{"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    403      0 --:--:-- --:--:-- --:--:--   404\n\r100 38368  100 38368    0     0  87779      0 --:--:-- --:--:-- --:--:-- 87779\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 (29.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a315d0fb37cdb9ae68ec4/rawLog.txt\nCompleted 7.0 KiB/7.0 KiB (118.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a315d0fb37cdb9ae68ec4/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 84%)\n  adding: outputs/Enzyme_clustering_in glucose_metabolism.sedml/ (stored 0%)\n  adding: outputs/Enzyme_clustering_in glucose_metabolism.sedml/plot_1_task1.pdf (deflated 29%)\n  adding: outputs/reports.h5 (deflated 41%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 90.1 KiB/90.1 KiB (809.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a315d0fb37cdb9ae68ec4/outputs/reports.h5\nCompleted 6.7 KiB/82.2 KiB (70.5 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a315d0fb37cdb9ae68ec4/outputs/plots.zip\nCompleted 6.7 KiB/82.2 KiB (70.5 KiB/s) with 3 file(s) remaining\rCompleted 16.3 KiB/82.2 KiB (169.4 KiB/s) with 3 file(s) remaining\rupload: outputs/Enzyme_clustering_in glucose_metabolism.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a315d0fb37cdb9ae68ec4/outputs/Enzyme_clustering_in glucose_metabolism.sedml/plot_1_task1.pdf\nCompleted 16.3 KiB/82.2 KiB (169.4 KiB/s) with 2 file(s) remaining\rCompleted 79.6 KiB/82.2 KiB (782.8 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a315d0fb37cdb9ae68ec4/output.zip\nCompleted 79.6 KiB/82.2 KiB (782.8 KiB/s) with 1 file(s) remaining\rCompleted 82.2 KiB/82.2 KiB (773.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a315d0fb37cdb9ae68ec4/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Enzyme_clustering_in glucose_metabolism-biopax2.owl  \n  inflating: contents/Enzyme_clustering_in glucose_metabolism-biopax3.owl  \n  inflating: contents/Enzyme_clustering_in glucose_metabolism-matlab.m  \n  inflating: contents/Enzyme_clustering_in glucose_metabolism-octave.m  \n  inflating: contents/Enzyme_clustering_in glucose_metabolism.cps  \n  inflating: contents/Enzyme_clustering_in glucose_metabolism.ode  \n  inflating: contents/Enzyme_clustering_in glucose_metabolism.sedml  \n  inflating: contents/Enzyme_clustering_in glucose_metabolism.xml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 46.2 KiB/501.3 KiB (673.1 KiB/s) with 10 file(s) remaining\rupload: contents/Enzyme_clustering_in glucose_metabolism-biopax2.owl to s3://files.biosimulations.org/simulations/647a315d0fb37cdb9ae68ec4/contents/Enzyme_clustering_in glucose_metabolism-biopax2.owl\nCompleted 46.2 KiB/501.3 KiB (673.1 KiB/s) with 9 file(s) remaining\rCompleted 47.6 KiB/501.3 KiB (387.8 KiB/s) with 9 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a315d0fb37cdb9ae68ec4/contents/manifest.xml\nCompleted 47.6 KiB/501.3 KiB (387.8 KiB/s) with 8 file(s) remaining\rCompleted 60.1 KiB/501.3 KiB (456.7 KiB/s) with 8 file(s) remaining\rupload: contents/Enzyme_clustering_in glucose_metabolism-matlab.m to s3://files.biosimulations.org/simulations/647a315d0fb37cdb9ae68ec4/contents/Enzyme_clustering_in glucose_metabolism-matlab.m\nCompleted 60.1 KiB/501.3 KiB (456.7 KiB/s) with 7 file(s) remaining\rCompleted 135.1 KiB/501.3 KiB (1010.5 KiB/s) with 7 file(s) remaining\rupload: contents/Enzyme_clustering_in glucose_metabolism-biopax3.owl to s3://files.biosimulations.org/simulations/647a315d0fb37cdb9ae68ec4/contents/Enzyme_clustering_in glucose_metabolism-biopax3.owl\nCompleted 135.1 KiB/501.3 KiB (1010.5 KiB/s) with 6 file(s) remaining\rCompleted 147.6 KiB/501.3 KiB (1.1 MiB/s) with 6 file(s) remaining   \rupload: contents/Enzyme_clustering_in glucose_metabolism-octave.m to s3://files.biosimulations.org/simulations/647a315d0fb37cdb9ae68ec4/contents/Enzyme_clustering_in glucose_metabolism-octave.m\nCompleted 147.6 KiB/501.3 KiB (1.1 MiB/s) with 5 file(s) remaining\rCompleted 289.2 KiB/501.3 KiB (2.0 MiB/s) with 5 file(s) remaining\rupload: contents/Enzyme_clustering_in glucose_metabolism.xml to s3://files.biosimulations.org/simulations/647a315d0fb37cdb9ae68ec4/contents/Enzyme_clustering_in glucose_metabolism.xml\nCompleted 289.2 KiB/501.3 KiB (2.0 MiB/s) with 4 file(s) remaining\rCompleted 299.7 KiB/501.3 KiB (2.0 MiB/s) with 4 file(s) remaining\rupload: contents/Enzyme_clustering_in glucose_metabolism.ode to s3://files.biosimulations.org/simulations/647a315d0fb37cdb9ae68ec4/contents/Enzyme_clustering_in glucose_metabolism.ode\nCompleted 299.7 KiB/501.3 KiB (2.0 MiB/s) with 3 file(s) remaining\rCompleted 347.9 KiB/501.3 KiB (2.2 MiB/s) with 3 file(s) remaining\rupload: contents/Enzyme_clustering_in glucose_metabolism.sedml to s3://files.biosimulations.org/simulations/647a315d0fb37cdb9ae68ec4/contents/Enzyme_clustering_in glucose_metabolism.sedml\nCompleted 347.9 KiB/501.3 KiB (2.2 MiB/s) with 2 file(s) remaining\rCompleted 500.1 KiB/501.3 KiB (3.1 MiB/s) with 2 file(s) remaining\rupload: contents/Enzyme_clustering_in glucose_metabolism.cps to s3://files.biosimulations.org/simulations/647a315d0fb37cdb9ae68ec4/contents/Enzyme_clustering_in glucose_metabolism.cps\nCompleted 500.1 KiB/501.3 KiB (3.1 MiB/s) with 1 file(s) remaining\rCompleted 501.3 KiB/501.3 KiB (3.0 MiB/s) with 1 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a315d0fb37cdb9ae68ec4/contents/metadata.rdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.5 KiB/7.5 KiB (116.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a315d0fb37cdb9ae68ec4/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Enzyme_clustering_in glucose_metabolism.sedml\ncreating dataset /Enzyme_clustering_in glucose_metabolism.sedml/autogen_report_for_task1, shape: (91, 201), type: float64\ndataset created, uuid: d-3e2c04c6-b7231a17-7f13-3f585b-67fe24, chunk_size: (91, 201)\ncreating dataset /Enzyme_clustering_in glucose_metabolism.sedml/plot_1_task1, shape: (4, 201), type: float64\ndataset created, uuid: d-3e2c04c6-b7231a17-c3a1-78b494-99d8ad, chunk_size: (4, 201)\ncreating attribute combineArchiveLocation in /Enzyme_clustering_in glucose_metabolism.sedml\ncreating attribute uri in /Enzyme_clustering_in glucose_metabolism.sedml\ncreating attribute _type in /Enzyme_clustering_in glucose_metabolism.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Enzyme_clustering_in glucose_metabolism.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Enzyme_clustering_in glucose_metabolism.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Enzyme_clustering_in glucose_metabolism.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Enzyme_clustering_in glucose_metabolism.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Enzyme_clustering_in glucose_metabolism.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Enzyme_clustering_in glucose_metabolism.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Enzyme_clustering_in glucose_metabolism.sedml/autogen_report_for_task1\ncreating attribute uri in /Enzyme_clustering_in glucose_metabolism.sedml/autogen_report_for_task1\ncreating attribute _type in /Enzyme_clustering_in glucose_metabolism.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Enzyme_clustering_in glucose_metabolism.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Enzyme_clustering_in glucose_metabolism.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Enzyme_clustering_in glucose_metabolism.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Enzyme_clustering_in glucose_metabolism.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Enzyme_clustering_in glucose_metabolism.sedml/plot_1_task1\ncreating attribute sedmlId in /Enzyme_clustering_in glucose_metabolism.sedml/plot_1_task1\ncreating attribute sedmlName in /Enzyme_clustering_in glucose_metabolism.sedml/plot_1_task1\ncreating attribute uri in /Enzyme_clustering_in glucose_metabolism.sedml/plot_1_task1\ncreate_links: /\ngot link: Enzyme_clustering_in glucose_metabolism.sedml\ncreate_links: /Enzyme_clustering_in glucose_metabolism.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Enzyme_clustering_in glucose_metabolism.sedml/autogen_report_for_task1 to tgt: /Enzyme_clustering_in glucose_metabolism.sedml/autogen_report_for_task1, shape: (91, 201), type: float64\niterating over chunks for /Enzyme_clustering_in glucose_metabolism.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 91, 1), slice(0, 201, 1))\ndone with dataload for /Enzyme_clustering_in glucose_metabolism.sedml/autogen_report_for_task1\nwrite_dataset src: /Enzyme_clustering_in glucose_metabolism.sedml/plot_1_task1 to tgt: /Enzyme_clustering_in glucose_metabolism.sedml/plot_1_task1, shape: (4, 201), type: float64\niterating over chunks for /Enzyme_clustering_in glucose_metabolism.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 201, 1))\ndone with dataload for /Enzyme_clustering_in glucose_metabolism.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a315d0fb37cdb9ae68ec4\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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.333283,"sedDocuments":[{"location":"Enzyme_clustering_in glucose_metabolism.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  Enzyme_clustering_in glucose_metabolism.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 91 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Enzyme_clustering_in glucose_metabolism.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":0.862716,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.233436,"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":0.29134,"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":0.178979,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Metabolic_outcome_of_Pentose_Phosphate_Shunt","status":"SUCCEEDED"},{"id":"autogen_task1_Metabolic_outcome_of_Serine_Biosynthesis_Flux","status":"SUCCEEDED"},{"id":"autogen_task1_Metabolic_outcome_of_Glycolytic_Flux","status":"SUCCEEDED"},{"id":"autogen_task1_Glucose","status":"SUCCEEDED"},{"id":"autogen_task1_Fructose_6_Phosphate","status":"SUCCEEDED"},{"id":"autogen_task1_Fructose_1_6_Bisphosphate","status":"SUCCEEDED"},{"id":"autogen_task1__3_Phosphoglycerate","status":"SUCCEEDED"},{"id":"autogen_task1_Phosphoenolpyruvate","status":"SUCCEEDED"},{"id":"autogen_task1_Pyruvate","status":"SUCCEEDED"},{"id":"autogen_task1_Oxaloacetate","status":"SUCCEEDED"},{"id":"autogen_task1_Phosphofructokinase_1","status":"SUCCEEDED"},{"id":"autogen_task1_Fructose_1_6_Bisphosphatase","status":"SUCCEEDED"},{"id":"autogen_task1_Large_sized_enzyme_clusters","status":"SUCCEEDED"},{"id":"autogen_task1_Medium_sized_enzyme_clusters","status":"SUCCEEDED"},{"id":"autogen_task1_Small_sized_enzyme_clusters","status":"SUCCEEDED"},{"id":"autogen_task1_Pyruvate_Kinase_M2_dimers","status":"SUCCEEDED"},{"id":"autogen_task1_Phosphoenolpyruvate_Carboxykinase_1","status":"SUCCEEDED"},{"id":"autogen_task1_Glycosylated_Phosphofructokinase","status":"SUCCEEDED"},{"id":"autogen_task1_Pyruvate_Kinase_M2_tetramers","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k_1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k_2","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_k_3","status":"SUCCEEDED"},{"id":"autogen_task1_k4","status":"SUCCEEDED"},{"id":"autogen_task1_k_4","status":"SUCCEEDED"},{"id":"autogen_task1_k5","status":"SUCCEEDED"},{"id":"autogen_task1_k_5","status":"SUCCEEDED"},{"id":"autogen_task1_k_6","status":"SUCCEEDED"},{"id":"autogen_task1_kas","status":"SUCCEEDED"},{"id":"autogen_task1_k_as","status":"SUCCEEDED"},{"id":"autogen_task1_kam","status":"SUCCEEDED"},{"id":"autogen_task1_k_am","status":"SUCCEEDED"},{"id":"autogen_task1_kal","status":"SUCCEEDED"},{"id":"autogen_task1_k_al","status":"SUCCEEDED"},{"id":"autogen_task1_kg","status":"SUCCEEDED"},{"id":"autogen_task1_k_g","status":"SUCCEEDED"},{"id":"autogen_task1_kd","status":"SUCCEEDED"},{"id":"autogen_task1_k_d","status":"SUCCEEDED"},{"id":"autogen_task1_kp","status":"SUCCEEDED"},{"id":"autogen_task1_ks","status":"SUCCEEDED"},{"id":"autogen_task1_kf","status":"SUCCEEDED"},{"id":"autogen_task1_delta_p","status":"SUCCEEDED"},{"id":"autogen_task1_delta_s","status":"SUCCEEDED"},{"id":"autogen_task1_delta_f","status":"SUCCEEDED"},{"id":"autogen_task1_c2","status":"SUCCEEDED"},{"id":"autogen_task1_c_2","status":"SUCCEEDED"},{"id":"autogen_task1_c_6","status":"SUCCEEDED"},{"id":"autogen_task1_e2","status":"SUCCEEDED"},{"id":"autogen_task1_e_2","status":"SUCCEEDED"},{"id":"autogen_task1_e_6","status":"SUCCEEDED"},{"id":"autogen_task1_e_d","status":"SUCCEEDED"},{"id":"autogen_task1_c_d","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_K1","status":"SUCCEEDED"},{"id":"autogen_task1_K2","status":"SUCCEEDED"},{"id":"autogen_task1_K3","status":"SUCCEEDED"},{"id":"autogen_task1_k0","status":"SUCCEEDED"},{"id":"autogen_task1_Cytoplasm","status":"SUCCEEDED"},{"id":"autogen_task1_R1","status":"SUCCEEDED"},{"id":"autogen_task1_R2","status":"SUCCEEDED"},{"id":"autogen_task1_R3","status":"SUCCEEDED"},{"id":"autogen_task1_R4","status":"SUCCEEDED"},{"id":"autogen_task1_R5","status":"SUCCEEDED"},{"id":"autogen_task1_R6","status":"SUCCEEDED"},{"id":"autogen_task1_R7","status":"SUCCEEDED"},{"id":"autogen_task1_R8","status":"SUCCEEDED"},{"id":"autogen_task1_R9","status":"SUCCEEDED"},{"id":"autogen_task1_R10","status":"SUCCEEDED"},{"id":"autogen_task1_R11","status":"SUCCEEDED"},{"id":"autogen_task1_R12","status":"SUCCEEDED"},{"id":"autogen_task1_R13","status":"SUCCEEDED"},{"id":"autogen_task1_R14","status":"SUCCEEDED"},{"id":"autogen_task1_R15","status":"SUCCEEDED"},{"id":"autogen_task1_R16","status":"SUCCEEDED"},{"id":"autogen_task1_R17","status":"SUCCEEDED"},{"id":"autogen_task1_R18","status":"SUCCEEDED"},{"id":"autogen_task1_R19","status":"SUCCEEDED"},{"id":"autogen_task1_R20","status":"SUCCEEDED"},{"id":"autogen_task1_R21","status":"SUCCEEDED"},{"id":"autogen_task1_R22","status":"SUCCEEDED"},{"id":"autogen_task1_R23","status":"SUCCEEDED"},{"id":"autogen_task1_R24","status":"SUCCEEDED"},{"id":"autogen_task1_R25","status":"SUCCEEDED"},{"id":"auto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