{"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    440      0 --:--:-- --:--:-- --:--:--   439\n\r100 89225  100 89225    0     0   207k      0 --:--:-- --:--:-- --:--:--  207k\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 (22.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b67195afd5df175f124/rawLog.txt\nCompleted 3.8 KiB/3.8 KiB (51.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b67195afd5df175f124/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/West2019 - Cellular interactions constrain tumor growth.sedml/ (stored 0%)\n  adding: outputs/West2019 - Cellular interactions constrain tumor growth.sedml/plot_1_task1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 15%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 174.2 KiB/174.2 KiB (1.7 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b67195afd5df175f124/outputs/reports.h5\nCompleted 160.4 KiB/188.0 KiB (2.0 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b67195afd5df175f124/output.zip\nCompleted 160.4 KiB/188.0 KiB (2.0 MiB/s) with 3 file(s) remaining\rCompleted 170.2 KiB/188.0 KiB (1.6 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b67195afd5df175f124/outputs/plots.zip\nCompleted 170.2 KiB/188.0 KiB (1.6 MiB/s) with 2 file(s) remaining\rCompleted 185.2 KiB/188.0 KiB (1.6 MiB/s) with 2 file(s) remaining\rupload: outputs/West2019 - Cellular interactions constrain tumor growth.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b67195afd5df175f124/outputs/West2019 - Cellular interactions constrain tumor growth.sedml/plot_1_task1.pdf\nCompleted 185.2 KiB/188.0 KiB (1.6 MiB/s) with 1 file(s) remaining\rCompleted 188.0 KiB/188.0 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b67195afd5df175f124/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Fig 2.png      \n  inflating: contents/West2019 - Cellular interactions constrain tumor growth-biopax2.owl  \n  inflating: contents/West2019 - Cellular interactions constrain tumor growth-biopax3.owl  \n  inflating: contents/West2019 - Cellular interactions constrain tumor growth-matlab.m  \n  inflating: contents/West2019 - Cellular interactions constrain tumor growth-octave.m  \n  inflating: contents/West2019 - Cellular interactions constrain tumor growth.cps  \n  inflating: contents/West2019 - Cellular interactions constrain tumor growth.ode  \n  inflating: contents/West2019 - Cellular interactions constrain tumor growth.sedml  \n  inflating: contents/West2019 - Cellular interactions constrain tumor growth.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 10.4 KiB/251.3 KiB (152.4 KiB/s) with 13 file(s) remaining\rupload: contents/West2019 - Cellular interactions constrain tumor growth-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b67195afd5df175f124/contents/West2019 - Cellular interactions constrain tumor growth-biopax2.owl\nCompleted 10.4 KiB/251.3 KiB (152.4 KiB/s) with 12 file(s) remaining\rCompleted 44.1 KiB/251.3 KiB (341.3 KiB/s) with 12 file(s) remaining\rupload: contents/Fig 2.png to s3://files.biosimulations.org/simulations/647a4b67195afd5df175f124/contents/Fig 2.png\nCompleted 44.1 KiB/251.3 KiB (341.3 KiB/s) with 11 file(s) remaining\rCompleted 59.2 KiB/251.3 KiB (451.3 KiB/s) with 11 file(s) remaining\rupload: contents/West2019 - Cellular interactions constrain tumor growth-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b67195afd5df175f124/contents/West2019 - Cellular interactions constrain tumor growth-biopax3.owl\nCompleted 59.2 KiB/251.3 KiB (451.3 KiB/s) with 10 file(s) remaining\rCompleted 65.6 KiB/251.3 KiB (468.2 KiB/s) with 10 file(s) remaining\rupload: contents/West2019 - Cellular interactions constrain tumor growth-matlab.m to s3://files.biosimulations.org/simulations/647a4b67195afd5df175f124/contents/West2019 - Cellular interactions constrain tumor growth-matlab.m\nCompleted 65.6 KiB/251.3 KiB (468.2 KiB/s) with 9 file(s) remaining\rCompleted 113.9 KiB/251.3 KiB (806.7 KiB/s) with 9 file(s) remaining\rupload: contents/West2019 - Cellular interactions constrain tumor growth.xml to s3://files.biosimulations.org/simulations/647a4b67195afd5df175f124/contents/West2019 - Cellular interactions constrain tumor growth.xml\nCompleted 113.9 KiB/251.3 KiB (806.7 KiB/s) with 8 file(s) remaining\rCompleted 147.6 KiB/251.3 KiB (1000.4 KiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b67195afd5df175f124/contents/curation_image.png\nCompleted 147.6 KiB/251.3 KiB (1000.4 KiB/s) with 7 file(s) remaining\rCompleted 216.7 KiB/251.3 KiB (1.4 MiB/s) with 7 file(s) remaining   \rupload: contents/West2019 - Cellular interactions constrain tumor growth.cps to s3://files.biosimulations.org/simulations/647a4b67195afd5df175f124/contents/West2019 - Cellular interactions constrain tumor growth.cps\nCompleted 216.7 KiB/251.3 KiB (1.4 MiB/s) with 6 file(s) remaining\rCompleted 216.9 KiB/251.3 KiB (1.4 MiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b67195afd5df175f124/contents/curation_notes.txt\nCompleted 216.9 KiB/251.3 KiB (1.4 MiB/s) with 5 file(s) remaining\rCompleted 218.7 KiB/251.3 KiB (1.3 MiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b67195afd5df175f124/contents/manifest.xml\nCompleted 218.7 KiB/251.3 KiB (1.3 MiB/s) with 4 file(s) remaining\rCompleted 223.3 KiB/251.3 KiB (1.2 MiB/s) with 4 file(s) remaining\rupload: contents/West2019 - Cellular interactions constrain tumor growth.ode to s3://files.biosimulations.org/simulations/647a4b67195afd5df175f124/contents/West2019 - Cellular interactions constrain tumor growth.ode\nCompleted 223.3 KiB/251.3 KiB (1.2 MiB/s) with 3 file(s) remaining\rCompleted 241.4 KiB/251.3 KiB (1.2 MiB/s) with 3 file(s) remaining\rupload: contents/West2019 - Cellular interactions constrain tumor growth.sedml to s3://files.biosimulations.org/simulations/647a4b67195afd5df175f124/contents/West2019 - Cellular interactions constrain tumor growth.sedml\nCompleted 241.4 KiB/251.3 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 247.8 KiB/251.3 KiB (1.2 MiB/s) with 2 file(s) remaining\rupload: contents/West2019 - Cellular interactions constrain tumor growth-octave.m to s3://files.biosimulations.org/simulations/647a4b67195afd5df175f124/contents/West2019 - Cellular interactions constrain tumor growth-octave.m\nCompleted 247.8 KiB/251.3 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 251.3 KiB/251.3 KiB (1.0 MiB/s) with 1 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b67195afd5df175f124/contents/metadata.rdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (86.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b67195afd5df175f124/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /West2019 - Cellular interactions constrain tumor growth.sedml\ncreating dataset /West2019 - Cellular interactions constrain tumor growth.sedml/autogen_report_for_task1, shape: (27, 1001), type: float64\ndataset created, uuid: d-1750b21d-fc51f115-7c9d-bdaebb-89d5d2, chunk_size: (27, 1001)\ncreating dataset /West2019 - Cellular interactions constrain tumor growth.sedml/plot_1_task1, shape: (8, 1001), type: float64\ndataset created, uuid: d-1750b21d-fc51f115-cc98-776951-aee776, chunk_size: (8, 1001)\ncreating attribute combineArchiveLocation in /West2019 - Cellular interactions constrain tumor growth.sedml\ncreating attribute uri in /West2019 - Cellular interactions constrain tumor growth.sedml\ncreating attribute _type in /West2019 - Cellular interactions constrain tumor growth.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /West2019 - Cellular interactions constrain tumor growth.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /West2019 - Cellular interactions constrain tumor growth.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /West2019 - Cellular interactions constrain tumor growth.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /West2019 - Cellular interactions constrain tumor growth.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /West2019 - Cellular interactions constrain tumor growth.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /West2019 - Cellular interactions constrain tumor growth.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /West2019 - Cellular interactions constrain tumor growth.sedml/autogen_report_for_task1\ncreating attribute uri in /West2019 - Cellular interactions constrain tumor growth.sedml/autogen_report_for_task1\ncreating attribute _type in /West2019 - Cellular interactions constrain tumor growth.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /West2019 - Cellular interactions constrain tumor growth.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /West2019 - Cellular interactions constrain tumor growth.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /West2019 - Cellular interactions constrain tumor growth.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /West2019 - Cellular interactions constrain tumor growth.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /West2019 - Cellular interactions constrain tumor growth.sedml/plot_1_task1\ncreating attribute sedmlId in /West2019 - Cellular interactions constrain tumor growth.sedml/plot_1_task1\ncreating attribute sedmlName in /West2019 - Cellular interactions constrain tumor growth.sedml/plot_1_task1\ncreating attribute uri in /West2019 - Cellular interactions constrain tumor growth.sedml/plot_1_task1\ncreate_links: /\ngot link: West2019 - Cellular interactions constrain tumor growth.sedml\ncreate_links: /West2019 - Cellular interactions constrain tumor growth.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /West2019 - Cellular interactions constrain tumor growth.sedml/autogen_report_for_task1 to tgt: /West2019 - Cellular interactions constrain tumor growth.sedml/autogen_report_for_task1, shape: (27, 1001), type: float64\niterating over chunks for /West2019 - Cellular interactions constrain tumor growth.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 27, 1), slice(0, 1001, 1))\ndone with dataload for /West2019 - Cellular interactions constrain tumor growth.sedml/autogen_report_for_task1\nwrite_dataset src: /West2019 - Cellular interactions constrain tumor growth.sedml/plot_1_task1 to tgt: /West2019 - Cellular interactions constrain tumor growth.sedml/plot_1_task1, shape: (8, 1001), type: float64\niterating over chunks for /West2019 - Cellular interactions constrain tumor growth.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 8, 1), slice(0, 1001, 1))\ndone with dataload for /West2019 - Cellular interactions constrain tumor growth.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b67195afd5df175f124\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 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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":1.474283,"sedDocuments":[{"location":"West2019 - Cellular interactions constrain tumor growth.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  West2019 - Cellular interactions constrain tumor growth.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: 7 curves\r\n\r\nExecuting SED-ML file 1: West2019 - Cellular interactions constrain tumor growth.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":1.052435,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.170849,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"deterministic"},{"key":"methodCode","value":22},{"key":"parameters","value":{"Absolute Tolerance":1e-12,"Integrate Reduced Model":false,"Max Internal Steps":10000,"Relative Tolerance":0.000001}}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.487464,"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":"p1_curve_6_task1","status":"SUCCEEDED"},{"id":"p1_curve_7_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.25436,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_tumor_at_Exp_growth","status":"SUCCEEDED"},{"id":"autogen_task1_tumor_at_Exp_Lin_growth","status":"SUCCEEDED"},{"id":"autogen_task1_tumor_at_Gen__logistic_growth","status":"SUCCEEDED"},{"id":"autogen_task1_tumor_at_Gomp__growth","status":"SUCCEEDED"},{"id":"autogen_task1_tumor_at_Logistic_growth","status":"SUCCEEDED"},{"id":"autogen_task1_tumor_at_Power_growth","status":"SUCCEEDED"},{"id":"autogen_task1_tumor_at_Von_Bert__growth","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_0","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_1","status":"SUCCEEDED"},{"id":"autogen_task1_tau","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_1_variable","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_0_variable","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_K","status":"SUCCEEDED"},{"id":"autogen_task1_nu","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_exponential_linear_growth","status":"SUCCEEDED"},{"id":"autogen_task1_generalized_logistic_growth","status":"SUCCEEDED"},{"id":"autogen_task1_Gompertz_growth","status":"SUCCEEDED"},{"id":"autogen_task1_power_law_model","status":"SUCCEEDED"},{"id":"autogen_task1_Von_Bertalanffy_equation","status":"SUCCEEDED"},{"id":"autogen_task1_exponential_growth","status":"SUCCEEDED"},{"id":"autogen_task1_logistic_growth","status":"SUCCEEDED"}]}]}]}