{"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    531      0 --:--:-- --:--:-- --:--:--   530\r100   139  100   139    0     0    528      0 --:--:-- --:--:-- --:--:--   528\n\r100  141k  100  141k    0     0   393k      0 --:--:-- --:--:-- --:--:--  393k\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 (30.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a313f0fb37cdb9ae6884e/rawLog.txt\nCompleted 3.4 KiB/3.4 KiB (60.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a313f0fb37cdb9ae6884e/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 75%)\n  adding: outputs/Kimmel2021 - Fig2(a) and (b).sedml/ (stored 0%)\n  adding: outputs/Kimmel2021 - Fig2(a) and (b).sedml/plot_1_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 20%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 104.6 KiB/104.6 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a313f0fb37cdb9ae6884e/outputs/reports.h5\nCompleted 7.3 KiB/114.9 KiB (79.4 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a313f0fb37cdb9ae6884e/outputs/plots.zip\nCompleted 7.3 KiB/114.9 KiB (79.4 KiB/s) with 3 file(s) remaining\rCompleted 18.3 KiB/114.9 KiB (194.7 KiB/s) with 3 file(s) remaining\rupload: outputs/Kimmel2021 - Fig2(a) and (b).sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a313f0fb37cdb9ae6884e/outputs/Kimmel2021 - Fig2(a) and (b).sedml/plot_1_task1.pdf\nCompleted 18.3 KiB/114.9 KiB (194.7 KiB/s) with 2 file(s) remaining\rCompleted 21.0 KiB/114.9 KiB (212.1 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a313f0fb37cdb9ae6884e/rawLog.txt\nCompleted 21.0 KiB/114.9 KiB (212.1 KiB/s) with 1 file(s) remaining\rCompleted 114.9 KiB/114.9 KiB (1.0 MiB/s) with 1 file(s) remaining \rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a313f0fb37cdb9ae6884e/output.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Fig2(a) and (b).png  \n  inflating: contents/Kimmel2021 - Fig2(a) and (b).sedml  \n  inflating: contents/Kimmel2021-biopax2.owl  \n  inflating: contents/Kimmel2021-biopax3.owl  \n  inflating: contents/Kimmel2021-matlab.m  \n  inflating: contents/Kimmel2021-octave.m  \n  inflating: contents/Kimmel2021.cps  \n  inflating: contents/Kimmel2021.ode  \n  inflating: contents/Kimmel2021.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 61.2 KiB/295.8 KiB (850.4 KiB/s) with 13 file(s) remaining\rupload: contents/Fig2(a) and (b).png to s3://files.biosimulations.org/simulations/647a313f0fb37cdb9ae6884e/contents/Fig2(a) and (b).png\nCompleted 61.2 KiB/295.8 KiB (850.4 KiB/s) with 12 file(s) remaining\rCompleted 64.4 KiB/295.8 KiB (627.1 KiB/s) with 12 file(s) remaining\rupload: contents/Kimmel2021.ode to s3://files.biosimulations.org/simulations/647a313f0fb37cdb9ae6884e/contents/Kimmel2021.ode\nCompleted 64.4 KiB/295.8 KiB (627.1 KiB/s) with 11 file(s) remaining\rCompleted 77.0 KiB/295.8 KiB (659.6 KiB/s) with 11 file(s) remaining\rupload: contents/Kimmel2021 - Fig2(a) and (b).sedml to s3://files.biosimulations.org/simulations/647a313f0fb37cdb9ae6884e/contents/Kimmel2021 - Fig2(a) and (b).sedml\nCompleted 77.0 KiB/295.8 KiB (659.6 KiB/s) with 10 file(s) remaining\rCompleted 87.8 KiB/295.8 KiB (719.1 KiB/s) with 10 file(s) remaining\rupload: contents/Kimmel2021-biopax2.owl to s3://files.biosimulations.org/simulations/647a313f0fb37cdb9ae6884e/contents/Kimmel2021-biopax2.owl\nCompleted 87.8 KiB/295.8 KiB (719.1 KiB/s) with 9 file(s) remaining\rCompleted 119.9 KiB/295.8 KiB (978.2 KiB/s) with 9 file(s) remaining\rupload: contents/Kimmel2021.xml to s3://files.biosimulations.org/simulations/647a313f0fb37cdb9ae6884e/contents/Kimmel2021.xml\nCompleted 119.9 KiB/295.8 KiB (978.2 KiB/s) with 8 file(s) remaining\rCompleted 205.6 KiB/295.8 KiB (1.5 MiB/s) with 8 file(s) remaining  \rupload: contents/Kimmel2021.cps to s3://files.biosimulations.org/simulations/647a313f0fb37cdb9ae6884e/contents/Kimmel2021.cps\nCompleted 205.6 KiB/295.8 KiB (1.5 MiB/s) with 7 file(s) remaining\rCompleted 205.9 KiB/295.8 KiB (1.5 MiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a313f0fb37cdb9ae6884e/contents/curation_notes.txt\nCompleted 205.9 KiB/295.8 KiB (1.5 MiB/s) with 6 file(s) remaining\rCompleted 210.1 KiB/295.8 KiB (1.5 MiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a313f0fb37cdb9ae6884e/contents/metadata.rdf\nCompleted 210.1 KiB/295.8 KiB (1.5 MiB/s) with 5 file(s) remaining\rCompleted 271.3 KiB/295.8 KiB (1.9 MiB/s) with 5 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a313f0fb37cdb9ae6884e/contents/curation_image.png\nCompleted 271.3 KiB/295.8 KiB (1.9 MiB/s) with 4 file(s) remaining\rCompleted 276.0 KiB/295.8 KiB (1.8 MiB/s) with 4 file(s) remaining\rupload: contents/Kimmel2021-octave.m to s3://files.biosimulations.org/simulations/647a313f0fb37cdb9ae6884e/contents/Kimmel2021-octave.m\nCompleted 276.0 KiB/295.8 KiB (1.8 MiB/s) with 3 file(s) remaining\rCompleted 277.5 KiB/295.8 KiB (1.6 MiB/s) with 3 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a313f0fb37cdb9ae6884e/contents/manifest.xml\nCompleted 277.5 KiB/295.8 KiB (1.6 MiB/s) with 2 file(s) remaining\rCompleted 291.1 KiB/295.8 KiB (1.7 MiB/s) with 2 file(s) remaining\rupload: contents/Kimmel2021-biopax3.owl to s3://files.biosimulations.org/simulations/647a313f0fb37cdb9ae6884e/contents/Kimmel2021-biopax3.owl\nCompleted 291.1 KiB/295.8 KiB (1.7 MiB/s) with 1 file(s) remaining\rCompleted 295.8 KiB/295.8 KiB (1.7 MiB/s) with 1 file(s) remaining\rupload: contents/Kimmel2021-matlab.m to s3://files.biosimulations.org/simulations/647a313f0fb37cdb9ae6884e/contents/Kimmel2021-matlab.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.9 KiB/7.9 KiB (142.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a313f0fb37cdb9ae6884e/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Kimmel2021 - Fig2(a) and (b).sedml\ncreating dataset /Kimmel2021 - Fig2(a) and (b).sedml/autogen_report_for_task1, shape: (20, 1001), type: float64\ndataset created, uuid: d-3b959b5f-d8d42709-ab9c-aeacd6-95d517, chunk_size: (20, 1001)\ncreating dataset /Kimmel2021 - Fig2(a) and (b).sedml/plot_1_task1, shape: (3, 1001), type: float64\ndataset created, uuid: d-3b959b5f-d8d42709-88a1-b3feb5-a78d85, chunk_size: (3, 1001)\ncreating attribute combineArchiveLocation in /Kimmel2021 - Fig2(a) and (b).sedml\ncreating attribute uri in /Kimmel2021 - Fig2(a) and (b).sedml\ncreating attribute _type in /Kimmel2021 - Fig2(a) and (b).sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Kimmel2021 - Fig2(a) and (b).sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Kimmel2021 - Fig2(a) and (b).sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Kimmel2021 - Fig2(a) and (b).sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Kimmel2021 - Fig2(a) and (b).sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Kimmel2021 - Fig2(a) and (b).sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Kimmel2021 - Fig2(a) and (b).sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Kimmel2021 - Fig2(a) and (b).sedml/autogen_report_for_task1\ncreating attribute uri in /Kimmel2021 - Fig2(a) and (b).sedml/autogen_report_for_task1\ncreating attribute _type in /Kimmel2021 - Fig2(a) and (b).sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Kimmel2021 - Fig2(a) and (b).sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Kimmel2021 - Fig2(a) and (b).sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Kimmel2021 - Fig2(a) and (b).sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Kimmel2021 - Fig2(a) and (b).sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Kimmel2021 - Fig2(a) and (b).sedml/plot_1_task1\ncreating attribute sedmlId in /Kimmel2021 - Fig2(a) and (b).sedml/plot_1_task1\ncreating attribute sedmlName in /Kimmel2021 - Fig2(a) and (b).sedml/plot_1_task1\ncreating attribute uri in /Kimmel2021 - Fig2(a) and (b).sedml/plot_1_task1\ncreate_links: /\ngot link: Kimmel2021 - Fig2(a) and (b).sedml\ncreate_links: /Kimmel2021 - Fig2(a) and (b).sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Kimmel2021 - Fig2(a) and (b).sedml/autogen_report_for_task1 to tgt: /Kimmel2021 - Fig2(a) and (b).sedml/autogen_report_for_task1, shape: (20, 1001), type: float64\niterating over chunks for /Kimmel2021 - Fig2(a) and (b).sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 20, 1), slice(0, 1001, 1))\ndone with dataload for /Kimmel2021 - Fig2(a) and (b).sedml/autogen_report_for_task1\nwrite_dataset src: /Kimmel2021 - Fig2(a) and (b).sedml/plot_1_task1 to tgt: /Kimmel2021 - Fig2(a) and (b).sedml/plot_1_task1, shape: (3, 1001), type: float64\niterating over chunks for /Kimmel2021 - Fig2(a) and (b).sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 1001, 1))\ndone with dataload for /Kimmel2021 - Fig2(a) and (b).sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a313f0fb37cdb9ae6884e\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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.196515,"sedDocuments":[{"location":"Kimmel2021 - Fig2(a) and (b).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  Kimmel2021 - Fig2(a) and (b).sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 20 data sets\r\n    Plots (1):\r\n      plot_1_task1: 2 curves\r\n\r\nExecuting SED-ML file 1: Kimmel2021 - Fig2(a) and (b).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":0.821162,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.203645,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"simulate"},{"key":"solver","value":"cvode"},{"key":"relative_tolerance","value":0.000001},{"key":"absolute_tolerance","value":1e-12},{"key":"stiff","value":true},{"key":"maximum_bdf_order","value":5},{"key":"maximum_adams_order","value":12},{"key":"maximum_num_steps","value":20000},{"key":"maximum_time_step","value":0},{"key":"minimum_time_step","value":0},{"key":"initial_time_step","value":0},{"key":"multiple_steps","value":false},{"key":"variable_step_size","value":false},{"key":"max_output_rows","value":100000}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.34811,"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":0.18118,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Normal_T_cells","status":"SUCCEEDED"},{"id":"autogen_task1_CAR_T_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Antigen_presenting_tumour_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Total_lymphocyte_count","status":"SUCCEEDED"},{"id":"autogen_task1_K_N","status":"SUCCEEDED"},{"id":"autogen_task1_K_C","status":"SUCCEEDED"},{"id":"autogen_task1_r_N","status":"SUCCEEDED"},{"id":"autogen_task1_rho_C","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_r_B","status":"SUCCEEDED"},{"id":"autogen_task1_gamma_B","status":"SUCCEEDED"},{"id":"autogen_task1_k_B","status":"SUCCEEDED"},{"id":"autogen_task1_r_C","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_Normal_T_cell_population_growth","status":"SUCCEEDED"},{"id":"autogen_task1_CAR_T_cell_population_growth","status":"SUCCEEDED"},{"id":"autogen_task1_Tumour_growth","status":"SUCCEEDED"},{"id":"autogen_task1_Tumour_killing","status":"SUCCEEDED"}]}]}]}