{"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    227      0 --:--:-- --:--:-- --:--:--   227\n\r100 25172  100 25172    0     0  35682      0 --:--:-- --:--:-- --:--:-- 35682\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 (30.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a315777b66696550567a7/rawLog.txt\nCompleted 4.2 KiB/4.2 KiB (60.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a315777b66696550567a7/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 77%)\n  adding: outputs/Tumor_cells_immune_system_competition.sedml/ (stored 0%)\n  adding: outputs/Tumor_cells_immune_system_competition.sedml/plot_1_task1.pdf (deflated 28%)\n  adding: outputs/reports.h5 (deflated 58%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 44.4 KiB/44.4 KiB (590.8 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a315777b66696550567a7/outputs/reports.h5\nCompleted 28.5 KiB/48.0 KiB (401.2 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a315777b66696550567a7/output.zip\nCompleted 28.5 KiB/48.0 KiB (401.2 KiB/s) with 3 file(s) remaining\rCompleted 35.5 KiB/48.0 KiB (365.4 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a315777b66696550567a7/outputs/plots.zip\nCompleted 35.5 KiB/48.0 KiB (365.4 KiB/s) with 2 file(s) remaining\rCompleted 45.4 KiB/48.0 KiB (456.6 KiB/s) with 2 file(s) remaining\rupload: outputs/Tumor_cells_immune_system_competition.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a315777b66696550567a7/outputs/Tumor_cells_immune_system_competition.sedml/plot_1_task1.pdf\nCompleted 45.4 KiB/48.0 KiB (456.6 KiB/s) with 1 file(s) remaining\rCompleted 48.0 KiB/48.0 KiB (429.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a315777b66696550567a7/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Tumor_cells_immune_system_competition-biopax2.owl  \n  inflating: contents/Tumor_cells_immune_system_competition-biopax3.owl  \n  inflating: contents/Tumor_cells_immune_system_competition-matlab.m  \n  inflating: contents/Tumor_cells_immune_system_competition-octave.m  \n  inflating: contents/Tumor_cells_immune_system_competition.cps  \n  inflating: contents/Tumor_cells_immune_system_competition.ode  \n  inflating: contents/Tumor_cells_immune_system_competition.sedml  \n  inflating: contents/Tumor_cells_immune_system_competition.xml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 16.9 KiB/237.8 KiB (231.7 KiB/s) with 10 file(s) remaining\rupload: contents/Tumor_cells_immune_system_competition-biopax2.owl to s3://files.biosimulations.org/simulations/647a315777b66696550567a7/contents/Tumor_cells_immune_system_competition-biopax2.owl\nCompleted 16.9 KiB/237.8 KiB (231.7 KiB/s) with 9 file(s) remaining\rCompleted 25.0 KiB/237.8 KiB (219.8 KiB/s) with 9 file(s) remaining\rupload: contents/Tumor_cells_immune_system_competition-matlab.m to s3://files.biosimulations.org/simulations/647a315777b66696550567a7/contents/Tumor_cells_immune_system_competition-matlab.m\nCompleted 25.0 KiB/237.8 KiB (219.8 KiB/s) with 8 file(s) remaining\rCompleted 26.3 KiB/237.8 KiB (225.3 KiB/s) with 8 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a315777b66696550567a7/contents/manifest.xml\nCompleted 26.3 KiB/237.8 KiB (225.3 KiB/s) with 7 file(s) remaining\rCompleted 27.6 KiB/237.8 KiB (219.7 KiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a315777b66696550567a7/contents/metadata.rdf\nCompleted 27.6 KiB/237.8 KiB (219.7 KiB/s) with 6 file(s) remaining\rCompleted 91.5 KiB/237.8 KiB (706.4 KiB/s) with 6 file(s) remaining\rupload: contents/Tumor_cells_immune_system_competition.xml to s3://files.biosimulations.org/simulations/647a315777b66696550567a7/contents/Tumor_cells_immune_system_competition.xml\nCompleted 91.5 KiB/237.8 KiB (706.4 KiB/s) with 5 file(s) remaining\rCompleted 99.5 KiB/237.8 KiB (753.5 KiB/s) with 5 file(s) remaining\rupload: contents/Tumor_cells_immune_system_competition-octave.m to s3://files.biosimulations.org/simulations/647a315777b66696550567a7/contents/Tumor_cells_immune_system_competition-octave.m\nCompleted 99.5 KiB/237.8 KiB (753.5 KiB/s) with 4 file(s) remaining\rCompleted 122.0 KiB/237.8 KiB (892.7 KiB/s) with 4 file(s) remaining\rupload: contents/Tumor_cells_immune_system_competition.sedml to s3://files.biosimulations.org/simulations/647a315777b66696550567a7/contents/Tumor_cells_immune_system_competition.sedml\nCompleted 122.0 KiB/237.8 KiB (892.7 KiB/s) with 3 file(s) remaining\rCompleted 146.9 KiB/237.8 KiB (1006.8 KiB/s) with 3 file(s) remaining\rupload: contents/Tumor_cells_immune_system_competition-biopax3.owl to s3://files.biosimulations.org/simulations/647a315777b66696550567a7/contents/Tumor_cells_immune_system_competition-biopax3.owl\nCompleted 146.9 KiB/237.8 KiB (1006.8 KiB/s) with 2 file(s) remaining\rCompleted 232.0 KiB/237.8 KiB (1.5 MiB/s) with 2 file(s) remaining   \rupload: contents/Tumor_cells_immune_system_competition.cps to s3://files.biosimulations.org/simulations/647a315777b66696550567a7/contents/Tumor_cells_immune_system_competition.cps\nCompleted 232.0 KiB/237.8 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 237.8 KiB/237.8 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: contents/Tumor_cells_immune_system_competition.ode to s3://files.biosimulations.org/simulations/647a315777b66696550567a7/contents/Tumor_cells_immune_system_competition.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.5 KiB/7.5 KiB (108.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a315777b66696550567a7/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Tumor_cells_immune_system_competition.sedml\ncreating dataset /Tumor_cells_immune_system_competition.sedml/autogen_report_for_task1, shape: (35, 101), type: float64\ndataset created, uuid: d-96c51569-ff192f6d-692e-89a642-f0329f, chunk_size: (35, 101)\ncreating dataset /Tumor_cells_immune_system_competition.sedml/plot_1_task1, shape: (4, 101), type: float64\ndataset created, uuid: d-96c51569-ff192f6d-a01d-a9cf2c-2dc5ce, chunk_size: (4, 101)\ncreating attribute combineArchiveLocation in /Tumor_cells_immune_system_competition.sedml\ncreating attribute uri in /Tumor_cells_immune_system_competition.sedml\ncreating attribute _type in /Tumor_cells_immune_system_competition.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Tumor_cells_immune_system_competition.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Tumor_cells_immune_system_competition.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Tumor_cells_immune_system_competition.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Tumor_cells_immune_system_competition.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Tumor_cells_immune_system_competition.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Tumor_cells_immune_system_competition.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Tumor_cells_immune_system_competition.sedml/autogen_report_for_task1\ncreating attribute uri in /Tumor_cells_immune_system_competition.sedml/autogen_report_for_task1\ncreating attribute _type in /Tumor_cells_immune_system_competition.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Tumor_cells_immune_system_competition.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Tumor_cells_immune_system_competition.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Tumor_cells_immune_system_competition.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Tumor_cells_immune_system_competition.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Tumor_cells_immune_system_competition.sedml/plot_1_task1\ncreating attribute sedmlId in /Tumor_cells_immune_system_competition.sedml/plot_1_task1\ncreating attribute sedmlName in /Tumor_cells_immune_system_competition.sedml/plot_1_task1\ncreating attribute uri in /Tumor_cells_immune_system_competition.sedml/plot_1_task1\ncreate_links: /\ngot link: Tumor_cells_immune_system_competition.sedml\ncreate_links: /Tumor_cells_immune_system_competition.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Tumor_cells_immune_system_competition.sedml/autogen_report_for_task1 to tgt: /Tumor_cells_immune_system_competition.sedml/autogen_report_for_task1, shape: (35, 101), type: float64\niterating over chunks for /Tumor_cells_immune_system_competition.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 35, 1), slice(0, 101, 1))\ndone with dataload for /Tumor_cells_immune_system_competition.sedml/autogen_report_for_task1\nwrite_dataset src: /Tumor_cells_immune_system_competition.sedml/plot_1_task1 to tgt: /Tumor_cells_immune_system_competition.sedml/plot_1_task1, shape: (4, 101), type: float64\niterating over chunks for /Tumor_cells_immune_system_competition.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 101, 1))\ndone with dataload for /Tumor_cells_immune_system_competition.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a315777b66696550567a7\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 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 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 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":0.965248,"sedDocuments":[{"location":"Tumor_cells_immune_system_competition.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  Tumor_cells_immune_system_competition.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 35 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Tumor_cells_immune_system_competition.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":0.595267,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.140194,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"deterministic"},{"key":"methodCode","value":22},{"key":"parameters","value":{"Absolute Tolerance":1e-12,"Integrate Reduced Model":false,"Max Internal Steps":100000,"Relative Tolerance":0.000001}}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.277379,"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":0.074724,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_I","status":"SUCCEEDED"},{"id":"autogen_task1_N","status":"SUCCEEDED"},{"id":"autogen_task1_T","status":"SUCCEEDED"},{"id":"autogen_task1_r","status":"SUCCEEDED"},{"id":"autogen_task1_beta1","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_alpha1","status":"SUCCEEDED"},{"id":"autogen_task1_alpha2","status":"SUCCEEDED"},{"id":"autogen_task1_beta2","status":"SUCCEEDED"},{"id":"autogen_task1_alpha3","status":"SUCCEEDED"},{"id":"autogen_task1_sigma","status":"SUCCEEDED"},{"id":"autogen_task1_delta","status":"SUCCEEDED"},{"id":"autogen_task1_rho","status":"SUCCEEDED"},{"id":"autogen_task1_m","status":"SUCCEEDED"},{"id":"autogen_task1_m1","status":"SUCCEEDED"},{"id":"autogen_task1_rho1","status":"SUCCEEDED"},{"id":"autogen_task1_mu","status":"SUCCEEDED"},{"id":"autogen_task1_mu1","status":"SUCCEEDED"},{"id":"autogen_task1_Tissue","status":"SUCCEEDED"},{"id":"autogen_task1_Normal_cell_proliferation","status":"SUCCEEDED"},{"id":"autogen_task1_division_of_normal_cells_into_abnormal_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Normal_cells_eradication_by_immune_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Normal_cells_eradication_or_inhibition_by_tumor_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_cells_proliferation","status":"SUCCEEDED"},{"id":"autogen_task1_decline_of_tumor_cells","status":"SUCCEEDED"},{"id":"autogen_task1_conversion_of_abnormal_cells_into_tumor_cells","status":"SUCCEEDED"},{"id":"autogen_task1_tumor_cell_eradication_or_inhibition_by_immune_cells","status":"SUCCEEDED"},{"id":"autogen_task1_constant_source_of_immune_system_response","status":"SUCCEEDED"},{"id":"autogen_task1_immune_cells_death","status":"SUCCEEDED"},{"id":"autogen_task1_elimination_of_tumor_cells_due_to_the_detection_of_their_appearance","status":"SUCCEEDED"},{"id":"autogen_task1_elimination_of_tumor_cells_due_to_the_detection_of_their_activity","status":"SUCCEEDED"},{"id":"autogen_task1_death_of_immune_cells_after_interaction_with_tumor","status":"SUCCEEDED"},{"id":"autogen_task1_suppression_of_immune_activity_by_tumor_cells","status":"SUCCEEDED"}]}]}]}