{"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    450      0 --:--:-- --:--:-- --:--:--   451\n\r100  179k  100  179k    0     0   416k      0 --:--:-- --:--:-- --:--:--  416k\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 (24.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a619c77b6669655064b84/rawLog.txt\nCompleted 5.5 KiB/5.5 KiB (50.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a619c77b6669655064b84/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 82%)\n  adding: outputs/Bakshi2020 minimal model.sedml/ (stored 0%)\n  adding: outputs/Bakshi2020 minimal model.sedml/plot_1_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 10%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 247.2 KiB/247.2 KiB (2.2 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a619c77b6669655064b84/outputs/reports.h5\nCompleted 2.6 KiB/257.4 KiB (22.2 KiB/s) with 4 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a619c77b6669655064b84/rawLog.txt\nCompleted 2.6 KiB/257.4 KiB (22.2 KiB/s) with 3 file(s) remaining\rCompleted 236.3 KiB/257.4 KiB (1.9 MiB/s) with 3 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a619c77b6669655064b84/output.zip\nCompleted 236.3 KiB/257.4 KiB (1.9 MiB/s) with 2 file(s) remaining\rCompleted 249.0 KiB/257.4 KiB (1.9 MiB/s) with 2 file(s) remaining\rupload: outputs/Bakshi2020 minimal model.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a619c77b6669655064b84/outputs/Bakshi2020 minimal model.sedml/plot_1_task1.pdf\nCompleted 249.0 KiB/257.4 KiB (1.9 MiB/s) with 1 file(s) remaining\rCompleted 257.4 KiB/257.4 KiB (1.7 MiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a619c77b6669655064b84/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Bakshi2020 minimal model-biopax2.owl  \n  inflating: contents/Bakshi2020 minimal model-biopax3.owl  \n  inflating: contents/Bakshi2020 minimal model-matlab.m  \n  inflating: contents/Bakshi2020 minimal model.cps  \n  inflating: contents/Bakshi2020 minimal model.ode  \n  inflating: contents/Bakshi2020 minimal model.sedml  \n  inflating: contents/Bakshi2020 minimal model.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 41.7 KiB/446.6 KiB (459.9 KiB/s) with 11 file(s) remaining\rupload: contents/Bakshi2020 minimal model-biopax3.owl to s3://files.biosimulations.org/simulations/647a619c77b6669655064b84/contents/Bakshi2020 minimal model-biopax3.owl\nCompleted 41.7 KiB/446.6 KiB (459.9 KiB/s) with 10 file(s) remaining\rCompleted 147.4 KiB/446.6 KiB (1.0 MiB/s) with 10 file(s) remaining \rupload: contents/Bakshi2020 minimal model.cps to s3://files.biosimulations.org/simulations/647a619c77b6669655064b84/contents/Bakshi2020 minimal model.cps\nCompleted 147.4 KiB/446.6 KiB (1.0 MiB/s) with 9 file(s) remaining\rCompleted 173.9 KiB/446.6 KiB (1.2 MiB/s) with 9 file(s) remaining\rupload: contents/Bakshi2020 minimal model-biopax2.owl to s3://files.biosimulations.org/simulations/647a619c77b6669655064b84/contents/Bakshi2020 minimal model-biopax2.owl\nCompleted 173.9 KiB/446.6 KiB (1.2 MiB/s) with 8 file(s) remaining\rCompleted 182.4 KiB/446.6 KiB (1.1 MiB/s) with 8 file(s) remaining\rupload: contents/Bakshi2020 minimal model-matlab.m to s3://files.biosimulations.org/simulations/647a619c77b6669655064b84/contents/Bakshi2020 minimal model-matlab.m\nCompleted 182.4 KiB/446.6 KiB (1.1 MiB/s) with 7 file(s) remaining\rCompleted 183.7 KiB/446.6 KiB (985.7 KiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a619c77b6669655064b84/contents/manifest.xml\nCompleted 183.7 KiB/446.6 KiB (985.7 KiB/s) with 6 file(s) remaining\rCompleted 186.9 KiB/446.6 KiB (986.9 KiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a619c77b6669655064b84/contents/metadata.rdf\nCompleted 186.9 KiB/446.6 KiB (986.9 KiB/s) with 5 file(s) remaining\rCompleted 256.1 KiB/446.6 KiB (1.3 MiB/s) with 5 file(s) remaining  \rupload: contents/Bakshi2020 minimal model.xml to s3://files.biosimulations.org/simulations/647a619c77b6669655064b84/contents/Bakshi2020 minimal model.xml\nCompleted 256.1 KiB/446.6 KiB (1.3 MiB/s) with 4 file(s) remaining\rCompleted 256.3 KiB/446.6 KiB (1.3 MiB/s) with 4 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a619c77b6669655064b84/contents/curation_notes.txt\nCompleted 256.3 KiB/446.6 KiB (1.3 MiB/s) with 3 file(s) remaining\rCompleted 285.9 KiB/446.6 KiB (1.4 MiB/s) with 3 file(s) remaining\rCompleted 440.4 KiB/446.6 KiB (2.2 MiB/s) with 3 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a619c77b6669655064b84/contents/curation_image.png\nCompleted 440.4 KiB/446.6 KiB (2.2 MiB/s) with 2 file(s) remaining\rupload: contents/Bakshi2020 minimal model.sedml to s3://files.biosimulations.org/simulations/647a619c77b6669655064b84/contents/Bakshi2020 minimal model.sedml\nCompleted 440.4 KiB/446.6 KiB (2.2 MiB/s) with 1 file(s) remaining\rCompleted 446.6 KiB/446.6 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: contents/Bakshi2020 minimal model.ode to s3://files.biosimulations.org/simulations/647a619c77b6669655064b84/contents/Bakshi2020 minimal model.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.4 KiB/7.4 KiB (104.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a619c77b6669655064b84/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Bakshi2020 minimal model.sedml\ncreating dataset /Bakshi2020 minimal model.sedml/autogen_report_for_task1, shape: (52, 1001), type: float64\ndataset created, uuid: d-a8aec2c8-958c88ba-693e-365916-bcc7a7, chunk_size: (52, 1001)\ncreating dataset /Bakshi2020 minimal model.sedml/plot_1_task1, shape: (10, 1001), type: float64\ndataset created, uuid: d-a8aec2c8-958c88ba-11e1-5dd6de-7a3a2d, chunk_size: (10, 1001)\ncreating attribute combineArchiveLocation in /Bakshi2020 minimal model.sedml\ncreating attribute uri in /Bakshi2020 minimal model.sedml\ncreating attribute _type in /Bakshi2020 minimal model.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Bakshi2020 minimal model.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Bakshi2020 minimal model.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Bakshi2020 minimal model.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Bakshi2020 minimal model.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Bakshi2020 minimal model.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Bakshi2020 minimal model.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Bakshi2020 minimal model.sedml/autogen_report_for_task1\ncreating attribute uri in /Bakshi2020 minimal model.sedml/autogen_report_for_task1\ncreating attribute _type in /Bakshi2020 minimal model.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Bakshi2020 minimal model.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Bakshi2020 minimal model.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Bakshi2020 minimal model.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Bakshi2020 minimal model.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Bakshi2020 minimal model.sedml/plot_1_task1\ncreating attribute sedmlId in /Bakshi2020 minimal model.sedml/plot_1_task1\ncreating attribute sedmlName in /Bakshi2020 minimal model.sedml/plot_1_task1\ncreating attribute uri in /Bakshi2020 minimal model.sedml/plot_1_task1\ncreate_links: /\ngot link: Bakshi2020 minimal model.sedml\ncreate_links: /Bakshi2020 minimal model.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Bakshi2020 minimal model.sedml/autogen_report_for_task1 to tgt: /Bakshi2020 minimal model.sedml/autogen_report_for_task1, shape: (52, 1001), type: float64\niterating over chunks for /Bakshi2020 minimal model.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 52, 1), slice(0, 1001, 1))\ndone with dataload for /Bakshi2020 minimal model.sedml/autogen_report_for_task1\nwrite_dataset src: /Bakshi2020 minimal model.sedml/plot_1_task1 to tgt: /Bakshi2020 minimal model.sedml/plot_1_task1, shape: (10, 1001), type: float64\niterating over chunks for /Bakshi2020 minimal model.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 10, 1), slice(0, 1001, 1))\ndone with dataload for /Bakshi2020 minimal model.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a619c77b6669655064b84\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 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 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":1.830633,"sedDocuments":[{"location":"Bakshi2020 minimal model.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  Bakshi2020 minimal model.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 52 data sets\r\n    Plots (1):\r\n      plot_1_task1: 9 curves\r\n\r\nExecuting SED-ML file 1: Bakshi2020 minimal model.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":1.334169,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.26518,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"simulate"},{"key":"solver","value":"cvode"},{"key":"relative_tolerance","value":0.000001},{"key":"absolute_tolerance","value":1e-12},{"key":"stiff","value":true},{"key":"maximum_bdf_order","value":5},{"key":"maximum_adams_order","value":12},{"key":"maximum_num_steps","value":20000},{"key":"maximum_time_step","value":0},{"key":"minimum_time_step","value":0},{"key":"initial_time_step","value":0},{"key":"multiple_steps","value":false},{"key":"variable_step_size","value":false},{"key":"max_output_rows","value":100000}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.514278,"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":"p1_curve_5_task1","status":"SUCCEEDED"},{"id":"p1_curve_6_task1","status":"SUCCEEDED"},{"id":"p1_curve_7_task1","status":"SUCCEEDED"},{"id":"p1_curve_8_task1","status":"SUCCEEDED"},{"id":"p1_curve_9_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.378952,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_C3","status":"SUCCEEDED"},{"id":"autogen_task1_C3b","status":"SUCCEEDED"},{"id":"autogen_task1_C3bB_closed","status":"SUCCEEDED"},{"id":"autogen_task1_C3bB_open","status":"SUCCEEDED"},{"id":"autogen_task1_C3bBb","status":"SUCCEEDED"},{"id":"autogen_task1_C3bBbH","status":"SUCCEEDED"},{"id":"autogen_task1_Factor_H","status":"SUCCEEDED"},{"id":"autogen_task1_Factor_B","status":"SUCCEEDED"},{"id":"autogen_task1_C3bH","status":"SUCCEEDED"},{"id":"autogen_task1_Bb","status":"SUCCEEDED"},{"id":"autogen_task1_Factor_I","status":"SUCCEEDED"},{"id":"autogen_task1_iC3b","status":"SUCCEEDED"},{"id":"autogen_task1_Factor_D","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_k4","status":"SUCCEEDED"},{"id":"autogen_task1_k5","status":"SUCCEEDED"},{"id":"autogen_task1_k6","status":"SUCCEEDED"},{"id":"autogen_task1_k7","status":"SUCCEEDED"},{"id":"autogen_task1_k8","status":"SUCCEEDED"},{"id":"autogen_task1_k9","status":"SUCCEEDED"},{"id":"autogen_task1_k10","status":"SUCCEEDED"},{"id":"autogen_task1_k15","status":"SUCCEEDED"},{"id":"autogen_task1_k16","status":"SUCCEEDED"},{"id":"autogen_task1_k19","status":"SUCCEEDED"},{"id":"autogen_task1_k20","status":"SUCCEEDED"},{"id":"autogen_task1_k21","status":"SUCCEEDED"},{"id":"autogen_task1_k25","status":"SUCCEEDED"},{"id":"autogen_task1_ks1","status":"SUCCEEDED"},{"id":"autogen_task1_ks2","status":"SUCCEEDED"},{"id":"autogen_task1_d1","status":"SUCCEEDED"},{"id":"autogen_task1_d2","status":"SUCCEEDED"},{"id":"autogen_task1_ks3","status":"SUCCEEDED"},{"id":"autogen_task1_d3","status":"SUCCEEDED"},{"id":"autogen_task1_Fluid_phase","status":"SUCCEEDED"},{"id":"autogen_task1_C3_hydrolysis","status":"SUCCEEDED"},{"id":"autogen_task1_C3bB_formation","status":"SUCCEEDED"},{"id":"autogen_task1_C3bB_conformational_change","status":"SUCCEEDED"},{"id":"autogen_task1_C3_convertase_formation","status":"SUCCEEDED"},{"id":"autogen_task1_Factor_H_binding_C3_convertase","status":"SUCCEEDED"},{"id":"autogen_task1_Factor_H_induced__C3_convertase_decay","status":"SUCCEEDED"},{"id":"autogen_task1_C3_convertase_decay","status":"SUCCEEDED"},{"id":"autogen_task1_Factor_H_binding_C3b","status":"SUCCEEDED"},{"id":"autogen_task1_C3b_inactivation","status":"SUCCEEDED"},{"id":"autogen_task1_C3_synthesis","status":"SUCCEEDED"},{"id":"autogen_task1_C3_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_Factor_B_synthesis","status":"SUCCEEDED"},{"id":"autogen_task1_Factor_B_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_Factor_H_synthesis","status":"SUCCEEDED"},{"id":"autogen_task1_Factor_H_degradation","status":"SUCCEEDED"}]}]}]}