{"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    463      0 --:--:-- --:--:-- --:--:--   464\n\r100  150k  100  150k    0     0   351k      0 --:--:-- --:--:-- --:--:--  351k\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 (24.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b56195afd5df175efd7/rawLog.txt\nCompleted 4.2 KiB/4.2 KiB (31.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b56195afd5df175efd7/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/Goldbeter1996.sedml/ (stored 0%)\n  adding: outputs/Goldbeter1996.sedml/plot_2_task1.pdf (deflated 21%)\n  adding: outputs/reports.h5 (deflated 19%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 176.6 KiB/176.6 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b56195afd5df175efd7/outputs/reports.h5\nCompleted 157.9 KiB/186.7 KiB (1.7 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b56195afd5df175efd7/output.zip\nCompleted 157.9 KiB/186.7 KiB (1.7 MiB/s) with 3 file(s) remaining\rCompleted 169.3 KiB/186.7 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b56195afd5df175efd7/outputs/plots.zip\nCompleted 169.3 KiB/186.7 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 184.1 KiB/186.7 KiB (1.5 MiB/s) with 2 file(s) remaining\rupload: outputs/Goldbeter1996.sedml/plot_2_task1.pdf to s3://files.biosimulations.org/simulations/647a4b56195afd5df175efd7/outputs/Goldbeter1996.sedml/plot_2_task1.pdf\nCompleted 184.1 KiB/186.7 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 186.7 KiB/186.7 KiB (1005.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b56195afd5df175efd7/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Goldbeter1996-biopax2.owl  \n  inflating: contents/Goldbeter1996-biopax3.owl  \n  inflating: contents/Goldbeter1996-matlab.m  \n  inflating: contents/Goldbeter1996-octave.m  \n  inflating: contents/Goldbeter1996.cps  \n  inflating: contents/Goldbeter1996.ode  \n  inflating: contents/Goldbeter1996.sedml  \n  inflating: contents/Goldbeter1996.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 13.5 KiB/303.4 KiB (173.1 KiB/s) with 12 file(s) remaining\rupload: contents/Goldbeter1996-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b56195afd5df175efd7/contents/Goldbeter1996-biopax3.owl\nCompleted 13.5 KiB/303.4 KiB (173.1 KiB/s) with 11 file(s) remaining\rCompleted 23.4 KiB/303.4 KiB (201.8 KiB/s) with 11 file(s) remaining\rupload: contents/Goldbeter1996-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b56195afd5df175efd7/contents/Goldbeter1996-biopax2.owl\nCompleted 23.4 KiB/303.4 KiB (201.8 KiB/s) with 10 file(s) remaining\rCompleted 28.3 KiB/303.4 KiB (231.5 KiB/s) with 10 file(s) remaining\rupload: contents/Goldbeter1996-matlab.m to s3://files.biosimulations.org/simulations/647a4b56195afd5df175efd7/contents/Goldbeter1996-matlab.m\nCompleted 28.3 KiB/303.4 KiB (231.5 KiB/s) with 9 file(s) remaining\rCompleted 29.7 KiB/303.4 KiB (213.2 KiB/s) with 9 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b56195afd5df175efd7/contents/manifest.xml\nCompleted 29.7 KiB/303.4 KiB (213.2 KiB/s) with 8 file(s) remaining\rCompleted 77.8 KiB/303.4 KiB (550.2 KiB/s) with 8 file(s) remaining\rupload: contents/Goldbeter1996.xml to s3://files.biosimulations.org/simulations/647a4b56195afd5df175efd7/contents/Goldbeter1996.xml\nCompleted 77.8 KiB/303.4 KiB (550.2 KiB/s) with 7 file(s) remaining\rCompleted 77.9 KiB/303.4 KiB (536.7 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b56195afd5df175efd7/contents/curation_notes.txt\nCompleted 77.9 KiB/303.4 KiB (536.7 KiB/s) with 6 file(s) remaining\rCompleted 94.1 KiB/303.4 KiB (639.0 KiB/s) with 6 file(s) remaining\rupload: contents/Goldbeter1996.sedml to s3://files.biosimulations.org/simulations/647a4b56195afd5df175efd7/contents/Goldbeter1996.sedml\nCompleted 94.1 KiB/303.4 KiB (639.0 KiB/s) with 5 file(s) remaining\rCompleted 96.5 KiB/303.4 KiB (618.0 KiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b56195afd5df175efd7/contents/metadata.rdf\nCompleted 96.5 KiB/303.4 KiB (618.0 KiB/s) with 4 file(s) remaining\rCompleted 229.3 KiB/303.4 KiB (1.4 MiB/s) with 4 file(s) remaining \rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b56195afd5df175efd7/contents/curation_image.png\nCompleted 229.3 KiB/303.4 KiB (1.4 MiB/s) with 3 file(s) remaining\rCompleted 234.1 KiB/303.4 KiB (1.2 MiB/s) with 3 file(s) remaining\rupload: contents/Goldbeter1996-octave.m to s3://files.biosimulations.org/simulations/647a4b56195afd5df175efd7/contents/Goldbeter1996-octave.m\nCompleted 234.1 KiB/303.4 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 237.3 KiB/303.4 KiB (1.2 MiB/s) with 2 file(s) remaining\rupload: contents/Goldbeter1996.ode to s3://files.biosimulations.org/simulations/647a4b56195afd5df175efd7/contents/Goldbeter1996.ode\nCompleted 237.3 KiB/303.4 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 303.4 KiB/303.4 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: contents/Goldbeter1996.cps to s3://files.biosimulations.org/simulations/647a4b56195afd5df175efd7/contents/Goldbeter1996.cps\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.4 KiB/7.4 KiB (110.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b56195afd5df175efd7/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Goldbeter1996.sedml\ncreating dataset /Goldbeter1996.sedml/autogen_report_for_task1, shape: (27, 1001), type: float64\ndataset created, uuid: d-a52003d1-ef8d0792-a104-183f30-425dd2, chunk_size: (27, 1001)\ncreating dataset /Goldbeter1996.sedml/plot_2_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-a52003d1-ef8d0792-9ef2-e9693b-637728, chunk_size: (4, 1001)\ncreating dataset /Goldbeter1996.sedml/report_task1, shape: (6, 1001), type: float64\ndataset created, uuid: d-a52003d1-ef8d0792-5a4c-7167f6-a4170c, chunk_size: (6, 1001)\ncreating attribute combineArchiveLocation in /Goldbeter1996.sedml\ncreating attribute uri in /Goldbeter1996.sedml\ncreating attribute _type in /Goldbeter1996.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Goldbeter1996.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Goldbeter1996.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Goldbeter1996.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Goldbeter1996.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Goldbeter1996.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Goldbeter1996.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Goldbeter1996.sedml/autogen_report_for_task1\ncreating attribute uri in /Goldbeter1996.sedml/autogen_report_for_task1\ncreating attribute _type in /Goldbeter1996.sedml/plot_2_task1\ncreating attribute sedmlDataSetDataTypes in /Goldbeter1996.sedml/plot_2_task1\ncreating attribute sedmlDataSetIds in /Goldbeter1996.sedml/plot_2_task1\ncreating attribute sedmlDataSetLabels in /Goldbeter1996.sedml/plot_2_task1\ncreating attribute sedmlDataSetNames in /Goldbeter1996.sedml/plot_2_task1\ncreating attribute sedmlDataSetShapes in /Goldbeter1996.sedml/plot_2_task1\ncreating attribute sedmlId in /Goldbeter1996.sedml/plot_2_task1\ncreating attribute sedmlName in /Goldbeter1996.sedml/plot_2_task1\ncreating attribute uri in /Goldbeter1996.sedml/plot_2_task1\ncreating attribute _type in /Goldbeter1996.sedml/report_task1\ncreating attribute sedmlDataSetDataTypes in /Goldbeter1996.sedml/report_task1\ncreating attribute sedmlDataSetIds in /Goldbeter1996.sedml/report_task1\ncreating attribute sedmlDataSetLabels in /Goldbeter1996.sedml/report_task1\ncreating attribute sedmlDataSetNames in /Goldbeter1996.sedml/report_task1\ncreating attribute sedmlDataSetShapes in /Goldbeter1996.sedml/report_task1\ncreating attribute sedmlId in /Goldbeter1996.sedml/report_task1\ncreating attribute sedmlName in /Goldbeter1996.sedml/report_task1\ncreating attribute uri in /Goldbeter1996.sedml/report_task1\ncreate_links: /\ngot link: Goldbeter1996.sedml\ncreate_links: /Goldbeter1996.sedml\ngot link: autogen_report_for_task1\ngot link: plot_2_task1\ngot link: report_task1\nwrite_dataset src: /Goldbeter1996.sedml/autogen_report_for_task1 to tgt: /Goldbeter1996.sedml/autogen_report_for_task1, shape: (27, 1001), type: float64\niterating over chunks for /Goldbeter1996.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 27, 1), slice(0, 1001, 1))\ndone with dataload for /Goldbeter1996.sedml/autogen_report_for_task1\nwrite_dataset src: /Goldbeter1996.sedml/plot_2_task1 to tgt: /Goldbeter1996.sedml/plot_2_task1, shape: (4, 1001), type: float64\niterating over chunks for /Goldbeter1996.sedml/plot_2_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /Goldbeter1996.sedml/plot_2_task1\nwrite_dataset src: /Goldbeter1996.sedml/report_task1 to tgt: /Goldbeter1996.sedml/report_task1, shape: (6, 1001), type: float64\niterating over chunks for /Goldbeter1996.sedml/report_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1001, 1))\ndone with dataload for /Goldbeter1996.sedml/report_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b56195afd5df175efd7\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 and upload the outputs of the simulation run ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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":1.693423,"sedDocuments":[{"location":"Goldbeter1996.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 2 reports, and 1 plots:\r\n  Goldbeter1996.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (2):\r\n      autogen_report_for_task1: 27 data sets\r\n      report_task1: 6 data sets\r\n    Plots (1):\r\n      plot_2_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Goldbeter1996.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_2_task1`\r\n      `report_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: `report_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":1.176693,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.229117,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"simulate"},{"key":"solver","value":"cvode"},{"key":"relative_tolerance","value":0.000001},{"key":"absolute_tolerance","value":1e-12},{"key":"stiff","value":true},{"key":"maximum_bdf_order","value":5},{"key":"maximum_adams_order","value":12},{"key":"maximum_num_steps","value":20000},{"key":"maximum_time_step","value":0},{"key":"minimum_time_step","value":0},{"key":"initial_time_step","value":0},{"key":"multiple_steps","value":false},{"key":"variable_step_size","value":false},{"key":"max_output_rows","value":100000}]}],"outputs":[{"id":"report_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.095153,"dataSets":[{"id":"ds_1_task1","status":"SUCCEEDED"},{"id":"ds_2_task1","status":"SUCCEEDED"},{"id":"ds_3_task1","status":"SUCCEEDED"},{"id":"ds_4_task1","status":"SUCCEEDED"},{"id":"ds_5_task1","status":"SUCCEEDED"},{"id":"ds_6_task1","status":"SUCCEEDED"}]},{"id":"plot_2_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.439586,"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":0.236361,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_C","status":"SUCCEEDED"},{"id":"autogen_task1_M","status":"SUCCEEDED"},{"id":"autogen_task1_X","status":"SUCCEEDED"},{"id":"autogen_task1_V1","status":"SUCCEEDED"},{"id":"autogen_task1_V3","status":"SUCCEEDED"},{"id":"autogen_task1_VM1","status":"SUCCEEDED"},{"id":"autogen_task1_V2","status":"SUCCEEDED"},{"id":"autogen_task1_VM3","status":"SUCCEEDED"},{"id":"autogen_task1_V4","status":"SUCCEEDED"},{"id":"autogen_task1_Kc","status":"SUCCEEDED"},{"id":"autogen_task1_vi","status":"SUCCEEDED"},{"id":"autogen_task1_vd","status":"SUCCEEDED"},{"id":"autogen_task1_Kd","status":"SUCCEEDED"},{"id":"autogen_task1_K1","status":"SUCCEEDED"},{"id":"autogen_task1_K2","status":"SUCCEEDED"},{"id":"autogen_task1_K3","status":"SUCCEEDED"},{"id":"autogen_task1_K4","status":"SUCCEEDED"},{"id":"autogen_task1_kd","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_Cyclin_synthesis","status":"SUCCEEDED"},{"id":"autogen_task1_Cyclin_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_Cyclin_decay","status":"SUCCEEDED"},{"id":"autogen_task1_Cdc2_kinase_activation","status":"SUCCEEDED"},{"id":"autogen_task1_Cdc2_kinase_inactivation","status":"SUCCEEDED"},{"id":"autogen_task1_X_activation","status":"SUCCEEDED"},{"id":"autogen_task1_X_inactivation","status":"SUCCEEDED"}]}]}]}