{"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    424      0 --:--:-- --:--:-- --:--:--   425\n\r100  249k  100  249k    0     0   554k      0 --:--:-- --:--:-- --:--:--  554k\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 (25.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/rawLog.txt\nCompleted 3.3 KiB/3.3 KiB (45.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 77%)\n  adding: outputs/Wodarz2007_model_2.sedml/ (stored 0%)\n  adding: outputs/Wodarz2007_model_2.sedml/plot_1_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 43%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 46.1 KiB/46.1 KiB (521.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/outputs/reports.h5\nCompleted 37.0 KiB/60.0 KiB (376.9 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/output.zip\nCompleted 37.0 KiB/60.0 KiB (376.9 KiB/s) with 3 file(s) remaining\rCompleted 49.2 KiB/60.0 KiB (447.6 KiB/s) with 3 file(s) remaining\rupload: outputs/Wodarz2007_model_2.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/outputs/Wodarz2007_model_2.sedml/plot_1_task1.pdf\nCompleted 49.2 KiB/60.0 KiB (447.6 KiB/s) with 2 file(s) remaining\rCompleted 57.4 KiB/60.0 KiB (506.5 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/outputs/plots.zip\nCompleted 57.4 KiB/60.0 KiB (506.5 KiB/s) with 1 file(s) remaining\rCompleted 60.0 KiB/60.0 KiB (469.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000663-biopax2.owl  \n  inflating: contents/BIOMD0000000663-biopax3.owl  \n  inflating: contents/BIOMD0000000663-matlab.m  \n  inflating: contents/BIOMD0000000663-octave.m  \n  inflating: contents/BIOMD0000000663.m  \n  inflating: contents/BIOMD0000000663.ode  \n  inflating: contents/BIOMD0000000663.pdf  \n  inflating: contents/BIOMD0000000663.png  \n  inflating: contents/BIOMD0000000663.svg  \n  inflating: contents/BIOMD0000000663_url.xml  \n  inflating: contents/Wodarz2007_model_2.cps  \n  inflating: contents/Wodarz2007_model_2.sedml  \n  inflating: contents/curation_image.jpeg  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 12.4 KiB/430.6 KiB (196.0 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000663-biopax2.owl to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/contents/BIOMD0000000663-biopax2.owl\nCompleted 12.4 KiB/430.6 KiB (196.0 KiB/s) with 15 file(s) remaining\rCompleted 17.3 KiB/430.6 KiB (152.5 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000663-matlab.m to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/contents/BIOMD0000000663-matlab.m\nCompleted 17.3 KiB/430.6 KiB (152.5 KiB/s) with 14 file(s) remaining\rCompleted 17.7 KiB/430.6 KiB (138.0 KiB/s) with 14 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/contents/curation_notes.txt\nCompleted 17.7 KiB/430.6 KiB (138.0 KiB/s) with 13 file(s) remaining\rCompleted 22.6 KiB/430.6 KiB (169.2 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000663-octave.m to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/contents/BIOMD0000000663-octave.m\nCompleted 22.6 KiB/430.6 KiB (169.2 KiB/s) with 12 file(s) remaining\rCompleted 41.3 KiB/430.6 KiB (299.0 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000663.svg to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/contents/BIOMD0000000663.svg\nCompleted 41.3 KiB/430.6 KiB (299.0 KiB/s) with 11 file(s) remaining\rCompleted 103.0 KiB/430.6 KiB (711.6 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000663.png to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/contents/BIOMD0000000663.png\nCompleted 103.0 KiB/430.6 KiB (711.6 KiB/s) with 10 file(s) remaining\rCompleted 115.4 KiB/430.6 KiB (712.5 KiB/s) with 10 file(s) remaining\rupload: contents/Wodarz2007_model_2.sedml to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/contents/Wodarz2007_model_2.sedml\nCompleted 115.4 KiB/430.6 KiB (712.5 KiB/s) with 9 file(s) remaining\rCompleted 160.7 KiB/430.6 KiB (967.8 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000663_url.xml to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/contents/BIOMD0000000663_url.xml\nCompleted 160.7 KiB/430.6 KiB (967.8 KiB/s) with 8 file(s) remaining\rCompleted 226.6 KiB/430.6 KiB (1.3 MiB/s) with 8 file(s) remaining  \rupload: contents/Wodarz2007_model_2.cps to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/contents/Wodarz2007_model_2.cps\nCompleted 226.6 KiB/430.6 KiB (1.3 MiB/s) with 7 file(s) remaining\rCompleted 231.2 KiB/430.6 KiB (1.3 MiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/contents/metadata.rdf\nCompleted 231.2 KiB/430.6 KiB (1.3 MiB/s) with 6 file(s) remaining\rCompleted 251.0 KiB/430.6 KiB (1.3 MiB/s) with 6 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/contents/curation_image.jpeg\nCompleted 251.0 KiB/430.6 KiB (1.3 MiB/s) with 5 file(s) remaining\rCompleted 255.9 KiB/430.6 KiB (1.3 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000663.m to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/contents/BIOMD0000000663.m\nCompleted 255.9 KiB/430.6 KiB (1.3 MiB/s) with 4 file(s) remaining\rCompleted 257.8 KiB/430.6 KiB (1.3 MiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/contents/manifest.xml\nCompleted 257.8 KiB/430.6 KiB (1.3 MiB/s) with 3 file(s) remaining\rCompleted 260.9 KiB/430.6 KiB (1.2 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000663.ode to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/contents/BIOMD0000000663.ode\nCompleted 260.9 KiB/430.6 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 278.5 KiB/430.6 KiB (1.2 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000663-biopax3.owl to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/contents/BIOMD0000000663-biopax3.owl\nCompleted 278.5 KiB/430.6 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 430.6 KiB/430.6 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000663.pdf to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/contents/BIOMD0000000663.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.8 KiB/8.8 KiB (139.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711be59a62a8be53f8c74f/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Wodarz2007_model_2.sedml\ncreating dataset /Wodarz2007_model_2.sedml/autogen_report_for_task1, shape: (21, 201), type: float64\ndataset created, uuid: d-5ec89333-f403ab07-63d9-98b4bb-65c2c3, chunk_size: (21, 201)\ncreating dataset /Wodarz2007_model_2.sedml/plot_1_task1, shape: (4, 201), type: float64\ndataset created, uuid: d-5ec89333-f403ab07-a2ee-931f08-7f281d, chunk_size: (4, 201)\ncreating attribute combineArchiveLocation in /Wodarz2007_model_2.sedml\ncreating attribute uri in /Wodarz2007_model_2.sedml\ncreating attribute _type in /Wodarz2007_model_2.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Wodarz2007_model_2.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Wodarz2007_model_2.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Wodarz2007_model_2.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Wodarz2007_model_2.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Wodarz2007_model_2.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Wodarz2007_model_2.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Wodarz2007_model_2.sedml/autogen_report_for_task1\ncreating attribute uri in /Wodarz2007_model_2.sedml/autogen_report_for_task1\ncreating attribute _type in /Wodarz2007_model_2.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Wodarz2007_model_2.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Wodarz2007_model_2.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Wodarz2007_model_2.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Wodarz2007_model_2.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Wodarz2007_model_2.sedml/plot_1_task1\ncreating attribute sedmlId in /Wodarz2007_model_2.sedml/plot_1_task1\ncreating attribute sedmlName in /Wodarz2007_model_2.sedml/plot_1_task1\ncreating attribute uri in /Wodarz2007_model_2.sedml/plot_1_task1\ncreate_links: /\ngot link: Wodarz2007_model_2.sedml\ncreate_links: /Wodarz2007_model_2.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Wodarz2007_model_2.sedml/autogen_report_for_task1 to tgt: /Wodarz2007_model_2.sedml/autogen_report_for_task1, shape: (21, 201), type: float64\niterating over chunks for /Wodarz2007_model_2.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 21, 1), slice(0, 201, 1))\ndone with dataload for /Wodarz2007_model_2.sedml/autogen_report_for_task1\nwrite_dataset src: /Wodarz2007_model_2.sedml/plot_1_task1 to tgt: /Wodarz2007_model_2.sedml/plot_1_task1, shape: (4, 201), type: float64\niterating over chunks for /Wodarz2007_model_2.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 201, 1))\ndone with dataload for /Wodarz2007_model_2.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711be59a62a8be53f8c74f\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.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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":1.331742,"sedDocuments":[{"location":"Wodarz2007_model_2.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  Wodarz2007_model_2.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 21 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Wodarz2007_model_2.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":0.865673,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.227228,"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":0.400285,"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":0.115499,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_v","status":"SUCCEEDED"},{"id":"autogen_task1_x","status":"SUCCEEDED"},{"id":"autogen_task1_y","status":"SUCCEEDED"},{"id":"autogen_task1_r","status":"SUCCEEDED"},{"id":"autogen_task1_k","status":"SUCCEEDED"},{"id":"autogen_task1_d","status":"SUCCEEDED"},{"id":"autogen_task1_Beta","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_eta","status":"SUCCEEDED"},{"id":"autogen_task1_u","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_reaction","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_1","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_2","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_3","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_4","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_5","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_6","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_7","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_8","status":"SUCCEEDED"}]}]}]}