{"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    428      0 --:--:-- --:--:-- --:--:--   429\n\r100  184k  100  184k    0     0   413k      0 --:--:-- --:--:-- --:--:--  413k\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/6471089249c0d898ffddbb5d/rawLog.txt\nCompleted 3.5 KiB/3.5 KiB (52.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471089249c0d898ffddbb5d/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/BIOMD0000000125_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000125_url.sedml/autogen_plot_for_task1.pdf (deflated 26%)\n  adding: outputs/reports.h5 (deflated 22%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 102.8 KiB/102.8 KiB (523.9 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471089249c0d898ffddbb5d/outputs/reports.h5\nCompleted 89.9 KiB/109.9 KiB (1.1 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471089249c0d898ffddbb5d/output.zip\nCompleted 89.9 KiB/109.9 KiB (1.1 MiB/s) with 3 file(s) remaining\rCompleted 97.2 KiB/109.9 KiB (970.5 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471089249c0d898ffddbb5d/outputs/plots.zip\nCompleted 97.2 KiB/109.9 KiB (970.5 KiB/s) with 2 file(s) remaining\rCompleted 107.2 KiB/109.9 KiB (1.0 MiB/s) with 2 file(s) remaining \rupload: outputs/BIOMD0000000125_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471089249c0d898ffddbb5d/outputs/BIOMD0000000125_url.sedml/autogen_plot_for_task1.pdf\nCompleted 107.2 KiB/109.9 KiB (1.0 MiB/s) with 1 file(s) remaining\rCompleted 109.9 KiB/109.9 KiB (915.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471089249c0d898ffddbb5d/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000125-biopax2.owl  \n  inflating: contents/BIOMD0000000125-biopax3.owl  \n  inflating: contents/BIOMD0000000125-matlab.m  \n  inflating: contents/BIOMD0000000125.m  \n  inflating: contents/BIOMD0000000125.ode  \n  inflating: contents/BIOMD0000000125.pdf  \n  inflating: contents/BIOMD0000000125.png  \n  inflating: contents/BIOMD0000000125.svg  \n  inflating: contents/BIOMD0000000125.vcml  \n  inflating: contents/BIOMD0000000125_url.sedml  \n  inflating: contents/BIOMD0000000125_url.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 11.8 KiB/324.1 KiB (173.7 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000125-biopax2.owl to s3://files.biosimulations.org/simulations/6471089249c0d898ffddbb5d/contents/BIOMD0000000125-biopax2.owl\nCompleted 11.8 KiB/324.1 KiB (173.7 KiB/s) with 14 file(s) remaining\rCompleted 24.3 KiB/324.1 KiB (189.3 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000125_url.sedml to s3://files.biosimulations.org/simulations/6471089249c0d898ffddbb5d/contents/BIOMD0000000125_url.sedml\nCompleted 24.3 KiB/324.1 KiB (189.3 KiB/s) with 13 file(s) remaining\rCompleted 49.5 KiB/324.1 KiB (377.2 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000125.vcml to s3://files.biosimulations.org/simulations/6471089249c0d898ffddbb5d/contents/BIOMD0000000125.vcml\nCompleted 49.5 KiB/324.1 KiB (377.2 KiB/s) with 12 file(s) remaining\rCompleted 51.9 KiB/324.1 KiB (386.9 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000125.ode to s3://files.biosimulations.org/simulations/6471089249c0d898ffddbb5d/contents/BIOMD0000000125.ode\nCompleted 51.9 KiB/324.1 KiB (386.9 KiB/s) with 11 file(s) remaining\rCompleted 54.8 KiB/324.1 KiB (397.4 KiB/s) with 11 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471089249c0d898ffddbb5d/contents/metadata.rdf\nCompleted 54.8 KiB/324.1 KiB (397.4 KiB/s) with 10 file(s) remaining\rCompleted 70.3 KiB/324.1 KiB (500.6 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000125-biopax3.owl to s3://files.biosimulations.org/simulations/6471089249c0d898ffddbb5d/contents/BIOMD0000000125-biopax3.owl\nCompleted 70.3 KiB/324.1 KiB (500.6 KiB/s) with 9 file(s) remaining\rCompleted 86.9 KiB/324.1 KiB (611.6 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000125.svg to s3://files.biosimulations.org/simulations/6471089249c0d898ffddbb5d/contents/BIOMD0000000125.svg\nCompleted 86.9 KiB/324.1 KiB (611.6 KiB/s) with 8 file(s) remaining\rCompleted 111.7 KiB/324.1 KiB (738.6 KiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6471089249c0d898ffddbb5d/contents/curation_image.png\nCompleted 111.7 KiB/324.1 KiB (738.6 KiB/s) with 7 file(s) remaining\rCompleted 111.7 KiB/324.1 KiB (686.5 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471089249c0d898ffddbb5d/contents/curation_notes.txt\nCompleted 111.7 KiB/324.1 KiB (686.5 KiB/s) with 6 file(s) remaining\rCompleted 113.4 KiB/324.1 KiB (664.8 KiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471089249c0d898ffddbb5d/contents/manifest.xml\nCompleted 113.4 KiB/324.1 KiB (664.8 KiB/s) with 5 file(s) remaining\rCompleted 130.1 KiB/324.1 KiB (648.0 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000125_url.xml to s3://files.biosimulations.org/simulations/6471089249c0d898ffddbb5d/contents/BIOMD0000000125_url.xml\nCompleted 130.1 KiB/324.1 KiB (648.0 KiB/s) with 4 file(s) remaining\rCompleted 134.5 KiB/324.1 KiB (661.1 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000125-matlab.m to s3://files.biosimulations.org/simulations/6471089249c0d898ffddbb5d/contents/BIOMD0000000125-matlab.m\nCompleted 134.5 KiB/324.1 KiB (661.1 KiB/s) with 3 file(s) remaining\rCompleted 138.9 KiB/324.1 KiB (663.6 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000125.m to s3://files.biosimulations.org/simulations/6471089249c0d898ffddbb5d/contents/BIOMD0000000125.m\nCompleted 138.9 KiB/324.1 KiB (663.6 KiB/s) with 2 file(s) remaining\rCompleted 164.8 KiB/324.1 KiB (688.8 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000125.png to s3://files.biosimulations.org/simulations/6471089249c0d898ffddbb5d/contents/BIOMD0000000125.png\nCompleted 164.8 KiB/324.1 KiB (688.8 KiB/s) with 1 file(s) remaining\rCompleted 324.1 KiB/324.1 KiB (1.3 MiB/s) with 1 file(s) remaining  \rupload: contents/BIOMD0000000125.pdf to s3://files.biosimulations.org/simulations/6471089249c0d898ffddbb5d/contents/BIOMD0000000125.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (146.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471089249c0d898ffddbb5d/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000125_url.sedml\ncreating dataset /BIOMD0000000125_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\ndataset created, uuid: d-f998e84c-368fcf48-3bb4-72d543-f26aba, chunk_size: (6, 1001)\ncreating dataset /BIOMD0000000125_url.sedml/autogen_report_for_task1, shape: (21, 1001), type: float64\ndataset created, uuid: d-f998e84c-368fcf48-8f2b-5dea62-cb6571, chunk_size: (21, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000125_url.sedml\ncreating attribute uri in /BIOMD0000000125_url.sedml\ncreating attribute _type in /BIOMD0000000125_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000125_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000125_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000125_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000125_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000125_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000125_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000125_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000125_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000125_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000125_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000125_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000125_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000125_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000125_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000125_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000125_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000125_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000125_url.sedml\ncreate_links: /BIOMD0000000125_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000125_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000125_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\niterating over chunks for /BIOMD0000000125_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000125_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000125_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000125_url.sedml/autogen_report_for_task1, shape: (21, 1001), type: float64\niterating over chunks for /BIOMD0000000125_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 21, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000125_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471089249c0d898ffddbb5d\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 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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.284815,"sedDocuments":[{"location":"BIOMD0000000125_url.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  BIOMD0000000125_url.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      autogen_plot_for_task1: 5 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000125_url.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_plot_for_task1`\r\n      `autogen_report_for_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: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_plot_for_task1` ...","duration":0.924057,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.190767,"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":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.191957,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_x1","status":"SUCCEEDED"},{"id":"autogen_task1_x2","status":"SUCCEEDED"},{"id":"autogen_task1_y2","status":"SUCCEEDED"},{"id":"autogen_task1_x0","status":"SUCCEEDED"},{"id":"autogen_task1_y0","status":"SUCCEEDED"},{"id":"autogen_task1_a1","status":"SUCCEEDED"},{"id":"autogen_task1_a2","status":"SUCCEEDED"},{"id":"autogen_task1_b1","status":"SUCCEEDED"},{"id":"autogen_task1_b2","status":"SUCCEEDED"},{"id":"autogen_task1_d1","status":"SUCCEEDED"},{"id":"autogen_task1_d2x","status":"SUCCEEDED"},{"id":"autogen_task1_d2y","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_0000001","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000001","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000002","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000003","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000004","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000005","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000006","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000007","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.416662,"curves":[{"id":"autogen_curve_task1_x1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_x2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_y2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_x0","status":"SUCCEEDED"},{"id":"autogen_curve_task1_y0","status":"SUCCEEDED"}]}]}]}