{"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    449      0 --:--:-- --:--:-- --:--:--   448\n\r100 64073  100 64073    0     0   146k      0 --:--:-- --:--:-- --:--:--  146k\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 (23.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b5b195afd5df175f048/rawLog.txt\nCompleted 3.3 KiB/3.3 KiB (45.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b5b195afd5df175f048/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 76%)\n  adding: outputs/Phan2017.sedml/ (stored 0%)\n  adding: outputs/Phan2017.sedml/plot_1_task1.pdf (deflated 27%)\n  adding: outputs/reports.h5 (deflated 39%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 52.2 KiB/52.2 KiB (571.0 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b5b195afd5df175f048/outputs/reports.h5\nCompleted 43.7 KiB/68.5 KiB (570.3 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b5b195afd5df175f048/output.zip\nCompleted 43.7 KiB/68.5 KiB (570.3 KiB/s) with 3 file(s) remaining\rCompleted 52.9 KiB/68.5 KiB (488.6 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b5b195afd5df175f048/outputs/plots.zip\nCompleted 52.9 KiB/68.5 KiB (488.6 KiB/s) with 2 file(s) remaining\rCompleted 65.8 KiB/68.5 KiB (584.7 KiB/s) with 2 file(s) remaining\rupload: outputs/Phan2017.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b5b195afd5df175f048/outputs/Phan2017.sedml/plot_1_task1.pdf\nCompleted 65.8 KiB/68.5 KiB (584.7 KiB/s) with 1 file(s) remaining\rCompleted 68.5 KiB/68.5 KiB (570.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b5b195afd5df175f048/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/Phan2017-biopax2.owl  \n  inflating: contents/Phan2017-biopax3.owl  \n  inflating: contents/Phan2017-matlab.m  \n  inflating: contents/Phan2017-octave.m  \n  inflating: contents/Phan2017.cps   \n  inflating: contents/Phan2017.ode   \n  inflating: contents/Phan2017.sedml  \n  inflating: contents/Phan2017.xml   \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 14.7 KiB/247.7 KiB (194.4 KiB/s) with 13 file(s) remaining\rupload: contents/Phan2017-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b5b195afd5df175f048/contents/Phan2017-biopax2.owl\nCompleted 14.7 KiB/247.7 KiB (194.4 KiB/s) with 12 file(s) remaining\rCompleted 35.6 KiB/247.7 KiB (306.1 KiB/s) with 12 file(s) remaining\rupload: contents/Phan2017-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b5b195afd5df175f048/contents/Phan2017-biopax3.owl\nCompleted 35.6 KiB/247.7 KiB (306.1 KiB/s) with 11 file(s) remaining\rCompleted 58.2 KiB/247.7 KiB (488.8 KiB/s) with 11 file(s) remaining\rupload: contents/Fig.2.png to s3://files.biosimulations.org/simulations/647a4b5b195afd5df175f048/contents/Fig.2.png\nCompleted 58.2 KiB/247.7 KiB (488.8 KiB/s) with 10 file(s) remaining\rCompleted 61.7 KiB/247.7 KiB (444.6 KiB/s) with 10 file(s) remaining\rupload: contents/Phan2017.ode to s3://files.biosimulations.org/simulations/647a4b5b195afd5df175f048/contents/Phan2017.ode\nCompleted 61.7 KiB/247.7 KiB (444.6 KiB/s) with 9 file(s) remaining\rCompleted 123.7 KiB/247.7 KiB (858.1 KiB/s) with 9 file(s) remaining\rupload: contents/Phan2017.xml to s3://files.biosimulations.org/simulations/647a4b5b195afd5df175f048/contents/Phan2017.xml\nCompleted 123.7 KiB/247.7 KiB (858.1 KiB/s) with 8 file(s) remaining\rCompleted 141.6 KiB/247.7 KiB (912.1 KiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b5b195afd5df175f048/contents/curation_image.png\nCompleted 141.6 KiB/247.7 KiB (912.1 KiB/s) with 7 file(s) remaining\rCompleted 141.8 KiB/247.7 KiB (874.0 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b5b195afd5df175f048/contents/curation_notes.txt\nCompleted 141.8 KiB/247.7 KiB (874.0 KiB/s) with 6 file(s) remaining\rCompleted 143.2 KiB/247.7 KiB (859.9 KiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b5b195afd5df175f048/contents/manifest.xml\nCompleted 143.2 KiB/247.7 KiB (859.9 KiB/s) with 5 file(s) remaining\rCompleted 146.2 KiB/247.7 KiB (863.6 KiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b5b195afd5df175f048/contents/metadata.rdf\nCompleted 146.2 KiB/247.7 KiB (863.6 KiB/s) with 4 file(s) remaining\rCompleted 161.8 KiB/247.7 KiB (907.5 KiB/s) with 4 file(s) remaining\rupload: contents/Phan2017.sedml to s3://files.biosimulations.org/simulations/647a4b5b195afd5df175f048/contents/Phan2017.sedml\nCompleted 161.8 KiB/247.7 KiB (907.5 KiB/s) with 3 file(s) remaining\rCompleted 167.5 KiB/247.7 KiB (927.2 KiB/s) with 3 file(s) remaining\rupload: contents/Phan2017-matlab.m to s3://files.biosimulations.org/simulations/647a4b5b195afd5df175f048/contents/Phan2017-matlab.m\nCompleted 167.5 KiB/247.7 KiB (927.2 KiB/s) with 2 file(s) remaining\rCompleted 242.1 KiB/247.7 KiB (1.2 MiB/s) with 2 file(s) remaining  \rupload: contents/Phan2017.cps to s3://files.biosimulations.org/simulations/647a4b5b195afd5df175f048/contents/Phan2017.cps\nCompleted 242.1 KiB/247.7 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 247.7 KiB/247.7 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: contents/Phan2017-octave.m to s3://files.biosimulations.org/simulations/647a4b5b195afd5df175f048/contents/Phan2017-octave.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.7 KiB/7.7 KiB (102.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b5b195afd5df175f048/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Phan2017.sedml\ncreating dataset /Phan2017.sedml/autogen_report_for_task1, shape: (25, 201), type: float64\ndataset created, uuid: d-e79d3572-d5c9c628-ce51-4e7eae-cbd77f, chunk_size: (25, 201)\ncreating dataset /Phan2017.sedml/plot_1_task1, shape: (5, 201), type: float64\ndataset created, uuid: d-e79d3572-d5c9c628-cb4a-027861-51130c, chunk_size: (5, 201)\ncreating attribute combineArchiveLocation in /Phan2017.sedml\ncreating attribute uri in /Phan2017.sedml\ncreating attribute _type in /Phan2017.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Phan2017.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Phan2017.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Phan2017.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Phan2017.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Phan2017.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Phan2017.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Phan2017.sedml/autogen_report_for_task1\ncreating attribute uri in /Phan2017.sedml/autogen_report_for_task1\ncreating attribute _type in /Phan2017.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Phan2017.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Phan2017.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Phan2017.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Phan2017.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Phan2017.sedml/plot_1_task1\ncreating attribute sedmlId in /Phan2017.sedml/plot_1_task1\ncreating attribute sedmlName in /Phan2017.sedml/plot_1_task1\ncreating attribute uri in /Phan2017.sedml/plot_1_task1\ncreate_links: /\ngot link: Phan2017.sedml\ncreate_links: /Phan2017.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Phan2017.sedml/autogen_report_for_task1 to tgt: /Phan2017.sedml/autogen_report_for_task1, shape: (25, 201), type: float64\niterating over chunks for /Phan2017.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 25, 1), slice(0, 201, 1))\ndone with dataload for /Phan2017.sedml/autogen_report_for_task1\nwrite_dataset src: /Phan2017.sedml/plot_1_task1 to tgt: /Phan2017.sedml/plot_1_task1, shape: (5, 201), type: float64\niterating over chunks for /Phan2017.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 201, 1))\ndone with dataload for /Phan2017.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b5b195afd5df175f048\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 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.\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 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":1.114551,"sedDocuments":[{"location":"Phan2017.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  Phan2017.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 25 data sets\r\n    Plots (1):\r\n      plot_1_task1: 4 curves\r\n\r\nExecuting SED-ML file 1: Phan2017.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":0.714267,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.144164,"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":0.346061,"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":0.097194,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_z","status":"SUCCEEDED"},{"id":"autogen_task1_y","status":"SUCCEEDED"},{"id":"autogen_task1_x","status":"SUCCEEDED"},{"id":"autogen_task1_v","status":"SUCCEEDED"},{"id":"autogen_task1_r","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_c","status":"SUCCEEDED"},{"id":"autogen_task1_d","status":"SUCCEEDED"},{"id":"autogen_task1_e","status":"SUCCEEDED"},{"id":"autogen_task1_m","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_b","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_cross_infection","status":"SUCCEEDED"},{"id":"autogen_task1_infected_tumor_killing","status":"SUCCEEDED"},{"id":"autogen_task1_infected_tumor_death","status":"SUCCEEDED"},{"id":"autogen_task1_virus_multiplication_in_infected_tumor","status":"SUCCEEDED"},{"id":"autogen_task1_virus_clearing","status":"SUCCEEDED"},{"id":"autogen_task1_virus_killing_by_immune","status":"SUCCEEDED"},{"id":"autogen_task1_immune_stimulation","status":"SUCCEEDED"},{"id":"autogen_task1_immune_cell_death","status":"SUCCEEDED"},{"id":"autogen_task1_infection","status":"SUCCEEDED"}]}]}]}