{"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    444      0 --:--:-- --:--:-- --:--:--   445\n\r100  100k  100  100k    0     0   234k      0 --:--:-- --:--:-- --:--:--  234k\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 3 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 3\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 (3):\n    Succeeded: 3\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 1.6 KiB/1.6 KiB (22.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b6b195afd5df175f177/rawLog.txt\nCompleted 4.5 KiB/4.5 KiB (57.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b6b195afd5df175f177/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 79%)\n  adding: outputs/Jung2019 simulation.sedml/ (stored 0%)\n  adding: outputs/Jung2019 simulation.sedml/plot_2_task1.pdf (deflated 21%)\n  adding: outputs/Jung2019 simulation.sedml/plot_1_task1.pdf (deflated 14%)\n  adding: outputs/reports.h5 (deflated 18%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 200.6 KiB/200.6 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b6b195afd5df175f177/outputs/reports.h5\nCompleted 202.0 KiB/279.3 KiB (2.0 MiB/s) with 5 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b6b195afd5df175f177/output.zip\nCompleted 202.0 KiB/279.3 KiB (2.0 MiB/s) with 4 file(s) remaining\rCompleted 215.8 KiB/279.3 KiB (1.8 MiB/s) with 4 file(s) remaining\rupload: outputs/Jung2019 simulation.sedml/plot_2_task1.pdf to s3://files.biosimulations.org/simulations/647a4b6b195afd5df175f177/outputs/Jung2019 simulation.sedml/plot_2_task1.pdf\nCompleted 215.8 KiB/279.3 KiB (1.8 MiB/s) with 3 file(s) remaining\rCompleted 242.9 KiB/279.3 KiB (1.9 MiB/s) with 3 file(s) remaining\rupload: outputs/Jung2019 simulation.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b6b195afd5df175f177/outputs/Jung2019 simulation.sedml/plot_1_task1.pdf\nCompleted 242.9 KiB/279.3 KiB (1.9 MiB/s) with 2 file(s) remaining\rCompleted 276.6 KiB/279.3 KiB (2.1 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b6b195afd5df175f177/outputs/plots.zip\nCompleted 276.6 KiB/279.3 KiB (2.1 MiB/s) with 1 file(s) remaining\rCompleted 279.3 KiB/279.3 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b6b195afd5df175f177/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Fig 8.png      \n  inflating: contents/Jung2019 model-biopax2.owl  \n  inflating: contents/Jung2019 model-biopax3.owl  \n  inflating: contents/Jung2019 model-matlab.m  \n  inflating: contents/Jung2019 model-octave.m  \n  inflating: contents/Jung2019 model.xml  \n  inflating: contents/Jung2019 simulation.sedml  \n  inflating: contents/Jung2019.cps   \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 15.2 KiB/327.4 KiB (216.8 KiB/s) with 12 file(s) remaining\rupload: contents/Jung2019 model-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b6b195afd5df175f177/contents/Jung2019 model-biopax2.owl\nCompleted 15.2 KiB/327.4 KiB (216.8 KiB/s) with 11 file(s) remaining\rCompleted 36.7 KiB/327.4 KiB (309.3 KiB/s) with 11 file(s) remaining\rupload: contents/Jung2019 model-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b6b195afd5df175f177/contents/Jung2019 model-biopax3.owl\nCompleted 36.7 KiB/327.4 KiB (309.3 KiB/s) with 10 file(s) remaining\rCompleted 74.1 KiB/327.4 KiB (604.5 KiB/s) with 10 file(s) remaining\rupload: contents/Fig 8.png to s3://files.biosimulations.org/simulations/647a4b6b195afd5df175f177/contents/Fig 8.png\nCompleted 74.1 KiB/327.4 KiB (604.5 KiB/s) with 9 file(s) remaining\rCompleted 74.4 KiB/327.4 KiB (560.1 KiB/s) with 9 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b6b195afd5df175f177/contents/curation_notes.txt\nCompleted 74.4 KiB/327.4 KiB (560.1 KiB/s) with 8 file(s) remaining\rCompleted 81.9 KiB/327.4 KiB (584.7 KiB/s) with 8 file(s) remaining\rupload: contents/Jung2019 model-octave.m to s3://files.biosimulations.org/simulations/647a4b6b195afd5df175f177/contents/Jung2019 model-octave.m\nCompleted 81.9 KiB/327.4 KiB (584.7 KiB/s) with 7 file(s) remaining\rCompleted 89.3 KiB/327.4 KiB (608.8 KiB/s) with 7 file(s) remaining\rupload: contents/Jung2019 model-matlab.m to s3://files.biosimulations.org/simulations/647a4b6b195afd5df175f177/contents/Jung2019 model-matlab.m\nCompleted 89.3 KiB/327.4 KiB (608.8 KiB/s) with 6 file(s) remaining\rCompleted 90.7 KiB/327.4 KiB (605.0 KiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b6b195afd5df175f177/contents/manifest.xml\nCompleted 90.7 KiB/327.4 KiB (605.0 KiB/s) with 5 file(s) remaining\rCompleted 128.2 KiB/327.4 KiB (771.2 KiB/s) with 5 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b6b195afd5df175f177/contents/curation_image.png\nCompleted 128.2 KiB/327.4 KiB (771.2 KiB/s) with 4 file(s) remaining\rCompleted 131.0 KiB/327.4 KiB (774.0 KiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b6b195afd5df175f177/contents/metadata.rdf\nCompleted 131.0 KiB/327.4 KiB (774.0 KiB/s) with 3 file(s) remaining\rCompleted 206.9 KiB/327.4 KiB (1.1 MiB/s) with 3 file(s) remaining  \rupload: contents/Jung2019 model.xml to s3://files.biosimulations.org/simulations/647a4b6b195afd5df175f177/contents/Jung2019 model.xml\nCompleted 206.9 KiB/327.4 KiB (1.1 MiB/s) with 2 file(s) remaining\rCompleted 305.4 KiB/327.4 KiB (1.6 MiB/s) with 2 file(s) remaining\rupload: contents/Jung2019.cps to s3://files.biosimulations.org/simulations/647a4b6b195afd5df175f177/contents/Jung2019.cps\nCompleted 305.4 KiB/327.4 KiB (1.6 MiB/s) with 1 file(s) remaining\rCompleted 327.4 KiB/327.4 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: contents/Jung2019 simulation.sedml to s3://files.biosimulations.org/simulations/647a4b6b195afd5df175f177/contents/Jung2019 simulation.sedml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.8 KiB/7.8 KiB (111.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b6b195afd5df175f177/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Jung2019 simulation.sedml\ncreating dataset /Jung2019 simulation.sedml/autogen_report_for_task1, shape: (37, 1001), type: float64\ndataset created, uuid: d-1695bb35-b982a295-3334-8c1549-d46e8e, chunk_size: (37, 1001)\ncreating dataset /Jung2019 simulation.sedml/plot_1_task1, shape: (9, 1001), type: float64\ndataset created, uuid: d-1695bb35-b982a295-34df-533ea4-bb97f2, chunk_size: (9, 1001)\ncreating dataset /Jung2019 simulation.sedml/plot_2_task1, shape: (2, 1001), type: float64\ndataset created, uuid: d-1695bb35-b982a295-4057-f8f38e-6ebdd2, chunk_size: (2, 1001)\ncreating attribute combineArchiveLocation in /Jung2019 simulation.sedml\ncreating attribute uri in /Jung2019 simulation.sedml\ncreating attribute _type in /Jung2019 simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Jung2019 simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Jung2019 simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Jung2019 simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Jung2019 simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Jung2019 simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Jung2019 simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Jung2019 simulation.sedml/autogen_report_for_task1\ncreating attribute uri in /Jung2019 simulation.sedml/autogen_report_for_task1\ncreating attribute _type in /Jung2019 simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Jung2019 simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Jung2019 simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Jung2019 simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Jung2019 simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Jung2019 simulation.sedml/plot_1_task1\ncreating attribute sedmlId in /Jung2019 simulation.sedml/plot_1_task1\ncreating attribute uri in /Jung2019 simulation.sedml/plot_1_task1\ncreating attribute _type in /Jung2019 simulation.sedml/plot_2_task1\ncreating attribute sedmlDataSetDataTypes in /Jung2019 simulation.sedml/plot_2_task1\ncreating attribute sedmlDataSetIds in /Jung2019 simulation.sedml/plot_2_task1\ncreating attribute sedmlDataSetLabels in /Jung2019 simulation.sedml/plot_2_task1\ncreating attribute sedmlDataSetNames in /Jung2019 simulation.sedml/plot_2_task1\ncreating attribute sedmlDataSetShapes in /Jung2019 simulation.sedml/plot_2_task1\ncreating attribute sedmlId in /Jung2019 simulation.sedml/plot_2_task1\ncreating attribute uri in /Jung2019 simulation.sedml/plot_2_task1\ncreate_links: /\ngot link: Jung2019 simulation.sedml\ncreate_links: /Jung2019 simulation.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\ngot link: plot_2_task1\nwrite_dataset src: /Jung2019 simulation.sedml/autogen_report_for_task1 to tgt: /Jung2019 simulation.sedml/autogen_report_for_task1, shape: (37, 1001), type: float64\niterating over chunks for /Jung2019 simulation.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 37, 1), slice(0, 1001, 1))\ndone with dataload for /Jung2019 simulation.sedml/autogen_report_for_task1\nwrite_dataset src: /Jung2019 simulation.sedml/plot_1_task1 to tgt: /Jung2019 simulation.sedml/plot_1_task1, shape: (9, 1001), type: float64\niterating over chunks for /Jung2019 simulation.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 1001, 1))\ndone with dataload for /Jung2019 simulation.sedml/plot_1_task1\nwrite_dataset src: /Jung2019 simulation.sedml/plot_2_task1 to tgt: /Jung2019 simulation.sedml/plot_2_task1, shape: (2, 1001), type: float64\niterating over chunks for /Jung2019 simulation.sedml/plot_2_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /Jung2019 simulation.sedml/plot_2_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b6b195afd5df175f177\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 metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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.\nProcess and upload the outputs of the simulation run ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.858218,"sedDocuments":[{"location":"Jung2019 simulation.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 2 plots:\r\n  Jung2019 simulation.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 37 data sets\r\n    Plots (2):\r\n      plot_1_task1: 8 curves\r\n      plot_2_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: Jung2019 simulation.sedml ...\r\n  Found 1 tasks and 3 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_report_for_task1`\r\n      `plot_1_task1`\r\n      `plot_2_task1`\r\n  Executing task 1: `task1`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 3 outputs ...\r\n      Generating output 1: `plot_1_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `plot_2_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 3: `autogen_report_for_task1` ...","duration":1.385391,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.211725,"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":10000,"Relative Tolerance":0.000001}}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.514372,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"},{"id":"p1_curve_4_task1","status":"SUCCEEDED"},{"id":"p1_curve_5_task1","status":"SUCCEEDED"},{"id":"p1_curve_6_task1","status":"SUCCEEDED"},{"id":"p1_curve_7_task1","status":"SUCCEEDED"},{"id":"p1_curve_8_task1","status":"SUCCEEDED"}]},{"id":"plot_2_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.163162,"curves":[{"id":"p2_curve_1_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.332648,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_u_1","status":"SUCCEEDED"},{"id":"autogen_task1_u_2","status":"SUCCEEDED"},{"id":"autogen_task1_AMPK_A","status":"SUCCEEDED"},{"id":"autogen_task1_Drug_D","status":"SUCCEEDED"},{"id":"autogen_task1_Glucose_G","status":"SUCCEEDED"},{"id":"autogen_task1_miR_451_M","status":"SUCCEEDED"},{"id":"autogen_task1_mTOR_R","status":"SUCCEEDED"},{"id":"autogen_task1_deltaD","status":"SUCCEEDED"},{"id":"autogen_task1_myu_G","status":"SUCCEEDED"},{"id":"autogen_task1_l_1","status":"SUCCEEDED"},{"id":"autogen_task1_l_2","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_l_3","status":"SUCCEEDED"},{"id":"autogen_task1_l_4","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_S_1","status":"SUCCEEDED"},{"id":"autogen_task1_epsilon_1","status":"SUCCEEDED"},{"id":"autogen_task1_l_5","status":"SUCCEEDED"},{"id":"autogen_task1_l_6","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_S_2","status":"SUCCEEDED"},{"id":"autogen_task1_epsilon_2","status":"SUCCEEDED"},{"id":"autogen_task1_myu_D","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_Dose_for_Glucose","status":"SUCCEEDED"},{"id":"autogen_task1_Dose_for_Drug","status":"SUCCEEDED"},{"id":"autogen_task1_Consumption_of_Glucose","status":"SUCCEEDED"},{"id":"autogen_task1_Decay_of_Drug","status":"SUCCEEDED"},{"id":"autogen_task1_Production_of_miR_451","status":"SUCCEEDED"},{"id":"autogen_task1_loss_of_miR_451","status":"SUCCEEDED"},{"id":"autogen_task1_signal_source_of_AMPK","status":"SUCCEEDED"},{"id":"autogen_task1_Production_of_AMPK","status":"SUCCEEDED"},{"id":"autogen_task1_loss_of_AMPK","status":"SUCCEEDED"},{"id":"autogen_task1_signal_source_of_mTOR","status":"SUCCEEDED"},{"id":"autogen_task1_Production_of_mTOR","status":"SUCCEEDED"},{"id":"autogen_task1_loss_of_mTOR","status":"SUCCEEDED"}]}]}]}