{"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    470      0 --:--:-- --:--:-- --:--:--   471\n\r100 38189  100 38189    0     0  95264      0 --:--:-- --:--:-- --:--:-- 95264\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 (14.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5f66195afd5df176219f/rawLog.txt\nCompleted 3.1 KiB/3.1 KiB (28.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a5f66195afd5df176219f/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 74%)\n  adding: outputs/Al-Tuwairqi2020 - Fig8 simulation.sedml/ (stored 0%)\n  adding: outputs/Al-Tuwairqi2020 - Fig8 simulation.sedml/plot_1_task1.pdf (deflated 29%)\n  adding: outputs/reports.h5 (deflated 18%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 117.8 KiB/117.8 KiB (930.0 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a5f66195afd5df176219f/outputs/reports.h5\nCompleted 10.0 KiB/136.4 KiB (92.0 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a5f66195afd5df176219f/outputs/plots.zip\nCompleted 10.0 KiB/136.4 KiB (92.0 KiB/s) with 3 file(s) remaining\rCompleted 119.5 KiB/136.4 KiB (843.8 KiB/s) with 3 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a5f66195afd5df176219f/output.zip\nCompleted 119.5 KiB/136.4 KiB (843.8 KiB/s) with 2 file(s) remaining\rCompleted 122.1 KiB/136.4 KiB (845.8 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5f66195afd5df176219f/rawLog.txt\nCompleted 122.1 KiB/136.4 KiB (845.8 KiB/s) with 1 file(s) remaining\rCompleted 136.4 KiB/136.4 KiB (867.7 KiB/s) with 1 file(s) remaining\rupload: outputs/Al-Tuwairqi2020 - Fig8 simulation.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a5f66195afd5df176219f/outputs/Al-Tuwairqi2020 - Fig8 simulation.sedml/plot_1_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Al-Tuwairqi2020 - Fig8 simulation.sedml  \n  inflating: contents/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment-biopax2.owl  \n  inflating: contents/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment-biopax3.owl  \n  inflating: contents/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment-matlab.m  \n  inflating: contents/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment-octave.m  \n  inflating: contents/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment.cps  \n  inflating: contents/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment.ode  \n  inflating: contents/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 13.4 KiB/180.6 KiB (138.6 KiB/s) with 12 file(s) remaining\rupload: contents/Al-Tuwairqi2020 - Fig8 simulation.sedml to s3://files.biosimulations.org/simulations/647a5f66195afd5df176219f/contents/Al-Tuwairqi2020 - Fig8 simulation.sedml\nCompleted 13.4 KiB/180.6 KiB (138.6 KiB/s) with 11 file(s) remaining\rCompleted 26.9 KiB/180.6 KiB (201.4 KiB/s) with 11 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a5f66195afd5df176219f/contents/curation_image.png\nCompleted 26.9 KiB/180.6 KiB (201.4 KiB/s) with 10 file(s) remaining\rCompleted 32.1 KiB/180.6 KiB (222.7 KiB/s) with 10 file(s) remaining\rupload: contents/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment-matlab.m to s3://files.biosimulations.org/simulations/647a5f66195afd5df176219f/contents/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment-matlab.m\nCompleted 32.1 KiB/180.6 KiB (222.7 KiB/s) with 9 file(s) remaining\rCompleted 33.8 KiB/180.6 KiB (217.2 KiB/s) with 9 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a5f66195afd5df176219f/contents/manifest.xml\nCompleted 33.8 KiB/180.6 KiB (217.2 KiB/s) with 8 file(s) remaining\rCompleted 33.9 KiB/180.6 KiB (214.1 KiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a5f66195afd5df176219f/contents/curation_notes.txt\nCompleted 33.9 KiB/180.6 KiB (214.1 KiB/s) with 7 file(s) remaining\rCompleted 69.6 KiB/180.6 KiB (433.0 KiB/s) with 7 file(s) remaining\rupload: contents/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment.xml to s3://files.biosimulations.org/simulations/647a5f66195afd5df176219f/contents/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment.xml\nCompleted 69.6 KiB/180.6 KiB (433.0 KiB/s) with 6 file(s) remaining\rCompleted 92.3 KiB/180.6 KiB (526.5 KiB/s) with 6 file(s) remaining\rupload: contents/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment-biopax3.owl to s3://files.biosimulations.org/simulations/647a5f66195afd5df176219f/contents/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment-biopax3.owl\nCompleted 92.3 KiB/180.6 KiB (526.5 KiB/s) with 5 file(s) remaining\rCompleted 97.5 KiB/180.6 KiB (533.3 KiB/s) with 5 file(s) remaining\rupload: contents/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment-octave.m to s3://files.biosimulations.org/simulations/647a5f66195afd5df176219f/contents/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment-octave.m\nCompleted 97.5 KiB/180.6 KiB (533.3 KiB/s) with 4 file(s) remaining\rCompleted 100.8 KiB/180.6 KiB (542.8 KiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a5f66195afd5df176219f/contents/metadata.rdf\nCompleted 100.8 KiB/180.6 KiB (542.8 KiB/s) with 3 file(s) remaining\rCompleted 104.1 KiB/180.6 KiB (527.6 KiB/s) with 3 file(s) remaining\rupload: contents/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment.ode to s3://files.biosimulations.org/simulations/647a5f66195afd5df176219f/contents/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment.ode\nCompleted 104.1 KiB/180.6 KiB (527.6 KiB/s) with 2 file(s) remaining\rCompleted 120.6 KiB/180.6 KiB (586.3 KiB/s) with 2 file(s) remaining\rupload: contents/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment-biopax2.owl to s3://files.biosimulations.org/simulations/647a5f66195afd5df176219f/contents/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment-biopax2.owl\nCompleted 120.6 KiB/180.6 KiB (586.3 KiB/s) with 1 file(s) remaining\rCompleted 180.6 KiB/180.6 KiB (865.4 KiB/s) with 1 file(s) remaining\rupload: contents/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment.cps to s3://files.biosimulations.org/simulations/647a5f66195afd5df176219f/contents/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment.cps\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.4 KiB/8.4 KiB (78.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5f66195afd5df176219f/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Al-Tuwairqi2020 - Fig8 simulation.sedml\ncreating dataset /Al-Tuwairqi2020 - Fig8 simulation.sedml/autogen_report_for_task1, shape: (19, 1001), type: float64\ndataset created, uuid: d-97bbd3b2-e25c9314-9fae-1ab271-87ee48, chunk_size: (19, 1001)\ncreating dataset /Al-Tuwairqi2020 - Fig8 simulation.sedml/plot_1_task1, shape: (5, 1001), type: float64\ndataset created, uuid: d-97bbd3b2-e25c9314-f8b6-aba676-32a6e8, chunk_size: (5, 1001)\ncreating attribute combineArchiveLocation in /Al-Tuwairqi2020 - Fig8 simulation.sedml\ncreating attribute uri in /Al-Tuwairqi2020 - Fig8 simulation.sedml\ncreating attribute _type in /Al-Tuwairqi2020 - Fig8 simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Al-Tuwairqi2020 - Fig8 simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Al-Tuwairqi2020 - Fig8 simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Al-Tuwairqi2020 - Fig8 simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Al-Tuwairqi2020 - Fig8 simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Al-Tuwairqi2020 - Fig8 simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Al-Tuwairqi2020 - Fig8 simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Al-Tuwairqi2020 - Fig8 simulation.sedml/autogen_report_for_task1\ncreating attribute uri in /Al-Tuwairqi2020 - Fig8 simulation.sedml/autogen_report_for_task1\ncreating attribute _type in /Al-Tuwairqi2020 - Fig8 simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Al-Tuwairqi2020 - Fig8 simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Al-Tuwairqi2020 - Fig8 simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Al-Tuwairqi2020 - Fig8 simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Al-Tuwairqi2020 - Fig8 simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Al-Tuwairqi2020 - Fig8 simulation.sedml/plot_1_task1\ncreating attribute sedmlId in /Al-Tuwairqi2020 - Fig8 simulation.sedml/plot_1_task1\ncreating attribute sedmlName in /Al-Tuwairqi2020 - Fig8 simulation.sedml/plot_1_task1\ncreating attribute uri in /Al-Tuwairqi2020 - Fig8 simulation.sedml/plot_1_task1\ncreate_links: /\ngot link: Al-Tuwairqi2020 - Fig8 simulation.sedml\ncreate_links: /Al-Tuwairqi2020 - Fig8 simulation.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Al-Tuwairqi2020 - Fig8 simulation.sedml/autogen_report_for_task1 to tgt: /Al-Tuwairqi2020 - Fig8 simulation.sedml/autogen_report_for_task1, shape: (19, 1001), type: float64\niterating over chunks for /Al-Tuwairqi2020 - Fig8 simulation.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 19, 1), slice(0, 1001, 1))\ndone with dataload for /Al-Tuwairqi2020 - Fig8 simulation.sedml/autogen_report_for_task1\nwrite_dataset src: /Al-Tuwairqi2020 - Fig8 simulation.sedml/plot_1_task1 to tgt: /Al-Tuwairqi2020 - Fig8 simulation.sedml/plot_1_task1, shape: (5, 1001), type: float64\niterating over chunks for /Al-Tuwairqi2020 - Fig8 simulation.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 1001, 1))\ndone with dataload for /Al-Tuwairqi2020 - Fig8 simulation.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a5f66195afd5df176219f\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.\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 and upload the outputs of the simulation run ... 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":1.19584,"sedDocuments":[{"location":"Al-Tuwairqi2020 - Fig8 simulation.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  Al-Tuwairqi2020 - Fig8 simulation.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: 4 curves\r\n\r\nExecuting SED-ML file 1: Al-Tuwairqi2020 - Fig8 simulation.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":0.819331,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.118938,"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":100000,"Relative Tolerance":0.000001}}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.404695,"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":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.179896,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_uninfected_cancer_cells","status":"SUCCEEDED"},{"id":"autogen_task1_infected_cancer_cells","status":"SUCCEEDED"},{"id":"autogen_task1_free_virus","status":"SUCCEEDED"},{"id":"autogen_task1_damaged_cancer_cells","status":"SUCCEEDED"},{"id":"autogen_task1_f","status":"SUCCEEDED"},{"id":"autogen_task1_h","status":"SUCCEEDED"},{"id":"autogen_task1_m","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_1","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_2","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_3","status":"SUCCEEDED"},{"id":"autogen_task1_Whole_organism","status":"SUCCEEDED"},{"id":"autogen_task1_uninfected_cancer_cell_growth","status":"SUCCEEDED"},{"id":"autogen_task1_cancer_cell_infection","status":"SUCCEEDED"},{"id":"autogen_task1_infected_cancer_cell_lysis","status":"SUCCEEDED"},{"id":"autogen_task1_virus_infection_removal","status":"SUCCEEDED"},{"id":"autogen_task1_radiotherapy_uninfected_cells","status":"SUCCEEDED"},{"id":"autogen_task1_radiotherapy_infected_cells","status":"SUCCEEDED"},{"id":"autogen_task1_damaged_cell_removal","status":"SUCCEEDED"}]}]}]}