{"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    460      0 --:--:-- --:--:-- --:--:--   461\n\r100 18458  100 18458    0     0  48905      0 --:--:-- --:--:-- --:--:-- 48905\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 (17.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c8c2321246e8866e4c96/rawLog.txt\nCompleted 2.9 KiB/2.9 KiB (29.8 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6480c8c2321246e8866e4c96/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 72%)\n  adding: outputs/Smith and moore2004-the SIR Model for Spread of Disease.sedml/ (stored 0%)\n  adding: outputs/Smith and moore2004-the SIR Model for Spread of Disease.sedml/plot_1_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 79%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 27.5 KiB/27.5 KiB (268.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6480c8c2321246e8866e4c96/outputs/reports.h5\nCompleted 9.4 KiB/43.5 KiB (96.6 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6480c8c2321246e8866e4c96/outputs/plots.zip\nCompleted 9.4 KiB/43.5 KiB (96.6 KiB/s) with 3 file(s) remaining\rCompleted 23.0 KiB/43.5 KiB (221.8 KiB/s) with 3 file(s) remaining\rupload: outputs/Smith and moore2004-the SIR Model for Spread of Disease.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/6480c8c2321246e8866e4c96/outputs/Smith and moore2004-the SIR Model for Spread of Disease.sedml/plot_1_task1.pdf\nCompleted 23.0 KiB/43.5 KiB (221.8 KiB/s) with 2 file(s) remaining\rCompleted 25.7 KiB/43.5 KiB (217.9 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c8c2321246e8866e4c96/rawLog.txt\nCompleted 25.7 KiB/43.5 KiB (217.9 KiB/s) with 1 file(s) remaining\rCompleted 43.5 KiB/43.5 KiB (361.6 KiB/s) with 1 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6480c8c2321246e8866e4c96/output.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Smith and moore2004-the SIR Model for Spread of Disease-biopax2.owl  \n  inflating: contents/Smith and moore2004-the SIR Model for Spread of Disease-biopax3.owl  \n  inflating: contents/Smith and moore2004-the SIR Model for Spread of Disease-matlab.m  \n  inflating: contents/Smith and moore2004-the SIR Model for Spread of Disease-octave.m  \n  inflating: contents/Smith and moore2004-the SIR Model for Spread of Disease.cps  \n  inflating: contents/Smith and moore2004-the SIR Model for Spread of Disease.ode  \n  inflating: contents/Smith and moore2004-the SIR Model for Spread of Disease.sedml  \n  inflating: contents/Smith and moore2004-the SIR Model for Spread of Disease.xml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 8.3 KiB/103.2 KiB (138.2 KiB/s) with 10 file(s) remaining\rupload: contents/Smith and moore2004-the SIR Model for Spread of Disease-biopax2.owl to s3://files.biosimulations.org/simulations/6480c8c2321246e8866e4c96/contents/Smith and moore2004-the SIR Model for Spread of Disease-biopax2.owl\nCompleted 8.3 KiB/103.2 KiB (138.2 KiB/s) with 9 file(s) remaining\rCompleted 18.8 KiB/103.2 KiB (177.9 KiB/s) with 9 file(s) remaining\rupload: contents/Smith and moore2004-the SIR Model for Spread of Disease-biopax3.owl to s3://files.biosimulations.org/simulations/6480c8c2321246e8866e4c96/contents/Smith and moore2004-the SIR Model for Spread of Disease-biopax3.owl\nCompleted 18.8 KiB/103.2 KiB (177.9 KiB/s) with 8 file(s) remaining\rCompleted 20.3 KiB/103.2 KiB (186.5 KiB/s) with 8 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6480c8c2321246e8866e4c96/contents/manifest.xml\nCompleted 20.3 KiB/103.2 KiB (186.5 KiB/s) with 7 file(s) remaining\rCompleted 23.5 KiB/103.2 KiB (177.1 KiB/s) with 7 file(s) remaining\rupload: contents/Smith and moore2004-the SIR Model for Spread of Disease-matlab.m to s3://files.biosimulations.org/simulations/6480c8c2321246e8866e4c96/contents/Smith and moore2004-the SIR Model for Spread of Disease-matlab.m\nCompleted 23.5 KiB/103.2 KiB (177.1 KiB/s) with 6 file(s) remaining\rCompleted 30.4 KiB/103.2 KiB (226.5 KiB/s) with 6 file(s) remaining\rupload: contents/Smith and moore2004-the SIR Model for Spread of Disease.sedml to s3://files.biosimulations.org/simulations/6480c8c2321246e8866e4c96/contents/Smith and moore2004-the SIR Model for Spread of Disease.sedml\nCompleted 30.4 KiB/103.2 KiB (226.5 KiB/s) with 5 file(s) remaining\rCompleted 33.6 KiB/103.2 KiB (242.7 KiB/s) with 5 file(s) remaining\rupload: contents/Smith and moore2004-the SIR Model for Spread of Disease-octave.m to s3://files.biosimulations.org/simulations/6480c8c2321246e8866e4c96/contents/Smith and moore2004-the SIR Model for Spread of Disease-octave.m\nCompleted 33.6 KiB/103.2 KiB (242.7 KiB/s) with 4 file(s) remaining\rCompleted 57.3 KiB/103.2 KiB (381.3 KiB/s) with 4 file(s) remaining\rupload: contents/Smith and moore2004-the SIR Model for Spread of Disease.xml to s3://files.biosimulations.org/simulations/6480c8c2321246e8866e4c96/contents/Smith and moore2004-the SIR Model for Spread of Disease.xml\nCompleted 57.3 KiB/103.2 KiB (381.3 KiB/s) with 3 file(s) remaining\rCompleted 58.9 KiB/103.2 KiB (344.2 KiB/s) with 3 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6480c8c2321246e8866e4c96/contents/metadata.rdf\nCompleted 58.9 KiB/103.2 KiB (344.2 KiB/s) with 2 file(s) remaining\rCompleted 60.4 KiB/103.2 KiB (291.6 KiB/s) with 2 file(s) remaining\rupload: contents/Smith and moore2004-the SIR Model for Spread of Disease.ode to s3://files.biosimulations.org/simulations/6480c8c2321246e8866e4c96/contents/Smith and moore2004-the SIR Model for Spread of Disease.ode\nCompleted 60.4 KiB/103.2 KiB (291.6 KiB/s) with 1 file(s) remaining\rCompleted 103.2 KiB/103.2 KiB (278.1 KiB/s) with 1 file(s) remaining\rupload: contents/Smith and moore2004-the SIR Model for Spread of Disease.cps to s3://files.biosimulations.org/simulations/6480c8c2321246e8866e4c96/contents/Smith and moore2004-the SIR Model for Spread of Disease.cps\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.0 KiB/8.0 KiB (128.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c8c2321246e8866e4c96/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Smith and moore2004-the SIR Model for Spread of Disease.sedml\ncreating dataset /Smith and moore2004-the SIR Model for Spread of Disease.sedml/autogen_report_for_task1, shape: (9, 57), type: float64\ndataset created, uuid: d-67c83faf-f7effb61-6bc2-5a6fa3-3a49be, chunk_size: (9, 57)\ncreating dataset /Smith and moore2004-the SIR Model for Spread of Disease.sedml/plot_1_task1, shape: (4, 57), type: float64\ndataset created, uuid: d-67c83faf-f7effb61-deb8-e30897-aeee91, chunk_size: (4, 57)\ncreating attribute combineArchiveLocation in /Smith and moore2004-the SIR Model for Spread of Disease.sedml\ncreating attribute uri in /Smith and moore2004-the SIR Model for Spread of Disease.sedml\ncreating attribute _type in /Smith and moore2004-the SIR Model for Spread of Disease.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Smith and moore2004-the SIR Model for Spread of Disease.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Smith and moore2004-the SIR Model for Spread of Disease.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Smith and moore2004-the SIR Model for Spread of Disease.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Smith and moore2004-the SIR Model for Spread of Disease.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Smith and moore2004-the SIR Model for Spread of Disease.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Smith and moore2004-the SIR Model for Spread of Disease.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Smith and moore2004-the SIR Model for Spread of Disease.sedml/autogen_report_for_task1\ncreating attribute uri in /Smith and moore2004-the SIR Model for Spread of Disease.sedml/autogen_report_for_task1\ncreating attribute _type in /Smith and moore2004-the SIR Model for Spread of Disease.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Smith and moore2004-the SIR Model for Spread of Disease.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Smith and moore2004-the SIR Model for Spread of Disease.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Smith and moore2004-the SIR Model for Spread of Disease.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Smith and moore2004-the SIR Model for Spread of Disease.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Smith and moore2004-the SIR Model for Spread of Disease.sedml/plot_1_task1\ncreating attribute sedmlId in /Smith and moore2004-the SIR Model for Spread of Disease.sedml/plot_1_task1\ncreating attribute sedmlName in /Smith and moore2004-the SIR Model for Spread of Disease.sedml/plot_1_task1\ncreating attribute uri in /Smith and moore2004-the SIR Model for Spread of Disease.sedml/plot_1_task1\ncreate_links: /\ngot link: Smith and moore2004-the SIR Model for Spread of Disease.sedml\ncreate_links: /Smith and moore2004-the SIR Model for Spread of Disease.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Smith and moore2004-the SIR Model for Spread of Disease.sedml/autogen_report_for_task1 to tgt: /Smith and moore2004-the SIR Model for Spread of Disease.sedml/autogen_report_for_task1, shape: (9, 57), type: float64\niterating over chunks for /Smith and moore2004-the SIR Model for Spread of Disease.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 57, 1))\ndone with dataload for /Smith and moore2004-the SIR Model for Spread of Disease.sedml/autogen_report_for_task1\nwrite_dataset src: /Smith and moore2004-the SIR Model for Spread of Disease.sedml/plot_1_task1 to tgt: /Smith and moore2004-the SIR Model for Spread of Disease.sedml/plot_1_task1, shape: (4, 57), type: float64\niterating over chunks for /Smith and moore2004-the SIR Model for Spread of Disease.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 57, 1))\ndone with dataload for /Smith and moore2004-the SIR Model for Spread of Disease.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6480c8c2321246e8866e4c96\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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.03564,"sedDocuments":[{"location":"Smith and moore2004-the SIR Model for Spread of Disease.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  Smith and moore2004-the SIR Model for Spread of Disease.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 9 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Smith and moore2004-the SIR Model for Spread of Disease.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":0.669779,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.17927,"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":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.318355,"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":0.069588,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Infected","status":"SUCCEEDED"},{"id":"autogen_task1_Recovered","status":"SUCCEEDED"},{"id":"autogen_task1_Susceptible","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_k","status":"SUCCEEDED"},{"id":"autogen_task1_New_York_1968_69","status":"SUCCEEDED"},{"id":"autogen_task1_Susceptible_to_Infected","status":"SUCCEEDED"},{"id":"autogen_task1_Infected_to_Recovered","status":"SUCCEEDED"}]}]}]}