{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"time"},{"status":"SUCCEEDED","id":"MDM2_mRNA"},{"status":"SUCCEEDED","id":"MDM2"}],"duration":0.053197,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"},{"curves":[{"status":"SUCCEEDED","id":"curve_MDM2_mRNA"},{"status":"SUCCEEDED","id":"curve_MDM2"}],"duration":0.222031,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"Figure"}],"tasks":[{"simulatorDetails":[{"value":["simulate({t_start => 0.0, t_end => 100.0, n_steps => 100, method => \"nf\"})"],"key":"actions"}],"algorithm":"KISAO_0000263","duration":5.141171,"output":"/usr/local/lib/python3.9/site-packages/biosimulators_bionetgen/core.py:226: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.\r\n  warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)\r\n","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task_1"}],"duration":11.402478,"output":"BioNetGen version 2.7.0\r\nReading from file /tmp/tmptlwca39x/Dolan2015.bngl (level 0)\r\nRead 73 parameters.\r\nRead 74 molecule types.\r\nRead 75 species.\r\nRead 176 observable(s).\r\nRead 9 functions.\r\nRead 2339 reaction rule(s).\r\nWrote model in xml format to ./Dolan2015.xml.\r\nFinished processing file /tmp/tmptlwca39x/Dolan2015.bngl.\r\nCPU TIME: total 4.54 s.\r\nArchive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n  Dolan2015.sedml:\r\n    Tasks (1):\r\n      task_1\r\n    Reports (1):\r\n      report: 3 data sets\r\n    Plots (1):\r\n      Figure: 2 curves\r\n\r\nExecuting SED-ML file 1: Dolan2015.sedml ...\r\nBioNetGen version 2.7.0\r\nReading from file /tmp/tmp59gevm6g/Dolan2015.bngl (level 0)\r\nRead 73 parameters.\r\nRead 74 molecule types.\r\nRead 75 species.\r\nRead 176 observable(s).\r\nRead 9 functions.\r\nRead 2339 reaction rule(s).\r\nWrote model in xml format to ./Dolan2015.xml.\r\nFinished processing file /tmp/tmp59gevm6g/Dolan2015.bngl.\r\nCPU TIME: total 4.16 s.\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task_1`\r\n    Outputs:\r\n      `Figure`\r\n      `report`\r\n  Executing task 1: `task_1`\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: `Figure` ...","skipReason":null,"exception":null,"status":"SUCCEEDED","location":"Dolan2015.sedml"}],"duration":18.240057,"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\r100   139  100   139    0     0    434      0 --:--:-- --:--:-- --:--:--   434\r100   139  100   139    0     0    429      0 --:--:-- --:--:-- --:--:--   429\n\r100  934k  100  934k    0     0  2027k      0 --:--:-- --:--:-- --:--:-- 2027k\n\n\u001b[0;36m============================================= Executing COMBINE archive =============================================\u001b[0m\nINFO:    Using cached SIF image\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 /Dolan2015.sedml\ncreating dataset /Dolan2015.sedml/Figure, shape: (3, 101), type: float64\ndataset created, uuid: d-7e3887c8-cf6263ec-e7d8-895e92-2135e1, chunk_size: (3, 101)\ncreating dataset /Dolan2015.sedml/report, shape: (3, 101), type: float64\ndataset created, uuid: d-7e3887c8-cf6263ec-9844-d97d98-ce7c04, chunk_size: (3, 101)\ncreating attribute combineArchiveLocation in /Dolan2015.sedml\ncreating attribute uri in /Dolan2015.sedml\ncreating attribute _type in /Dolan2015.sedml/Figure\ncreating attribute sedmlDataSetDataTypes in /Dolan2015.sedml/Figure\ncreating attribute sedmlDataSetIds in /Dolan2015.sedml/Figure\ncreating attribute sedmlDataSetLabels in /Dolan2015.sedml/Figure\ncreating attribute sedmlDataSetNames in /Dolan2015.sedml/Figure\ncreating attribute sedmlDataSetShapes in /Dolan2015.sedml/Figure\ncreating attribute sedmlId in /Dolan2015.sedml/Figure\ncreating attribute uri in /Dolan2015.sedml/Figure\ncreating attribute _type in /Dolan2015.sedml/report\ncreating attribute sedmlDataSetDataTypes in /Dolan2015.sedml/report\ncreating attribute sedmlDataSetIds in /Dolan2015.sedml/report\ncreating attribute sedmlDataSetLabels in /Dolan2015.sedml/report\ncreating attribute sedmlDataSetNames in /Dolan2015.sedml/report\ncreating attribute sedmlDataSetShapes in /Dolan2015.sedml/report\ncreating attribute sedmlId in /Dolan2015.sedml/report\ncreating attribute uri in /Dolan2015.sedml/report\ncreate_links: /\ngot link: Dolan2015.sedml\ncreate_links: /Dolan2015.sedml\ngot link: Figure\ngot link: report\nwrite_dataset src: /Dolan2015.sedml/Figure to tgt: /Dolan2015.sedml/Figure, shape: (3, 101), type: float64\niterating over chunks for /Dolan2015.sedml/Figure\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 101, 1))\ndone with dataload for /Dolan2015.sedml/Figure\nwrite_dataset src: /Dolan2015.sedml/report to tgt: /Dolan2015.sedml/report, shape: (3, 101), type: float64\niterating over chunks for /Dolan2015.sedml/report\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 101, 1))\ndone with dataload for /Dolan2015.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/61fea499f499ccf25faafc6b\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 65%)\n  adding: outputs/Dolan2015.sedml/ (stored 0%)\n  adding: outputs/Dolan2015.sedml/Figure.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 93%)\n  adding: rawLog.txt (deflated 76%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 11.5 KiB/32.3 KiB (176.6 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/61fea499f499ccf25faafc6b/output.zip\nCompleted 11.5 KiB/32.3 KiB (176.6 KiB/s) with 3 file(s) remaining\rCompleted 21.5 KiB/32.3 KiB (217.2 KiB/s) with 3 file(s) remaining\rupload: outputs/Dolan2015.sedml/Figure.pdf to s3://files.biosimulations.org/simulations/61fea499f499ccf25faafc6b/outputs/Dolan2015.sedml/Figure.pdf\nCompleted 21.5 KiB/32.3 KiB (217.2 KiB/s) with 2 file(s) remaining\rCompleted 28.2 KiB/32.3 KiB (254.8 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/61fea499f499ccf25faafc6b/outputs/plots.zip\nCompleted 28.2 KiB/32.3 KiB (254.8 KiB/s) with 1 file(s) remaining\rCompleted 32.3 KiB/32.3 KiB (281.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/61fea499f499ccf25faafc6b/rawLog.txt\nCompleted 24.6 KiB/24.6 KiB (229.0 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/61fea499f499ccf25faafc6b/outputs/reports.h5\nCompleted 2.7 KiB/2.7 KiB (32.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/61fea499f499ccf25faafc6b/outputs/log.yml\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\n\u001b[0;32mProcess and upload the outputs of the simulation run.....Succeeded\nPost 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\nProcess the manifest file in the combine archive.....Succeeded\nExtract the files in the combine archive.....Succeeded\nPost the Metadata to the API.....Succeeded\nProcess the Metadata in the combine archive.....Succeeded\nPost the SED-ML file to the API.....Succeeded\nProcess the SED-ML file in the combine archive.....Succeeded\nPost the logs to the API.....Succeeded\nRetrieve the logs of the simulation run.....Succeeded\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","skipReason":null,"exception":null,"status":"SUCCEEDED"}