{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_V"},{"status":"SUCCEEDED","id":"data_set_W"}],"duration":0.077164,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"},{"curves":[{"status":"SUCCEEDED","id":"curve_1"}],"duration":0.187472,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"plot"}],"tasks":[{"simulatorDetails":[{"value":"100000.0","key":"total"},{"value":"euler","key":"meth"},{"value":"0.1","key":"dt"},{"value":"0.0","key":"t0"},{"value":"1000","key":"njmp"}],"algorithm":"KISAO_0000030","duration":0.448006,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.82837,"output":"Archive contains 2 SED-ML documents with 2 models, 2 simulations, 2 tasks, 2 reports, and 2 plots:\r\n  2d-ML.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 3 data sets\r\n    Plots (1):\r\n      plot: 1 curves\r\n  3d-ML.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 4 data sets\r\n    Plots (1):\r\n      plot: 1 curves\r\n\r\nExecuting SED-ML file 1: 2d-ML.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":"2d-ML.sedml"},{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_V"},{"status":"SUCCEEDED","id":"data_set_Y"},{"status":"SUCCEEDED","id":"data_set_Z"}],"duration":0.073251,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"},{"curves":[{"status":"SUCCEEDED","id":"curve_1"}],"duration":0.146484,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"plot"}],"tasks":[{"simulatorDetails":[{"value":"100000.0","key":"total"},{"value":"euler","key":"meth"},{"value":"0.1","key":"dt"},{"value":"0.0","key":"t0"},{"value":"1000","key":"njmp"}],"algorithm":"KISAO_0000030","duration":0.608033,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.941317,"output":" \u001b[34msucceeded\u001b[0m\r\n\r\n  Executed 1 tasks and 2 outputs:\r\n    Tasks:\r\n      Succeeded: 1\r\n      Skipped: 0\r\n      Failed: 0\r\n    Outputs:\r\n      Succeeded: 2\r\n      Skipped: 0\r\n      Failed: 0\r\nExecuting SED-ML file 2: 3d-ML.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":"3d-ML.sedml"}],"duration":2.17943,"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    479      0 --:--:-- --:--:-- --:--:--   480\n\r100 1000k  100 1000k    0     0  2320k      0 --:--:-- --:--:-- --:--:-- 2320k\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 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 (4):\n    Succeeded: 4\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.html    \n  inflating: contents/2d-ML.ode      \n  inflating: contents/3d-ML.ode      \n  inflating: contents/2d-ML.sedml    \n  inflating: contents/3d-ML.sedml    \n  inflating: contents/metadata.rdf   \n  inflating: contents/article-figures/PMC2551735/pcbi.1000198.g001.jpg  \n  inflating: contents/article-figures/PMC2551735/pcbi.1000198.g002.jpg  \n  inflating: contents/article-figures/PMC2551735/pcbi.1000198.g003.jpg  \n  inflating: contents/article-figures/PMC2551735/pcbi.1000198.g004.jpg  \n  inflating: contents/article-figures/PMC2551735/pcbi.1000198.g005.jpg  \n  inflating: contents/article-figures/PMC2551735/pcbi.1000198.g006.jpg  \n  inflating: contents/article-figures/PMC2551735/pcbi.1000198.g007.jpg  \n  inflating: contents/article-figures/PMC2551735/pcbi.1000198.g008.jpg  \n  inflating: contents/article-figures/PMC2551735/pcbi.1000198.g009.jpg  \n  inflating: contents/article-figures/PMC2551735/pcbi.1000198.g010.jpg  \n  inflating: contents/article-figures/PMC2551735/pcbi.1000198.g011.jpg  \n  inflating: contents/manifest.xml   \nCompleted 3.2 KiB/1.0 MiB (38.9 KiB/s) with 18 file(s) remaining\rupload: contents/2d-ML.sedml to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/contents/2d-ML.sedml\nCompleted 3.2 KiB/1.0 MiB (38.9 KiB/s) with 17 file(s) remaining\rCompleted 6.1 KiB/1.0 MiB (44.7 KiB/s) with 17 file(s) remaining\rupload: contents/3d-ML.ode to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/contents/3d-ML.ode\nCompleted 6.1 KiB/1.0 MiB (44.7 KiB/s) with 16 file(s) remaining\rCompleted 10.1 KiB/1.0 MiB (70.0 KiB/s) with 16 file(s) remaining\rupload: contents/3d-ML.sedml to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/contents/3d-ML.sedml\nCompleted 10.1 KiB/1.0 MiB (70.0 KiB/s) with 15 file(s) remaining\rCompleted 13.0 KiB/1.0 MiB (88.9 KiB/s) with 15 file(s) remaining\rupload: contents/2d-ML.ode to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/contents/2d-ML.ode\nCompleted 13.0 KiB/1.0 MiB (88.9 KiB/s) with 14 file(s) remaining\rCompleted 133.2 KiB/1.0 MiB (814.3 KiB/s) with 14 file(s) remaining\rupload: contents/article-figures/PMC2551735/pcbi.1000198.g007.jpg to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/contents/article-figures/PMC2551735/pcbi.1000198.g007.jpg\nCompleted 133.2 KiB/1.0 MiB (814.3 KiB/s) with 13 file(s) remaining\rCompleted 246.6 KiB/1.0 MiB (1.4 MiB/s) with 13 file(s) remaining  \rupload: contents/article-figures/PMC2551735/pcbi.1000198.g002.jpg to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/contents/article-figures/PMC2551735/pcbi.1000198.g002.jpg\nCompleted 246.6 KiB/1.0 MiB (1.4 MiB/s) with 12 file(s) remaining\rCompleted 361.1 KiB/1.0 MiB (1.9 MiB/s) with 12 file(s) remaining\rCompleted 500.5 KiB/1.0 MiB (2.6 MiB/s) with 12 file(s) remaining\rupload: contents/article-figures/PMC2551735/pcbi.1000198.g001.jpg to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/contents/article-figures/PMC2551735/pcbi.1000198.g001.jpg\nCompleted 500.5 KiB/1.0 MiB (2.6 MiB/s) with 11 file(s) remaining\rCompleted 540.5 KiB/1.0 MiB (2.7 MiB/s) with 11 file(s) remaining\rupload: contents/article-figures/PMC2551735/pcbi.1000198.g011.jpg to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/contents/article-figures/PMC2551735/pcbi.1000198.g011.jpg\nCompleted 540.5 KiB/1.0 MiB (2.7 MiB/s) with 10 file(s) remaining\rupload: contents/article-figures/PMC2551735/pcbi.1000198.g009.jpg to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/contents/article-figures/PMC2551735/pcbi.1000198.g009.jpg\nCompleted 540.5 KiB/1.0 MiB (2.7 MiB/s) with 9 file(s) remaining\rCompleted 605.9 KiB/1.0 MiB (2.9 MiB/s) with 9 file(s) remaining\rupload: contents/article-figures/PMC2551735/pcbi.1000198.g010.jpg to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/contents/article-figures/PMC2551735/pcbi.1000198.g010.jpg\nCompleted 605.9 KiB/1.0 MiB (2.9 MiB/s) with 8 file(s) remaining\rCompleted 621.7 KiB/1.0 MiB (2.9 MiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/contents/metadata.rdf\nCompleted 621.7 KiB/1.0 MiB (2.9 MiB/s) with 7 file(s) remaining\rCompleted 624.0 KiB/1.0 MiB (2.8 MiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/contents/manifest.xml\nCompleted 624.0 KiB/1.0 MiB (2.8 MiB/s) with 6 file(s) remaining\rCompleted 793.2 KiB/1.0 MiB (3.4 MiB/s) with 6 file(s) remaining\rupload: contents/article-figures/PMC2551735/pcbi.1000198.g008.jpg to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/contents/article-figures/PMC2551735/pcbi.1000198.g008.jpg\nCompleted 793.2 KiB/1.0 MiB (3.4 MiB/s) with 5 file(s) remaining\rCompleted 869.7 KiB/1.0 MiB (3.7 MiB/s) with 5 file(s) remaining\rupload: contents/article-figures/PMC2551735/pcbi.1000198.g003.jpg to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/contents/article-figures/PMC2551735/pcbi.1000198.g003.jpg\nCompleted 869.7 KiB/1.0 MiB (3.7 MiB/s) with 4 file(s) remaining\rCompleted 873.5 KiB/1.0 MiB (3.4 MiB/s) with 4 file(s) remaining\rupload: contents/readme.html to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/contents/readme.html\nCompleted 873.5 KiB/1.0 MiB (3.4 MiB/s) with 3 file(s) remaining\rCompleted 943.5 KiB/1.0 MiB (3.5 MiB/s) with 3 file(s) remaining\rupload: contents/article-figures/PMC2551735/pcbi.1000198.g005.jpg to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/contents/article-figures/PMC2551735/pcbi.1000198.g005.jpg\nCompleted 943.5 KiB/1.0 MiB (3.5 MiB/s) with 2 file(s) remaining\rCompleted 993.8 KiB/1.0 MiB (2.7 MiB/s) with 2 file(s) remaining\rupload: contents/article-figures/PMC2551735/pcbi.1000198.g006.jpg to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/contents/article-figures/PMC2551735/pcbi.1000198.g006.jpg\nCompleted 993.8 KiB/1.0 MiB (2.7 MiB/s) with 1 file(s) remaining\rCompleted 1.0 MiB/1.0 MiB (2.7 MiB/s) with 1 file(s) remaining  \rupload: contents/article-figures/PMC2551735/pcbi.1000198.g004.jpg to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/contents/article-figures/PMC2551735/pcbi.1000198.g004.jpg\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /2d-ML.sedml\ncreating dataset /2d-ML.sedml/plot, shape: (2, 1001), type: float64\ndataset created, uuid: d-8f5fcf5e-6eead536-e1e1-e5a670-956341, chunk_size: (2, 1001)\ncreating dataset /2d-ML.sedml/report, shape: (3, 1001), type: float64\ndataset created, uuid: d-8f5fcf5e-6eead536-25af-cc9d58-bbcf4a, chunk_size: (3, 1001)\ncreating group /3d-ML.sedml\ncreating dataset /3d-ML.sedml/plot, shape: (2, 1001), type: float64\ndataset created, uuid: d-8f5fcf5e-6eead536-ac36-b772f3-7b287a, chunk_size: (2, 1001)\ncreating dataset /3d-ML.sedml/report, shape: (4, 1001), type: float64\ndataset created, uuid: d-8f5fcf5e-6eead536-7aa5-43c7a7-c3ea51, chunk_size: (4, 1001)\ncreating attribute combineArchiveLocation in /2d-ML.sedml\ncreating attribute uri in /2d-ML.sedml\ncreating attribute _type in /2d-ML.sedml/plot\ncreating attribute sedmlDataSetDataTypes in /2d-ML.sedml/plot\ncreating attribute sedmlDataSetIds in /2d-ML.sedml/plot\ncreating attribute sedmlDataSetLabels in /2d-ML.sedml/plot\ncreating attribute sedmlDataSetNames in /2d-ML.sedml/plot\ncreating attribute sedmlDataSetShapes in /2d-ML.sedml/plot\ncreating attribute sedmlId in /2d-ML.sedml/plot\ncreating attribute uri in /2d-ML.sedml/plot\ncreating attribute _type in /2d-ML.sedml/report\ncreating attribute sedmlDataSetDataTypes in /2d-ML.sedml/report\ncreating attribute sedmlDataSetIds in /2d-ML.sedml/report\ncreating attribute sedmlDataSetLabels in /2d-ML.sedml/report\ncreating attribute sedmlDataSetNames in /2d-ML.sedml/report\ncreating attribute sedmlDataSetShapes in /2d-ML.sedml/report\ncreating attribute sedmlId in /2d-ML.sedml/report\ncreating attribute sedmlName in /2d-ML.sedml/report\ncreating attribute uri in /2d-ML.sedml/report\ncreating attribute combineArchiveLocation in /3d-ML.sedml\ncreating attribute uri in /3d-ML.sedml\ncreating attribute _type in /3d-ML.sedml/plot\ncreating attribute sedmlDataSetDataTypes in /3d-ML.sedml/plot\ncreating attribute sedmlDataSetIds in /3d-ML.sedml/plot\ncreating attribute sedmlDataSetLabels in /3d-ML.sedml/plot\ncreating attribute sedmlDataSetNames in /3d-ML.sedml/plot\ncreating attribute sedmlDataSetShapes in /3d-ML.sedml/plot\ncreating attribute sedmlId in /3d-ML.sedml/plot\ncreating attribute uri in /3d-ML.sedml/plot\ncreating attribute _type in /3d-ML.sedml/report\ncreating attribute sedmlDataSetDataTypes in /3d-ML.sedml/report\ncreating attribute sedmlDataSetIds in /3d-ML.sedml/report\ncreating attribute sedmlDataSetLabels in /3d-ML.sedml/report\ncreating attribute sedmlDataSetNames in /3d-ML.sedml/report\ncreating attribute sedmlDataSetShapes in /3d-ML.sedml/report\ncreating attribute sedmlId in /3d-ML.sedml/report\ncreating attribute sedmlName in /3d-ML.sedml/report\ncreating attribute uri in /3d-ML.sedml/report\ncreate_links: /\ngot link: 2d-ML.sedml\ngot link: 3d-ML.sedml\ncreate_links: /2d-ML.sedml\ngot link: plot\ngot link: report\ncreate_links: /3d-ML.sedml\ngot link: plot\ngot link: report\nwrite_dataset src: /2d-ML.sedml/plot to tgt: /2d-ML.sedml/plot, shape: (2, 1001), type: float64\niterating over chunks for /2d-ML.sedml/plot\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /2d-ML.sedml/plot\nwrite_dataset src: /2d-ML.sedml/report to tgt: /2d-ML.sedml/report, shape: (3, 1001), type: float64\niterating over chunks for /2d-ML.sedml/report\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 1001, 1))\ndone with dataload for /2d-ML.sedml/report\nwrite_dataset src: /3d-ML.sedml/plot to tgt: /3d-ML.sedml/plot, shape: (2, 1001), type: float64\niterating over chunks for /3d-ML.sedml/plot\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /3d-ML.sedml/plot\nwrite_dataset src: /3d-ML.sedml/report to tgt: /3d-ML.sedml/report, shape: (4, 1001), type: float64\niterating over chunks for /3d-ML.sedml/report\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /3d-ML.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/621d42a687550e369891ba75\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/3d-ML.sedml/ (stored 0%)\n  adding: outputs/3d-ML.sedml/plot.pdf (deflated 36%)\n  adding: outputs/log.yml (deflated 76%)\n  adding: outputs/2d-ML.sedml/ (stored 0%)\n  adding: outputs/2d-ML.sedml/plot.pdf (deflated 35%)\n  adding: outputs/reports.h5 (deflated 86%)\n  adding: rawLog.txt (deflated 84%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 20.2 KiB/57.2 KiB (319.3 KiB/s) with 5 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/output.zip\nCompleted 20.2 KiB/57.2 KiB (319.3 KiB/s) with 4 file(s) remaining\rCompleted 27.5 KiB/57.2 KiB (279.1 KiB/s) with 4 file(s) remaining\rupload: outputs/3d-ML.sedml/plot.pdf to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/outputs/3d-ML.sedml/plot.pdf\nCompleted 27.5 KiB/57.2 KiB (279.1 KiB/s) with 3 file(s) remaining\rCompleted 35.2 KiB/57.2 KiB (342.8 KiB/s) with 3 file(s) remaining\rupload: outputs/2d-ML.sedml/plot.pdf to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/outputs/2d-ML.sedml/plot.pdf\nCompleted 35.2 KiB/57.2 KiB (342.8 KiB/s) with 2 file(s) remaining\rCompleted 44.5 KiB/57.2 KiB (427.2 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/outputs/plots.zip\nCompleted 44.5 KiB/57.2 KiB (427.2 KiB/s) with 1 file(s) remaining\rCompleted 57.2 KiB/57.2 KiB (534.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/rawLog.txt\nCompleted 47.4 KiB/47.4 KiB (647.2 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/outputs/reports.h5\nCompleted 3.7 KiB/3.7 KiB (70.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/621d42a687550e369891ba75/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 metadata in the COMBINE archive ... succeeded.\nPost the metadata 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 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"}