{"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    432      0 --:--:-- --:--:-- --:--:--   433\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100  231k  100  231k    0     0   535k      0 --:--:-- --:--:-- --:--:-- 2518k\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 (25.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/rawLog.txt\nCompleted 4.1 KiB/4.1 KiB (41.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 78%)\n  adding: outputs/reports.h5 (deflated 35%)\n  adding: outputs/MODEL1006230047_curated_annotated.sedml/ (stored 0%)\n  adding: outputs/MODEL1006230047_curated_annotated.sedml/plot_1_task1.pdf (deflated 23%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 73.6 KiB/73.6 KiB (819.9 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/outputs/reports.h5\nCompleted 61.2 KiB/87.7 KiB (672.2 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/output.zip\nCompleted 61.2 KiB/87.7 KiB (672.2 KiB/s) with 3 file(s) remaining\rCompleted 74.7 KiB/87.7 KiB (673.7 KiB/s) with 3 file(s) remaining\rupload: outputs/MODEL1006230047_curated_annotated.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/outputs/MODEL1006230047_curated_annotated.sedml/plot_1_task1.pdf\nCompleted 74.7 KiB/87.7 KiB (673.7 KiB/s) with 2 file(s) remaining\rCompleted 85.0 KiB/87.7 KiB (750.5 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/outputs/plots.zip\nCompleted 85.0 KiB/87.7 KiB (750.5 KiB/s) with 1 file(s) remaining\rCompleted 87.7 KiB/87.7 KiB (759.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/MODEL1006230047-biopax2.owl  \n  inflating: contents/MODEL1006230047-biopax3.owl  \n  inflating: contents/MODEL1006230047-matlab.m  \n  inflating: contents/MODEL1006230047-octave.m  \n  inflating: contents/MODEL1006230047.m  \n  inflating: contents/MODEL1006230047.ode  \n  inflating: contents/MODEL1006230047.pdf  \n  inflating: contents/MODEL1006230047.png  \n  inflating: contents/MODEL1006230047.svg  \n  inflating: contents/MODEL1006230047.xml  \n  inflating: contents/MODEL1006230047_curated_annotated.cps  \n  inflating: contents/MODEL1006230047_curated_annotated.sedml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 15.5 KiB/433.5 KiB (212.7 KiB/s) with 16 file(s) remaining\rupload: contents/MODEL1006230047-biopax2.owl to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/contents/MODEL1006230047-biopax2.owl\nCompleted 15.5 KiB/433.5 KiB (212.7 KiB/s) with 15 file(s) remaining\rCompleted 21.6 KiB/433.5 KiB (203.1 KiB/s) with 15 file(s) remaining\rupload: contents/MODEL1006230047-octave.m to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/contents/MODEL1006230047-octave.m\nCompleted 21.6 KiB/433.5 KiB (203.1 KiB/s) with 14 file(s) remaining\rCompleted 27.6 KiB/433.5 KiB (249.8 KiB/s) with 14 file(s) remaining\rupload: contents/MODEL1006230047-matlab.m to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/contents/MODEL1006230047-matlab.m\nCompleted 27.6 KiB/433.5 KiB (249.8 KiB/s) with 13 file(s) remaining\rCompleted 32.7 KiB/433.5 KiB (271.1 KiB/s) with 13 file(s) remaining\rupload: contents/MODEL1006230047.png to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/contents/MODEL1006230047.png\nCompleted 32.7 KiB/433.5 KiB (271.1 KiB/s) with 12 file(s) remaining\rCompleted 33.0 KiB/433.5 KiB (225.9 KiB/s) with 12 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/contents/curation_notes.txt\nCompleted 33.0 KiB/433.5 KiB (225.9 KiB/s) with 11 file(s) remaining\rCompleted 78.6 KiB/433.5 KiB (494.9 KiB/s) with 11 file(s) remaining\rupload: contents/MODEL1006230047.xml to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/contents/MODEL1006230047.xml\nCompleted 78.6 KiB/433.5 KiB (494.9 KiB/s) with 10 file(s) remaining\rCompleted 79.8 KiB/433.5 KiB (492.4 KiB/s) with 10 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/contents/metadata.rdf\nCompleted 79.8 KiB/433.5 KiB (492.4 KiB/s) with 9 file(s) remaining\rCompleted 146.7 KiB/433.5 KiB (891.7 KiB/s) with 9 file(s) remaining\rupload: contents/MODEL1006230047_curated_annotated.cps to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/contents/MODEL1006230047_curated_annotated.cps\nCompleted 146.7 KiB/433.5 KiB (891.7 KiB/s) with 8 file(s) remaining\rCompleted 169.7 KiB/433.5 KiB (904.4 KiB/s) with 8 file(s) remaining\rupload: contents/MODEL1006230047-biopax3.owl to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/contents/MODEL1006230047-biopax3.owl\nCompleted 169.7 KiB/433.5 KiB (904.4 KiB/s) with 7 file(s) remaining\rCompleted 170.5 KiB/433.5 KiB (895.6 KiB/s) with 7 file(s) remaining\rupload: contents/MODEL1006230047.svg to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/contents/MODEL1006230047.svg\nCompleted 170.5 KiB/433.5 KiB (895.6 KiB/s) with 6 file(s) remaining\rCompleted 306.7 KiB/433.5 KiB (1.5 MiB/s) with 6 file(s) remaining  \rupload: contents/MODEL1006230047.pdf to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/contents/MODEL1006230047.pdf\nCompleted 306.7 KiB/433.5 KiB (1.5 MiB/s) with 5 file(s) remaining\rCompleted 308.5 KiB/433.5 KiB (1.5 MiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/contents/manifest.xml\nCompleted 308.5 KiB/433.5 KiB (1.5 MiB/s) with 4 file(s) remaining\rCompleted 311.5 KiB/433.5 KiB (1.5 MiB/s) with 4 file(s) remaining\rupload: contents/MODEL1006230047.m to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/contents/MODEL1006230047.m\nCompleted 311.5 KiB/433.5 KiB (1.5 MiB/s) with 3 file(s) remaining\rCompleted 329.3 KiB/433.5 KiB (1.6 MiB/s) with 3 file(s) remaining\rupload: contents/MODEL1006230047_curated_annotated.sedml to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/contents/MODEL1006230047_curated_annotated.sedml\nCompleted 329.3 KiB/433.5 KiB (1.6 MiB/s) with 2 file(s) remaining\rCompleted 429.3 KiB/433.5 KiB (2.0 MiB/s) with 2 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/contents/curation_image.png\nCompleted 429.3 KiB/433.5 KiB (2.0 MiB/s) with 1 file(s) remaining\rCompleted 433.5 KiB/433.5 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: contents/MODEL1006230047.ode to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/contents/MODEL1006230047.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.0 KiB/9.0 KiB (115.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c7d49c0d898ffdf2d16/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /MODEL1006230047_curated_annotated.sedml\ncreating dataset /MODEL1006230047_curated_annotated.sedml/autogen_report_for_task1, shape: (27, 301), type: float64\ndataset created, uuid: d-69fc8f0d-fae7a7f2-bbde-9034ab-dd7e0e, chunk_size: (27, 301)\ncreating dataset /MODEL1006230047_curated_annotated.sedml/plot_1_task1, shape: (6, 301), type: float64\ndataset created, uuid: d-69fc8f0d-fae7a7f2-0070-aee066-819234, chunk_size: (6, 301)\ncreating attribute combineArchiveLocation in /MODEL1006230047_curated_annotated.sedml\ncreating attribute uri in /MODEL1006230047_curated_annotated.sedml\ncreating attribute _type in /MODEL1006230047_curated_annotated.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /MODEL1006230047_curated_annotated.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /MODEL1006230047_curated_annotated.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /MODEL1006230047_curated_annotated.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /MODEL1006230047_curated_annotated.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /MODEL1006230047_curated_annotated.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /MODEL1006230047_curated_annotated.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /MODEL1006230047_curated_annotated.sedml/autogen_report_for_task1\ncreating attribute uri in /MODEL1006230047_curated_annotated.sedml/autogen_report_for_task1\ncreating attribute _type in /MODEL1006230047_curated_annotated.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /MODEL1006230047_curated_annotated.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /MODEL1006230047_curated_annotated.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /MODEL1006230047_curated_annotated.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /MODEL1006230047_curated_annotated.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /MODEL1006230047_curated_annotated.sedml/plot_1_task1\ncreating attribute sedmlId in /MODEL1006230047_curated_annotated.sedml/plot_1_task1\ncreating attribute sedmlName in /MODEL1006230047_curated_annotated.sedml/plot_1_task1\ncreating attribute uri in /MODEL1006230047_curated_annotated.sedml/plot_1_task1\ncreate_links: /\ngot link: MODEL1006230047_curated_annotated.sedml\ncreate_links: /MODEL1006230047_curated_annotated.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /MODEL1006230047_curated_annotated.sedml/autogen_report_for_task1 to tgt: /MODEL1006230047_curated_annotated.sedml/autogen_report_for_task1, shape: (27, 301), type: float64\niterating over chunks for /MODEL1006230047_curated_annotated.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 27, 1), slice(0, 301, 1))\ndone with dataload for /MODEL1006230047_curated_annotated.sedml/autogen_report_for_task1\nwrite_dataset src: /MODEL1006230047_curated_annotated.sedml/plot_1_task1 to tgt: /MODEL1006230047_curated_annotated.sedml/plot_1_task1, shape: (6, 301), type: float64\niterating over chunks for /MODEL1006230047_curated_annotated.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 301, 1))\ndone with dataload for /MODEL1006230047_curated_annotated.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711c7d49c0d898ffdf2d16\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 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.\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":1.423131,"sedDocuments":[{"location":"MODEL1006230047_curated_annotated.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  MODEL1006230047_curated_annotated.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 27 data sets\r\n    Plots (1):\r\n      plot_1_task1: 5 curves\r\n\r\nExecuting SED-ML file 1: MODEL1006230047_curated_annotated.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":0.932732,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.23404,"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":0.409585,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"},{"id":"p1_curve_4_task1","status":"SUCCEEDED"},{"id":"p1_curve_5_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.135097,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Pathogen_Virus","status":"SUCCEEDED"},{"id":"autogen_task1_Recombinant_Virus","status":"SUCCEEDED"},{"id":"autogen_task1_Normal_Th_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Single_Infected_Th_Cells","status":"SUCCEEDED"},{"id":"autogen_task1_Double_Infected_Th_Cells","status":"SUCCEEDED"},{"id":"autogen_task1_d","status":"SUCCEEDED"},{"id":"autogen_task1_lamda","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_k","status":"SUCCEEDED"},{"id":"autogen_task1_u","status":"SUCCEEDED"},{"id":"autogen_task1_c","status":"SUCCEEDED"},{"id":"autogen_task1_q","status":"SUCCEEDED"},{"id":"autogen_task1_Plasma","status":"SUCCEEDED"},{"id":"autogen_task1_Production_of_Normal_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Degradation_of_Normal_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Infection_of_Normal_cells_with_Pathogen","status":"SUCCEEDED"},{"id":"autogen_task1_Degradation_of_Single_Infected_Cells","status":"SUCCEEDED"},{"id":"autogen_task1_Infection_of_Single_Infeced_Cells_with_Recombinant_Virus","status":"SUCCEEDED"},{"id":"autogen_task1_Release_of_Pathogen","status":"SUCCEEDED"},{"id":"autogen_task1_Degradation_of_Double_Infected_Cells","status":"SUCCEEDED"},{"id":"autogen_task1_Release_of_Recombinant_Virus","status":"SUCCEEDED"},{"id":"autogen_task1_Degradation_of_Pathogen_Virus","status":"SUCCEEDED"},{"id":"autogen_task1_Degradation_of_Recombinant_Virus","status":"SUCCEEDED"}]}]}]}