{"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    467      0 --:--:-- --:--:-- --:--:--   469\n\r100  342k  100  342k    0     0   795k      0 --:--:-- --:--:-- --:--:--  795k\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 (19.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/rawLog.txt\nCompleted 5.0 KiB/5.0 KiB (76.8 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 81%)\n  adding: outputs/BIOMD0000000017_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000017_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 17%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 147.6 KiB/147.6 KiB (1.7 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/outputs/reports.h5\nCompleted 11.2 KiB/166.8 KiB (89.0 KiB/s) with 4 file(s) remaining\rCompleted 27.6 KiB/166.8 KiB (215.1 KiB/s) with 4 file(s) remaining\rupload: outputs/BIOMD0000000017_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/outputs/BIOMD0000000017_url.sedml/autogen_plot_for_task1.pdf\nCompleted 27.6 KiB/166.8 KiB (215.1 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/outputs/plots.zip\nCompleted 27.6 KiB/166.8 KiB (215.1 KiB/s) with 2 file(s) remaining\rCompleted 164.2 KiB/166.8 KiB (1.2 MiB/s) with 2 file(s) remaining \rupload: ./output.zip to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/output.zip\nCompleted 164.2 KiB/166.8 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 166.8 KiB/166.8 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000017-biopax2.owl  \n  inflating: contents/BIOMD0000000017-biopax3.owl  \n  inflating: contents/BIOMD0000000017-matlab.m  \n  inflating: contents/BIOMD0000000017-octave.m  \n  inflating: contents/BIOMD0000000017.m  \n  inflating: contents/BIOMD0000000017.ode  \n  inflating: contents/BIOMD0000000017.pdf  \n  inflating: contents/BIOMD0000000017.png  \n  inflating: contents/BIOMD0000000017.sci  \n  inflating: contents/BIOMD0000000017.svg  \n  inflating: contents/BIOMD0000000017.vcml  \n  inflating: contents/BIOMD0000000017_url.sedml  \n  inflating: contents/BIOMD0000000017_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 47.0 KiB/751.2 KiB (549.3 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000017-biopax2.owl to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/contents/BIOMD0000000017-biopax2.owl\nCompleted 47.0 KiB/751.2 KiB (549.3 KiB/s) with 16 file(s) remaining\rCompleted 60.8 KiB/751.2 KiB (534.2 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000017-octave.m to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/contents/BIOMD0000000017-octave.m\nCompleted 60.8 KiB/751.2 KiB (534.2 KiB/s) with 15 file(s) remaining\rCompleted 74.6 KiB/751.2 KiB (601.0 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000017-matlab.m to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/contents/BIOMD0000000017-matlab.m\nCompleted 74.6 KiB/751.2 KiB (601.0 KiB/s) with 14 file(s) remaining\rCompleted 211.2 KiB/751.2 KiB (1.6 MiB/s) with 14 file(s) remaining \rupload: contents/BIOMD0000000017.png to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/contents/BIOMD0000000017.png\nCompleted 211.2 KiB/751.2 KiB (1.6 MiB/s) with 13 file(s) remaining\rCompleted 211.3 KiB/751.2 KiB (1.4 MiB/s) with 13 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/contents/curation_notes.txt\nCompleted 211.3 KiB/751.2 KiB (1.4 MiB/s) with 12 file(s) remaining\rCompleted 244.2 KiB/751.2 KiB (1.6 MiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000017.svg to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/contents/BIOMD0000000017.svg\nCompleted 244.2 KiB/751.2 KiB (1.6 MiB/s) with 11 file(s) remaining\rCompleted 315.5 KiB/751.2 KiB (1.9 MiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000017.vcml to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/contents/BIOMD0000000017.vcml\nCompleted 315.5 KiB/751.2 KiB (1.9 MiB/s) with 10 file(s) remaining\rCompleted 330.2 KiB/751.2 KiB (2.0 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000017.sci to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/contents/BIOMD0000000017.sci\nCompleted 330.2 KiB/751.2 KiB (2.0 MiB/s) with 9 file(s) remaining\rCompleted 332.2 KiB/751.2 KiB (1.9 MiB/s) with 9 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/contents/manifest.xml\nCompleted 332.2 KiB/751.2 KiB (1.9 MiB/s) with 8 file(s) remaining\rCompleted 353.1 KiB/751.2 KiB (2.0 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000017_url.sedml to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/contents/BIOMD0000000017_url.sedml\nCompleted 353.1 KiB/751.2 KiB (2.0 MiB/s) with 7 file(s) remaining\rCompleted 413.8 KiB/751.2 KiB (2.2 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000017_url.xml to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/contents/BIOMD0000000017_url.xml\nCompleted 413.8 KiB/751.2 KiB (2.2 MiB/s) with 6 file(s) remaining\rCompleted 434.0 KiB/751.2 KiB (2.3 MiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/contents/curation_image.png\nCompleted 434.0 KiB/751.2 KiB (2.3 MiB/s) with 5 file(s) remaining\rCompleted 499.6 KiB/751.2 KiB (2.3 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000017-biopax3.owl to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/contents/BIOMD0000000017-biopax3.owl\nCompleted 499.6 KiB/751.2 KiB (2.3 MiB/s) with 4 file(s) remaining\rCompleted 504.3 KiB/751.2 KiB (2.2 MiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/contents/metadata.rdf\nCompleted 504.3 KiB/751.2 KiB (2.2 MiB/s) with 3 file(s) remaining\rCompleted 514.2 KiB/751.2 KiB (2.2 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000017.ode to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/contents/BIOMD0000000017.ode\nCompleted 514.2 KiB/751.2 KiB (2.2 MiB/s) with 2 file(s) remaining\rCompleted 528.0 KiB/751.2 KiB (2.3 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000017.m to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/contents/BIOMD0000000017.m\nCompleted 528.0 KiB/751.2 KiB (2.3 MiB/s) with 1 file(s) remaining\rCompleted 751.2 KiB/751.2 KiB (3.2 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000017.pdf to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/contents/BIOMD0000000017.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.1 KiB/9.1 KiB (143.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107280dcacb55678b38b1/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000017_url.sedml\ncreating dataset /BIOMD0000000017_url.sedml/autogen_plot_for_task1, shape: (20, 1001), type: float64\ndataset created, uuid: d-2a8868ec-03e55301-d023-537a43-46e01c, chunk_size: (20, 1001)\ncreating dataset /BIOMD0000000017_url.sedml/autogen_report_for_task1, shape: (35, 1001), type: float64\ndataset created, uuid: d-2a8868ec-03e55301-90b4-bd3dee-f77682, chunk_size: (35, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000017_url.sedml\ncreating attribute uri in /BIOMD0000000017_url.sedml\ncreating attribute _type in /BIOMD0000000017_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000017_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000017_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000017_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000017_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000017_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000017_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000017_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000017_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000017_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000017_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000017_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000017_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000017_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000017_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000017_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000017_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000017_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000017_url.sedml\ncreate_links: /BIOMD0000000017_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000017_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000017_url.sedml/autogen_plot_for_task1, shape: (20, 1001), type: float64\niterating over chunks for /BIOMD0000000017_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 20, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000017_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000017_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000017_url.sedml/autogen_report_for_task1, shape: (35, 1001), type: float64\niterating over chunks for /BIOMD0000000017_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 35, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000017_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647107280dcacb55678b38b1\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 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.\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.\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","duration":1.986586,"sedDocuments":[{"location":"BIOMD0000000017_url.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  BIOMD0000000017_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 35 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 19 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000017_url.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_plot_for_task1`\r\n      `autogen_report_for_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: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_plot_for_task1` ...","duration":1.484276,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.277792,"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":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.29595,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_ADP","status":"SUCCEEDED"},{"id":"autogen_task1_NAD","status":"SUCCEEDED"},{"id":"autogen_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_task1_NADH","status":"SUCCEEDED"},{"id":"autogen_task1_pyruvate","status":"SUCCEEDED"},{"id":"autogen_task1_lactate","status":"SUCCEEDED"},{"id":"autogen_task1_CoA","status":"SUCCEEDED"},{"id":"autogen_task1_halfglucose","status":"SUCCEEDED"},{"id":"autogen_task1_AcCoA","status":"SUCCEEDED"},{"id":"autogen_task1_AcP","status":"SUCCEEDED"},{"id":"autogen_task1_Ac","status":"SUCCEEDED"},{"id":"autogen_task1_AcO","status":"SUCCEEDED"},{"id":"autogen_task1_EtOH","status":"SUCCEEDED"},{"id":"autogen_task1_AcLac","status":"SUCCEEDED"},{"id":"autogen_task1_AcetoinIn","status":"SUCCEEDED"},{"id":"autogen_task1_AcetoinOut","status":"SUCCEEDED"},{"id":"autogen_task1_Butanediol","status":"SUCCEEDED"},{"id":"autogen_task1_O2","status":"SUCCEEDED"},{"id":"autogen_task1_PO4","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_R1","status":"SUCCEEDED"},{"id":"autogen_task1_R2","status":"SUCCEEDED"},{"id":"autogen_task1_R3","status":"SUCCEEDED"},{"id":"autogen_task1_R4","status":"SUCCEEDED"},{"id":"autogen_task1_R5","status":"SUCCEEDED"},{"id":"autogen_task1_R6","status":"SUCCEEDED"},{"id":"autogen_task1_R7","status":"SUCCEEDED"},{"id":"autogen_task1_R8","status":"SUCCEEDED"},{"id":"autogen_task1_R9","status":"SUCCEEDED"},{"id":"autogen_task1_R10","status":"SUCCEEDED"},{"id":"autogen_task1_R11","status":"SUCCEEDED"},{"id":"autogen_task1_R12","status":"SUCCEEDED"},{"id":"autogen_task1_R13","status":"SUCCEEDED"},{"id":"autogen_task1_R14","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.752415,"curves":[{"id":"autogen_curve_task1_ADP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NAD","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_pyruvate","status":"SUCCEEDED"},{"id":"autogen_curve_task1_lactate","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CoA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_halfglucose","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AcCoA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AcP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ac","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AcO","status":"SUCCEEDED"},{"id":"autogen_curve_task1_EtOH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AcLac","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AcetoinIn","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AcetoinOut","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Butanediol","status":"SUCCEEDED"},{"id":"autogen_curve_task1_O2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PO4","status":"SUCCEEDED"}]}]}]}