{"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    459      0 --:--:-- --:--:-- --:--:--   460\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100  211k  100  211k    0     0   376k      0 --:--:-- --:--:-- --:--:--  879k\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 (26.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/rawLog.txt\nCompleted 3.2 KiB/3.2 KiB (41.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 75%)\n  adding: outputs/BIOMD0000000039_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000039_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 14%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 147.5 KiB/147.5 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/outputs/reports.h5\nCompleted 136.6 KiB/157.6 KiB (1.4 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/output.zip\nCompleted 136.6 KiB/157.6 KiB (1.4 MiB/s) with 3 file(s) remaining\rCompleted 139.3 KiB/157.6 KiB (1.2 MiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/rawLog.txt\nCompleted 139.3 KiB/157.6 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 146.7 KiB/157.6 KiB (1.2 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/outputs/plots.zip\nCompleted 146.7 KiB/157.6 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 157.6 KiB/157.6 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000039_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/outputs/BIOMD0000000039_url.sedml/autogen_plot_for_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000039-biopax2.owl  \n  inflating: contents/BIOMD0000000039-biopax3.owl  \n  inflating: contents/BIOMD0000000039-matlab.m  \n  inflating: contents/BIOMD0000000039-octave.m  \n  inflating: contents/BIOMD0000000039.m  \n  inflating: contents/BIOMD0000000039.ode  \n  inflating: contents/BIOMD0000000039.pdf  \n  inflating: contents/BIOMD0000000039.png  \n  inflating: contents/BIOMD0000000039.sci  \n  inflating: contents/BIOMD0000000039.svg  \n  inflating: contents/BIOMD0000000039_url.sedml  \n  inflating: contents/BIOMD0000000039_url.xml  \n  inflating: contents/curation_image.jpeg  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 16.8 KiB/366.2 KiB (230.2 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000039-biopax2.owl to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/contents/BIOMD0000000039-biopax2.owl\nCompleted 16.8 KiB/366.2 KiB (230.2 KiB/s) with 15 file(s) remaining\rCompleted 21.6 KiB/366.2 KiB (193.9 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000039-matlab.m to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/contents/BIOMD0000000039-matlab.m\nCompleted 21.6 KiB/366.2 KiB (193.9 KiB/s) with 14 file(s) remaining\rCompleted 26.5 KiB/366.2 KiB (234.2 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000039-octave.m to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/contents/BIOMD0000000039-octave.m\nCompleted 26.5 KiB/366.2 KiB (234.2 KiB/s) with 13 file(s) remaining\rCompleted 28.4 KiB/366.2 KiB (221.2 KiB/s) with 13 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/contents/manifest.xml\nCompleted 28.4 KiB/366.2 KiB (221.2 KiB/s) with 12 file(s) remaining\rCompleted 76.1 KiB/366.2 KiB (565.5 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000039.png to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/contents/BIOMD0000000039.png\nCompleted 76.1 KiB/366.2 KiB (565.5 KiB/s) with 11 file(s) remaining\rCompleted 91.0 KiB/366.2 KiB (655.2 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000039.svg to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/contents/BIOMD0000000039.svg\nCompleted 91.0 KiB/366.2 KiB (655.2 KiB/s) with 10 file(s) remaining\rCompleted 112.0 KiB/366.2 KiB (740.2 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000039_url.xml to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/contents/BIOMD0000000039_url.xml\nCompleted 112.0 KiB/366.2 KiB (740.2 KiB/s) with 9 file(s) remaining\rCompleted 121.7 KiB/366.2 KiB (795.7 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000039_url.sedml to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/contents/BIOMD0000000039_url.sedml\nCompleted 121.7 KiB/366.2 KiB (795.7 KiB/s) with 8 file(s) remaining\rCompleted 124.8 KiB/366.2 KiB (783.5 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000039.sci to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/contents/BIOMD0000000039.sci\nCompleted 124.8 KiB/366.2 KiB (783.5 KiB/s) with 7 file(s) remaining\rCompleted 125.0 KiB/366.2 KiB (773.6 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/contents/curation_notes.txt\nCompleted 125.0 KiB/366.2 KiB (773.6 KiB/s) with 6 file(s) remaining\rCompleted 164.2 KiB/366.2 KiB (968.5 KiB/s) with 6 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/contents/curation_image.jpeg\nCompleted 164.2 KiB/366.2 KiB (968.5 KiB/s) with 5 file(s) remaining\rCompleted 167.9 KiB/366.2 KiB (969.2 KiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/contents/metadata.rdf\nCompleted 167.9 KiB/366.2 KiB (969.2 KiB/s) with 4 file(s) remaining\rCompleted 170.7 KiB/366.2 KiB (871.0 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000039.ode to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/contents/BIOMD0000000039.ode\nCompleted 170.7 KiB/366.2 KiB (871.0 KiB/s) with 3 file(s) remaining\rCompleted 175.6 KiB/366.2 KiB (882.8 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000039.m to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/contents/BIOMD0000000039.m\nCompleted 175.6 KiB/366.2 KiB (882.8 KiB/s) with 2 file(s) remaining\rCompleted 198.9 KiB/366.2 KiB (988.9 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000039-biopax3.owl to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/contents/BIOMD0000000039-biopax3.owl\nCompleted 198.9 KiB/366.2 KiB (988.9 KiB/s) with 1 file(s) remaining\rCompleted 366.2 KiB/366.2 KiB (1.8 MiB/s) with 1 file(s) remaining  \rupload: contents/BIOMD0000000039.pdf to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/contents/BIOMD0000000039.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (123.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471077049c0d898ffdd9789/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000039_url.sedml\ncreating dataset /BIOMD0000000039_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\ndataset created, uuid: d-50ad17a1-bbe51931-db8f-4f56fe-979033, chunk_size: (6, 1001)\ncreating dataset /BIOMD0000000039_url.sedml/autogen_report_for_task1, shape: (16, 1001), type: float64\ndataset created, uuid: d-50ad17a1-bbe51931-b18c-805d6c-7c160e, chunk_size: (16, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000039_url.sedml\ncreating attribute uri in /BIOMD0000000039_url.sedml\ncreating attribute _type in /BIOMD0000000039_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000039_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000039_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000039_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000039_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000039_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000039_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000039_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000039_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000039_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000039_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000039_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000039_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000039_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000039_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000039_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000039_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000039_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000039_url.sedml\ncreate_links: /BIOMD0000000039_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000039_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000039_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\niterating over chunks for /BIOMD0000000039_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000039_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000039_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000039_url.sedml/autogen_report_for_task1, shape: (16, 1001), type: float64\niterating over chunks for /BIOMD0000000039_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 16, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000039_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471077049c0d898ffdd9789\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 and upload the outputs of the simulation run ... succeeded.\nProcess 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.\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":1.287419,"sedDocuments":[{"location":"BIOMD0000000039_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  BIOMD0000000039_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 16 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 5 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000039_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":0.849896,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.187752,"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":0.14556,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Ca_cyt","status":"SUCCEEDED"},{"id":"autogen_task1_CaER","status":"SUCCEEDED"},{"id":"autogen_task1_CaM","status":"SUCCEEDED"},{"id":"autogen_task1_CaPr","status":"SUCCEEDED"},{"id":"autogen_task1_Pr","status":"SUCCEEDED"},{"id":"autogen_task1_Cytosol","status":"SUCCEEDED"},{"id":"autogen_task1_Endoplasmic_Reticulum","status":"SUCCEEDED"},{"id":"autogen_task1_Mitochondria","status":"SUCCEEDED"},{"id":"autogen_task1_v1","status":"SUCCEEDED"},{"id":"autogen_task1_v3","status":"SUCCEEDED"},{"id":"autogen_task1_v5","status":"SUCCEEDED"},{"id":"autogen_task1_v7","status":"SUCCEEDED"},{"id":"autogen_task1_v9","status":"SUCCEEDED"},{"id":"autogen_task1_v11","status":"SUCCEEDED"},{"id":"autogen_task1_v12","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.409251,"curves":[{"id":"autogen_curve_task1_Ca_cyt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CaER","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CaM","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CaPr","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Pr","status":"SUCCEEDED"}]}]}]}