{"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    430      0 --:--:-- --:--:-- --:--:--   431\n\r100  111k  100  111k    0     0   248k      0 --:--:-- --:--:-- --:--:--  248k\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 3 outputs:\n    Tasks:\n      Succeeded: 1\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 (1):\n    Succeeded: 1\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 (22.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a309177b66696550534e3/rawLog.txt\nCompleted 4.3 KiB/4.3 KiB (56.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a309177b66696550534e3/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 80%)\n  adding: outputs/Sarkar2020.sedml/ (stored 0%)\n  adding: outputs/Sarkar2020.sedml/plot_2_task1.pdf (deflated 31%)\n  adding: outputs/Sarkar2020.sedml/plot_1_task1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 67%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 48.6 KiB/48.6 KiB (514.3 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a309177b66696550534e3/outputs/reports.h5\nCompleted 33.2 KiB/71.2 KiB (440.5 KiB/s) with 5 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a309177b66696550534e3/output.zip\nCompleted 33.2 KiB/71.2 KiB (440.5 KiB/s) with 4 file(s) remaining\rCompleted 43.1 KiB/71.2 KiB (376.2 KiB/s) with 4 file(s) remaining\rupload: outputs/Sarkar2020.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a309177b66696550534e3/outputs/Sarkar2020.sedml/plot_1_task1.pdf\nCompleted 43.1 KiB/71.2 KiB (376.2 KiB/s) with 3 file(s) remaining\rCompleted 57.2 KiB/71.2 KiB (486.7 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a309177b66696550534e3/outputs/plots.zip\nCompleted 57.2 KiB/71.2 KiB (486.7 KiB/s) with 2 file(s) remaining\rCompleted 59.9 KiB/71.2 KiB (463.2 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a309177b66696550534e3/rawLog.txt\nCompleted 59.9 KiB/71.2 KiB (463.2 KiB/s) with 1 file(s) remaining\rCompleted 71.2 KiB/71.2 KiB (518.7 KiB/s) with 1 file(s) remaining\rupload: outputs/Sarkar2020.sedml/plot_2_task1.pdf to s3://files.biosimulations.org/simulations/647a309177b66696550534e3/outputs/Sarkar2020.sedml/plot_2_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Sarkar2020-biopax2.owl  \n  inflating: contents/Sarkar2020-biopax3.owl  \n  inflating: contents/Sarkar2020-matlab.m  \n  inflating: contents/Sarkar2020-octave.m  \n  inflating: contents/Sarkar2020.cps  \n  inflating: contents/Sarkar2020.ode  \n  inflating: contents/Sarkar2020.sedml  \n  inflating: contents/Sarkar2020.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 34.4 KiB/357.4 KiB (431.5 KiB/s) with 12 file(s) remaining\rupload: contents/Sarkar2020-biopax3.owl to s3://files.biosimulations.org/simulations/647a309177b66696550534e3/contents/Sarkar2020-biopax3.owl\nCompleted 34.4 KiB/357.4 KiB (431.5 KiB/s) with 11 file(s) remaining\rCompleted 42.7 KiB/357.4 KiB (386.3 KiB/s) with 11 file(s) remaining\rupload: contents/Sarkar2020-matlab.m to s3://files.biosimulations.org/simulations/647a309177b66696550534e3/contents/Sarkar2020-matlab.m\nCompleted 42.7 KiB/357.4 KiB (386.3 KiB/s) with 10 file(s) remaining\rCompleted 65.2 KiB/357.4 KiB (481.3 KiB/s) with 10 file(s) remaining\rupload: contents/Sarkar2020.sedml to s3://files.biosimulations.org/simulations/647a309177b66696550534e3/contents/Sarkar2020.sedml\nCompleted 65.2 KiB/357.4 KiB (481.3 KiB/s) with 9 file(s) remaining\rCompleted 73.5 KiB/357.4 KiB (534.2 KiB/s) with 9 file(s) remaining\rupload: contents/Sarkar2020-octave.m to s3://files.biosimulations.org/simulations/647a309177b66696550534e3/contents/Sarkar2020-octave.m\nCompleted 73.5 KiB/357.4 KiB (534.2 KiB/s) with 8 file(s) remaining\rCompleted 73.7 KiB/357.4 KiB (528.0 KiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a309177b66696550534e3/contents/curation_notes.txt\nCompleted 73.7 KiB/357.4 KiB (528.0 KiB/s) with 7 file(s) remaining\rCompleted 75.0 KiB/357.4 KiB (524.6 KiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a309177b66696550534e3/contents/manifest.xml\nCompleted 75.0 KiB/357.4 KiB (524.6 KiB/s) with 6 file(s) remaining\rCompleted 96.6 KiB/357.4 KiB (640.3 KiB/s) with 6 file(s) remaining\rupload: contents/Sarkar2020-biopax2.owl to s3://files.biosimulations.org/simulations/647a309177b66696550534e3/contents/Sarkar2020-biopax2.owl\nCompleted 96.6 KiB/357.4 KiB (640.3 KiB/s) with 5 file(s) remaining\rCompleted 99.7 KiB/357.4 KiB (652.9 KiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a309177b66696550534e3/contents/metadata.rdf\nCompleted 99.7 KiB/357.4 KiB (652.9 KiB/s) with 4 file(s) remaining\rCompleted 189.1 KiB/357.4 KiB (1.2 MiB/s) with 4 file(s) remaining \rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a309177b66696550534e3/contents/curation_image.png\nCompleted 189.1 KiB/357.4 KiB (1.2 MiB/s) with 3 file(s) remaining\rCompleted 194.7 KiB/357.4 KiB (1.1 MiB/s) with 3 file(s) remaining\rupload: contents/Sarkar2020.ode to s3://files.biosimulations.org/simulations/647a309177b66696550534e3/contents/Sarkar2020.ode\nCompleted 194.7 KiB/357.4 KiB (1.1 MiB/s) with 2 file(s) remaining\rCompleted 258.3 KiB/357.4 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: contents/Sarkar2020.xml to s3://files.biosimulations.org/simulations/647a309177b66696550534e3/contents/Sarkar2020.xml\nCompleted 258.3 KiB/357.4 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 357.4 KiB/357.4 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: contents/Sarkar2020.cps to s3://files.biosimulations.org/simulations/647a309177b66696550534e3/contents/Sarkar2020.cps\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.7 KiB/7.7 KiB (114.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a309177b66696550534e3/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Sarkar2020.sedml\ncreating dataset /Sarkar2020.sedml/autogen_report_for_task1, shape: (36, 91), type: float64\ndataset created, uuid: d-38cf28ae-dbdd89eb-d1ac-fc5185-fcfeef, chunk_size: (36, 91)\ncreating dataset /Sarkar2020.sedml/plot_1_task1, shape: (2, 91), type: float64\ndataset created, uuid: d-38cf28ae-dbdd89eb-0071-341797-68ab18, chunk_size: (2, 91)\ncreating dataset /Sarkar2020.sedml/plot_2_task1, shape: (2, 91), type: float64\ndataset created, uuid: d-38cf28ae-dbdd89eb-e251-a5dadf-9ca3c7, chunk_size: (2, 91)\ncreating attribute combineArchiveLocation in /Sarkar2020.sedml\ncreating attribute uri in /Sarkar2020.sedml\ncreating attribute _type in /Sarkar2020.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Sarkar2020.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Sarkar2020.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Sarkar2020.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Sarkar2020.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Sarkar2020.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Sarkar2020.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Sarkar2020.sedml/autogen_report_for_task1\ncreating attribute uri in /Sarkar2020.sedml/autogen_report_for_task1\ncreating attribute _type in /Sarkar2020.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Sarkar2020.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Sarkar2020.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Sarkar2020.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Sarkar2020.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Sarkar2020.sedml/plot_1_task1\ncreating attribute sedmlId in /Sarkar2020.sedml/plot_1_task1\ncreating attribute sedmlName in /Sarkar2020.sedml/plot_1_task1\ncreating attribute uri in /Sarkar2020.sedml/plot_1_task1\ncreating attribute _type in /Sarkar2020.sedml/plot_2_task1\ncreating attribute sedmlDataSetDataTypes in /Sarkar2020.sedml/plot_2_task1\ncreating attribute sedmlDataSetIds in /Sarkar2020.sedml/plot_2_task1\ncreating attribute sedmlDataSetLabels in /Sarkar2020.sedml/plot_2_task1\ncreating attribute sedmlDataSetNames in /Sarkar2020.sedml/plot_2_task1\ncreating attribute sedmlDataSetShapes in /Sarkar2020.sedml/plot_2_task1\ncreating attribute sedmlId in /Sarkar2020.sedml/plot_2_task1\ncreating attribute sedmlName in /Sarkar2020.sedml/plot_2_task1\ncreating attribute uri in /Sarkar2020.sedml/plot_2_task1\ncreate_links: /\ngot link: Sarkar2020.sedml\ncreate_links: /Sarkar2020.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\ngot link: plot_2_task1\nwrite_dataset src: /Sarkar2020.sedml/autogen_report_for_task1 to tgt: /Sarkar2020.sedml/autogen_report_for_task1, shape: (36, 91), type: float64\niterating over chunks for /Sarkar2020.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 36, 1), slice(0, 91, 1))\ndone with dataload for /Sarkar2020.sedml/autogen_report_for_task1\nwrite_dataset src: /Sarkar2020.sedml/plot_1_task1 to tgt: /Sarkar2020.sedml/plot_1_task1, shape: (2, 91), type: float64\niterating over chunks for /Sarkar2020.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 91, 1))\ndone with dataload for /Sarkar2020.sedml/plot_1_task1\nwrite_dataset src: /Sarkar2020.sedml/plot_2_task1 to tgt: /Sarkar2020.sedml/plot_2_task1, shape: (2, 91), type: float64\niterating over chunks for /Sarkar2020.sedml/plot_2_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 91, 1))\ndone with dataload for /Sarkar2020.sedml/plot_2_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a309177b66696550534e3\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 SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata 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":18.72309,"sedDocuments":[{"location":"Sarkar2020.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 2 plots:\r\n  Sarkar2020.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 36 data sets\r\n    Plots (2):\r\n      plot_1_task1: 1 curves\r\n      plot_2_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: Sarkar2020.sedml ...\r\n  Found 1 tasks and 3 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_report_for_task1`\r\n      `plot_1_task1`\r\n      `plot_2_task1`\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_1_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `plot_2_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 3: `autogen_report_for_task1` ...","duration":18.380511,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":17.821929,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.171558,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"}]},{"id":"plot_2_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.129273,"curves":[{"id":"p2_curve_1_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.081378,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Infected","status":"SUCCEEDED"},{"id":"autogen_task1_Cumulative_cases","status":"SUCCEEDED"},{"id":"autogen_task1_Susceptible","status":"SUCCEEDED"},{"id":"autogen_task1_Asymptomatic","status":"SUCCEEDED"},{"id":"autogen_task1_Susceptible_quarantined","status":"SUCCEEDED"},{"id":"autogen_task1_Exposed_quarantined","status":"SUCCEEDED"},{"id":"autogen_task1_Recovered","status":"SUCCEEDED"},{"id":"autogen_task1_lambda_s","status":"SUCCEEDED"},{"id":"autogen_task1_beta_s","status":"SUCCEEDED"},{"id":"autogen_task1_rho_s","status":"SUCCEEDED"},{"id":"autogen_task1_epsilon_s","status":"SUCCEEDED"},{"id":"autogen_task1_delta","status":"SUCCEEDED"},{"id":"autogen_task1_m_s","status":"SUCCEEDED"},{"id":"autogen_task1_gamma_a","status":"SUCCEEDED"},{"id":"autogen_task1_xi_a","status":"SUCCEEDED"},{"id":"autogen_task1_gamma_i","status":"SUCCEEDED"},{"id":"autogen_task1_xi_i","status":"SUCCEEDED"},{"id":"autogen_task1_xi_q","status":"SUCCEEDED"},{"id":"autogen_task1_Total_population","status":"SUCCEEDED"},{"id":"autogen_task1_Wuhan","status":"SUCCEEDED"},{"id":"autogen_task1_Susceptible_to_Susceptible_quarantined","status":"SUCCEEDED"},{"id":"autogen_task1_Infected_to_Recovered","status":"SUCCEEDED"},{"id":"autogen_task1_Susceptible_quarantined_to_Susceptible","status":"SUCCEEDED"},{"id":"autogen_task1_Susceptible_to_Deceased","status":"SUCCEEDED"},{"id":"autogen_task1_Susceptible_quarantined_to_Deceased","status":"SUCCEEDED"},{"id":"autogen_task1_Susceptible_to_Asymptomatic","status":"SUCCEEDED"},{"id":"autogen_task1_Susceptible_to_Infected_quarantined","status":"SUCCEEDED"},{"id":"autogen_task1_Asymptomatic_to_Infected","status":"SUCCEEDED"},{"id":"autogen_task1_Asymptomatic_to_Recovered","status":"SUCCEEDED"},{"id":"autogen_task1_Asymptomatic_to_Deceased","status":"SUCCEEDED"},{"id":"autogen_task1_Infected_to_Deceased","status":"SUCCEEDED"},{"id":"autogen_task1_Infected_to_Infected_quarantined","status":"SUCCEEDED"},{"id":"autogen_task1_Infected_quarantined_to_Recovered","status":"SUCCEEDED"},{"id":"autogen_task1_Infected_quarantined_to_Deceased","status":"SUCCEEDED"},{"id":"autogen_task1_Recovered_to_Deceased","status":"SUCCEEDED"}]}]}]}