{"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    422      0 --:--:-- --:--:-- --:--:--   421\n\r100  144k  100  144k    0     0   331k      0 --:--:-- --:--:-- --:--:--  331k\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 (25.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/rawLog.txt\nCompleted 3.9 KiB/3.9 KiB (42.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/BIOMD0000000241_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000241_url.sedml/autogen_plot_for_task1.pdf (deflated 19%)\n  adding: outputs/log.yml (deflated 79%)\n  adding: outputs/reports.h5 (deflated 24%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 116.4 KiB/116.4 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/outputs/reports.h5\nCompleted 104.7 KiB/137.6 KiB (1.1 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/output.zip\nCompleted 104.7 KiB/137.6 KiB (1.1 MiB/s) with 3 file(s) remaining\rCompleted 121.5 KiB/137.6 KiB (1.1 MiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000241_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/outputs/BIOMD0000000241_url.sedml/autogen_plot_for_task1.pdf\nCompleted 121.5 KiB/137.6 KiB (1.1 MiB/s) with 2 file(s) remaining\rCompleted 124.2 KiB/137.6 KiB (1.1 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/rawLog.txt\nCompleted 124.2 KiB/137.6 KiB (1.1 MiB/s) with 1 file(s) remaining\rCompleted 137.6 KiB/137.6 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000241-biopax2.owl  \n  inflating: contents/BIOMD0000000241-biopax3.owl  \n  inflating: contents/BIOMD0000000241-matlab.m  \n  inflating: contents/BIOMD0000000241-octave.m  \n  inflating: contents/BIOMD0000000241.m  \n  inflating: contents/BIOMD0000000241.ode  \n  inflating: contents/BIOMD0000000241.pdf  \n  inflating: contents/BIOMD0000000241.png  \n  inflating: contents/BIOMD0000000241.svg  \n  inflating: contents/BIOMD0000000241_url.sedml  \n  inflating: contents/BIOMD0000000241_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 6.5 KiB/240.5 KiB (91.1 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000241-biopax2.owl to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/contents/BIOMD0000000241-biopax2.owl\nCompleted 6.5 KiB/240.5 KiB (91.1 KiB/s) with 14 file(s) remaining\rCompleted 9.3 KiB/240.5 KiB (68.9 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000241.ode to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/contents/BIOMD0000000241.ode\nCompleted 9.3 KiB/240.5 KiB (68.9 KiB/s) with 13 file(s) remaining\rCompleted 14.4 KiB/240.5 KiB (104.1 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000241.png to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/contents/BIOMD0000000241.png\nCompleted 14.4 KiB/240.5 KiB (104.1 KiB/s) with 12 file(s) remaining\rCompleted 15.2 KiB/240.5 KiB (107.0 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000241.svg to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/contents/BIOMD0000000241.svg\nCompleted 15.2 KiB/240.5 KiB (107.0 KiB/s) with 11 file(s) remaining\rCompleted 20.1 KiB/240.5 KiB (136.0 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000241-octave.m to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/contents/BIOMD0000000241-octave.m\nCompleted 20.1 KiB/240.5 KiB (136.0 KiB/s) with 10 file(s) remaining\rCompleted 173.6 KiB/240.5 KiB (1.1 MiB/s) with 10 file(s) remaining \rupload: contents/BIOMD0000000241.pdf to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/contents/BIOMD0000000241.pdf\nCompleted 173.6 KiB/240.5 KiB (1.1 MiB/s) with 9 file(s) remaining\rCompleted 178.5 KiB/240.5 KiB (1.1 MiB/s) with 9 file(s) remaining\rCompleted 185.6 KiB/240.5 KiB (1.2 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000241-matlab.m to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/contents/BIOMD0000000241-matlab.m\nCompleted 185.6 KiB/240.5 KiB (1.2 MiB/s) with 8 file(s) remaining\rCompleted 190.5 KiB/240.5 KiB (1.2 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000241-biopax3.owl to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/contents/BIOMD0000000241-biopax3.owl\nCompleted 190.5 KiB/240.5 KiB (1.2 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000241.m to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/contents/BIOMD0000000241.m\nCompleted 190.5 KiB/240.5 KiB (1.2 MiB/s) with 6 file(s) remaining\rCompleted 206.7 KiB/240.5 KiB (1.3 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000241_url.sedml to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/contents/BIOMD0000000241_url.sedml\nCompleted 206.7 KiB/240.5 KiB (1.3 MiB/s) with 5 file(s) remaining\rCompleted 228.2 KiB/240.5 KiB (1.4 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000241_url.xml to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/contents/BIOMD0000000241_url.xml\nCompleted 228.2 KiB/240.5 KiB (1.4 MiB/s) with 4 file(s) remaining\rCompleted 233.8 KiB/240.5 KiB (1.1 MiB/s) with 4 file(s) remaining\rCompleted 235.6 KiB/240.5 KiB (1.1 MiB/s) with 4 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/contents/curation_image.png\nCompleted 235.6 KiB/240.5 KiB (1.1 MiB/s) with 3 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/contents/manifest.xml\nCompleted 235.6 KiB/240.5 KiB (1.1 MiB/s) with 2 file(s) remaining\rCompleted 240.1 KiB/240.5 KiB (1.1 MiB/s) with 2 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/contents/metadata.rdf\nCompleted 240.1 KiB/240.5 KiB (1.1 MiB/s) with 1 file(s) remaining\rCompleted 240.5 KiB/240.5 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/contents/curation_notes.txt\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (132.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c474195afd5df1769325/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000241_url.sedml\ncreating dataset /BIOMD0000000241_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\ndataset created, uuid: d-df6ced87-b01e5e8d-3d9e-4bf15f-196bb4, chunk_size: (6, 1001)\ncreating dataset /BIOMD0000000241_url.sedml/autogen_report_for_task1, shape: (30, 1001), type: float64\ndataset created, uuid: d-df6ced87-b01e5e8d-bae2-8efc16-8d60be, chunk_size: (30, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000241_url.sedml\ncreating attribute uri in /BIOMD0000000241_url.sedml\ncreating attribute _type in /BIOMD0000000241_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000241_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000241_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000241_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000241_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000241_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000241_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000241_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000241_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000241_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000241_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000241_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000241_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000241_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000241_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000241_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000241_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000241_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000241_url.sedml\ncreate_links: /BIOMD0000000241_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000241_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000241_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\niterating over chunks for /BIOMD0000000241_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000241_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000241_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000241_url.sedml/autogen_report_for_task1, shape: (30, 1001), type: float64\niterating over chunks for /BIOMD0000000241_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 30, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000241_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6480c474195afd5df1769325\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 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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.476301,"sedDocuments":[{"location":"BIOMD0000000241_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  BIOMD0000000241_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 30 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 5 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000241_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":1.029972,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.206602,"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":0.257279,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_X_gut","status":"SUCCEEDED"},{"id":"autogen_task1_C_p","status":"SUCCEEDED"},{"id":"autogen_task1_C_per","status":"SUCCEEDED"},{"id":"autogen_task1_C_e","status":"SUCCEEDED"},{"id":"autogen_task1_C_t","status":"SUCCEEDED"},{"id":"autogen_task1_CL","status":"SUCCEEDED"},{"id":"autogen_task1_V_C","status":"SUCCEEDED"},{"id":"autogen_task1_k_a","status":"SUCCEEDED"},{"id":"autogen_task1_t_lag","status":"SUCCEEDED"},{"id":"autogen_task1_k10","status":"SUCCEEDED"},{"id":"autogen_task1_k12","status":"SUCCEEDED"},{"id":"autogen_task1_k21","status":"SUCCEEDED"},{"id":"autogen_task1_t_half","status":"SUCCEEDED"},{"id":"autogen_task1_F","status":"SUCCEEDED"},{"id":"autogen_task1_k_eo","status":"SUCCEEDED"},{"id":"autogen_task1_k_tol","status":"SUCCEEDED"},{"id":"autogen_task1_E_0","status":"SUCCEEDED"},{"id":"autogen_task1_S","status":"SUCCEEDED"},{"id":"autogen_task1_T_50","status":"SUCCEEDED"},{"id":"autogen_task1_E","status":"SUCCEEDED"},{"id":"autogen_task1_t_int","status":"SUCCEEDED"},{"id":"autogen_task1_cupsize","status":"SUCCEEDED"},{"id":"autogen_task1_bodyweight","status":"SUCCEEDED"},{"id":"autogen_task1_cups","status":"SUCCEEDED"},{"id":"autogen_task1_Gut","status":"SUCCEEDED"},{"id":"autogen_task1_C","status":"SUCCEEDED"},{"id":"autogen_task1_P","status":"SUCCEEDED"},{"id":"autogen_task1_Tol","status":"SUCCEEDED"},{"id":"autogen_task1_Eff","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.441127,"curves":[{"id":"autogen_curve_task1_X_gut","status":"SUCCEEDED"},{"id":"autogen_curve_task1_C_p","status":"SUCCEEDED"},{"id":"autogen_curve_task1_C_per","status":"SUCCEEDED"},{"id":"autogen_curve_task1_C_e","status":"SUCCEEDED"},{"id":"autogen_curve_task1_C_t","status":"SUCCEEDED"}]}]}]}