{"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    439      0 --:--:-- --:--:-- --:--:--   439\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100  291k  100  291k    0     0   666k      0 --:--:-- --:--:-- --:--:-- 3832k\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 (25.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b8077b6669655061461/rawLog.txt\nCompleted 3.2 KiB/3.2 KiB (45.8 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b8077b6669655061461/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 73%)\n  adding: outputs/Dubey2007_model1.sedml/ (stored 0%)\n  adding: outputs/Dubey2007_model1.sedml/plot_1_task1.pdf (deflated 28%)\n  adding: outputs/reports.h5 (deflated 64%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 31.4 KiB/31.4 KiB (388.2 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b8077b6669655061461/outputs/reports.h5\nCompleted 21.6 KiB/42.6 KiB (306.6 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b8077b6669655061461/output.zip\nCompleted 21.6 KiB/42.6 KiB (306.6 KiB/s) with 3 file(s) remaining\rCompleted 29.2 KiB/42.6 KiB (306.3 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b8077b6669655061461/outputs/plots.zip\nCompleted 29.2 KiB/42.6 KiB (306.3 KiB/s) with 2 file(s) remaining\rCompleted 39.9 KiB/42.6 KiB (352.8 KiB/s) with 2 file(s) remaining\rupload: outputs/Dubey2007_model1.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b8077b6669655061461/outputs/Dubey2007_model1.sedml/plot_1_task1.pdf\nCompleted 39.9 KiB/42.6 KiB (352.8 KiB/s) with 1 file(s) remaining\rCompleted 42.6 KiB/42.6 KiB (347.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b8077b6669655061461/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nsrun: Job 6631020 step creation temporarily disabled, retrying\nsrun: Step created for job 6631020\nArchive:  archive.omex\n  inflating: contents/Dubey2007_model1-biopax2.owl  \n  inflating: contents/Dubey2007_model1-biopax3.owl  \n  inflating: contents/Dubey2007_model1-matlab.m  \n  inflating: contents/Dubey2007_model1-octave.m  \n  inflating: contents/Dubey2007_model1.cps  \n  inflating: contents/Dubey2007_model1.ode  \n  inflating: contents/Dubey2007_model1.sedml  \n  inflating: contents/Dubey2007_model1.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 13.9 KiB/485.8 KiB (173.9 KiB/s) with 12 file(s) remaining\rupload: contents/Dubey2007_model1-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b8077b6669655061461/contents/Dubey2007_model1-biopax3.owl\nCompleted 13.9 KiB/485.8 KiB (173.9 KiB/s) with 11 file(s) remaining\rCompleted 23.7 KiB/485.8 KiB (233.4 KiB/s) with 11 file(s) remaining\rupload: contents/Dubey2007_model1-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b8077b6669655061461/contents/Dubey2007_model1-biopax2.owl\nCompleted 23.7 KiB/485.8 KiB (233.4 KiB/s) with 10 file(s) remaining\rCompleted 30.0 KiB/485.8 KiB (276.2 KiB/s) with 10 file(s) remaining\rupload: contents/Dubey2007_model1-matlab.m to s3://files.biosimulations.org/simulations/647a4b8077b6669655061461/contents/Dubey2007_model1-matlab.m\nCompleted 30.0 KiB/485.8 KiB (276.2 KiB/s) with 9 file(s) remaining\rCompleted 286.0 KiB/485.8 KiB (2.6 MiB/s) with 9 file(s) remaining \rCompleted 292.3 KiB/485.8 KiB (2.0 MiB/s) with 9 file(s) remaining \rupload: contents/Dubey2007_model1-octave.m to s3://files.biosimulations.org/simulations/647a4b8077b6669655061461/contents/Dubey2007_model1-octave.m\nCompleted 292.3 KiB/485.8 KiB (2.0 MiB/s) with 8 file(s) remaining\rCompleted 305.9 KiB/485.8 KiB (2.0 MiB/s) with 8 file(s) remaining\rupload: contents/Dubey2007_model1.sedml to s3://files.biosimulations.org/simulations/647a4b8077b6669655061461/contents/Dubey2007_model1.sedml\nCompleted 305.9 KiB/485.8 KiB (2.0 MiB/s) with 7 file(s) remaining\rCompleted 306.1 KiB/485.8 KiB (1.8 MiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b8077b6669655061461/contents/curation_notes.txt\nCompleted 306.1 KiB/485.8 KiB (1.8 MiB/s) with 6 file(s) remaining\rCompleted 389.3 KiB/485.8 KiB (2.3 MiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b8077b6669655061461/contents/curation_image.png\nCompleted 389.3 KiB/485.8 KiB (2.3 MiB/s) with 5 file(s) remaining\rCompleted 390.7 KiB/485.8 KiB (2.3 MiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b8077b6669655061461/contents/manifest.xml\nCompleted 390.7 KiB/485.8 KiB (2.3 MiB/s) with 4 file(s) remaining\rCompleted 393.0 KiB/485.8 KiB (2.3 MiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b8077b6669655061461/contents/metadata.rdf\nCompleted 393.0 KiB/485.8 KiB (2.3 MiB/s) with 3 file(s) remaining\rCompleted 423.3 KiB/485.8 KiB (2.3 MiB/s) with 3 file(s) remaining\rupload: contents/Dubey2007_model1.xml to s3://files.biosimulations.org/simulations/647a4b8077b6669655061461/contents/Dubey2007_model1.xml\nCompleted 423.3 KiB/485.8 KiB (2.3 MiB/s) with 2 file(s) remaining\rCompleted 481.7 KiB/485.8 KiB (2.6 MiB/s) with 2 file(s) remaining\rupload: contents/Dubey2007_model1.cps to s3://files.biosimulations.org/simulations/647a4b8077b6669655061461/contents/Dubey2007_model1.cps\nCompleted 481.7 KiB/485.8 KiB (2.6 MiB/s) with 1 file(s) remaining\rCompleted 485.8 KiB/485.8 KiB (2.6 MiB/s) with 1 file(s) remaining\rupload: contents/Dubey2007_model1.ode to s3://files.biosimulations.org/simulations/647a4b8077b6669655061461/contents/Dubey2007_model1.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.7 KiB/7.7 KiB (112.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b8077b6669655061461/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Dubey2007_model1.sedml\ncreating dataset /Dubey2007_model1.sedml/autogen_report_for_task1, shape: (20, 101), type: float64\ndataset created, uuid: d-9a8d7fbe-159b18d9-6720-996dd6-125d8f, chunk_size: (20, 101)\ncreating dataset /Dubey2007_model1.sedml/plot_1_task1, shape: (4, 101), type: float64\ndataset created, uuid: d-9a8d7fbe-159b18d9-7461-76a4f2-17bd7a, chunk_size: (4, 101)\ncreating attribute combineArchiveLocation in /Dubey2007_model1.sedml\ncreating attribute uri in /Dubey2007_model1.sedml\ncreating attribute _type in /Dubey2007_model1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Dubey2007_model1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Dubey2007_model1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Dubey2007_model1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Dubey2007_model1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Dubey2007_model1.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Dubey2007_model1.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Dubey2007_model1.sedml/autogen_report_for_task1\ncreating attribute uri in /Dubey2007_model1.sedml/autogen_report_for_task1\ncreating attribute _type in /Dubey2007_model1.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Dubey2007_model1.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Dubey2007_model1.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Dubey2007_model1.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Dubey2007_model1.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Dubey2007_model1.sedml/plot_1_task1\ncreating attribute sedmlId in /Dubey2007_model1.sedml/plot_1_task1\ncreating attribute sedmlName in /Dubey2007_model1.sedml/plot_1_task1\ncreating attribute uri in /Dubey2007_model1.sedml/plot_1_task1\ncreate_links: /\ngot link: Dubey2007_model1.sedml\ncreate_links: /Dubey2007_model1.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Dubey2007_model1.sedml/autogen_report_for_task1 to tgt: /Dubey2007_model1.sedml/autogen_report_for_task1, shape: (20, 101), type: float64\niterating over chunks for /Dubey2007_model1.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 20, 1), slice(0, 101, 1))\ndone with dataload for /Dubey2007_model1.sedml/autogen_report_for_task1\nwrite_dataset src: /Dubey2007_model1.sedml/plot_1_task1 to tgt: /Dubey2007_model1.sedml/plot_1_task1, shape: (4, 101), type: float64\niterating over chunks for /Dubey2007_model1.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 101, 1))\ndone with dataload for /Dubey2007_model1.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b8077b6669655061461\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\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 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.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file 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":1.016634,"sedDocuments":[{"location":"Dubey2007_model1.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  Dubey2007_model1.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 20 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Dubey2007_model1.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":0.630268,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.113792,"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":0.335427,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.069625,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_P","status":"SUCCEEDED"},{"id":"autogen_task1_I","status":"SUCCEEDED"},{"id":"autogen_task1_M","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_beta0","status":"SUCCEEDED"},{"id":"autogen_task1_mu","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_alpha0","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_increase_in_the_amount_of_pathogenic_micro_organism","status":"SUCCEEDED"},{"id":"autogen_task1_Decrease_in_the_amount_of_pathogenic_micro_organism","status":"SUCCEEDED"},{"id":"autogen_task1_Increase_of_appropriate_immune_response_with_respect_to_pathogen","status":"SUCCEEDED"},{"id":"autogen_task1_Reduction_of_immune_response","status":"SUCCEEDED"},{"id":"autogen_task1_betterment_of_relative_characteristics_of_the_damaged_part_of_the_organ","status":"SUCCEEDED"},{"id":"autogen_task1_removal_of_relative_characteristics_of_the_damaged_part_of_the_organ","status":"SUCCEEDED"}]}]}]}