{"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    426      0 --:--:-- --:--:-- --:--:--   427\n\r100  160k  100  160k    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 2 tasks and 3 outputs:\n    Tasks:\n      Succeeded: 2\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 (2):\n    Succeeded: 2\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 (22.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711f140dcacb55678d4963/rawLog.txt\nCompleted 5.0 KiB/5.0 KiB (80.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711f140dcacb55678d4963/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/Mwalili2020.sedml/ (stored 0%)\n  adding: outputs/Mwalili2020.sedml/plot_4_task2.pdf (deflated 25%)\n  adding: outputs/Mwalili2020.sedml/plot_3_task2.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 65%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 136.4 KiB/136.4 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711f140dcacb55678d4963/outputs/reports.h5\nCompleted 18.7 KiB/125.7 KiB (252.6 KiB/s) with 5 file(s) remaining\rupload: outputs/Mwalili2020.sedml/plot_4_task2.pdf to s3://files.biosimulations.org/simulations/64711f140dcacb55678d4963/outputs/Mwalili2020.sedml/plot_4_task2.pdf\nCompleted 18.7 KiB/125.7 KiB (252.6 KiB/s) with 4 file(s) remaining\rCompleted 29.9 KiB/125.7 KiB (260.6 KiB/s) with 4 file(s) remaining\rupload: outputs/Mwalili2020.sedml/plot_3_task2.pdf to s3://files.biosimulations.org/simulations/64711f140dcacb55678d4963/outputs/Mwalili2020.sedml/plot_3_task2.pdf\nCompleted 29.9 KiB/125.7 KiB (260.6 KiB/s) with 3 file(s) remaining\rCompleted 51.0 KiB/125.7 KiB (411.6 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711f140dcacb55678d4963/outputs/plots.zip\nCompleted 51.0 KiB/125.7 KiB (411.6 KiB/s) with 2 file(s) remaining\rCompleted 53.7 KiB/125.7 KiB (409.7 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711f140dcacb55678d4963/rawLog.txt\nCompleted 53.7 KiB/125.7 KiB (409.7 KiB/s) with 1 file(s) remaining\rCompleted 125.7 KiB/125.7 KiB (523.6 KiB/s) with 1 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711f140dcacb55678d4963/output.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Mwalili2020-biopax2.owl  \n  inflating: contents/Mwalili2020-biopax3.owl  \n  inflating: contents/Mwalili2020-matlab.m  \n  inflating: contents/Mwalili2020-octave.m  \n  inflating: contents/Mwalili2020.cps  \n  inflating: contents/Mwalili2020.ode  \n  inflating: contents/Mwalili2020.sedml  \n  inflating: contents/Mwalili2020.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 32.3 KiB/412.9 KiB (432.7 KiB/s) with 12 file(s) remaining\rupload: contents/Mwalili2020-biopax3.owl to s3://files.biosimulations.org/simulations/64711f140dcacb55678d4963/contents/Mwalili2020-biopax3.owl\nCompleted 32.3 KiB/412.9 KiB (432.7 KiB/s) with 11 file(s) remaining\rCompleted 40.1 KiB/412.9 KiB (314.0 KiB/s) with 11 file(s) remaining\rupload: contents/Mwalili2020-matlab.m to s3://files.biosimulations.org/simulations/64711f140dcacb55678d4963/contents/Mwalili2020-matlab.m\nCompleted 40.1 KiB/412.9 KiB (314.0 KiB/s) with 10 file(s) remaining\rCompleted 61.7 KiB/412.9 KiB (460.1 KiB/s) with 10 file(s) remaining\rupload: contents/Mwalili2020-biopax2.owl to s3://files.biosimulations.org/simulations/64711f140dcacb55678d4963/contents/Mwalili2020-biopax2.owl\nCompleted 61.7 KiB/412.9 KiB (460.1 KiB/s) with 9 file(s) remaining\rCompleted 85.6 KiB/412.9 KiB (583.5 KiB/s) with 9 file(s) remaining\rupload: contents/Mwalili2020.sedml to s3://files.biosimulations.org/simulations/64711f140dcacb55678d4963/contents/Mwalili2020.sedml\nCompleted 85.6 KiB/412.9 KiB (583.5 KiB/s) with 8 file(s) remaining\rCompleted 85.8 KiB/412.9 KiB (577.3 KiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711f140dcacb55678d4963/contents/curation_notes.txt\nCompleted 85.8 KiB/412.9 KiB (577.3 KiB/s) with 7 file(s) remaining\rCompleted 88.2 KiB/412.9 KiB (586.5 KiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711f140dcacb55678d4963/contents/metadata.rdf\nCompleted 88.2 KiB/412.9 KiB (586.5 KiB/s) with 6 file(s) remaining\rCompleted 95.9 KiB/412.9 KiB (626.9 KiB/s) with 6 file(s) remaining\rupload: contents/Mwalili2020-octave.m to s3://files.biosimulations.org/simulations/64711f140dcacb55678d4963/contents/Mwalili2020-octave.m\nCompleted 95.9 KiB/412.9 KiB (626.9 KiB/s) with 5 file(s) remaining\rCompleted 232.7 KiB/412.9 KiB (1.4 MiB/s) with 5 file(s) remaining \rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64711f140dcacb55678d4963/contents/curation_image.png\nCompleted 232.7 KiB/412.9 KiB (1.4 MiB/s) with 4 file(s) remaining\rCompleted 234.1 KiB/412.9 KiB (1.3 MiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711f140dcacb55678d4963/contents/manifest.xml\nCompleted 234.1 KiB/412.9 KiB (1.3 MiB/s) with 3 file(s) remaining\rCompleted 305.2 KiB/412.9 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: contents/Mwalili2020.xml to s3://files.biosimulations.org/simulations/64711f140dcacb55678d4963/contents/Mwalili2020.xml\nCompleted 305.2 KiB/412.9 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 310.6 KiB/412.9 KiB (1.5 MiB/s) with 2 file(s) remaining\rupload: contents/Mwalili2020.ode to s3://files.biosimulations.org/simulations/64711f140dcacb55678d4963/contents/Mwalili2020.ode\nCompleted 310.6 KiB/412.9 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 412.9 KiB/412.9 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: contents/Mwalili2020.cps to s3://files.biosimulations.org/simulations/64711f140dcacb55678d4963/contents/Mwalili2020.cps\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.7 KiB/7.7 KiB (111.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711f140dcacb55678d4963/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Mwalili2020.sedml\ncreating dataset /Mwalili2020.sedml/autogen_report_for_task2, shape: (38, 11, 1, 101), type: float64\ndataset created, uuid: d-08610ae4-ac6c93f6-cb9e-fcab02-563df9, chunk_size: (38, 11, 1, 101)\ncreating dataset /Mwalili2020.sedml/plot_3_task2, shape: (2, 11, 1, 101), type: float64\ndataset created, uuid: d-08610ae4-ac6c93f6-c93a-4eb801-e4538f, chunk_size: (2, 11, 1, 101)\ncreating dataset /Mwalili2020.sedml/plot_4_task2, shape: (6, 11, 1, 101), type: float64\ndataset created, uuid: d-08610ae4-ac6c93f6-a5ec-ec2efa-b73044, chunk_size: (6, 11, 1, 101)\ncreating attribute combineArchiveLocation in /Mwalili2020.sedml\ncreating attribute uri in /Mwalili2020.sedml\ncreating attribute _type in /Mwalili2020.sedml/autogen_report_for_task2\ncreating attribute sedmlDataSetDataTypes in /Mwalili2020.sedml/autogen_report_for_task2\ncreating attribute sedmlDataSetIds in /Mwalili2020.sedml/autogen_report_for_task2\ncreating attribute sedmlDataSetLabels in /Mwalili2020.sedml/autogen_report_for_task2\ncreating attribute sedmlDataSetNames in /Mwalili2020.sedml/autogen_report_for_task2\ncreating attribute sedmlDataSetShapes in /Mwalili2020.sedml/autogen_report_for_task2\ncreating attribute sedmlId in /Mwalili2020.sedml/autogen_report_for_task2\ncreating attribute sedmlName in /Mwalili2020.sedml/autogen_report_for_task2\ncreating attribute uri in /Mwalili2020.sedml/autogen_report_for_task2\ncreating attribute _type in /Mwalili2020.sedml/plot_3_task2\ncreating attribute sedmlDataSetDataTypes in /Mwalili2020.sedml/plot_3_task2\ncreating attribute sedmlDataSetIds in /Mwalili2020.sedml/plot_3_task2\ncreating attribute sedmlDataSetLabels in /Mwalili2020.sedml/plot_3_task2\ncreating attribute sedmlDataSetNames in /Mwalili2020.sedml/plot_3_task2\ncreating attribute sedmlDataSetShapes in /Mwalili2020.sedml/plot_3_task2\ncreating attribute sedmlId in /Mwalili2020.sedml/plot_3_task2\ncreating attribute sedmlName in /Mwalili2020.sedml/plot_3_task2\ncreating attribute uri in /Mwalili2020.sedml/plot_3_task2\ncreating attribute _type in /Mwalili2020.sedml/plot_4_task2\ncreating attribute sedmlDataSetDataTypes in /Mwalili2020.sedml/plot_4_task2\ncreating attribute sedmlDataSetIds in /Mwalili2020.sedml/plot_4_task2\ncreating attribute sedmlDataSetLabels in /Mwalili2020.sedml/plot_4_task2\ncreating attribute sedmlDataSetNames in /Mwalili2020.sedml/plot_4_task2\ncreating attribute sedmlDataSetShapes in /Mwalili2020.sedml/plot_4_task2\ncreating attribute sedmlId in /Mwalili2020.sedml/plot_4_task2\ncreating attribute sedmlName in /Mwalili2020.sedml/plot_4_task2\ncreating attribute uri in /Mwalili2020.sedml/plot_4_task2\ncreate_links: /\ngot link: Mwalili2020.sedml\ncreate_links: /Mwalili2020.sedml\ngot link: autogen_report_for_task2\ngot link: plot_3_task2\ngot link: plot_4_task2\nwrite_dataset src: /Mwalili2020.sedml/autogen_report_for_task2 to tgt: /Mwalili2020.sedml/autogen_report_for_task2, shape: (38, 11, 1, 101), type: float64\niterating over chunks for /Mwalili2020.sedml/autogen_report_for_task2\nwriting dataset data for slice: (slice(0, 38, 1), slice(0, 11, 1), slice(0, 1, 1), slice(0, 101, 1))\ndone with dataload for /Mwalili2020.sedml/autogen_report_for_task2\nwrite_dataset src: /Mwalili2020.sedml/plot_3_task2 to tgt: /Mwalili2020.sedml/plot_3_task2, shape: (2, 11, 1, 101), type: float64\niterating over chunks for /Mwalili2020.sedml/plot_3_task2\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 11, 1), slice(0, 1, 1), slice(0, 101, 1))\ndone with dataload for /Mwalili2020.sedml/plot_3_task2\nwrite_dataset src: /Mwalili2020.sedml/plot_4_task2 to tgt: /Mwalili2020.sedml/plot_4_task2, shape: (6, 11, 1, 101), type: float64\niterating over chunks for /Mwalili2020.sedml/plot_4_task2\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 11, 1), slice(0, 1, 1), slice(0, 101, 1))\ndone with dataload for /Mwalili2020.sedml/plot_4_task2\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711f140dcacb55678d4963\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mRetrieve 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.\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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":139.684928,"sedDocuments":[{"location":"Mwalili2020.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 1 reports, and 2 plots:\r\n  Mwalili2020.sedml:\r\n    Tasks (2):\r\n      task1\r\n      task2\r\n    Reports (1):\r\n      autogen_report_for_task2: 38 data sets\r\n    Plots (2):\r\n      plot_3_task2: 1 curves\r\n      plot_4_task2: 5 curves\r\n\r\nExecuting SED-ML file 1: Mwalili2020.sedml ...\r\n  Found 2 tasks and 3 outputs:\r\n    Tasks:\r\n      `task1`\r\n      `task2`\r\n    Outputs:\r\n      `autogen_report_for_task2`\r\n      `plot_3_task2`\r\n      `plot_4_task2`\r\n  Executing task 1: `task1`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 3 outputs ...\r\n      Generating output 1: `plot_3_task2` ... \u001b[36mqueued\u001b[0m\r\n      Generating output 2: `plot_4_task2` ... \u001b[36mqueued\u001b[0m\r\n      Generating output 3: `autogen_report_for_task2` ... \u001b[36mqueued\u001b[0m\r\n  Executing task 2: `task2`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 3 outputs ...\r\n      Generating output 1: `plot_3_task2` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `plot_4_task2` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 3: `autogen_report_for_task2` ...","duration":139.256765,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":8.860422,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]},{"id":"task2","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":128.741568,"algorithm":null,"simulatorDetails":null}],"outputs":[{"id":"plot_3_task2","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.18698,"curves":[{"id":"p1_curve_1_task2","status":"SUCCEEDED"}]},{"id":"plot_4_task2","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.30668,"curves":[{"id":"p2_curve_1_task2","status":"SUCCEEDED"},{"id":"p2_curve_2_task2","status":"SUCCEEDED"},{"id":"p2_curve_3_task2","status":"SUCCEEDED"},{"id":"p2_curve_4_task2","status":"SUCCEEDED"},{"id":"p2_curve_5_task2","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task2","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.325791,"dataSets":[{"id":"autogen_time_for_task2","status":"SUCCEEDED"},{"id":"autogen_task2_Pathogen_0","status":"SUCCEEDED"},{"id":"autogen_task2_Susceptible","status":"SUCCEEDED"},{"id":"autogen_task2_Exposed","status":"SUCCEEDED"},{"id":"autogen_task2_Infected_Symptomatic","status":"SUCCEEDED"},{"id":"autogen_task2_Infected_Asymptomatic","status":"SUCCEEDED"},{"id":"autogen_task2_Recovered","status":"SUCCEEDED"},{"id":"autogen_task2_alpha_1","status":"SUCCEEDED"},{"id":"autogen_task2_alpha_2","status":"SUCCEEDED"},{"id":"autogen_task2_b","status":"SUCCEEDED"},{"id":"autogen_task2_mu","status":"SUCCEEDED"},{"id":"autogen_task2_mu_p","status":"SUCCEEDED"},{"id":"autogen_task2_beta_1","status":"SUCCEEDED"},{"id":"autogen_task2_beta_2","status":"SUCCEEDED"},{"id":"autogen_task2_delta","status":"SUCCEEDED"},{"id":"autogen_task2_psi","status":"SUCCEEDED"},{"id":"autogen_task2_omega","status":"SUCCEEDED"},{"id":"autogen_task2_sigma","status":"SUCCEEDED"},{"id":"autogen_task2_gamma_S","status":"SUCCEEDED"},{"id":"autogen_task2_gamma_A","status":"SUCCEEDED"},{"id":"autogen_task2_eta_S","status":"SUCCEEDED"},{"id":"autogen_task2_eta_A","status":"SUCCEEDED"},{"id":"autogen_task2_Human","status":"SUCCEEDED"},{"id":"autogen_task2_Pathogen","status":"SUCCEEDED"},{"id":"autogen_task2_Birth_Rate","status":"SUCCEEDED"},{"id":"autogen_task2_Exposed_to_Susceptible","status":"SUCCEEDED"},{"id":"autogen_task2_Susceptible_to_Exposed","status":"SUCCEEDED"},{"id":"autogen_task2_Death_rate_Susceptible","status":"SUCCEEDED"},{"id":"autogen_task2_Death_rate_Exposed","status":"SUCCEEDED"},{"id":"autogen_task2_Symptomatic_infection_from_Exposed","status":"SUCCEEDED"},{"id":"autogen_task2_Asymptomatic_infection_from_Exposed","status":"SUCCEEDED"},{"id":"autogen_task2_Death_rate_Symptomatic_infected","status":"SUCCEEDED"},{"id":"autogen_task2_Death_rate_Asymptomatic_infected","status":"SUCCEEDED"},{"id":"autogen_task2_Recovery_from_Symptomatic_infection","status":"SUCCEEDED"},{"id":"autogen_task2_Recovery_from_Asymptomatic_infection","status":"SUCCEEDED"},{"id":"autogen_task2_Death_rate_Recovered","status":"SUCCEEDED"},{"id":"autogen_task2_Rate_of_pathogen_increase","status":"SUCCEEDED"},{"id":"autogen_task2_Death_rate_of_Pathogen","status":"SUCCEEDED"}]}]}]}