{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_KO"},{"status":"SUCCEEDED","id":"data_set_NAI"}],"duration":0.078156,"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":0.183466,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.333685,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n  Cressman_et_al_JCNS_1_reducedmodel.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 3 data sets\r\n\r\nExecuting SED-ML file 1: Cressman_et_al_JCNS_1_reducedmodel.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":"Cressman_et_al_JCNS_1_reducedmodel.sedml"}],"duration":0.603366,"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    477      0 --:--:-- --:--:-- --:--:--   479\n\r100  6263  100  6263    0     0  15443      0 --:--:-- --:--:-- --:--:-- 15443\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/Cressman_et_al_JCNS_1_reducedmodel.ode  \n  inflating: contents/README.txt     \n  inflating: contents/Cressman_et_al_JCNS_1_fullmodel_RK4.c  \n  inflating: contents/Cressman_et_al_JCNS_1_reducedmodel.sedml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 756 Bytes/17.7 KiB (5.7 KiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/621d42aad8a14a834cbf3dfc/contents/manifest.xml\nCompleted 756 Bytes/17.7 KiB (5.7 KiB/s) with 5 file(s) remaining\rCompleted 7.5 KiB/17.7 KiB (56.2 KiB/s) with 5 file(s) remaining \rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/621d42aad8a14a834cbf3dfc/contents/metadata.rdf\nCompleted 7.5 KiB/17.7 KiB (56.2 KiB/s) with 4 file(s) remaining\rCompleted 7.9 KiB/17.7 KiB (54.8 KiB/s) with 4 file(s) remaining\rupload: contents/README.txt to s3://files.biosimulations.org/simulations/621d42aad8a14a834cbf3dfc/contents/README.txt\nCompleted 7.9 KiB/17.7 KiB (54.8 KiB/s) with 3 file(s) remaining\rCompleted 12.5 KiB/17.7 KiB (77.3 KiB/s) with 3 file(s) remaining\rupload: contents/Cressman_et_al_JCNS_1_fullmodel_RK4.c to s3://files.biosimulations.org/simulations/621d42aad8a14a834cbf3dfc/contents/Cressman_et_al_JCNS_1_fullmodel_RK4.c\nCompleted 12.5 KiB/17.7 KiB (77.3 KiB/s) with 2 file(s) remaining\rCompleted 15.0 KiB/17.7 KiB (89.8 KiB/s) with 2 file(s) remaining\rupload: contents/Cressman_et_al_JCNS_1_reducedmodel.sedml to s3://files.biosimulations.org/simulations/621d42aad8a14a834cbf3dfc/contents/Cressman_et_al_JCNS_1_reducedmodel.sedml\nCompleted 15.0 KiB/17.7 KiB (89.8 KiB/s) with 1 file(s) remaining\rCompleted 17.7 KiB/17.7 KiB (96.3 KiB/s) with 1 file(s) remaining\rupload: contents/Cressman_et_al_JCNS_1_reducedmodel.ode to s3://files.biosimulations.org/simulations/621d42aad8a14a834cbf3dfc/contents/Cressman_et_al_JCNS_1_reducedmodel.ode\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Cressman_et_al_JCNS_1_reducedmodel.sedml\ncreating dataset /Cressman_et_al_JCNS_1_reducedmodel.sedml/report, shape: (3, 1001), type: float64\ndataset created, uuid: d-e8e2cfd7-c9fb948b-f6c0-fbb904-2b5e4c, chunk_size: (3, 1001)\ncreating attribute combineArchiveLocation in /Cressman_et_al_JCNS_1_reducedmodel.sedml\ncreating attribute uri in /Cressman_et_al_JCNS_1_reducedmodel.sedml\ncreating attribute _type in /Cressman_et_al_JCNS_1_reducedmodel.sedml/report\ncreating attribute sedmlDataSetDataTypes in /Cressman_et_al_JCNS_1_reducedmodel.sedml/report\ncreating attribute sedmlDataSetIds in /Cressman_et_al_JCNS_1_reducedmodel.sedml/report\ncreating attribute sedmlDataSetLabels in /Cressman_et_al_JCNS_1_reducedmodel.sedml/report\ncreating attribute sedmlDataSetNames in /Cressman_et_al_JCNS_1_reducedmodel.sedml/report\ncreating attribute sedmlDataSetShapes in /Cressman_et_al_JCNS_1_reducedmodel.sedml/report\ncreating attribute sedmlId in /Cressman_et_al_JCNS_1_reducedmodel.sedml/report\ncreating attribute sedmlName in /Cressman_et_al_JCNS_1_reducedmodel.sedml/report\ncreating attribute uri in /Cressman_et_al_JCNS_1_reducedmodel.sedml/report\ncreate_links: /\ngot link: Cressman_et_al_JCNS_1_reducedmodel.sedml\ncreate_links: /Cressman_et_al_JCNS_1_reducedmodel.sedml\ngot link: report\nwrite_dataset src: /Cressman_et_al_JCNS_1_reducedmodel.sedml/report to tgt: /Cressman_et_al_JCNS_1_reducedmodel.sedml/report, shape: (3, 1001), type: float64\niterating over chunks for /Cressman_et_al_JCNS_1_reducedmodel.sedml/report\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 1001, 1))\ndone with dataload for /Cressman_et_al_JCNS_1_reducedmodel.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/621d42aad8a14a834cbf3dfc\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 61%)\n  adding: outputs/reports.h5 (deflated 48%)\n  adding: rawLog.txt (deflated 77%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 16.4 KiB/22.3 KiB (231.1 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/621d42aad8a14a834cbf3dfc/output.zip\nCompleted 16.4 KiB/22.3 KiB (231.1 KiB/s) with 1 file(s) remaining\rCompleted 22.3 KiB/22.3 KiB (181.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/621d42aad8a14a834cbf3dfc/rawLog.txt\nCompleted 26.4 KiB/26.4 KiB (388.7 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/621d42aad8a14a834cbf3dfc/outputs/reports.h5\nCompleted 1.8 KiB/1.8 KiB (17.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/621d42aad8a14a834cbf3dfc/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.\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.\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"}