{"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    429      0 --:--:-- --:--:-- --:--:--   430\n\r100 33780  100 33780    0     0  80333      0 --:--:-- --:--:-- --:--:-- 80333\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 (26.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b5c0fb37cdb9ae735f1/rawLog.txt\nCompleted 3.2 KiB/3.2 KiB (35.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b5c0fb37cdb9ae735f1/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/Figueredo2013_1.sedml/ (stored 0%)\n  adding: outputs/Figueredo2013_1.sedml/plot_1_task1.pdf (deflated 33%)\n  adding: outputs/reports.h5 (deflated 47%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 42.4 KiB/42.4 KiB (496.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b5c0fb37cdb9ae735f1/outputs/reports.h5\nCompleted 31.3 KiB/50.2 KiB (364.2 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b5c0fb37cdb9ae735f1/output.zip\nCompleted 31.3 KiB/50.2 KiB (364.2 KiB/s) with 3 file(s) remaining\rCompleted 41.2 KiB/50.2 KiB (405.4 KiB/s) with 3 file(s) remaining\rupload: outputs/Figueredo2013_1.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b5c0fb37cdb9ae735f1/outputs/Figueredo2013_1.sedml/plot_1_task1.pdf\nCompleted 41.2 KiB/50.2 KiB (405.4 KiB/s) with 2 file(s) remaining\rCompleted 47.6 KiB/50.2 KiB (415.9 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b5c0fb37cdb9ae735f1/outputs/plots.zip\nCompleted 47.6 KiB/50.2 KiB (415.9 KiB/s) with 1 file(s) remaining\rCompleted 50.2 KiB/50.2 KiB (374.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b5c0fb37cdb9ae735f1/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Figueredo2013_1-biopax2.owl  \n  inflating: contents/Figueredo2013_1-biopax3.owl  \n  inflating: contents/Figueredo2013_1-matlab.m  \n  inflating: contents/Figueredo2013_1-octave.m  \n  inflating: contents/Figueredo2013_1.cps  \n  inflating: contents/Figueredo2013_1.ode  \n  inflating: contents/Figueredo2013_1.sedml  \n  inflating: contents/Figueredo2013_1.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 13.2 KiB/167.4 KiB (195.8 KiB/s) with 12 file(s) remaining\rupload: contents/Figueredo2013_1-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b5c0fb37cdb9ae735f1/contents/Figueredo2013_1-biopax3.owl\nCompleted 13.2 KiB/167.4 KiB (195.8 KiB/s) with 11 file(s) remaining\rCompleted 23.1 KiB/167.4 KiB (195.2 KiB/s) with 11 file(s) remaining\rupload: contents/Figueredo2013_1-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b5c0fb37cdb9ae735f1/contents/Figueredo2013_1-biopax2.owl\nCompleted 23.1 KiB/167.4 KiB (195.2 KiB/s) with 10 file(s) remaining\rCompleted 27.2 KiB/167.4 KiB (223.4 KiB/s) with 10 file(s) remaining\rupload: contents/Figueredo2013_1-matlab.m to s3://files.biosimulations.org/simulations/647a4b5c0fb37cdb9ae735f1/contents/Figueredo2013_1-matlab.m\nCompleted 27.2 KiB/167.4 KiB (223.4 KiB/s) with 9 file(s) remaining\rCompleted 28.6 KiB/167.4 KiB (211.7 KiB/s) with 9 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b5c0fb37cdb9ae735f1/contents/manifest.xml\nCompleted 28.6 KiB/167.4 KiB (211.7 KiB/s) with 8 file(s) remaining\rCompleted 31.1 KiB/167.4 KiB (224.7 KiB/s) with 8 file(s) remaining\rupload: contents/Figueredo2013_1.ode to s3://files.biosimulations.org/simulations/647a4b5c0fb37cdb9ae735f1/contents/Figueredo2013_1.ode\nCompleted 31.1 KiB/167.4 KiB (224.7 KiB/s) with 7 file(s) remaining\rCompleted 35.2 KiB/167.4 KiB (227.0 KiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b5c0fb37cdb9ae735f1/contents/metadata.rdf\nCompleted 35.2 KiB/167.4 KiB (227.0 KiB/s) with 6 file(s) remaining\rCompleted 35.4 KiB/167.4 KiB (223.7 KiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b5c0fb37cdb9ae735f1/contents/curation_notes.txt\nCompleted 35.4 KiB/167.4 KiB (223.7 KiB/s) with 5 file(s) remaining\rCompleted 46.8 KiB/167.4 KiB (292.0 KiB/s) with 5 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b5c0fb37cdb9ae735f1/contents/curation_image.png\nCompleted 46.8 KiB/167.4 KiB (292.0 KiB/s) with 4 file(s) remaining\rCompleted 51.0 KiB/167.4 KiB (313.8 KiB/s) with 4 file(s) remaining\rupload: contents/Figueredo2013_1-octave.m to s3://files.biosimulations.org/simulations/647a4b5c0fb37cdb9ae735f1/contents/Figueredo2013_1-octave.m\nCompleted 51.0 KiB/167.4 KiB (313.8 KiB/s) with 3 file(s) remaining\rCompleted 62.5 KiB/167.4 KiB (348.3 KiB/s) with 3 file(s) remaining\rupload: contents/Figueredo2013_1.sedml to s3://files.biosimulations.org/simulations/647a4b5c0fb37cdb9ae735f1/contents/Figueredo2013_1.sedml\nCompleted 62.5 KiB/167.4 KiB (348.3 KiB/s) with 2 file(s) remaining\rCompleted 107.1 KiB/167.4 KiB (555.7 KiB/s) with 2 file(s) remaining\rupload: contents/Figueredo2013_1.xml to s3://files.biosimulations.org/simulations/647a4b5c0fb37cdb9ae735f1/contents/Figueredo2013_1.xml\nCompleted 107.1 KiB/167.4 KiB (555.7 KiB/s) with 1 file(s) remaining\rCompleted 167.4 KiB/167.4 KiB (855.5 KiB/s) with 1 file(s) remaining\rupload: contents/Figueredo2013_1.cps to s3://files.biosimulations.org/simulations/647a4b5c0fb37cdb9ae735f1/contents/Figueredo2013_1.cps\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.5 KiB/7.5 KiB (98.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b5c0fb37cdb9ae735f1/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Figueredo2013_1.sedml\ncreating dataset /Figueredo2013_1.sedml/autogen_report_for_task1, shape: (19, 401), type: float64\ndataset created, uuid: d-2c380677-b23bc928-7ad6-82edce-cbca06, chunk_size: (19, 401)\ncreating dataset /Figueredo2013_1.sedml/plot_1_task1, shape: (3, 401), type: float64\ndataset created, uuid: d-2c380677-b23bc928-ee5b-e926ae-d0343f, chunk_size: (3, 401)\ncreating attribute combineArchiveLocation in /Figueredo2013_1.sedml\ncreating attribute uri in /Figueredo2013_1.sedml\ncreating attribute _type in /Figueredo2013_1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Figueredo2013_1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Figueredo2013_1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Figueredo2013_1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Figueredo2013_1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Figueredo2013_1.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Figueredo2013_1.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Figueredo2013_1.sedml/autogen_report_for_task1\ncreating attribute uri in /Figueredo2013_1.sedml/autogen_report_for_task1\ncreating attribute _type in /Figueredo2013_1.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Figueredo2013_1.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Figueredo2013_1.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Figueredo2013_1.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Figueredo2013_1.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Figueredo2013_1.sedml/plot_1_task1\ncreating attribute sedmlId in /Figueredo2013_1.sedml/plot_1_task1\ncreating attribute sedmlName in /Figueredo2013_1.sedml/plot_1_task1\ncreating attribute uri in /Figueredo2013_1.sedml/plot_1_task1\ncreate_links: /\ngot link: Figueredo2013_1.sedml\ncreate_links: /Figueredo2013_1.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Figueredo2013_1.sedml/autogen_report_for_task1 to tgt: /Figueredo2013_1.sedml/autogen_report_for_task1, shape: (19, 401), type: float64\niterating over chunks for /Figueredo2013_1.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 19, 1), slice(0, 401, 1))\ndone with dataload for /Figueredo2013_1.sedml/autogen_report_for_task1\nwrite_dataset src: /Figueredo2013_1.sedml/plot_1_task1 to tgt: /Figueredo2013_1.sedml/plot_1_task1, shape: (3, 401), type: float64\niterating over chunks for /Figueredo2013_1.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 401, 1))\ndone with dataload for /Figueredo2013_1.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b5c0fb37cdb9ae735f1\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 and upload the outputs of the simulation run ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.314795,"sedDocuments":[{"location":"Figueredo2013_1.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  Figueredo2013_1.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 19 data sets\r\n    Plots (1):\r\n      plot_1_task1: 2 curves\r\n\r\nExecuting SED-ML file 1: Figueredo2013_1.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":0.843852,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.220325,"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":0.390591,"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":0.109441,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_E","status":"SUCCEEDED"},{"id":"autogen_task1_T","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_p","status":"SUCCEEDED"},{"id":"autogen_task1_g","status":"SUCCEEDED"},{"id":"autogen_task1_m","status":"SUCCEEDED"},{"id":"autogen_task1_d","status":"SUCCEEDED"},{"id":"autogen_task1_s","status":"SUCCEEDED"},{"id":"autogen_task1_tumor_microenvironment","status":"SUCCEEDED"},{"id":"autogen_task1_tumor_growth","status":"SUCCEEDED"},{"id":"autogen_task1_tumor_death","status":"SUCCEEDED"},{"id":"autogen_task1_tumor_killing","status":"SUCCEEDED"},{"id":"autogen_task1_immune_stimulation","status":"SUCCEEDED"},{"id":"autogen_task1_immune_exhaustion","status":"SUCCEEDED"},{"id":"autogen_task1_immune_death","status":"SUCCEEDED"},{"id":"autogen_task1_immune_source","status":"SUCCEEDED"}]}]}]}