{"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    430      0 --:--:-- --:--:-- --:--:--   430\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100 41306  100 41306    0     0  96458      0 --:--:-- --:--:-- --:--:--  420k\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 (24.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b9a195afd5df175f59b/rawLog.txt\nCompleted 2.5 KiB/2.5 KiB (36.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b9a195afd5df175f59b/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 72%)\n  adding: outputs/Alharbi2019 TNM - Fig10.sedml/ (stored 0%)\n  adding: outputs/Alharbi2019 TNM - Fig10.sedml/plot_1_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 75%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 31.9 KiB/31.9 KiB (444.5 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b9a195afd5df175f59b/outputs/reports.h5\nCompleted 17.9 KiB/38.7 KiB (229.1 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b9a195afd5df175f59b/output.zip\nCompleted 17.9 KiB/38.7 KiB (229.1 KiB/s) with 3 file(s) remaining\rCompleted 25.3 KiB/38.7 KiB (247.1 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b9a195afd5df175f59b/outputs/plots.zip\nCompleted 25.3 KiB/38.7 KiB (247.1 KiB/s) with 2 file(s) remaining\rCompleted 36.0 KiB/38.7 KiB (324.7 KiB/s) with 2 file(s) remaining\rupload: outputs/Alharbi2019 TNM - Fig10.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b9a195afd5df175f59b/outputs/Alharbi2019 TNM - Fig10.sedml/plot_1_task1.pdf\nCompleted 36.0 KiB/38.7 KiB (324.7 KiB/s) with 1 file(s) remaining\rCompleted 38.7 KiB/38.7 KiB (314.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b9a195afd5df175f59b/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Alharbi2019 TNM - Fig10.sedml  \n  inflating: contents/Alharbi2019 TNM-biopax2.owl  \n  inflating: contents/Alharbi2019 TNM-biopax3.owl  \n  inflating: contents/Alharbi2019 TNM-matlab.m  \n  inflating: contents/Alharbi2019 TNM-octave.m  \n  inflating: contents/Alharbi2019 TNM.cps  \n  inflating: contents/Alharbi2019 TNM.ode  \n  inflating: contents/Alharbi2019 TNM.xml  \n  inflating: contents/Fig10.png      \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 8.4 KiB/137.4 KiB (113.9 KiB/s) with 13 file(s) remaining\rupload: contents/Alharbi2019 TNM-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b9a195afd5df175f59b/contents/Alharbi2019 TNM-biopax2.owl\nCompleted 8.4 KiB/137.4 KiB (113.9 KiB/s) with 12 file(s) remaining\rCompleted 18.6 KiB/137.4 KiB (162.7 KiB/s) with 12 file(s) remaining\rupload: contents/Alharbi2019 TNM-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b9a195afd5df175f59b/contents/Alharbi2019 TNM-biopax3.owl\nCompleted 18.6 KiB/137.4 KiB (162.7 KiB/s) with 11 file(s) remaining\rCompleted 42.3 KiB/137.4 KiB (346.7 KiB/s) with 11 file(s) remaining\rupload: contents/Alharbi2019 TNM.xml to s3://files.biosimulations.org/simulations/647a4b9a195afd5df175f59b/contents/Alharbi2019 TNM.xml\nCompleted 42.3 KiB/137.4 KiB (346.7 KiB/s) with 10 file(s) remaining\rCompleted 51.2 KiB/137.4 KiB (407.9 KiB/s) with 10 file(s) remaining\rupload: contents/Alharbi2019 TNM - Fig10.sedml to s3://files.biosimulations.org/simulations/647a4b9a195afd5df175f59b/contents/Alharbi2019 TNM - Fig10.sedml\nCompleted 51.2 KiB/137.4 KiB (407.9 KiB/s) with 9 file(s) remaining\rCompleted 61.3 KiB/137.4 KiB (439.4 KiB/s) with 9 file(s) remaining\rupload: contents/Fig10.png to s3://files.biosimulations.org/simulations/647a4b9a195afd5df175f59b/contents/Fig10.png\nCompleted 61.3 KiB/137.4 KiB (439.4 KiB/s) with 8 file(s) remaining\rCompleted 61.5 KiB/137.4 KiB (428.2 KiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b9a195afd5df175f59b/contents/curation_notes.txt\nCompleted 61.5 KiB/137.4 KiB (428.2 KiB/s) with 7 file(s) remaining\rCompleted 71.6 KiB/137.4 KiB (491.9 KiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b9a195afd5df175f59b/contents/curation_image.png\nCompleted 71.6 KiB/137.4 KiB (491.9 KiB/s) with 6 file(s) remaining\rCompleted 73.8 KiB/137.4 KiB (500.3 KiB/s) with 6 file(s) remaining\rupload: contents/Alharbi2019 TNM.ode to s3://files.biosimulations.org/simulations/647a4b9a195afd5df175f59b/contents/Alharbi2019 TNM.ode\nCompleted 73.8 KiB/137.4 KiB (500.3 KiB/s) with 5 file(s) remaining\rCompleted 75.3 KiB/137.4 KiB (475.1 KiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b9a195afd5df175f59b/contents/manifest.xml\nCompleted 75.3 KiB/137.4 KiB (475.1 KiB/s) with 4 file(s) remaining\rCompleted 79.2 KiB/137.4 KiB (451.2 KiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b9a195afd5df175f59b/contents/metadata.rdf\nCompleted 79.2 KiB/137.4 KiB (451.2 KiB/s) with 3 file(s) remaining\rCompleted 82.9 KiB/137.4 KiB (460.2 KiB/s) with 3 file(s) remaining\rupload: contents/Alharbi2019 TNM-matlab.m to s3://files.biosimulations.org/simulations/647a4b9a195afd5df175f59b/contents/Alharbi2019 TNM-matlab.m\nCompleted 82.9 KiB/137.4 KiB (460.2 KiB/s) with 2 file(s) remaining\rCompleted 86.6 KiB/137.4 KiB (468.4 KiB/s) with 2 file(s) remaining\rupload: contents/Alharbi2019 TNM-octave.m to s3://files.biosimulations.org/simulations/647a4b9a195afd5df175f59b/contents/Alharbi2019 TNM-octave.m\nCompleted 86.6 KiB/137.4 KiB (468.4 KiB/s) with 1 file(s) remaining\rCompleted 137.4 KiB/137.4 KiB (710.0 KiB/s) with 1 file(s) remaining\rupload: contents/Alharbi2019 TNM.cps to s3://files.biosimulations.org/simulations/647a4b9a195afd5df175f59b/contents/Alharbi2019 TNM.cps\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.9 KiB/7.9 KiB (112.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b9a195afd5df175f59b/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Alharbi2019 TNM - Fig10.sedml\ncreating dataset /Alharbi2019 TNM - Fig10.sedml/autogen_report_for_task1, shape: (13, 101), type: float64\ndataset created, uuid: d-b5025c9f-31d27111-86f7-f27ba0-13fdf6, chunk_size: (13, 101)\ncreating dataset /Alharbi2019 TNM - Fig10.sedml/plot_1_task1, shape: (3, 101), type: float64\ndataset created, uuid: d-b5025c9f-31d27111-6a0e-196717-45bfb8, chunk_size: (3, 101)\ncreating attribute combineArchiveLocation in /Alharbi2019 TNM - Fig10.sedml\ncreating attribute uri in /Alharbi2019 TNM - Fig10.sedml\ncreating attribute _type in /Alharbi2019 TNM - Fig10.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Alharbi2019 TNM - Fig10.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Alharbi2019 TNM - Fig10.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Alharbi2019 TNM - Fig10.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Alharbi2019 TNM - Fig10.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Alharbi2019 TNM - Fig10.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Alharbi2019 TNM - Fig10.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Alharbi2019 TNM - Fig10.sedml/autogen_report_for_task1\ncreating attribute uri in /Alharbi2019 TNM - Fig10.sedml/autogen_report_for_task1\ncreating attribute _type in /Alharbi2019 TNM - Fig10.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Alharbi2019 TNM - Fig10.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Alharbi2019 TNM - Fig10.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Alharbi2019 TNM - Fig10.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Alharbi2019 TNM - Fig10.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Alharbi2019 TNM - Fig10.sedml/plot_1_task1\ncreating attribute sedmlId in /Alharbi2019 TNM - Fig10.sedml/plot_1_task1\ncreating attribute sedmlName in /Alharbi2019 TNM - Fig10.sedml/plot_1_task1\ncreating attribute uri in /Alharbi2019 TNM - Fig10.sedml/plot_1_task1\ncreate_links: /\ngot link: Alharbi2019 TNM - Fig10.sedml\ncreate_links: /Alharbi2019 TNM - Fig10.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Alharbi2019 TNM - Fig10.sedml/autogen_report_for_task1 to tgt: /Alharbi2019 TNM - Fig10.sedml/autogen_report_for_task1, shape: (13, 101), type: float64\niterating over chunks for /Alharbi2019 TNM - Fig10.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 13, 1), slice(0, 101, 1))\ndone with dataload for /Alharbi2019 TNM - Fig10.sedml/autogen_report_for_task1\nwrite_dataset src: /Alharbi2019 TNM - Fig10.sedml/plot_1_task1 to tgt: /Alharbi2019 TNM - Fig10.sedml/plot_1_task1, shape: (3, 101), type: float64\niterating over chunks for /Alharbi2019 TNM - Fig10.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 101, 1))\ndone with dataload for /Alharbi2019 TNM - Fig10.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b9a195afd5df175f59b\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 metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess 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 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 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":17.282229,"sedDocuments":[{"location":"Alharbi2019 TNM - Fig10.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  Alharbi2019 TNM - Fig10.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 13 data sets\r\n    Plots (1):\r\n      plot_1_task1: 2 curves\r\n\r\nExecuting SED-ML file 1: Alharbi2019 TNM - Fig10.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":16.973622,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":16.591629,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.203082,"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":0.06823,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Normal_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_cells","status":"SUCCEEDED"},{"id":"autogen_task1_r","status":"SUCCEEDED"},{"id":"autogen_task1_beta1","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_alpha1","status":"SUCCEEDED"},{"id":"autogen_task1_alpha2","status":"SUCCEEDED"},{"id":"autogen_task1_beta2","status":"SUCCEEDED"},{"id":"autogen_task1_Whole_organism","status":"SUCCEEDED"},{"id":"autogen_task1_Normal_cell_growth","status":"SUCCEEDED"},{"id":"autogen_task1_Normal_cell_death_inhibition","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_cell_growth","status":"SUCCEEDED"}]}]}]}