{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_CAD"},{"status":"SUCCEEDED","id":"data_set_CD"},{"status":"SUCCEEDED","id":"data_set_GKC"},{"status":"SUCCEEDED","id":"data_set_GKQ"},{"status":"SUCCEEDED","id":"data_set_HS"},{"status":"SUCCEEDED","id":"data_set_NS"},{"status":"SUCCEEDED","id":"data_set_QD"},{"status":"SUCCEEDED","id":"data_set_SD"},{"status":"SUCCEEDED","id":"data_set_VD"},{"status":"SUCCEEDED","id":"data_set_VS"}],"duration":0.122145,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"}],"tasks":[{"simulatorDetails":[{"value":"1500.0","key":"total"},{"value":"cvode","key":"meth"},{"value":"0.0001","key":"atoler"},{"value":"0.0001","key":"toler"},{"value":"0.0","key":"t0"},{"value":"1.5","key":"dt"},{"value":"1","key":"njmp"}],"algorithm":"KISAO_0000019","duration":0.105696,"output":"/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mModel `model` may be invalid.\r\n  - The model file `/tmp/tmpiu_pldux/booth_bose.ode` has warnings.\r\n    - The XPP file may be not be formulated correctly\r\n      - GKC is a duplicate name\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.317481,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n  booth_bose.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 11 data sets\r\n\r\nExecuting SED-ML file 1: booth_bose.sedml ...\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n  - Model `model` has warnings.\r\n    - The model file `booth_bose.ode` has warnings.\r\n      - The XPP file may be not be formulated correctly\r\n        - GKC is a duplicate name\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\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":"booth_bose.sedml"}],"duration":0.658303,"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    451      0 --:--:-- --:--:-- --:--:--   452\n\r100  304k  100  304k    0     0   687k      0 --:--:-- --:--:-- --:--:--  687k\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/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n  - Model `model` has warnings.\r\n    - The model file `booth_bose.ode` has warnings.\r\n      - The XPP file may be not be formulated correctly\r\n        - GKC is a duplicate name\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n  - The SED-ML file at location `booth_bose.sedml` has warnings.\r\n    - Model `model` has warnings.\r\n      - The model file `booth_bose.ode` has warnings.\r\n        - The XPP file may be not be formulated correctly\r\n          - GKC is a duplicate name\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/batch_a.hoc    \n  inflating: contents/matrix.mod     \n  inflating: contents/vecst.mod      \n  inflating: contents/passiv.mod     \n  inflating: contents/geneval_cvode.inc  \n  inflating: contents/xpp.dat        \n  inflating: contents/cal.mod        \n  inflating: contents/README         \n  inflating: contents/booth_bose.ode  \n  inflating: contents/nafPR.mod      \n  inflating: contents/xtmp           \n  inflating: contents/rcadecay.mod   \n  inflating: contents/kcRT03.mod     \n  inflating: contents/rkq.mod        \n  inflating: contents/mosinit.hoc    \n  inflating: contents/kdr.mod        \n  inflating: contents/booth_bose.sedml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 1.8 KiB/850.1 KiB (10.9 KiB/s) with 19 file(s) remaining\rupload: contents/booth_bose.ode to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/contents/booth_bose.ode\nCompleted 1.8 KiB/850.1 KiB (10.9 KiB/s) with 18 file(s) remaining\rCompleted 8.6 KiB/850.1 KiB (48.2 KiB/s) with 18 file(s) remaining\rupload: contents/booth_bose.sedml to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/contents/booth_bose.sedml\nCompleted 8.6 KiB/850.1 KiB (48.2 KiB/s) with 17 file(s) remaining\rCompleted 12.9 KiB/850.1 KiB (70.4 KiB/s) with 17 file(s) remaining\rupload: contents/README to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/contents/README\nCompleted 12.9 KiB/850.1 KiB (70.4 KiB/s) with 16 file(s) remaining\rCompleted 13.0 KiB/850.1 KiB (68.7 KiB/s) with 16 file(s) remaining\rupload: contents/mosinit.hoc to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/contents/mosinit.hoc\nCompleted 13.0 KiB/850.1 KiB (68.7 KiB/s) with 15 file(s) remaining\rCompleted 21.2 KiB/850.1 KiB (106.0 KiB/s) with 15 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/contents/metadata.rdf\nCompleted 21.2 KiB/850.1 KiB (106.0 KiB/s) with 14 file(s) remaining\rCompleted 177.3 KiB/850.1 KiB (876.9 KiB/s) with 14 file(s) remaining\rupload: contents/batch_a.hoc to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/contents/batch_a.hoc\nCompleted 177.3 KiB/850.1 KiB (876.9 KiB/s) with 13 file(s) remaining\rCompleted 180.4 KiB/850.1 KiB (838.2 KiB/s) with 13 file(s) remaining\rupload: contents/nafPR.mod to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/contents/nafPR.mod\nCompleted 180.4 KiB/850.1 KiB (838.2 KiB/s) with 12 file(s) remaining\rCompleted 190.9 KiB/850.1 KiB (865.0 KiB/s) with 12 file(s) remaining\rupload: contents/matrix.mod to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/contents/matrix.mod\nCompleted 190.9 KiB/850.1 KiB (865.0 KiB/s) with 11 file(s) remaining\rCompleted 446.9 KiB/850.1 KiB (1.9 MiB/s) with 11 file(s) remaining  \rCompleted 702.9 KiB/850.1 KiB (3.0 MiB/s) with 11 file(s) remaining  \rCompleted 706.0 KiB/850.1 KiB (2.7 MiB/s) with 11 file(s) remaining  \rupload: contents/passiv.mod to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/contents/passiv.mod\nCompleted 706.0 KiB/850.1 KiB (2.7 MiB/s) with 10 file(s) remaining\rCompleted 708.0 KiB/850.1 KiB (2.6 MiB/s) with 10 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/contents/manifest.xml\nCompleted 708.0 KiB/850.1 KiB (2.6 MiB/s) with 9 file(s) remaining\rupload: contents/xtmp to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/contents/xtmp\nCompleted 708.0 KiB/850.1 KiB (2.6 MiB/s) with 8 file(s) remaining\rCompleted 708.6 KiB/850.1 KiB (2.4 MiB/s) with 8 file(s) remaining\rupload: contents/rcadecay.mod to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/contents/rcadecay.mod\nCompleted 708.6 KiB/850.1 KiB (2.4 MiB/s) with 7 file(s) remaining\rCompleted 709.4 KiB/850.1 KiB (2.4 MiB/s) with 7 file(s) remaining\rupload: contents/rkq.mod to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/contents/rkq.mod\nCompleted 709.4 KiB/850.1 KiB (2.4 MiB/s) with 6 file(s) remaining\rCompleted 710.0 KiB/850.1 KiB (2.3 MiB/s) with 6 file(s) remaining\rupload: contents/kdr.mod to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/contents/kdr.mod\nCompleted 710.0 KiB/850.1 KiB (2.3 MiB/s) with 5 file(s) remaining\rCompleted 743.2 KiB/850.1 KiB (2.2 MiB/s) with 5 file(s) remaining\rupload: contents/vecst.mod to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/contents/vecst.mod\nCompleted 743.2 KiB/850.1 KiB (2.2 MiB/s) with 4 file(s) remaining\rCompleted 843.6 KiB/850.1 KiB (2.4 MiB/s) with 4 file(s) remaining\rupload: contents/xpp.dat to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/contents/xpp.dat\nCompleted 843.6 KiB/850.1 KiB (2.4 MiB/s) with 3 file(s) remaining\rCompleted 848.3 KiB/850.1 KiB (2.4 MiB/s) with 3 file(s) remaining\rupload: contents/geneval_cvode.inc to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/contents/geneval_cvode.inc\nCompleted 848.3 KiB/850.1 KiB (2.4 MiB/s) with 2 file(s) remaining\rCompleted 849.5 KiB/850.1 KiB (2.3 MiB/s) with 2 file(s) remaining\rupload: contents/kcRT03.mod to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/contents/kcRT03.mod\nCompleted 849.5 KiB/850.1 KiB (2.3 MiB/s) with 1 file(s) remaining\rCompleted 850.1 KiB/850.1 KiB (2.2 MiB/s) with 1 file(s) remaining\rupload: contents/cal.mod to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/contents/cal.mod\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /booth_bose.sedml\ncreating dataset /booth_bose.sedml/report, shape: (11, 1001), type: float64\ndataset created, uuid: d-ebfee6c2-abf6225a-963b-e011ec-c59ddc, chunk_size: (11, 1001)\ncreating attribute combineArchiveLocation in /booth_bose.sedml\ncreating attribute uri in /booth_bose.sedml\ncreating attribute _type in /booth_bose.sedml/report\ncreating attribute sedmlDataSetDataTypes in /booth_bose.sedml/report\ncreating attribute sedmlDataSetIds in /booth_bose.sedml/report\ncreating attribute sedmlDataSetLabels in /booth_bose.sedml/report\ncreating attribute sedmlDataSetNames in /booth_bose.sedml/report\ncreating attribute sedmlDataSetShapes in /booth_bose.sedml/report\ncreating attribute sedmlId in /booth_bose.sedml/report\ncreating attribute sedmlName in /booth_bose.sedml/report\ncreating attribute uri in /booth_bose.sedml/report\ncreate_links: /\ngot link: booth_bose.sedml\ncreate_links: /booth_bose.sedml\ngot link: report\nwrite_dataset src: /booth_bose.sedml/report to tgt: /booth_bose.sedml/report, shape: (11, 1001), type: float64\niterating over chunks for /booth_bose.sedml/report\nwriting dataset data for slice: (slice(0, 11, 1), slice(0, 1001, 1))\ndone with dataload for /booth_bose.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/621d4295b50991044c79acc0\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 75%)\n  adding: outputs/reports.h5 (deflated 14%)\n  adding: rawLog.txt (deflated 81%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 78.2 KiB/88.1 KiB (657.5 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/output.zip\nCompleted 78.2 KiB/88.1 KiB (657.5 KiB/s) with 1 file(s) remaining\rCompleted 88.1 KiB/88.1 KiB (511.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/rawLog.txt\nCompleted 86.7 KiB/86.7 KiB (810.4 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/outputs/reports.h5\nCompleted 4.0 KiB/4.0 KiB (49.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/621d4295b50991044c79acc0/outputs/log.yml\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mProcess 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.\nProcess and upload the outputs of the simulation run ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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"}