{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_FF"},{"status":"SUCCEEDED","id":"data_set_KAPD"},{"status":"SUCCEEDED","id":"data_set_KAPUD"},{"status":"SUCCEEDED","id":"data_set_SIGHAT"},{"status":"SUCCEEDED","id":"data_set_SOBJ"},{"status":"SUCCEEDED","id":"data_set_THETA"},{"status":"SUCCEEDED","id":"data_set_THOBJ"},{"status":"SUCCEEDED","id":"data_set_XCEN"},{"status":"SUCCEEDED","id":"data_set_XLEN"},{"status":"SUCCEEDED","id":"data_set_XU"},{"status":"SUCCEEDED","id":"data_set_XX"},{"status":"SUCCEEDED","id":"data_set_XXAUX"},{"status":"SUCCEEDED","id":"data_set_YCEN"},{"status":"SUCCEEDED","id":"data_set_YY"},{"status":"SUCCEEDED","id":"data_set_YYAUX"}],"duration":0.139789,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"},{"curves":[{"status":"SUCCEEDED","id":"curve_1"}],"duration":0.165336,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"plot"}],"tasks":[{"simulatorDetails":[{"value":"1.0","key":"total"},{"value":"rungekutta","key":"meth"},{"value":"0.001","key":"dt"},{"value":"0.0","key":"t0"},{"value":"1","key":"njmp"}],"algorithm":"KISAO_0000032","duration":0.084724,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.488456,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n  conical_whisker.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 16 data sets\r\n    Plots (1):\r\n      plot: 1 curves\r\n\r\nExecuting SED-ML file 1: conical_whisker.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":"conical_whisker.sedml"}],"duration":0.816552,"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    444      0 --:--:-- --:--:-- --:--:--   445\n\r100  585k  100  585k    0     0  1328k      0 --:--:-- --:--:-- --:--:-- 1328k\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 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 contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/readme.txt     \n  inflating: contents/conical_whisker.ode  \n  inflating: contents/conical_whisker.sedml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/article-figures/PMC3828597/elife01350f001.jpg  \n  inflating: contents/article-figures/PMC3828597/elife01350f002.jpg  \n  inflating: contents/article-figures/PMC3828597/elife01350f003.jpg  \n  inflating: contents/article-figures/PMC3828597/elife01350f004.jpg  \n  inflating: contents/article-figures/PMC3828597/elife01350f005.jpg  \n  inflating: contents/article-figures/PMC3828597/elife01350f006.jpg  \n  inflating: contents/article-figures/PMC3828597/elife01350f007.jpg  \n  inflating: contents/manifest.xml   \nCompleted 83.2 KiB/879.0 KiB (1.1 MiB/s) with 12 file(s) remaining\rupload: contents/article-figures/PMC3828597/elife01350f002.jpg to s3://files.biosimulations.org/simulations/621d42afd8a14a834cbf3e47/contents/article-figures/PMC3828597/elife01350f002.jpg\nCompleted 83.2 KiB/879.0 KiB (1.1 MiB/s) with 11 file(s) remaining\rCompleted 271.8 KiB/879.0 KiB (2.0 MiB/s) with 11 file(s) remaining\rupload: contents/article-figures/PMC3828597/elife01350f003.jpg to s3://files.biosimulations.org/simulations/621d42afd8a14a834cbf3e47/contents/article-figures/PMC3828597/elife01350f003.jpg\nCompleted 271.8 KiB/879.0 KiB (2.0 MiB/s) with 10 file(s) remaining\rCompleted 280.9 KiB/879.0 KiB (2.0 MiB/s) with 10 file(s) remaining\rupload: contents/conical_whisker.sedml to s3://files.biosimulations.org/simulations/621d42afd8a14a834cbf3e47/contents/conical_whisker.sedml\nCompleted 280.9 KiB/879.0 KiB (2.0 MiB/s) with 9 file(s) remaining\rCompleted 392.7 KiB/879.0 KiB (2.7 MiB/s) with 9 file(s) remaining\rupload: contents/article-figures/PMC3828597/elife01350f007.jpg to s3://files.biosimulations.org/simulations/621d42afd8a14a834cbf3e47/contents/article-figures/PMC3828597/elife01350f007.jpg\nCompleted 392.7 KiB/879.0 KiB (2.7 MiB/s) with 8 file(s) remaining\rCompleted 506.5 KiB/879.0 KiB (3.2 MiB/s) with 8 file(s) remaining\rupload: contents/article-figures/PMC3828597/elife01350f001.jpg to s3://files.biosimulations.org/simulations/621d42afd8a14a834cbf3e47/contents/article-figures/PMC3828597/elife01350f001.jpg\nCompleted 506.5 KiB/879.0 KiB (3.2 MiB/s) with 7 file(s) remaining\rCompleted 637.4 KiB/879.0 KiB (3.3 MiB/s) with 7 file(s) remaining\rupload: contents/article-figures/PMC3828597/elife01350f006.jpg to s3://files.biosimulations.org/simulations/621d42afd8a14a834cbf3e47/contents/article-figures/PMC3828597/elife01350f006.jpg\nCompleted 637.4 KiB/879.0 KiB (3.3 MiB/s) with 6 file(s) remaining\rCompleted 645.0 KiB/879.0 KiB (3.3 MiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/621d42afd8a14a834cbf3e47/contents/metadata.rdf\nCompleted 645.0 KiB/879.0 KiB (3.3 MiB/s) with 5 file(s) remaining\rCompleted 740.3 KiB/879.0 KiB (3.7 MiB/s) with 5 file(s) remaining\rupload: contents/article-figures/PMC3828597/elife01350f004.jpg to s3://files.biosimulations.org/simulations/621d42afd8a14a834cbf3e47/contents/article-figures/PMC3828597/elife01350f004.jpg\nCompleted 740.3 KiB/879.0 KiB (3.7 MiB/s) with 4 file(s) remaining\rCompleted 742.5 KiB/879.0 KiB (3.7 MiB/s) with 4 file(s) remaining\rupload: contents/conical_whisker.ode to s3://files.biosimulations.org/simulations/621d42afd8a14a834cbf3e47/contents/conical_whisker.ode\nCompleted 742.5 KiB/879.0 KiB (3.7 MiB/s) with 3 file(s) remaining\rCompleted 877.2 KiB/879.0 KiB (3.8 MiB/s) with 3 file(s) remaining\rupload: contents/article-figures/PMC3828597/elife01350f005.jpg to s3://files.biosimulations.org/simulations/621d42afd8a14a834cbf3e47/contents/article-figures/PMC3828597/elife01350f005.jpg\nCompleted 877.2 KiB/879.0 KiB (3.8 MiB/s) with 2 file(s) remaining\rCompleted 877.4 KiB/879.0 KiB (3.5 MiB/s) with 2 file(s) remaining\rupload: contents/readme.txt to s3://files.biosimulations.org/simulations/621d42afd8a14a834cbf3e47/contents/readme.txt\nCompleted 877.4 KiB/879.0 KiB (3.5 MiB/s) with 1 file(s) remaining\rCompleted 879.0 KiB/879.0 KiB (3.2 MiB/s) with 1 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/621d42afd8a14a834cbf3e47/contents/manifest.xml\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /conical_whisker.sedml\ncreating dataset /conical_whisker.sedml/plot, shape: (2, 1001), type: float64\ndataset created, uuid: d-53cda0bb-74c1edca-80ea-d3ea75-5503bc, chunk_size: (2, 1001)\ncreating dataset /conical_whisker.sedml/report, shape: (16, 1001), type: float64\ndataset created, uuid: d-53cda0bb-74c1edca-3d9a-224a6f-90bfdd, chunk_size: (16, 1001)\ncreating attribute combineArchiveLocation in /conical_whisker.sedml\ncreating attribute uri in /conical_whisker.sedml\ncreating attribute _type in /conical_whisker.sedml/plot\ncreating attribute sedmlDataSetDataTypes in /conical_whisker.sedml/plot\ncreating attribute sedmlDataSetIds in /conical_whisker.sedml/plot\ncreating attribute sedmlDataSetLabels in /conical_whisker.sedml/plot\ncreating attribute sedmlDataSetNames in /conical_whisker.sedml/plot\ncreating attribute sedmlDataSetShapes in /conical_whisker.sedml/plot\ncreating attribute sedmlId in /conical_whisker.sedml/plot\ncreating attribute uri in /conical_whisker.sedml/plot\ncreating attribute _type in /conical_whisker.sedml/report\ncreating attribute sedmlDataSetDataTypes in /conical_whisker.sedml/report\ncreating attribute sedmlDataSetIds in /conical_whisker.sedml/report\ncreating attribute sedmlDataSetLabels in /conical_whisker.sedml/report\ncreating attribute sedmlDataSetNames in /conical_whisker.sedml/report\ncreating attribute sedmlDataSetShapes in /conical_whisker.sedml/report\ncreating attribute sedmlId in /conical_whisker.sedml/report\ncreating attribute sedmlName in /conical_whisker.sedml/report\ncreating attribute uri in /conical_whisker.sedml/report\ncreate_links: /\ngot link: conical_whisker.sedml\ncreate_links: /conical_whisker.sedml\ngot link: plot\ngot link: report\nwrite_dataset src: /conical_whisker.sedml/plot to tgt: /conical_whisker.sedml/plot, shape: (2, 1001), type: float64\niterating over chunks for /conical_whisker.sedml/plot\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /conical_whisker.sedml/plot\nwrite_dataset src: /conical_whisker.sedml/report to tgt: /conical_whisker.sedml/report, shape: (16, 1001), type: float64\niterating over chunks for /conical_whisker.sedml/report\nwriting dataset data for slice: (slice(0, 16, 1), slice(0, 1001, 1))\ndone with dataload for /conical_whisker.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/621d42afd8a14a834cbf3e47\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 69%)\n  adding: outputs/conical_whisker.sedml/ (stored 0%)\n  adding: outputs/conical_whisker.sedml/plot.pdf (deflated 35%)\n  adding: outputs/reports.h5 (deflated 23%)\n  adding: rawLog.txt (deflated 82%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 74.0 KiB/93.6 KiB (749.6 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/621d42afd8a14a834cbf3e47/output.zip\nCompleted 74.0 KiB/93.6 KiB (749.6 KiB/s) with 3 file(s) remaining\rCompleted 80.6 KiB/93.6 KiB (742.2 KiB/s) with 3 file(s) remaining\rupload: outputs/conical_whisker.sedml/plot.pdf to s3://files.biosimulations.org/simulations/621d42afd8a14a834cbf3e47/outputs/conical_whisker.sedml/plot.pdf\nCompleted 80.6 KiB/93.6 KiB (742.2 KiB/s) with 2 file(s) remaining\rCompleted 89.4 KiB/93.6 KiB (705.9 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/621d42afd8a14a834cbf3e47/rawLog.txt\nCompleted 89.4 KiB/93.6 KiB (705.9 KiB/s) with 1 file(s) remaining\rCompleted 93.6 KiB/93.6 KiB (711.5 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/621d42afd8a14a834cbf3e47/outputs/plots.zip\nCompleted 86.4 KiB/86.4 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/621d42afd8a14a834cbf3e47/outputs/reports.h5\nCompleted 2.7 KiB/2.7 KiB (47.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/621d42afd8a14a834cbf3e47/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.\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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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"}