{"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    555      0 --:--:-- --:--:-- --:--:--   556\n\r100 33597  100 33597    0     0  94215      0 --:--:-- --:--:-- --:--:-- 94215\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 (27.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711e349a62a8be53f92465/rawLog.txt\nCompleted 3.4 KiB/3.4 KiB (50.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711e349a62a8be53f92465/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/Ontah2019.sedml/ (stored 0%)\n  adding: outputs/Ontah2019.sedml/plot_1_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 15%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 137.3 KiB/137.3 KiB (1.7 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711e349a62a8be53f92465/outputs/reports.h5\nCompleted 125.3 KiB/143.7 KiB (1.7 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711e349a62a8be53f92465/output.zip\nCompleted 125.3 KiB/143.7 KiB (1.7 MiB/s) with 3 file(s) remaining\rCompleted 131.7 KiB/143.7 KiB (1.1 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711e349a62a8be53f92465/outputs/plots.zip\nCompleted 131.7 KiB/143.7 KiB (1.1 MiB/s) with 2 file(s) remaining\rCompleted 141.1 KiB/143.7 KiB (1.2 MiB/s) with 2 file(s) remaining\rupload: outputs/Ontah2019.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711e349a62a8be53f92465/outputs/Ontah2019.sedml/plot_1_task1.pdf\nCompleted 141.1 KiB/143.7 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 143.7 KiB/143.7 KiB (1.0 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711e349a62a8be53f92465/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Ontah2019-biopax2.owl  \n  inflating: contents/Ontah2019-biopax3.owl  \n  inflating: contents/Ontah2019-matlab.m  \n  inflating: contents/Ontah2019-octave.m  \n  inflating: contents/Ontah2019.cps  \n  inflating: contents/Ontah2019.ode  \n  inflating: contents/Ontah2019.sedml  \n  inflating: contents/Ontah2019.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 13.7 KiB/188.1 KiB (194.6 KiB/s) with 12 file(s) remaining\rupload: contents/Ontah2019-biopax2.owl to s3://files.biosimulations.org/simulations/64711e349a62a8be53f92465/contents/Ontah2019-biopax2.owl\nCompleted 13.7 KiB/188.1 KiB (194.6 KiB/s) with 11 file(s) remaining\rCompleted 19.3 KiB/188.1 KiB (178.4 KiB/s) with 11 file(s) remaining\rupload: contents/Ontah2019-matlab.m to s3://files.biosimulations.org/simulations/64711e349a62a8be53f92465/contents/Ontah2019-matlab.m\nCompleted 19.3 KiB/188.1 KiB (178.4 KiB/s) with 10 file(s) remaining\rCompleted 30.2 KiB/188.1 KiB (261.8 KiB/s) with 10 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64711e349a62a8be53f92465/contents/curation_image.png\nCompleted 30.2 KiB/188.1 KiB (261.8 KiB/s) with 9 file(s) remaining\rCompleted 30.3 KiB/188.1 KiB (242.8 KiB/s) with 9 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711e349a62a8be53f92465/contents/curation_notes.txt\nCompleted 30.3 KiB/188.1 KiB (242.8 KiB/s) with 8 file(s) remaining\rCompleted 68.6 KiB/188.1 KiB (541.6 KiB/s) with 8 file(s) remaining\rupload: contents/Ontah2019.xml to s3://files.biosimulations.org/simulations/64711e349a62a8be53f92465/contents/Ontah2019.xml\nCompleted 68.6 KiB/188.1 KiB (541.6 KiB/s) with 7 file(s) remaining\rCompleted 84.4 KiB/188.1 KiB (663.6 KiB/s) with 7 file(s) remaining\rupload: contents/Ontah2019.sedml to s3://files.biosimulations.org/simulations/64711e349a62a8be53f92465/contents/Ontah2019.sedml\nCompleted 84.4 KiB/188.1 KiB (663.6 KiB/s) with 6 file(s) remaining\rCompleted 86.2 KiB/188.1 KiB (637.2 KiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711e349a62a8be53f92465/contents/metadata.rdf\nCompleted 86.2 KiB/188.1 KiB (637.2 KiB/s) with 5 file(s) remaining\rCompleted 105.2 KiB/188.1 KiB (773.7 KiB/s) with 5 file(s) remaining\rupload: contents/Ontah2019-biopax3.owl to s3://files.biosimulations.org/simulations/64711e349a62a8be53f92465/contents/Ontah2019-biopax3.owl\nCompleted 105.2 KiB/188.1 KiB (773.7 KiB/s) with 4 file(s) remaining\rCompleted 106.5 KiB/188.1 KiB (718.2 KiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711e349a62a8be53f92465/contents/manifest.xml\nCompleted 106.5 KiB/188.1 KiB (718.2 KiB/s) with 3 file(s) remaining\rCompleted 110.3 KiB/188.1 KiB (686.2 KiB/s) with 3 file(s) remaining\rupload: contents/Ontah2019.ode to s3://files.biosimulations.org/simulations/64711e349a62a8be53f92465/contents/Ontah2019.ode\nCompleted 110.3 KiB/188.1 KiB (686.2 KiB/s) with 2 file(s) remaining\rCompleted 115.9 KiB/188.1 KiB (699.8 KiB/s) with 2 file(s) remaining\rupload: contents/Ontah2019-octave.m to s3://files.biosimulations.org/simulations/64711e349a62a8be53f92465/contents/Ontah2019-octave.m\nCompleted 115.9 KiB/188.1 KiB (699.8 KiB/s) with 1 file(s) remaining\rCompleted 188.1 KiB/188.1 KiB (858.8 KiB/s) with 1 file(s) remaining\rupload: contents/Ontah2019.cps to s3://files.biosimulations.org/simulations/64711e349a62a8be53f92465/contents/Ontah2019.cps\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.3 KiB/7.3 KiB (115.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711e349a62a8be53f92465/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Ontah2019.sedml\ncreating dataset /Ontah2019.sedml/autogen_report_for_task1, shape: (27, 1001), type: float64\ndataset created, uuid: d-216bb19a-7d17b0f9-a4ef-c7137d-39cd8b, chunk_size: (27, 1001)\ncreating dataset /Ontah2019.sedml/plot_1_task1, shape: (5, 1001), type: float64\ndataset created, uuid: d-216bb19a-7d17b0f9-6da4-668d84-0a7c38, chunk_size: (5, 1001)\ncreating attribute combineArchiveLocation in /Ontah2019.sedml\ncreating attribute uri in /Ontah2019.sedml\ncreating attribute _type in /Ontah2019.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Ontah2019.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Ontah2019.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Ontah2019.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Ontah2019.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Ontah2019.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Ontah2019.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Ontah2019.sedml/autogen_report_for_task1\ncreating attribute uri in /Ontah2019.sedml/autogen_report_for_task1\ncreating attribute _type in /Ontah2019.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Ontah2019.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Ontah2019.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Ontah2019.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Ontah2019.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Ontah2019.sedml/plot_1_task1\ncreating attribute sedmlId in /Ontah2019.sedml/plot_1_task1\ncreating attribute sedmlName in /Ontah2019.sedml/plot_1_task1\ncreating attribute uri in /Ontah2019.sedml/plot_1_task1\ncreate_links: /\ngot link: Ontah2019.sedml\ncreate_links: /Ontah2019.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Ontah2019.sedml/autogen_report_for_task1 to tgt: /Ontah2019.sedml/autogen_report_for_task1, shape: (27, 1001), type: float64\niterating over chunks for /Ontah2019.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 27, 1), slice(0, 1001, 1))\ndone with dataload for /Ontah2019.sedml/autogen_report_for_task1\nwrite_dataset src: /Ontah2019.sedml/plot_1_task1 to tgt: /Ontah2019.sedml/plot_1_task1, shape: (5, 1001), type: float64\niterating over chunks for /Ontah2019.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 1001, 1))\ndone with dataload for /Ontah2019.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711e349a62a8be53f92465\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\nsrun: Job 6618172 step creation temporarily disabled, retrying\nsrun: Step created for job 6618172\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 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.\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":1.18437,"sedDocuments":[{"location":"Ontah2019.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  Ontah2019.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: 4 curves\r\n\r\nExecuting SED-ML file 1: Ontah2019.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":0.821365,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.130848,"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":0.356512,"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":0.232327,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_C","status":"SUCCEEDED"},{"id":"autogen_task1_I","status":"SUCCEEDED"},{"id":"autogen_task1_U","status":"SUCCEEDED"},{"id":"autogen_task1_V","status":"SUCCEEDED"},{"id":"autogen_task1_r","status":"SUCCEEDED"},{"id":"autogen_task1_K","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_delta_u","status":"SUCCEEDED"},{"id":"autogen_task1_K_c","status":"SUCCEEDED"},{"id":"autogen_task1_delta","status":"SUCCEEDED"},{"id":"autogen_task1_delta_i","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_mu","status":"SUCCEEDED"},{"id":"autogen_task1_psi","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_Growth","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_Cell_Infection","status":"SUCCEEDED"},{"id":"autogen_task1_Uninfected_Tumor_Lysis_Drug","status":"SUCCEEDED"},{"id":"autogen_task1_Infected_Tumor_Lysis_Drug","status":"SUCCEEDED"},{"id":"autogen_task1_Infected_Tumor_Death","status":"SUCCEEDED"},{"id":"autogen_task1_Virus_Production","status":"SUCCEEDED"},{"id":"autogen_task1_Virus_Decay","status":"SUCCEEDED"},{"id":"autogen_task1_Drug_Injection","status":"SUCCEEDED"},{"id":"autogen_task1_Drug_Decay","status":"SUCCEEDED"}]}]}]}