{"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    435      0 --:--:-- --:--:-- --:--:--   435\n\r100 46924  100 46924    0     0   109k      0 --:--:-- --:--:-- --:--:--  109k\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 (26.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c909a62a8be53f8dd39/rawLog.txt\nCompleted 4.0 KiB/4.0 KiB (53.5 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711c909a62a8be53f8dd39/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/Epidemic Model with the impact of Media Reactions.sedml/ (stored 0%)\n  adding: outputs/Epidemic Model with the impact of Media Reactions.sedml/plot_1_task1.pdf (deflated 29%)\n  adding: outputs/reports.h5 (deflated 62%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 41.7 KiB/41.7 KiB (352.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711c909a62a8be53f8dd39/outputs/reports.h5\nCompleted 25.9 KiB/46.6 KiB (372.0 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711c909a62a8be53f8dd39/output.zip\nCompleted 25.9 KiB/46.6 KiB (372.0 KiB/s) with 3 file(s) remaining\rCompleted 33.3 KiB/46.6 KiB (318.3 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711c909a62a8be53f8dd39/outputs/plots.zip\nCompleted 33.3 KiB/46.6 KiB (318.3 KiB/s) with 2 file(s) remaining\rCompleted 44.0 KiB/46.6 KiB (388.9 KiB/s) with 2 file(s) remaining\rupload: outputs/Epidemic Model with the impact of Media Reactions.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711c909a62a8be53f8dd39/outputs/Epidemic Model with the impact of Media Reactions.sedml/plot_1_task1.pdf\nCompleted 44.0 KiB/46.6 KiB (388.9 KiB/s) with 1 file(s) remaining\rCompleted 46.6 KiB/46.6 KiB (404.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c909a62a8be53f8dd39/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Epidemic Model with the impact of Media Reactions-biopax2.owl  \n  inflating: contents/Epidemic Model with the impact of Media Reactions-biopax3.owl  \n  inflating: contents/Epidemic Model with the impact of Media Reactions-matlab.m  \n  inflating: contents/Epidemic Model with the impact of Media Reactions-octave.m  \n  inflating: contents/Epidemic Model with the impact of Media Reactions.cps  \n  inflating: contents/Epidemic Model with the impact of Media Reactions.ode  \n  inflating: contents/Epidemic Model with the impact of Media Reactions.sedml  \n  inflating: contents/Epidemic Model with the impact of Media Reactions.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 12.3 KiB/190.9 KiB (183.9 KiB/s) with 12 file(s) remaining\rupload: contents/Epidemic Model with the impact of Media Reactions-biopax2.owl to s3://files.biosimulations.org/simulations/64711c909a62a8be53f8dd39/contents/Epidemic Model with the impact of Media Reactions-biopax2.owl\nCompleted 12.3 KiB/190.9 KiB (183.9 KiB/s) with 11 file(s) remaining\rCompleted 18.0 KiB/190.9 KiB (149.0 KiB/s) with 11 file(s) remaining\rupload: contents/Epidemic Model with the impact of Media Reactions-matlab.m to s3://files.biosimulations.org/simulations/64711c909a62a8be53f8dd39/contents/Epidemic Model with the impact of Media Reactions-matlab.m\nCompleted 18.0 KiB/190.9 KiB (149.0 KiB/s) with 10 file(s) remaining\rCompleted 23.6 KiB/190.9 KiB (187.1 KiB/s) with 10 file(s) remaining\rupload: contents/Epidemic Model with the impact of Media Reactions-octave.m to s3://files.biosimulations.org/simulations/64711c909a62a8be53f8dd39/contents/Epidemic Model with the impact of Media Reactions-octave.m\nCompleted 23.6 KiB/190.9 KiB (187.1 KiB/s) with 9 file(s) remaining\rCompleted 40.4 KiB/190.9 KiB (316.6 KiB/s) with 9 file(s) remaining\rupload: contents/Epidemic Model with the impact of Media Reactions.sedml to s3://files.biosimulations.org/simulations/64711c909a62a8be53f8dd39/contents/Epidemic Model with the impact of Media Reactions.sedml\nCompleted 40.4 KiB/190.9 KiB (316.6 KiB/s) with 8 file(s) remaining\rCompleted 74.2 KiB/190.9 KiB (528.0 KiB/s) with 8 file(s) remaining\rupload: contents/Epidemic Model with the impact of Media Reactions.xml to s3://files.biosimulations.org/simulations/64711c909a62a8be53f8dd39/contents/Epidemic Model with the impact of Media Reactions.xml\nCompleted 74.2 KiB/190.9 KiB (528.0 KiB/s) with 7 file(s) remaining\rCompleted 100.1 KiB/190.9 KiB (706.5 KiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64711c909a62a8be53f8dd39/contents/curation_image.png\nCompleted 100.1 KiB/190.9 KiB (706.5 KiB/s) with 6 file(s) remaining\rCompleted 101.3 KiB/190.9 KiB (686.9 KiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711c909a62a8be53f8dd39/contents/metadata.rdf\nCompleted 101.3 KiB/190.9 KiB (686.9 KiB/s) with 5 file(s) remaining\rCompleted 103.0 KiB/190.9 KiB (655.9 KiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711c909a62a8be53f8dd39/contents/manifest.xml\nCompleted 103.0 KiB/190.9 KiB (655.9 KiB/s) with 4 file(s) remaining\rCompleted 168.2 KiB/190.9 KiB (963.6 KiB/s) with 4 file(s) remaining\rupload: contents/Epidemic Model with the impact of Media Reactions.cps to s3://files.biosimulations.org/simulations/64711c909a62a8be53f8dd39/contents/Epidemic Model with the impact of Media Reactions.cps\nCompleted 168.2 KiB/190.9 KiB (963.6 KiB/s) with 3 file(s) remaining\rCompleted 187.0 KiB/190.9 KiB (1003.5 KiB/s) with 3 file(s) remaining\rupload: contents/Epidemic Model with the impact of Media Reactions-biopax3.owl to s3://files.biosimulations.org/simulations/64711c909a62a8be53f8dd39/contents/Epidemic Model with the impact of Media Reactions-biopax3.owl\nCompleted 187.0 KiB/190.9 KiB (1003.5 KiB/s) with 2 file(s) remaining\rCompleted 187.2 KiB/190.9 KiB (868.0 KiB/s) with 2 file(s) remaining \rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711c909a62a8be53f8dd39/contents/curation_notes.txt\nCompleted 187.2 KiB/190.9 KiB (868.0 KiB/s) with 1 file(s) remaining\rCompleted 190.9 KiB/190.9 KiB (823.3 KiB/s) with 1 file(s) remaining\rupload: contents/Epidemic Model with the impact of Media Reactions.ode to s3://files.biosimulations.org/simulations/64711c909a62a8be53f8dd39/contents/Epidemic Model with the impact of Media Reactions.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.4 KiB/8.4 KiB (135.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c909a62a8be53f8dd39/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Epidemic Model with the impact of Media Reactions.sedml\ncreating dataset /Epidemic Model with the impact of Media Reactions.sedml/autogen_report_for_task1, shape: (29, 101), type: float64\ndataset created, uuid: d-0507fdf4-7d571e73-64b3-70a67e-c937d8, chunk_size: (29, 101)\ncreating dataset /Epidemic Model with the impact of Media Reactions.sedml/plot_1_task1, shape: (6, 101), type: float64\ndataset created, uuid: d-0507fdf4-7d571e73-2f26-515be6-ea4a58, chunk_size: (6, 101)\ncreating attribute combineArchiveLocation in /Epidemic Model with the impact of Media Reactions.sedml\ncreating attribute uri in /Epidemic Model with the impact of Media Reactions.sedml\ncreating attribute _type in /Epidemic Model with the impact of Media Reactions.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Epidemic Model with the impact of Media Reactions.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Epidemic Model with the impact of Media Reactions.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Epidemic Model with the impact of Media Reactions.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Epidemic Model with the impact of Media Reactions.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Epidemic Model with the impact of Media Reactions.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Epidemic Model with the impact of Media Reactions.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Epidemic Model with the impact of Media Reactions.sedml/autogen_report_for_task1\ncreating attribute uri in /Epidemic Model with the impact of Media Reactions.sedml/autogen_report_for_task1\ncreating attribute _type in /Epidemic Model with the impact of Media Reactions.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Epidemic Model with the impact of Media Reactions.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Epidemic Model with the impact of Media Reactions.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Epidemic Model with the impact of Media Reactions.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Epidemic Model with the impact of Media Reactions.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Epidemic Model with the impact of Media Reactions.sedml/plot_1_task1\ncreating attribute sedmlId in /Epidemic Model with the impact of Media Reactions.sedml/plot_1_task1\ncreating attribute sedmlName in /Epidemic Model with the impact of Media Reactions.sedml/plot_1_task1\ncreating attribute uri in /Epidemic Model with the impact of Media Reactions.sedml/plot_1_task1\ncreate_links: /\ngot link: Epidemic Model with the impact of Media Reactions.sedml\ncreate_links: /Epidemic Model with the impact of Media Reactions.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Epidemic Model with the impact of Media Reactions.sedml/autogen_report_for_task1 to tgt: /Epidemic Model with the impact of Media Reactions.sedml/autogen_report_for_task1, shape: (29, 101), type: float64\niterating over chunks for /Epidemic Model with the impact of Media Reactions.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 29, 1), slice(0, 101, 1))\ndone with dataload for /Epidemic Model with the impact of Media Reactions.sedml/autogen_report_for_task1\nwrite_dataset src: /Epidemic Model with the impact of Media Reactions.sedml/plot_1_task1 to tgt: /Epidemic Model with the impact of Media Reactions.sedml/plot_1_task1, shape: (6, 101), type: float64\niterating over chunks for /Epidemic Model with the impact of Media Reactions.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 101, 1))\ndone with dataload for /Epidemic Model with the impact of Media Reactions.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711c909a62a8be53f8dd39\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":1.259659,"sedDocuments":[{"location":"Epidemic Model with the impact of Media Reactions.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  Epidemic Model with the impact of Media Reactions.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 29 data sets\r\n    Plots (1):\r\n      plot_1_task1: 5 curves\r\n\r\nExecuting SED-ML file 1: Epidemic Model with the impact of Media Reactions.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":0.804104,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.222512,"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":0.364538,"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":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.076355,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_E","status":"SUCCEEDED"},{"id":"autogen_task1_I","status":"SUCCEEDED"},{"id":"autogen_task1_M","status":"SUCCEEDED"},{"id":"autogen_task1_N","status":"SUCCEEDED"},{"id":"autogen_task1_S","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_rho","status":"SUCCEEDED"},{"id":"autogen_task1_mu1","status":"SUCCEEDED"},{"id":"autogen_task1_mu2","status":"SUCCEEDED"},{"id":"autogen_task1_mu3","status":"SUCCEEDED"},{"id":"autogen_task1_alpha1","status":"SUCCEEDED"},{"id":"autogen_task1_alpha2","status":"SUCCEEDED"},{"id":"autogen_task1_tau","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_1","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_2","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_3","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_4","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_5","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_6","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_7","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_8","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_9","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_10","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_11","status":"SUCCEEDED"}]}]}]}