{"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    458      0 --:--:-- --:--:-- --:--:--   458\n\r100  100k  100  100k    0     0   165k      0 --:--:-- --:--:-- --:--:--  165k\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 (22.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/rawLog.txt\nCompleted 3.4 KiB/3.4 KiB (38.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/Malinzi2018 - tumour-immune interaction model.sedml/ (stored 0%)\n  adding: outputs/Malinzi2018 - tumour-immune interaction model.sedml/plot_1_task1.pdf (deflated 31%)\n  adding: outputs/log.yml (deflated 76%)\n  adding: outputs/reports.h5 (deflated 63%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 41.8 KiB/41.8 KiB (572.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/outputs/reports.h5\nCompleted 26.7 KiB/50.5 KiB (375.5 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/output.zip\nCompleted 26.7 KiB/50.5 KiB (375.5 KiB/s) with 3 file(s) remaining\rCompleted 35.2 KiB/50.5 KiB (299.6 KiB/s) with 3 file(s) remaining\rCompleted 37.9 KiB/50.5 KiB (316.8 KiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/rawLog.txt\nCompleted 37.9 KiB/50.5 KiB (316.8 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/outputs/plots.zip\nCompleted 37.9 KiB/50.5 KiB (316.8 KiB/s) with 1 file(s) remaining\rCompleted 50.5 KiB/50.5 KiB (412.1 KiB/s) with 1 file(s) remaining\rupload: outputs/Malinzi2018 - tumour-immune interaction model.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/outputs/Malinzi2018 - tumour-immune interaction model.sedml/plot_1_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Malinzi2018 - tumour-immune interaction model-biopax2.owl  \n  inflating: contents/Malinzi2018 - tumour-immune interaction model-biopax3.owl  \n  inflating: contents/Malinzi2018 - tumour-immune interaction model-matlab.m  \n  inflating: contents/Malinzi2018 - tumour-immune interaction model-octave.m  \n  inflating: contents/Malinzi2018 - tumour-immune interaction model.cps  \n  inflating: contents/Malinzi2018 - tumour-immune interaction model.ode  \n  inflating: contents/Malinzi2018 - tumour-immune interaction model.sedml  \n  inflating: contents/Malinzi2018 - tumour-immune interaction model.xml  \n  inflating: contents/call_mvb.m     \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/figure 2.png   \n  inflating: contents/metadata.rdf   \n  inflating: contents/mvb.m          \n  inflating: contents/manifest.xml   \nCompleted 16.2 KiB/287.6 KiB (212.4 KiB/s) with 15 file(s) remaining\rupload: contents/Malinzi2018 - tumour-immune interaction model-biopax3.owl to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/contents/Malinzi2018 - tumour-immune interaction model-biopax3.owl\nCompleted 16.2 KiB/287.6 KiB (212.4 KiB/s) with 14 file(s) remaining\rCompleted 27.8 KiB/287.6 KiB (245.4 KiB/s) with 14 file(s) remaining\rupload: contents/Malinzi2018 - tumour-immune interaction model-biopax2.owl to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/contents/Malinzi2018 - tumour-immune interaction model-biopax2.owl\nCompleted 27.8 KiB/287.6 KiB (245.4 KiB/s) with 13 file(s) remaining\rCompleted 34.0 KiB/287.6 KiB (287.9 KiB/s) with 13 file(s) remaining\rupload: contents/Malinzi2018 - tumour-immune interaction model-matlab.m to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/contents/Malinzi2018 - tumour-immune interaction model-matlab.m\nCompleted 34.0 KiB/287.6 KiB (287.9 KiB/s) with 12 file(s) remaining\rCompleted 40.1 KiB/287.6 KiB (324.5 KiB/s) with 12 file(s) remaining\rupload: contents/Malinzi2018 - tumour-immune interaction model-octave.m to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/contents/Malinzi2018 - tumour-immune interaction model-octave.m\nCompleted 40.1 KiB/287.6 KiB (324.5 KiB/s) with 11 file(s) remaining\rCompleted 40.6 KiB/287.6 KiB (294.1 KiB/s) with 11 file(s) remaining\rupload: contents/mvb.m to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/contents/mvb.m\nCompleted 40.6 KiB/287.6 KiB (294.1 KiB/s) with 10 file(s) remaining\rCompleted 43.2 KiB/287.6 KiB (303.7 KiB/s) with 10 file(s) remaining\rupload: contents/call_mvb.m to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/contents/call_mvb.m\nCompleted 43.2 KiB/287.6 KiB (303.7 KiB/s) with 9 file(s) remaining\rCompleted 43.6 KiB/287.6 KiB (296.4 KiB/s) with 9 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/contents/curation_notes.txt\nCompleted 43.6 KiB/287.6 KiB (296.4 KiB/s) with 8 file(s) remaining\rCompleted 90.7 KiB/287.6 KiB (574.3 KiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/contents/curation_image.png\nCompleted 90.7 KiB/287.6 KiB (574.3 KiB/s) with 7 file(s) remaining\rCompleted 106.7 KiB/287.6 KiB (633.0 KiB/s) with 7 file(s) remaining\rupload: contents/Malinzi2018 - tumour-immune interaction model.sedml to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/contents/Malinzi2018 - tumour-immune interaction model.sedml\nCompleted 106.7 KiB/287.6 KiB (633.0 KiB/s) with 6 file(s) remaining\rCompleted 153.8 KiB/287.6 KiB (868.2 KiB/s) with 6 file(s) remaining\rupload: contents/figure 2.png to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/contents/figure 2.png\nCompleted 153.8 KiB/287.6 KiB (868.2 KiB/s) with 5 file(s) remaining\rCompleted 155.7 KiB/287.6 KiB (866.9 KiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/contents/manifest.xml\nCompleted 155.7 KiB/287.6 KiB (866.9 KiB/s) with 4 file(s) remaining\rCompleted 158.1 KiB/287.6 KiB (865.6 KiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/contents/metadata.rdf\nCompleted 158.1 KiB/287.6 KiB (865.6 KiB/s) with 3 file(s) remaining\rCompleted 212.8 KiB/287.6 KiB (1.1 MiB/s) with 3 file(s) remaining  \rupload: contents/Malinzi2018 - tumour-immune interaction model.xml to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/contents/Malinzi2018 - tumour-immune interaction model.xml\nCompleted 212.8 KiB/287.6 KiB (1.1 MiB/s) with 2 file(s) remaining\rCompleted 283.3 KiB/287.6 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: contents/Malinzi2018 - tumour-immune interaction model.cps to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/contents/Malinzi2018 - tumour-immune interaction model.cps\nCompleted 283.3 KiB/287.6 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 287.6 KiB/287.6 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: contents/Malinzi2018 - tumour-immune interaction model.ode to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/contents/Malinzi2018 - tumour-immune interaction model.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.2 KiB/9.2 KiB (143.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711d730dcacb55678cead0/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Malinzi2018 - tumour-immune interaction model.sedml\ncreating dataset /Malinzi2018 - tumour-immune interaction model.sedml/autogen_report_for_task1, shape: (28, 101), type: float64\ndataset created, uuid: d-34a40526-b8b016c3-ef5b-d88cfa-c4fb32, chunk_size: (28, 101)\ncreating dataset /Malinzi2018 - tumour-immune interaction model.sedml/plot_1_task1, shape: (3, 101), type: float64\ndataset created, uuid: d-34a40526-b8b016c3-bff9-24df03-0a7edc, chunk_size: (3, 101)\ncreating attribute combineArchiveLocation in /Malinzi2018 - tumour-immune interaction model.sedml\ncreating attribute uri in /Malinzi2018 - tumour-immune interaction model.sedml\ncreating attribute _type in /Malinzi2018 - tumour-immune interaction model.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Malinzi2018 - tumour-immune interaction model.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Malinzi2018 - tumour-immune interaction model.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Malinzi2018 - tumour-immune interaction model.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Malinzi2018 - tumour-immune interaction model.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Malinzi2018 - tumour-immune interaction model.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Malinzi2018 - tumour-immune interaction model.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Malinzi2018 - tumour-immune interaction model.sedml/autogen_report_for_task1\ncreating attribute uri in /Malinzi2018 - tumour-immune interaction model.sedml/autogen_report_for_task1\ncreating attribute _type in /Malinzi2018 - tumour-immune interaction model.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Malinzi2018 - tumour-immune interaction model.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Malinzi2018 - tumour-immune interaction model.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Malinzi2018 - tumour-immune interaction model.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Malinzi2018 - tumour-immune interaction model.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Malinzi2018 - tumour-immune interaction model.sedml/plot_1_task1\ncreating attribute sedmlId in /Malinzi2018 - tumour-immune interaction model.sedml/plot_1_task1\ncreating attribute sedmlName in /Malinzi2018 - tumour-immune interaction model.sedml/plot_1_task1\ncreating attribute uri in /Malinzi2018 - tumour-immune interaction model.sedml/plot_1_task1\ncreate_links: /\ngot link: Malinzi2018 - tumour-immune interaction model.sedml\ncreate_links: /Malinzi2018 - tumour-immune interaction model.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Malinzi2018 - tumour-immune interaction model.sedml/autogen_report_for_task1 to tgt: /Malinzi2018 - tumour-immune interaction model.sedml/autogen_report_for_task1, shape: (28, 101), type: float64\niterating over chunks for /Malinzi2018 - tumour-immune interaction model.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 28, 1), slice(0, 101, 1))\ndone with dataload for /Malinzi2018 - tumour-immune interaction model.sedml/autogen_report_for_task1\nwrite_dataset src: /Malinzi2018 - tumour-immune interaction model.sedml/plot_1_task1 to tgt: /Malinzi2018 - tumour-immune interaction model.sedml/plot_1_task1, shape: (3, 101), type: float64\niterating over chunks for /Malinzi2018 - tumour-immune interaction model.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 101, 1))\ndone with dataload for /Malinzi2018 - tumour-immune interaction model.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711d730dcacb55678cead0\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 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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.097938,"sedDocuments":[{"location":"Malinzi2018 - tumour-immune interaction model.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  Malinzi2018 - tumour-immune interaction model.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 28 data sets\r\n    Plots (1):\r\n      plot_1_task1: 2 curves\r\n\r\nExecuting SED-ML file 1: Malinzi2018 - tumour-immune interaction model.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":0.694056,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.14179,"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":10000,"Relative Tolerance":0.000001}}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.340543,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.077177,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_x","status":"SUCCEEDED"},{"id":"autogen_task1_y","status":"SUCCEEDED"},{"id":"autogen_task1_u","status":"SUCCEEDED"},{"id":"autogen_task1_ystar","status":"SUCCEEDED"},{"id":"autogen_task1_R","status":"SUCCEEDED"},{"id":"autogen_task1_phi_1","status":"SUCCEEDED"},{"id":"autogen_task1_phi_2","status":"SUCCEEDED"},{"id":"autogen_task1_delta","status":"SUCCEEDED"},{"id":"autogen_task1_nu_1","status":"SUCCEEDED"},{"id":"autogen_task1_sigma_1","status":"SUCCEEDED"},{"id":"autogen_task1_sigma_2","status":"SUCCEEDED"},{"id":"autogen_task1_nu_2","status":"SUCCEEDED"},{"id":"autogen_task1_nu_3","status":"SUCCEEDED"},{"id":"autogen_task1_myu_1","status":"SUCCEEDED"},{"id":"autogen_task1_rho","status":"SUCCEEDED"},{"id":"autogen_task1_myu_2","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_x_logistic_growth","status":"SUCCEEDED"},{"id":"autogen_task1_x_proliferation","status":"SUCCEEDED"},{"id":"autogen_task1_x_immune_inactivation","status":"SUCCEEDED"},{"id":"autogen_task1_y_logistic_growth","status":"SUCCEEDED"},{"id":"autogen_task1_y_tumour_lysis","status":"SUCCEEDED"},{"id":"autogen_task1_u_production","status":"SUCCEEDED"},{"id":"autogen_task1_u_decay","status":"SUCCEEDED"},{"id":"autogen_task1_ystar_formation","status":"SUCCEEDED"},{"id":"autogen_task1_ystar_decay","status":"SUCCEEDED"}]}]}]}