{"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    459      0 --:--:-- --:--:-- --:--:--   460\n\r100 51034  100 51034    0     0   120k      0 --:--:-- --:--:-- --:--:--  120k\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 (25.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b9777b666965506171a/rawLog.txt\nCompleted 2.5 KiB/2.5 KiB (35.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b9777b666965506171a/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 72%)\n  adding: outputs/Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/ (stored 0%)\n  adding: outputs/Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/plot_1_task1.pdf (deflated 26%)\n  adding: outputs/reports.h5 (deflated 26%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 93.0 KiB/93.0 KiB (1001.9 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b9777b666965506171a/outputs/reports.h5\nCompleted 81.2 KiB/106.2 KiB (981.7 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b9777b666965506171a/output.zip\nCompleted 81.2 KiB/106.2 KiB (981.7 KiB/s) with 3 file(s) remaining\rCompleted 94.1 KiB/106.2 KiB (857.6 KiB/s) with 3 file(s) remaining\rupload: outputs/Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b9777b666965506171a/outputs/Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/plot_1_task1.pdf\nCompleted 94.1 KiB/106.2 KiB (857.6 KiB/s) with 2 file(s) remaining\rCompleted 96.7 KiB/106.2 KiB (811.7 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b9777b666965506171a/rawLog.txt\nCompleted 96.7 KiB/106.2 KiB (811.7 KiB/s) with 1 file(s) remaining\rCompleted 106.2 KiB/106.2 KiB (853.3 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b9777b666965506171a/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml  \n  inflating: contents/Chaudhury2020 Eq 4-5-biopax2.owl  \n  inflating: contents/Chaudhury2020 Eq 4-5-biopax3.owl  \n  inflating: contents/Chaudhury2020 Eq 4-5-matlab.m  \n  inflating: contents/Chaudhury2020 Eq 4-5-octave.m  \n  inflating: contents/Chaudhury2020 Eq 4-5.cps  \n  inflating: contents/Chaudhury2020 Eq 4-5.ode  \n  inflating: contents/Chaudhury2020 Eq 4-5.xml  \n  inflating: contents/Fig 3(C) - Cyclic behaviour.png  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 8.6 KiB/150.5 KiB (128.4 KiB/s) with 13 file(s) remaining\rupload: contents/Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml to s3://files.biosimulations.org/simulations/647a4b9777b666965506171a/contents/Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml\nCompleted 8.6 KiB/150.5 KiB (128.4 KiB/s) with 12 file(s) remaining\rCompleted 33.4 KiB/150.5 KiB (260.7 KiB/s) with 12 file(s) remaining\rupload: contents/Chaudhury2020 Eq 4-5.xml to s3://files.biosimulations.org/simulations/647a4b9777b666965506171a/contents/Chaudhury2020 Eq 4-5.xml\nCompleted 33.4 KiB/150.5 KiB (260.7 KiB/s) with 11 file(s) remaining\rCompleted 35.6 KiB/150.5 KiB (272.4 KiB/s) with 11 file(s) remaining\rupload: contents/Chaudhury2020 Eq 4-5.ode to s3://files.biosimulations.org/simulations/647a4b9777b666965506171a/contents/Chaudhury2020 Eq 4-5.ode\nCompleted 35.6 KiB/150.5 KiB (272.4 KiB/s) with 10 file(s) remaining\rCompleted 39.3 KiB/150.5 KiB (293.2 KiB/s) with 10 file(s) remaining\rupload: contents/Chaudhury2020 Eq 4-5-matlab.m to s3://files.biosimulations.org/simulations/647a4b9777b666965506171a/contents/Chaudhury2020 Eq 4-5-matlab.m\nCompleted 39.3 KiB/150.5 KiB (293.2 KiB/s) with 9 file(s) remaining\rCompleted 52.9 KiB/150.5 KiB (379.1 KiB/s) with 9 file(s) remaining\rupload: contents/Chaudhury2020 Eq 4-5-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b9777b666965506171a/contents/Chaudhury2020 Eq 4-5-biopax3.owl\nCompleted 52.9 KiB/150.5 KiB (379.1 KiB/s) with 8 file(s) remaining\rCompleted 68.1 KiB/150.5 KiB (481.4 KiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b9777b666965506171a/contents/curation_image.png\nCompleted 68.1 KiB/150.5 KiB (481.4 KiB/s) with 7 file(s) remaining\rCompleted 83.3 KiB/150.5 KiB (582.5 KiB/s) with 7 file(s) remaining\rupload: contents/Fig 3(C) - Cyclic behaviour.png to s3://files.biosimulations.org/simulations/647a4b9777b666965506171a/contents/Fig 3(C) - Cyclic behaviour.png\nCompleted 83.3 KiB/150.5 KiB (582.5 KiB/s) with 6 file(s) remaining\rCompleted 83.4 KiB/150.5 KiB (556.8 KiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b9777b666965506171a/contents/curation_notes.txt\nCompleted 83.4 KiB/150.5 KiB (556.8 KiB/s) with 5 file(s) remaining\rCompleted 85.0 KiB/150.5 KiB (560.2 KiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b9777b666965506171a/contents/manifest.xml\nCompleted 85.0 KiB/150.5 KiB (560.2 KiB/s) with 4 file(s) remaining\rCompleted 88.0 KiB/150.5 KiB (565.8 KiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b9777b666965506171a/contents/metadata.rdf\nCompleted 88.0 KiB/150.5 KiB (565.8 KiB/s) with 3 file(s) remaining\rCompleted 135.6 KiB/150.5 KiB (783.5 KiB/s) with 3 file(s) remaining\rupload: contents/Chaudhury2020 Eq 4-5.cps to s3://files.biosimulations.org/simulations/647a4b9777b666965506171a/contents/Chaudhury2020 Eq 4-5.cps\nCompleted 135.6 KiB/150.5 KiB (783.5 KiB/s) with 2 file(s) remaining\rCompleted 146.7 KiB/150.5 KiB (727.9 KiB/s) with 2 file(s) remaining\rupload: contents/Chaudhury2020 Eq 4-5-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b9777b666965506171a/contents/Chaudhury2020 Eq 4-5-biopax2.owl\nCompleted 146.7 KiB/150.5 KiB (727.9 KiB/s) with 1 file(s) remaining\rCompleted 150.5 KiB/150.5 KiB (736.3 KiB/s) with 1 file(s) remaining\rupload: contents/Chaudhury2020 Eq 4-5-octave.m to s3://files.biosimulations.org/simulations/647a4b9777b666965506171a/contents/Chaudhury2020 Eq 4-5-octave.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.1 KiB/8.1 KiB (120.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b9777b666965506171a/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml\ncreating dataset /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/autogen_report_for_task1, shape: (12, 1001), type: float64\ndataset created, uuid: d-443078f3-4595068d-1dfe-0e0b6a-8e1758, chunk_size: (12, 1001)\ncreating dataset /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/plot_1_task1, shape: (3, 1001), type: float64\ndataset created, uuid: d-443078f3-4595068d-77f9-c67a70-cc8a0c, chunk_size: (3, 1001)\ncreating attribute combineArchiveLocation in /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml\ncreating attribute uri in /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml\ncreating attribute _type in /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/autogen_report_for_task1\ncreating attribute uri in /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/autogen_report_for_task1\ncreating attribute _type in /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/plot_1_task1\ncreating attribute sedmlId in /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/plot_1_task1\ncreating attribute sedmlName in /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/plot_1_task1\ncreating attribute uri in /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/plot_1_task1\ncreate_links: /\ngot link: Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml\ncreate_links: /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/autogen_report_for_task1 to tgt: /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/autogen_report_for_task1, shape: (12, 1001), type: float64\niterating over chunks for /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 12, 1), slice(0, 1001, 1))\ndone with dataload for /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/autogen_report_for_task1\nwrite_dataset src: /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/plot_1_task1 to tgt: /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/plot_1_task1, shape: (3, 1001), type: float64\niterating over chunks for /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 1001, 1))\ndone with dataload for /Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b9777b666965506171a\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 metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... 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.\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":13.937986,"sedDocuments":[{"location":"Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.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  Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 12 data sets\r\n    Plots (1):\r\n      plot_1_task1: 2 curves\r\n\r\nExecuting SED-ML file 1: Chaudhury2020 Eq 4-5 - Fig 3(C) simulation.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":13.684386,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":12.904402,"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":0.534315,"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":0.12993,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Expanding_CAR_T_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_cells","status":"SUCCEEDED"},{"id":"autogen_task1_rho","status":"SUCCEEDED"},{"id":"autogen_task1_k_E","status":"SUCCEEDED"},{"id":"autogen_task1_g","status":"SUCCEEDED"},{"id":"autogen_task1_d","status":"SUCCEEDED"},{"id":"autogen_task1_Whole_organism_blood","status":"SUCCEEDED"},{"id":"autogen_task1_Expanding_CAR_T_cell_proliferation","status":"SUCCEEDED"},{"id":"autogen_task1_Expanding_CAR_T_cell_death","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_cell_growth","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_cell_death","status":"SUCCEEDED"}]}]}]}