{"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    456      0 --:--:-- --:--:-- --:--:--   457\n\r100 34472  100 34472    0     0  84339      0 --:--:-- --:--:-- --:--:-- 84339\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 (24.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b630fb37cdb9ae7365d/rawLog.txt\nCompleted 4.3 KiB/4.3 KiB (70.5 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b630fb37cdb9ae7365d/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 79%)\n  adding: outputs/reports.h5 (deflated 17%)\n  adding: outputs/Hu2018.sedml/ (stored 0%)\n  adding: outputs/Hu2018.sedml/plot_1_task1.pdf (deflated 32%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 158.6 KiB/158.6 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b630fb37cdb9ae7365d/outputs/reports.h5\nCompleted 141.9 KiB/163.5 KiB (1.6 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b630fb37cdb9ae7365d/output.zip\nCompleted 141.9 KiB/163.5 KiB (1.6 MiB/s) with 3 file(s) remaining\rCompleted 144.5 KiB/163.5 KiB (1.1 MiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b630fb37cdb9ae7365d/rawLog.txt\nCompleted 144.5 KiB/163.5 KiB (1.1 MiB/s) with 2 file(s) remaining\rCompleted 152.0 KiB/163.5 KiB (1.0 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b630fb37cdb9ae7365d/outputs/plots.zip\nCompleted 152.0 KiB/163.5 KiB (1.0 MiB/s) with 1 file(s) remaining\rCompleted 163.5 KiB/163.5 KiB (390.4 KiB/s) with 1 file(s) remaining\rupload: outputs/Hu2018.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b630fb37cdb9ae7365d/outputs/Hu2018.sedml/plot_1_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Hu2018-biopax2.owl  \n  inflating: contents/Hu2018-biopax3.owl  \n  inflating: contents/Hu2018-matlab.m  \n  inflating: contents/Hu2018-octave.m  \n  inflating: contents/Hu2018.cps     \n  inflating: contents/Hu2018.ode     \n  inflating: contents/Hu2018.sedml   \n  inflating: contents/Hu2018.xml     \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 22.8 KiB/226.6 KiB (227.2 KiB/s) with 12 file(s) remaining\rupload: contents/Hu2018-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b630fb37cdb9ae7365d/contents/Hu2018-biopax3.owl\nCompleted 22.8 KiB/226.6 KiB (227.2 KiB/s) with 11 file(s) remaining\rCompleted 38.7 KiB/226.6 KiB (293.7 KiB/s) with 11 file(s) remaining\rupload: contents/Hu2018-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b630fb37cdb9ae7365d/contents/Hu2018-biopax2.owl\nCompleted 38.7 KiB/226.6 KiB (293.7 KiB/s) with 10 file(s) remaining\rCompleted 45.9 KiB/226.6 KiB (344.6 KiB/s) with 10 file(s) remaining\rupload: contents/Hu2018-octave.m to s3://files.biosimulations.org/simulations/647a4b630fb37cdb9ae7365d/contents/Hu2018-octave.m\nCompleted 45.9 KiB/226.6 KiB (344.6 KiB/s) with 9 file(s) remaining\rCompleted 53.1 KiB/226.6 KiB (377.7 KiB/s) with 9 file(s) remaining\rupload: contents/Hu2018-matlab.m to s3://files.biosimulations.org/simulations/647a4b630fb37cdb9ae7365d/contents/Hu2018-matlab.m\nCompleted 53.1 KiB/226.6 KiB (377.7 KiB/s) with 8 file(s) remaining\rCompleted 53.3 KiB/226.6 KiB (342.2 KiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b630fb37cdb9ae7365d/contents/curation_notes.txt\nCompleted 53.3 KiB/226.6 KiB (342.2 KiB/s) with 7 file(s) remaining\rCompleted 62.1 KiB/226.6 KiB (387.5 KiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b630fb37cdb9ae7365d/contents/curation_image.png\nCompleted 62.1 KiB/226.6 KiB (387.5 KiB/s) with 6 file(s) remaining\rCompleted 63.4 KiB/226.6 KiB (391.9 KiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b630fb37cdb9ae7365d/contents/manifest.xml\nCompleted 63.4 KiB/226.6 KiB (391.9 KiB/s) with 5 file(s) remaining\rCompleted 66.2 KiB/226.6 KiB (383.9 KiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b630fb37cdb9ae7365d/contents/metadata.rdf\nCompleted 66.2 KiB/226.6 KiB (383.9 KiB/s) with 4 file(s) remaining\rCompleted 147.2 KiB/226.6 KiB (759.7 KiB/s) with 4 file(s) remaining\rupload: contents/Hu2018.cps to s3://files.biosimulations.org/simulations/647a4b630fb37cdb9ae7365d/contents/Hu2018.cps\nCompleted 147.2 KiB/226.6 KiB (759.7 KiB/s) with 3 file(s) remaining\rCompleted 168.7 KiB/226.6 KiB (840.0 KiB/s) with 3 file(s) remaining\rupload: contents/Hu2018.sedml to s3://files.biosimulations.org/simulations/647a4b630fb37cdb9ae7365d/contents/Hu2018.sedml\nCompleted 168.7 KiB/226.6 KiB (840.0 KiB/s) with 2 file(s) remaining\rCompleted 174.4 KiB/226.6 KiB (853.6 KiB/s) with 2 file(s) remaining\rupload: contents/Hu2018.ode to s3://files.biosimulations.org/simulations/647a4b630fb37cdb9ae7365d/contents/Hu2018.ode\nCompleted 174.4 KiB/226.6 KiB (853.6 KiB/s) with 1 file(s) remaining\rCompleted 226.6 KiB/226.6 KiB (1.1 MiB/s) with 1 file(s) remaining  \rupload: contents/Hu2018.xml to s3://files.biosimulations.org/simulations/647a4b630fb37cdb9ae7365d/contents/Hu2018.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.3 KiB/7.3 KiB (103.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b630fb37cdb9ae7365d/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Hu2018.sedml\ncreating dataset /Hu2018.sedml/autogen_report_for_task1, shape: (37, 1001), type: float64\ndataset created, uuid: d-b3998406-7278dfdc-294d-ca30b8-a47c33, chunk_size: (37, 1001)\ncreating dataset /Hu2018.sedml/plot_1_task1, shape: (3, 1001), type: float64\ndataset created, uuid: d-b3998406-7278dfdc-4a50-3f45c2-4b2515, chunk_size: (3, 1001)\ncreating attribute combineArchiveLocation in /Hu2018.sedml\ncreating attribute uri in /Hu2018.sedml\ncreating attribute _type in /Hu2018.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Hu2018.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Hu2018.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Hu2018.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Hu2018.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Hu2018.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Hu2018.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Hu2018.sedml/autogen_report_for_task1\ncreating attribute uri in /Hu2018.sedml/autogen_report_for_task1\ncreating attribute _type in /Hu2018.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Hu2018.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Hu2018.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Hu2018.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Hu2018.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Hu2018.sedml/plot_1_task1\ncreating attribute sedmlId in /Hu2018.sedml/plot_1_task1\ncreating attribute sedmlName in /Hu2018.sedml/plot_1_task1\ncreating attribute uri in /Hu2018.sedml/plot_1_task1\ncreate_links: /\ngot link: Hu2018.sedml\ncreate_links: /Hu2018.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Hu2018.sedml/autogen_report_for_task1 to tgt: /Hu2018.sedml/autogen_report_for_task1, shape: (37, 1001), type: float64\niterating over chunks for /Hu2018.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 37, 1), slice(0, 1001, 1))\ndone with dataload for /Hu2018.sedml/autogen_report_for_task1\nwrite_dataset src: /Hu2018.sedml/plot_1_task1 to tgt: /Hu2018.sedml/plot_1_task1, shape: (3, 1001), type: float64\niterating over chunks for /Hu2018.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 1001, 1))\ndone with dataload for /Hu2018.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b630fb37cdb9ae7365d\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 metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nRetrieve 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 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":1.607493,"sedDocuments":[{"location":"Hu2018.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  Hu2018.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 37 data sets\r\n    Plots (1):\r\n      plot_1_task1: 2 curves\r\n\r\nExecuting SED-ML file 1: Hu2018.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":1.125414,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.252057,"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":0.42076,"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":0.30718,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Host_Cells_1e8","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_Cells_1e8","status":"SUCCEEDED"},{"id":"autogen_task1_x_Tumor_Cells","status":"SUCCEEDED"},{"id":"autogen_task1_y_CD4_T_Cells","status":"SUCCEEDED"},{"id":"autogen_task1_z_Cytokine","status":"SUCCEEDED"},{"id":"autogen_task1_w_Healthy_Tissue","status":"SUCCEEDED"},{"id":"autogen_task1_r_1","status":"SUCCEEDED"},{"id":"autogen_task1_b_1","status":"SUCCEEDED"},{"id":"autogen_task1_c_1","status":"SUCCEEDED"},{"id":"autogen_task1_a_1","status":"SUCCEEDED"},{"id":"autogen_task1_delta_1","status":"SUCCEEDED"},{"id":"autogen_task1_beta_1","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_1","status":"SUCCEEDED"},{"id":"autogen_task1_mu_1","status":"SUCCEEDED"},{"id":"autogen_task1_delta_2","status":"SUCCEEDED"},{"id":"autogen_task1_beta_2","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_2","status":"SUCCEEDED"},{"id":"autogen_task1_mu_2","status":"SUCCEEDED"},{"id":"autogen_task1_r_2","status":"SUCCEEDED"},{"id":"autogen_task1_b_2","status":"SUCCEEDED"},{"id":"autogen_task1_delta_3","status":"SUCCEEDED"},{"id":"autogen_task1_I_2","status":"SUCCEEDED"},{"id":"autogen_task1_I_1","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_Growth","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_Killing_Cytokine","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_Competition_Normal_Cells","status":"SUCCEEDED"},{"id":"autogen_task1_CD4T_Production","status":"SUCCEEDED"},{"id":"autogen_task1_CD4T_Natural_Death","status":"SUCCEEDED"},{"id":"autogen_task1_CD4T_Depletion","status":"SUCCEEDED"},{"id":"autogen_task1_CD4T_Treatment","status":"SUCCEEDED"},{"id":"autogen_task1_Cytokine_Production","status":"SUCCEEDED"},{"id":"autogen_task1_Cytokine_Decay","status":"SUCCEEDED"},{"id":"autogen_task1_Cytokine_Treatment","status":"SUCCEEDED"},{"id":"autogen_task1_Normal_Tissue_Growth","status":"SUCCEEDED"},{"id":"autogen_task1_Normal_Tissue_Competition_Tumor_Cells","status":"SUCCEEDED"}]}]}]}