{"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    453      0 --:--:-- --:--:-- --:--:--   454\n\r 29  273k   29 82060    0     0   190k      0  0:00:01 --:--:--  0:00:01  190k\r100  273k  100  273k    0     0   633k      0 --:--:-- --:--:-- --:--:-- 17.1M\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 (20.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a619f0fb37cdb9ae76ead/rawLog.txt\nCompleted 3.5 KiB/3.5 KiB (29.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a619f0fb37cdb9ae76ead/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 77%)\n  adding: outputs/Cappuccio2007 - Fig1.sedml/ (stored 0%)\n  adding: outputs/Cappuccio2007 - Fig1.sedml/plot_1_task1.pdf (deflated 24%)\n  adding: outputs/reports.h5 (deflated 18%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 117.1 KiB/117.1 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a619f0fb37cdb9ae76ead/outputs/reports.h5\nCompleted 11.8 KiB/141.3 KiB (102.3 KiB/s) with 4 file(s) remaining\rCompleted 122.7 KiB/141.3 KiB (1.0 MiB/s) with 4 file(s) remaining \rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a619f0fb37cdb9ae76ead/output.zip\nCompleted 122.7 KiB/141.3 KiB (1.0 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a619f0fb37cdb9ae76ead/outputs/plots.zip\nCompleted 122.7 KiB/141.3 KiB (1.0 MiB/s) with 2 file(s) remaining\rCompleted 138.7 KiB/141.3 KiB (1.1 MiB/s) with 2 file(s) remaining\rupload: outputs/Cappuccio2007 - Fig1.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a619f0fb37cdb9ae76ead/outputs/Cappuccio2007 - Fig1.sedml/plot_1_task1.pdf\nCompleted 138.7 KiB/141.3 KiB (1.1 MiB/s) with 1 file(s) remaining\rCompleted 141.3 KiB/141.3 KiB (1.0 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a619f0fb37cdb9ae76ead/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Cappuccio2007 - Fig1.sedml  \n  inflating: contents/Cappuccio2007-biopax2.owl  \n  inflating: contents/Cappuccio2007-biopax3.owl  \n  inflating: contents/Cappuccio2007-matlab.m  \n  inflating: contents/Cappuccio2007-octave.m  \n  inflating: contents/Cappuccio2007.cps  \n  inflating: contents/Cappuccio2007.ode  \n  inflating: contents/Cappuccio2007.xml  \n  inflating: contents/Fig1.png       \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 11.2 KiB/416.3 KiB (143.0 KiB/s) with 13 file(s) remaining\rupload: contents/Cappuccio2007-biopax2.owl to s3://files.biosimulations.org/simulations/647a619f0fb37cdb9ae76ead/contents/Cappuccio2007-biopax2.owl\nCompleted 11.2 KiB/416.3 KiB (143.0 KiB/s) with 12 file(s) remaining\rCompleted 25.6 KiB/416.3 KiB (194.2 KiB/s) with 12 file(s) remaining\rupload: contents/Cappuccio2007-biopax3.owl to s3://files.biosimulations.org/simulations/647a619f0fb37cdb9ae76ead/contents/Cappuccio2007-biopax3.owl\nCompleted 25.6 KiB/416.3 KiB (194.2 KiB/s) with 11 file(s) remaining\rCompleted 25.8 KiB/416.3 KiB (175.9 KiB/s) with 11 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a619f0fb37cdb9ae76ead/contents/curation_notes.txt\nCompleted 25.8 KiB/416.3 KiB (175.9 KiB/s) with 10 file(s) remaining\rCompleted 40.0 KiB/416.3 KiB (261.4 KiB/s) with 10 file(s) remaining\rupload: contents/Cappuccio2007 - Fig1.sedml to s3://files.biosimulations.org/simulations/647a619f0fb37cdb9ae76ead/contents/Cappuccio2007 - Fig1.sedml\nCompleted 40.0 KiB/416.3 KiB (261.4 KiB/s) with 9 file(s) remaining\rCompleted 165.8 KiB/416.3 KiB (1008.7 KiB/s) with 9 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a619f0fb37cdb9ae76ead/contents/curation_image.png\nCompleted 165.8 KiB/416.3 KiB (1008.7 KiB/s) with 8 file(s) remaining\rCompleted 200.5 KiB/416.3 KiB (1.2 MiB/s) with 8 file(s) remaining   \rupload: contents/Cappuccio2007.xml to s3://files.biosimulations.org/simulations/647a619f0fb37cdb9ae76ead/contents/Cappuccio2007.xml\nCompleted 200.5 KiB/416.3 KiB (1.2 MiB/s) with 7 file(s) remaining\rCompleted 326.3 KiB/416.3 KiB (1.9 MiB/s) with 7 file(s) remaining\rupload: contents/Fig1.png to s3://files.biosimulations.org/simulations/647a619f0fb37cdb9ae76ead/contents/Fig1.png\nCompleted 326.3 KiB/416.3 KiB (1.9 MiB/s) with 6 file(s) remaining\rCompleted 327.8 KiB/416.3 KiB (1.9 MiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a619f0fb37cdb9ae76ead/contents/manifest.xml\nCompleted 327.8 KiB/416.3 KiB (1.9 MiB/s) with 5 file(s) remaining\rCompleted 332.3 KiB/416.3 KiB (1.8 MiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a619f0fb37cdb9ae76ead/contents/metadata.rdf\nCompleted 332.3 KiB/416.3 KiB (1.8 MiB/s) with 4 file(s) remaining\rCompleted 335.6 KiB/416.3 KiB (1.8 MiB/s) with 4 file(s) remaining\rupload: contents/Cappuccio2007.ode to s3://files.biosimulations.org/simulations/647a619f0fb37cdb9ae76ead/contents/Cappuccio2007.ode\nCompleted 335.6 KiB/416.3 KiB (1.8 MiB/s) with 3 file(s) remaining\rCompleted 406.1 KiB/416.3 KiB (2.2 MiB/s) with 3 file(s) remaining\rupload: contents/Cappuccio2007.cps to s3://files.biosimulations.org/simulations/647a619f0fb37cdb9ae76ead/contents/Cappuccio2007.cps\nCompleted 406.1 KiB/416.3 KiB (2.2 MiB/s) with 2 file(s) remaining\rCompleted 411.2 KiB/416.3 KiB (2.0 MiB/s) with 2 file(s) remaining\rupload: contents/Cappuccio2007-matlab.m to s3://files.biosimulations.org/simulations/647a619f0fb37cdb9ae76ead/contents/Cappuccio2007-matlab.m\nCompleted 411.2 KiB/416.3 KiB (2.0 MiB/s) with 1 file(s) remaining\rCompleted 416.3 KiB/416.3 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: contents/Cappuccio2007-octave.m to s3://files.biosimulations.org/simulations/647a619f0fb37cdb9ae76ead/contents/Cappuccio2007-octave.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.8 KiB/7.8 KiB (77.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a619f0fb37cdb9ae76ead/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Cappuccio2007 - Fig1.sedml\ncreating dataset /Cappuccio2007 - Fig1.sedml/autogen_report_for_task1, shape: (24, 1001), type: float64\ndataset created, uuid: d-2256337a-8835f7f0-1a86-1eda82-61da61, chunk_size: (24, 1001)\ncreating dataset /Cappuccio2007 - Fig1.sedml/plot_1_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-2256337a-8835f7f0-1aec-69fa45-0438f8, chunk_size: (4, 1001)\ncreating attribute combineArchiveLocation in /Cappuccio2007 - Fig1.sedml\ncreating attribute uri in /Cappuccio2007 - Fig1.sedml\ncreating attribute _type in /Cappuccio2007 - Fig1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Cappuccio2007 - Fig1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Cappuccio2007 - Fig1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Cappuccio2007 - Fig1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Cappuccio2007 - Fig1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Cappuccio2007 - Fig1.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Cappuccio2007 - Fig1.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Cappuccio2007 - Fig1.sedml/autogen_report_for_task1\ncreating attribute uri in /Cappuccio2007 - Fig1.sedml/autogen_report_for_task1\ncreating attribute _type in /Cappuccio2007 - Fig1.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Cappuccio2007 - Fig1.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Cappuccio2007 - Fig1.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Cappuccio2007 - Fig1.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Cappuccio2007 - Fig1.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Cappuccio2007 - Fig1.sedml/plot_1_task1\ncreating attribute sedmlId in /Cappuccio2007 - Fig1.sedml/plot_1_task1\ncreating attribute sedmlName in /Cappuccio2007 - Fig1.sedml/plot_1_task1\ncreating attribute uri in /Cappuccio2007 - Fig1.sedml/plot_1_task1\ncreate_links: /\ngot link: Cappuccio2007 - Fig1.sedml\ncreate_links: /Cappuccio2007 - Fig1.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Cappuccio2007 - Fig1.sedml/autogen_report_for_task1 to tgt: /Cappuccio2007 - Fig1.sedml/autogen_report_for_task1, shape: (24, 1001), type: float64\niterating over chunks for /Cappuccio2007 - Fig1.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 24, 1), slice(0, 1001, 1))\ndone with dataload for /Cappuccio2007 - Fig1.sedml/autogen_report_for_task1\nwrite_dataset src: /Cappuccio2007 - Fig1.sedml/plot_1_task1 to tgt: /Cappuccio2007 - Fig1.sedml/plot_1_task1, shape: (4, 1001), type: float64\niterating over chunks for /Cappuccio2007 - Fig1.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /Cappuccio2007 - Fig1.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a619f0fb37cdb9ae76ead\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 and upload the outputs of the simulation run ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.399165,"sedDocuments":[{"location":"Cappuccio2007 - Fig1.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  Cappuccio2007 - Fig1.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 24 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Cappuccio2007 - Fig1.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":0.943474,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.216078,"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":0.397064,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.198895,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Effector_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_cells","status":"SUCCEEDED"},{"id":"autogen_task1_IL_2","status":"SUCCEEDED"},{"id":"autogen_task1_c","status":"SUCCEEDED"},{"id":"autogen_task1_mu2","status":"SUCCEEDED"},{"id":"autogen_task1_p1","status":"SUCCEEDED"},{"id":"autogen_task1_g1","status":"SUCCEEDED"},{"id":"autogen_task1_s1","status":"SUCCEEDED"},{"id":"autogen_task1_r2","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_g2","status":"SUCCEEDED"},{"id":"autogen_task1_p2","status":"SUCCEEDED"},{"id":"autogen_task1_g3","status":"SUCCEEDED"},{"id":"autogen_task1_mu3","status":"SUCCEEDED"},{"id":"autogen_task1_s2","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_microenvironment","status":"SUCCEEDED"},{"id":"autogen_task1_Effector_cell_stimulation","status":"SUCCEEDED"},{"id":"autogen_task1_Effector_cell_decay","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_growth","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_killing","status":"SUCCEEDED"},{"id":"autogen_task1_IL_2_production","status":"SUCCEEDED"},{"id":"autogen_task1_IL_2_decay","status":"SUCCEEDED"}]}]}]}