nai.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":"One_full_cell_fixed_Ko_and_Nai.sedml"},{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_H"},{"status":"SUCCEEDED","id":"data_set_KO"},{"status":"SUCCEEDED","id":"data_set_N"},{"status":"SUCCEEDED","id":"data_set_NAI"},{"status":"SUCCEEDED","id":"data_set_V"}],"duration":0.086251,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"}],"tasks":[{"simulatorDetails":[{"value":"10000.0","key":"total"},{"value":"rungekutta","key":"meth"},{"value":"0.05","key":"dt"},{"value":"0.0","key":"t0"},{"value":"200","key":"njmp"}],"algorithm":"KISAO_0000032","duration":0.849677,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":1.03219,"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: One_full_cell_with_dyn_ion_conc.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":"One_full_cell_with_dyn_ion_conc.sedml"}],"duration":1.770613,"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    491      0 --:--:-- --:--:-- --:--:--   492\n\r100  771k  100  771k    0     0  1258k      0 --:--:-- --:--:-- --:--:-- 1258k\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/FullModel_RK4_JBP.c  \n  inflating: contents/One_full_cell_fixed_Ko_and_Nai.ode  \n  inflating: contents/One_full_cell_with_dyn_ion_conc.ode  \n  inflating: contents/One_full_cell_fixed_Ko_and_Nai.sedml  \n  inflating: contents/One_full_cell_with_dyn_ion_conc.sedml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/fig4A.jpg      \n  inflating: contents/fig4B.jpg      \n  inflating: contents/fig4C.jpg      \n  inflating: contents/fig4D.jpg      \n  inflating: contents/manifest.xml   \nCompleted 4.5 KiB/904.6 KiB (49.7 KiB/s) with 12 file(s) remaining\rupload: contents/FullModel_RK4_JBP.c to s3://files.biosimulations.org/simulations/621d42ac87550e369891baa5/contents/FullModel_RK4_JBP.c\nCompleted 4.5 KiB/904.6 KiB (49.7 KiB/s) with 11 file(s) remaining\rCompleted 5.8 KiB/904.6 KiB (44.2 KiB/s) with 11 file(s) remaining\rupload: contents/One_full_cell_fixed_Ko_and_Nai.ode to s3://files.biosimulations.org/simulations/621d42ac87550e369891baa5/contents/One_full_cell_fixed_Ko_and_Nai.ode\nCompleted 5.8 KiB/904.6 KiB (44.2 KiB/s) with 10 file(s) remaining\rCompleted 15.7 KiB/904.6 KiB (109.7 KiB/s) with 10 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/621d42ac87550e369891baa5/contents/metadata.rdf\nCompleted 15.7 KiB/904.6 KiB (109.7 KiB/s) with 9 file(s) remaining\rCompleted 20.3 KiB/904.6 KiB (136.0 KiB/s) with 9 file(s) remaining\rupload: contents/One_full_cell_with_dyn_ion_conc.sedml to s3://files.biosimulations.org/simulations/621d42ac87550e369891baa5/contents/One_full_cell_with_dyn_ion_conc.sedml\nCompleted 20.3 KiB/904.6 KiB (136.0 KiB/s) with 8 file(s) remaining\rCompleted 237.1 KiB/904.6 KiB (1.4 MiB/s) with 8 file(s) remaining \rupload: contents/fig4D.jpg to s3://files.biosimulations.org/simulations/621d42ac87550e369891baa5/contents/fig4D.jpg\nCompleted 237.1 KiB/904.6 KiB (1.4 MiB/s) with 7 file(s) remaining\rCompleted 451.2 KiB/904.6 KiB (2.6 MiB/s) with 7 file(s) remaining\rupload: contents/fig4A.jpg to s3://files.biosimulations.org/simulations/621d42ac87550e369891baa5/contents/fig4A.jpg\nCompleted 451.2 KiB/904.6 KiB (2.6 MiB/s) with 6 file(s) remaining\rCompleted 452.5 KiB/904.6 KiB (2.4 MiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/621d42ac87550e369891baa5/contents/manifest.xml\nCompleted 452.5 KiB/904.6 KiB (2.4 MiB/s) with 5 file(s) remaining\rCompleted 456.0 KiB/904.6 KiB (2.4 MiB/s) with 5 file(s) remaining\rupload: contents/One_full_cell_fixed_Ko_and_Nai.sedml to s3://files.biosimulations.org/simulations/621d42ac87550e369891baa5/contents/One_full_cell_fixed_Ko_and_Nai.sedml\nCompleted 456.0 KiB/904.6 KiB (2.4 MiB/s) with 4 file(s) remaining\rCompleted 458.0 KiB/904.6 KiB (2.4 MiB/s) with 4 file(s) remaining\rupload: contents/One_full_cell_with_dyn_ion_conc.ode to s3://files.biosimulations.org/simulations/621d42ac87550e369891baa5/contents/One_full_cell_with_dyn_ion_conc.ode\nCompleted 458.0 KiB/904.6 KiB (2.4 MiB/s) with 3 file(s) remaining\rCompleted 458.9 KiB/904.6 KiB (2.3 MiB/s) with 3 file(s) remaining\rupload: contents/README.txt to s3://files.biosimulations.org/simulations/621d42ac87550e369891baa5/contents/README.txt\nCompleted 458.9 KiB/904.6 KiB (2.3 MiB/s) with 2 file(s) remaining\rCompleted 652.9 KiB/904.6 KiB (3.1 MiB/s) with 2 file(s) remaining\rupload: contents/fig4B.jpg to s3://files.biosimulations.org/simulations/621d42ac87550e369891baa5/contents/fig4B.jpg\nCompleted 652.9 KiB/904.6 KiB (3.1 MiB/s) with 1 file(s) remaining\rCompleted 904.6 KiB/904.6 KiB (3.4 MiB/s) with 1 file(s) remaining\rupload: contents/fig4C.jpg to s3://files.biosimulations.org/simulations/621d42ac87550e369891baa5/contents/fig4C.jpg\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /One_full_cell_fixed_Ko_and_Nai.sedml\ncreating dataset /One_full_cell_fixed_Ko_and_Nai.sedml/report, shape: (4, 1001), type: float64\ndataset created, uuid: d-41153605-85bb0f2b-576c-eab6c6-06a320, chunk_size: (4, 1001)\ncreating group /One_full_cell_with_dyn_ion_conc.sedml\ncreating dataset /One_full_cell_with_dyn_ion_conc.sedml/report, shape: (6, 1001), type: float64\ndataset created, uuid: d-41153605-85bb0f2b-b4a5-eff28f-2b9a38, chunk_size: (6, 1001)\ncreating attribute combineArchiveLocation in /One_full_cell_fixed_Ko_and_Nai.sedml\ncreating attribute uri in /One_full_cell_fixed_Ko_and_Nai.sedml\ncreating attribute _type in /One_full_cell_fixed_Ko_and_Nai.sedml/report\ncreating attribute sedmlDataSetDataTypes in /One_full_cell_fixed_Ko_and_Nai.sedml/report\ncreating attribute sedmlDataSetIds in /One_full_cell_fixed_Ko_and_Nai.sedml/report\ncreating attribute sedmlDataSetLabels in /One_full_cell_fixed_Ko_and_Nai.sedml/report\ncreating attribute sedmlDataSetNames in /One_full_cell_fixed_Ko_and_Nai.sedml/report\ncreating attribute sedmlDataSetShapes in /One_full_cell_fixed_Ko_and_Nai.sedml/report\ncreating attribute sedmlId in /One_full_cell_fixed_Ko_and_Nai.sedml/report\ncreating attribute sedmlName in /One_full_cell_fixed_Ko_and_Nai.sedml/report\ncreating attribute uri in /One_full_cell_fixed_Ko_and_Nai.sedml/report\ncreating attribute combineArchiveLocation in /One_full_cell_with_dyn_ion_conc.sedml\ncreating attribute uri in /One_full_cell_with_dyn_ion_conc.sedml\ncreating attribute _type in /One_full_cell_with_dyn_ion_conc.sedml/report\ncreating attribute sedmlDataSetDataTypes in /One_full_cell_with_dyn_ion_conc.sedml/report\ncreating attribute sedmlDataSetIds in /One_full_cell_with_dyn_ion_conc.sedml/report\ncreating attribute sedmlDataSetLabels in /One_full_cell_with_dyn_ion_conc.sedml/report\ncreating attribute sedmlDataSetNames in /One_full_cell_with_dyn_ion_conc.sedml/report\ncreating attribute sedmlDataSetShapes in /One_full_cell_with_dyn_ion_conc.sedml/report\ncreating attribute sedmlId in /One_full_cell_with_dyn_ion_conc.sedml/report\ncreating attribute sedmlName in /One_full_cell_with_dyn_ion_conc.sedml/report\ncreating attribute uri in /One_full_cell_with_dyn_ion_conc.sedml/report\ncreate_links: /\ngot link: One_full_cell_fixed_Ko_and_Nai.sedml\ngot link: One_full_cell_with_dyn_ion_conc.sedml\ncreate_links: /One_full_cell_fixed_Ko_and_Nai.sedml\ngot link: report\ncreate_links: /One_full_cell_with_dyn_ion_conc.sedml\ngot link: report\nwrite_dataset src: /One_full_cell_fixed_Ko_and_Nai.sedml/report to tgt: /One_full_cell_fixed_Ko_and_Nai.sedml/report, shape: (4, 1001), type: float64\niterating over chunks for /One_full_cell_fixed_Ko_and_Nai.sedml/report\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /One_full_cell_fixed_Ko_and_Nai.sedml/report\nwrite_dataset src: /One_full_cell_with_dyn_ion_conc.sedml/report to tgt: /One_full_cell_with_dyn_ion_conc.sedml/report, shape: (6, 1001), type: float64\niterating over chunks for /One_full_cell_with_dyn_ion_conc.sedml/report\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1001, 1))\ndone with dataload for /One_full_cell_with_dyn_ion_conc.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/621d42ac87550e369891baa5\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 74%)\n  adding: outputs/reports.h5 (deflated 39%)\n  adding: rawLog.txt (deflated 82%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 40.8 KiB/49.9 KiB (602.5 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/621d42ac87550e369891baa5/output.zip\nCompleted 40.8 KiB/49.9 KiB (602.5 KiB/s) with 1 file(s) remaining\rCompleted 49.9 KiB/49.9 KiB (560.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/621d42ac87550e369891baa5/rawLog.txt\nCompleted 61.6 KiB/61.6 KiB (905.9 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/621d42ac87550e369891baa5/outputs/reports.h5\nCompleted 3.4 KiB/3.4 KiB (52.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/621d42ac87550e369891baa5/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.\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.\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"}