{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_time"},{"status":"SUCCEEDED","id":"data_set_v"},{"status":"SUCCEEDED","id":"data_set_m"},{"status":"SUCCEEDED","id":"data_set_h"},{"status":"SUCCEEDED","id":"data_set_n"}],"duration":0.996207,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"},{"curves":[{"status":"SUCCEEDED","id":"curve_v"},{"status":"SUCCEEDED","id":"curve_m"},{"status":"SUCCEEDED","id":"curve_h"},{"status":"SUCCEEDED","id":"curve_n"}],"duration":2.055955,"output":"/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"plot"}],"tasks":[{"simulatorDetails":[{"value":"pyneuroml.pynml.run_lems_with_jneuroml","key":"method"},{"value":{"length":"0.3s","method":"eulerTree","step":"9.999999999999999e-06s"},"key":"lemsSimulation"}],"algorithm":"KISAO_0000030","duration":4.932272,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":9.312046,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n  simulation.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 5 data sets\r\n    Plots (1):\r\n      plot: 4 curves\r\n\r\nExecuting SED-ML file 1: simulation.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task`\r\n    Outputs:\r\n      `plot`\r\n      `report`\r\n  Executing task 1: `task`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `report` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `plot` ...","skipReason":null,"exception":null,"status":"SUCCEEDED","location":"simulation.sedml"}],"duration":11.068873,"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 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    444      0 --:--:-- --:--:-- --:--:--   444\n\r100 1266k  100 1266k    0     0  2773k      0 --:--:-- --:--:-- --:--:-- 2773k\n\n\u001b[0;36m============================================= Executing COMBINE 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 may be invalid.\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 2 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 2\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 (2):\n    Succeeded: 2\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /simulation.sedml\ncreating dataset /simulation.sedml/plot, shape: (5, 30001), type: float64\ndataset created, uuid: d-5412f28e-6bc957bf-a70b-521cf7-20af42, chunk_size: (5, 30001)\ncreating dataset /simulation.sedml/report, shape: (5, 30001), type: float64\ndataset created, uuid: d-5412f28e-6bc957bf-a527-86c871-b64471, chunk_size: (5, 30001)\ncreating attribute combineArchiveLocation in /simulation.sedml\ncreating attribute uri in /simulation.sedml\ncreating attribute _type in /simulation.sedml/plot\ncreating attribute sedmlDataSetDataTypes in /simulation.sedml/plot\ncreating attribute sedmlDataSetIds in /simulation.sedml/plot\ncreating attribute sedmlDataSetLabels in /simulation.sedml/plot\ncreating attribute sedmlDataSetNames in /simulation.sedml/plot\ncreating attribute sedmlDataSetShapes in /simulation.sedml/plot\ncreating attribute sedmlId in /simulation.sedml/plot\ncreating attribute uri in /simulation.sedml/plot\ncreating attribute _type in /simulation.sedml/report\ncreating attribute sedmlDataSetDataTypes in /simulation.sedml/report\ncreating attribute sedmlDataSetIds in /simulation.sedml/report\ncreating attribute sedmlDataSetLabels in /simulation.sedml/report\ncreating attribute sedmlDataSetNames in /simulation.sedml/report\ncreating attribute sedmlDataSetShapes in /simulation.sedml/report\ncreating attribute sedmlId in /simulation.sedml/report\ncreating attribute uri in /simulation.sedml/report\ncreate_links: /\ngot link: simulation.sedml\ncreate_links: /simulation.sedml\ngot link: plot\ngot link: report\nwrite_dataset src: /simulation.sedml/plot to tgt: /simulation.sedml/plot, shape: (5, 30001), type: float64\niterating over chunks for /simulation.sedml/plot\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 30001, 1))\ndone with dataload for /simulation.sedml/plot\nwrite_dataset src: /simulation.sedml/report to tgt: /simulation.sedml/report, shape: (5, 30001), type: float64\niterating over chunks for /simulation.sedml/report\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 30001, 1))\ndone with dataload for /simulation.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/61fea490f499ccf25faafc55\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/simulation.sedml/ (stored 0%)\n  adding: outputs/simulation.sedml/plot.pdf (deflated 17%)\n  adding: outputs/log.yml (deflated 65%)\n  adding: outputs/reports.h5 (deflated 2%)\n  adding: rawLog.txt (deflated 74%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/1.3 MiB (2.8 MiB/s) with 4 file(s) remaining\rCompleted 512.0 KiB/1.3 MiB (5.2 MiB/s) with 4 file(s) remaining\rCompleted 531.4 KiB/1.3 MiB (5.0 MiB/s) with 4 file(s) remaining\rupload: outputs/simulation.sedml/plot.pdf to s3://files.biosimulations.org/simulations/61fea490f499ccf25faafc55/outputs/simulation.sedml/plot.pdf\nCompleted 531.4 KiB/1.3 MiB (5.0 MiB/s) with 3 file(s) remaining\rCompleted 787.4 KiB/1.3 MiB (7.3 MiB/s) with 3 file(s) remaining\rCompleted 1.0 MiB/1.3 MiB (9.4 MiB/s) with 3 file(s) remaining  \rCompleted 1.0 MiB/1.3 MiB (7.8 MiB/s) with 3 file(s) remaining  \rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/61fea490f499ccf25faafc55/outputs/plots.zip\nCompleted 1.0 MiB/1.3 MiB (7.8 MiB/s) with 2 file(s) remaining\rCompleted 1.0 MiB/1.3 MiB (7.5 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/61fea490f499ccf25faafc55/rawLog.txt\nCompleted 1.0 MiB/1.3 MiB (7.5 MiB/s) with 1 file(s) remaining\rCompleted 1.3 MiB/1.3 MiB (6.2 MiB/s) with 1 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/61fea490f499ccf25faafc55/output.zip\nCompleted 256.0 KiB/1.3 MiB (5.0 MiB/s) with 1 file(s) remaining\rCompleted 512.0 KiB/1.3 MiB (8.8 MiB/s) with 1 file(s) remaining\rCompleted 768.0 KiB/1.3 MiB (11.8 MiB/s) with 1 file(s) remaining\rCompleted 1.0 MiB/1.3 MiB (14.5 MiB/s) with 1 file(s) remaining  \rCompleted 1.2 MiB/1.3 MiB (17.7 MiB/s) with 1 file(s) remaining  \rCompleted 1.3 MiB/1.3 MiB (9.5 MiB/s) with 1 file(s) remaining   \rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/61fea490f499ccf25faafc55/outputs/reports.h5\nCompleted 2.6 KiB/2.6 KiB (37.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/61fea490f499ccf25faafc55/outputs/log.yml\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\n\u001b[0;32mPost thumbnails to the API.....Succeeded\nCreate thumbnails from the images specified in the manifest.....Succeeded\nRead the manifest and post the files to the API.....Succeeded\nExtract the files in the combine archive.....Succeeded\nProcess the manifest file in the combine archive.....Succeeded\nPost the logs to the API.....Succeeded\nRetrieve the logs of the simulation run.....Succeeded\nPost the Metadata to the API.....Succeeded\nProcess the Metadata in the combine archive.....Succeeded\nProcess and upload the outputs of the simulation run.....Succeeded\nPost the SED-ML file to the API.....Succeeded\nProcess the SED-ML file in the combine archive.....Succeeded\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","skipReason":null,"exception":null,"status":"SUCCEEDED"}