{"status":"SUCCEEDED","exception":null,"skipReason":null,"output":"\u001b[0;36mThank you for using runBioSimulations!\u001b[0m\n\n\u001b[0;36m================================================ Loading Singularity ================================================\u001b[0m\n\n\u001b[0;36m=================================================== Set up storage ==================================================\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    524      0 --:--:-- --:--:-- --:--:--   526\n\r100  763k  100  763k    0     0  2018k      0 --:--:-- --:--:-- --:--:-- 2018k\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX 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 log ====================================================\u001b[0m\nCompleted 1.6 KiB/1.6 KiB (16.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/rawLog.txt\nCompleted 3.2 KiB/3.2 KiB (53.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/outputs/log.yml\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 67%)\n  adding: outputs/Lenbury2001.sedml/ (stored 0%)\n  adding: outputs/Lenbury2001.sedml/plot_1_task1.pdf (deflated 28%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 30.4 KiB/30.4 KiB (427.1 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/outputs/reports.h5\nCompleted 20.8 KiB/43.2 KiB (293.8 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/output.zip\nCompleted 20.8 KiB/43.2 KiB (293.8 KiB/s) with 3 file(s) remaining\rCompleted 32.4 KiB/43.2 KiB (300.3 KiB/s) with 3 file(s) remaining\rupload: outputs/Lenbury2001.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/outputs/Lenbury2001.sedml/plot_1_task1.pdf\nCompleted 32.4 KiB/43.2 KiB (300.3 KiB/s) with 2 file(s) remaining\rCompleted 40.6 KiB/43.2 KiB (370.8 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/outputs/plots.zip\nCompleted 40.6 KiB/43.2 KiB (370.8 KiB/s) with 1 file(s) remaining\rCompleted 43.2 KiB/43.2 KiB (392.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Lenbury2001-biopax2.owl  \n  inflating: contents/Lenbury2001-biopax3.owl  \n  inflating: contents/Lenbury2001-matlab.m  \n  inflating: contents/Lenbury2001-octave.m  \n  inflating: contents/Lenbury2001.cps  \n  inflating: contents/Lenbury2001.ode  \n  inflating: contents/Lenbury2001.sedml  \n  inflating: contents/Lenbury2001.xml  \n  inflating: contents/MODEL1201140002-biopax2.owl  \n  inflating: contents/MODEL1201140002-biopax3.owl  \n  inflating: contents/MODEL1201140002-matlab.m  \n  inflating: contents/MODEL1201140002-octave.m  \n  inflating: contents/MODEL1201140002.m  \n  inflating: contents/MODEL1201140002.ode  \n  inflating: contents/MODEL1201140002.pdf  \n  inflating: contents/MODEL1201140002.png  \n  inflating: contents/MODEL1201140002.sci  \n  inflating: contents/MODEL1201140002.svg  \n  inflating: contents/MODEL1201140002_url.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 9.2 KiB/996.7 KiB (132.1 KiB/s) with 23 file(s) remaining\rupload: contents/Lenbury2001-biopax2.owl to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/Lenbury2001-biopax2.owl\nCompleted 9.2 KiB/996.7 KiB (132.1 KiB/s) with 22 file(s) remaining\rCompleted 21.7 KiB/996.7 KiB (210.6 KiB/s) with 22 file(s) remaining\rupload: contents/Lenbury2001-biopax3.owl to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/Lenbury2001-biopax3.owl\nCompleted 21.7 KiB/996.7 KiB (210.6 KiB/s) with 21 file(s) remaining\rCompleted 26.9 KiB/996.7 KiB (237.3 KiB/s) with 21 file(s) remaining\rupload: contents/Lenbury2001-octave.m to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/Lenbury2001-octave.m\nCompleted 26.9 KiB/996.7 KiB (237.3 KiB/s) with 20 file(s) remaining\rCompleted 30.0 KiB/996.7 KiB (239.5 KiB/s) with 20 file(s) remaining\rupload: contents/MODEL1201140002-biopax3.owl to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/MODEL1201140002-biopax3.owl\nCompleted 30.0 KiB/996.7 KiB (239.5 KiB/s) with 19 file(s) remaining\rCompleted 72.2 KiB/996.7 KiB (536.7 KiB/s) with 19 file(s) remaining\rupload: contents/Lenbury2001.xml to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/Lenbury2001.xml\nCompleted 72.2 KiB/996.7 KiB (536.7 KiB/s) with 18 file(s) remaining\rCompleted 75.2 KiB/996.7 KiB (538.6 KiB/s) with 18 file(s) remaining\rupload: contents/MODEL1201140002-biopax2.owl to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/MODEL1201140002-biopax2.owl\nCompleted 75.2 KiB/996.7 KiB (538.6 KiB/s) with 17 file(s) remaining\rCompleted 78.7 KiB/996.7 KiB (538.7 KiB/s) with 17 file(s) remaining\rupload: contents/MODEL1201140002-matlab.m to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/MODEL1201140002-matlab.m\nCompleted 78.7 KiB/996.7 KiB (538.7 KiB/s) with 16 file(s) remaining\rCompleted 82.2 KiB/996.7 KiB (533.4 KiB/s) with 16 file(s) remaining\rupload: contents/MODEL1201140002-octave.m to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/MODEL1201140002-octave.m\nCompleted 82.2 KiB/996.7 KiB (533.4 KiB/s) with 15 file(s) remaining\rCompleted 211.0 KiB/996.7 KiB (1.3 MiB/s) with 15 file(s) remaining \rupload: contents/MODEL1201140002.pdf to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/MODEL1201140002.pdf\nCompleted 211.0 KiB/996.7 KiB (1.3 MiB/s) with 14 file(s) remaining\rCompleted 216.0 KiB/996.7 KiB (1.3 MiB/s) with 14 file(s) remaining\rupload: contents/MODEL1201140002.png to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/MODEL1201140002.png\nCompleted 216.0 KiB/996.7 KiB (1.3 MiB/s) with 13 file(s) remaining\rCompleted 217.7 KiB/996.7 KiB (1.3 MiB/s) with 13 file(s) remaining\rupload: contents/MODEL1201140002.ode to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/MODEL1201140002.ode\nCompleted 217.7 KiB/996.7 KiB (1.3 MiB/s) with 12 file(s) remaining\rCompleted 473.7 KiB/996.7 KiB (2.7 MiB/s) with 12 file(s) remaining\rCompleted 476.4 KiB/996.7 KiB (2.7 MiB/s) with 12 file(s) remaining\rupload: contents/MODEL1201140002.m to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/MODEL1201140002.m\nCompleted 476.4 KiB/996.7 KiB (2.7 MiB/s) with 11 file(s) remaining\rCompleted 732.4 KiB/996.7 KiB (4.0 MiB/s) with 11 file(s) remaining\rCompleted 733.8 KiB/996.7 KiB (4.0 MiB/s) with 11 file(s) remaining\rupload: contents/MODEL1201140002.sci to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/MODEL1201140002.sci\nCompleted 733.8 KiB/996.7 KiB (4.0 MiB/s) with 10 file(s) remaining\rCompleted 741.8 KiB/996.7 KiB (3.8 MiB/s) with 10 file(s) remaining\rupload: contents/MODEL1201140002_url.xml to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/MODEL1201140002_url.xml\nCompleted 741.8 KiB/996.7 KiB (3.8 MiB/s) with 9 file(s) remaining\rCompleted 742.1 KiB/996.7 KiB (3.5 MiB/s) with 9 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/curation_notes.txt\nCompleted 742.1 KiB/996.7 KiB (3.5 MiB/s) with 8 file(s) remaining\rCompleted 747.2 KiB/996.7 KiB (3.5 MiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/metadata.rdf\nCompleted 747.2 KiB/996.7 KiB (3.5 MiB/s) with 7 file(s) remaining\rCompleted 749.8 KiB/996.7 KiB (3.5 MiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/manifest.xml\nCompleted 749.8 KiB/996.7 KiB (3.5 MiB/s) with 6 file(s) remaining\rCompleted 764.1 KiB/996.7 KiB (3.5 MiB/s) with 6 file(s) remaining\rupload: contents/Lenbury2001.sedml to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/Lenbury2001.sedml\nCompleted 764.1 KiB/996.7 KiB (3.5 MiB/s) with 5 file(s) remaining\rCompleted 769.3 KiB/996.7 KiB (3.4 MiB/s) with 5 file(s) remaining\rupload: contents/Lenbury2001-matlab.m to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/Lenbury2001-matlab.m\nCompleted 769.3 KiB/996.7 KiB (3.4 MiB/s) with 4 file(s) remaining\rCompleted 770.2 KiB/996.7 KiB (3.2 MiB/s) with 4 file(s) remaining\rupload: contents/MODEL1201140002.svg to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/MODEL1201140002.svg\nCompleted 770.2 KiB/996.7 KiB (3.2 MiB/s) with 3 file(s) remaining\rCompleted 773.6 KiB/996.7 KiB (3.2 MiB/s) with 3 file(s) remaining\rupload: contents/Lenbury2001.ode to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/Lenbury2001.ode\nCompleted 773.6 KiB/996.7 KiB (3.2 MiB/s) with 2 file(s) remaining\rCompleted 929.3 KiB/996.7 KiB (3.7 MiB/s) with 2 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/curation_image.png\nCompleted 929.3 KiB/996.7 KiB (3.7 MiB/s) with 1 file(s) remaining\rCompleted 996.7 KiB/996.7 KiB (4.0 MiB/s) with 1 file(s) remaining\rupload: contents/Lenbury2001.cps to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/contents/Lenbury2001.cps\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 11.0 KiB/11.0 KiB (154.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711e3749c0d898ffdf76a1/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Lenbury2001.sedml\ncreating dataset /Lenbury2001.sedml/autogen_report_for_task1, shape: (24, 81), type: float64\ndataset created, uuid: d-07fecc9e-2ceb122f-e548-204ca1-65c738, chunk_size: (24, 81)\ncreating dataset /Lenbury2001.sedml/plot_1_task1, shape: (4, 81), type: float64\ndataset created, uuid: d-07fecc9e-2ceb122f-8ea4-683524-f14403, chunk_size: (4, 81)\ncreating attribute combineArchiveLocation in /Lenbury2001.sedml\ncreating attribute uri in /Lenbury2001.sedml\ncreating attribute _type in /Lenbury2001.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Lenbury2001.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Lenbury2001.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Lenbury2001.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Lenbury2001.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Lenbury2001.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Lenbury2001.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Lenbury2001.sedml/autogen_report_for_task1\ncreating attribute uri in /Lenbury2001.sedml/autogen_report_for_task1\ncreating attribute _type in /Lenbury2001.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Lenbury2001.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Lenbury2001.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Lenbury2001.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Lenbury2001.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Lenbury2001.sedml/plot_1_task1\ncreating attribute sedmlId in /Lenbury2001.sedml/plot_1_task1\ncreating attribute sedmlName in /Lenbury2001.sedml/plot_1_task1\ncreating attribute uri in /Lenbury2001.sedml/plot_1_task1\ncreate_links: /\ngot link: Lenbury2001.sedml\ncreate_links: /Lenbury2001.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Lenbury2001.sedml/autogen_report_for_task1 to tgt: /Lenbury2001.sedml/autogen_report_for_task1, shape: (24, 81), type: float64\niterating over chunks for /Lenbury2001.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 24, 1), slice(0, 81, 1))\ndone with dataload for /Lenbury2001.sedml/autogen_report_for_task1\nwrite_dataset src: /Lenbury2001.sedml/plot_1_task1 to tgt: /Lenbury2001.sedml/plot_1_task1, shape: (4, 81), type: float64\niterating over chunks for /Lenbury2001.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 81, 1))\ndone with dataload for /Lenbury2001.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711e3749c0d898ffdf76a1\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mProcess 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.\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 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","duration":0.962821,"sedDocuments":[{"location":"Lenbury2001.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n  Lenbury2001.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 24 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Lenbury2001.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_report_for_task1`\r\n      `plot_1_task1`\r\n  Executing task 1: `task1`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `plot_1_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_report_for_task1` ...","duration":0.590407,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.137858,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"deterministic"},{"key":"methodCode","value":22},{"key":"parameters","value":{"Absolute Tolerance":1e-12,"Integrate Reduced Model":false,"Max Internal Steps":100000,"Relative Tolerance":0.000001}}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.298823,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.062117,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_x","status":"SUCCEEDED"},{"id":"autogen_task1_y","status":"SUCCEEDED"},{"id":"autogen_task1_z","status":"SUCCEEDED"},{"id":"autogen_task1_time_environment","status":"SUCCEEDED"},{"id":"autogen_task1_r_1","status":"SUCCEEDED"},{"id":"autogen_task1_r_2","status":"SUCCEEDED"},{"id":"autogen_task1_c_1","status":"SUCCEEDED"},{"id":"autogen_task1_r_3","status":"SUCCEEDED"},{"id":"autogen_task1_r_4","status":"SUCCEEDED"},{"id":"autogen_task1_c_2","status":"SUCCEEDED"},{"id":"autogen_task1_r_5","status":"SUCCEEDED"},{"id":"autogen_task1_r_6","status":"SUCCEEDED"},{"id":"autogen_task1_r_7","status":"SUCCEEDED"},{"id":"autogen_task1_z_hat","status":"SUCCEEDED"},{"id":"autogen_task1_y_hat","status":"SUCCEEDED"},{"id":"autogen_task1_epsilon","status":"SUCCEEDED"},{"id":"autogen_task1_COMpartment","status":"SUCCEEDED"},{"id":"autogen_task1_Production_of_insulin","status":"SUCCEEDED"},{"id":"autogen_task1_Utilisation_of_insulin","status":"SUCCEEDED"},{"id":"autogen_task1_Production_of_glucose","status":"SUCCEEDED"},{"id":"autogen_task1_utilisation_of_glucose","status":"SUCCEEDED"},{"id":"autogen_task1_Production_of_Beta_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Removal_of_Beta_Cell","status":"SUCCEEDED"}]}]}]}