{"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    437      0 --:--:-- --:--:-- --:--:--   438\n\r100  342k  100  342k    0     0   760k      0 --:--:-- --:--:-- --:--:--  760k\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 (19.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/rawLog.txt\nCompleted 4.5 KiB/4.5 KiB (59.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/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/BIOMD0000000017_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000017_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 24%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 104.6 KiB/104.6 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/outputs/reports.h5\nCompleted 93.5 KiB/123.6 KiB (1.0 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/output.zip\nCompleted 93.5 KiB/123.6 KiB (1.0 MiB/s) with 3 file(s) remaining\rCompleted 96.1 KiB/123.6 KiB (908.6 KiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/rawLog.txt\nCompleted 96.1 KiB/123.6 KiB (908.6 KiB/s) with 2 file(s) remaining\rCompleted 107.3 KiB/123.6 KiB (963.8 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/outputs/plots.zip\nCompleted 107.3 KiB/123.6 KiB (963.8 KiB/s) with 1 file(s) remaining\rCompleted 123.6 KiB/123.6 KiB (1.0 MiB/s) with 1 file(s) remaining  \rupload: outputs/BIOMD0000000017_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/outputs/BIOMD0000000017_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/BIOMD0000000017-biopax2.owl  \n  inflating: contents/BIOMD0000000017-biopax3.owl  \n  inflating: contents/BIOMD0000000017-matlab.m  \n  inflating: contents/BIOMD0000000017-octave.m  \n  inflating: contents/BIOMD0000000017.m  \n  inflating: contents/BIOMD0000000017.ode  \n  inflating: contents/BIOMD0000000017.pdf  \n  inflating: contents/BIOMD0000000017.png  \n  inflating: contents/BIOMD0000000017.sci  \n  inflating: contents/BIOMD0000000017.svg  \n  inflating: contents/BIOMD0000000017.vcml  \n  inflating: contents/BIOMD0000000017_url.sedml  \n  inflating: contents/BIOMD0000000017_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 13.8 KiB/751.2 KiB (134.0 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000017-matlab.m to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/contents/BIOMD0000000017-matlab.m\nCompleted 13.8 KiB/751.2 KiB (134.0 KiB/s) with 16 file(s) remaining\rCompleted 28.5 KiB/751.2 KiB (206.6 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000017.sci to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/contents/BIOMD0000000017.sci\nCompleted 28.5 KiB/751.2 KiB (206.6 KiB/s) with 15 file(s) remaining\rCompleted 94.1 KiB/751.2 KiB (673.5 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000017-biopax3.owl to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/contents/BIOMD0000000017-biopax3.owl\nCompleted 94.1 KiB/751.2 KiB (673.5 KiB/s) with 14 file(s) remaining\rCompleted 141.1 KiB/751.2 KiB (967.4 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000017-biopax2.owl to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/contents/BIOMD0000000017-biopax2.owl\nCompleted 141.1 KiB/751.2 KiB (967.4 KiB/s) with 13 file(s) remaining\rCompleted 154.9 KiB/751.2 KiB (1.0 MiB/s) with 13 file(s) remaining  \rupload: contents/BIOMD0000000017-octave.m to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/contents/BIOMD0000000017-octave.m\nCompleted 154.9 KiB/751.2 KiB (1.0 MiB/s) with 12 file(s) remaining\rCompleted 187.8 KiB/751.2 KiB (1.2 MiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000017.svg to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/contents/BIOMD0000000017.svg\nCompleted 187.8 KiB/751.2 KiB (1.2 MiB/s) with 11 file(s) remaining\rCompleted 187.9 KiB/751.2 KiB (1.1 MiB/s) with 11 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/contents/curation_notes.txt\nCompleted 187.9 KiB/751.2 KiB (1.1 MiB/s) with 10 file(s) remaining\rCompleted 259.2 KiB/751.2 KiB (1.4 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000017.vcml to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/contents/BIOMD0000000017.vcml\nCompleted 259.2 KiB/751.2 KiB (1.4 MiB/s) with 9 file(s) remaining\rCompleted 280.2 KiB/751.2 KiB (1.5 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000017_url.sedml to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/contents/BIOMD0000000017_url.sedml\nCompleted 280.2 KiB/751.2 KiB (1.5 MiB/s) with 8 file(s) remaining\rCompleted 300.4 KiB/751.2 KiB (1.6 MiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/contents/curation_image.png\nCompleted 300.4 KiB/751.2 KiB (1.6 MiB/s) with 7 file(s) remaining\rCompleted 361.0 KiB/751.2 KiB (1.8 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000017_url.xml to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/contents/BIOMD0000000017_url.xml\nCompleted 361.0 KiB/751.2 KiB (1.8 MiB/s) with 6 file(s) remaining\rCompleted 363.0 KiB/751.2 KiB (1.7 MiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/contents/manifest.xml\nCompleted 363.0 KiB/751.2 KiB (1.7 MiB/s) with 5 file(s) remaining\rCompleted 376.8 KiB/751.2 KiB (1.7 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000017.m to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/contents/BIOMD0000000017.m\nCompleted 376.8 KiB/751.2 KiB (1.7 MiB/s) with 4 file(s) remaining\rCompleted 513.4 KiB/751.2 KiB (2.3 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000017.png to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/contents/BIOMD0000000017.png\nCompleted 513.4 KiB/751.2 KiB (2.3 MiB/s) with 3 file(s) remaining\rCompleted 523.3 KiB/751.2 KiB (2.3 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000017.ode to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/contents/BIOMD0000000017.ode\nCompleted 523.3 KiB/751.2 KiB (2.3 MiB/s) with 2 file(s) remaining\rCompleted 746.5 KiB/751.2 KiB (3.2 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000017.pdf to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/contents/BIOMD0000000017.pdf\nCompleted 746.5 KiB/751.2 KiB (3.2 MiB/s) with 1 file(s) remaining\rCompleted 751.2 KiB/751.2 KiB (3.2 MiB/s) with 1 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/contents/metadata.rdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.1 KiB/9.1 KiB (143.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471072949c0d898ffdd8f3d/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000017_url.sedml\ncreating dataset /BIOMD0000000017_url.sedml/autogen_plot_for_task1, shape: (20, 1001), type: float64\ndataset created, uuid: d-5b55cbea-386f8d39-c997-6ca89d-9a48d9, chunk_size: (20, 1001)\ncreating dataset /BIOMD0000000017_url.sedml/autogen_report_for_task1, shape: (35, 1001), type: float64\ndataset created, uuid: d-5b55cbea-386f8d39-1111-0f0c6f-7ee31d, chunk_size: (35, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000017_url.sedml\ncreating attribute uri in /BIOMD0000000017_url.sedml\ncreating attribute _type in /BIOMD0000000017_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000017_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000017_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000017_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000017_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000017_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000017_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000017_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000017_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000017_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000017_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000017_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000017_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000017_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000017_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000017_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000017_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000017_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000017_url.sedml\ncreate_links: /BIOMD0000000017_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000017_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000017_url.sedml/autogen_plot_for_task1, shape: (20, 1001), type: float64\niterating over chunks for /BIOMD0000000017_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 20, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000017_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000017_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000017_url.sedml/autogen_report_for_task1, shape: (35, 1001), type: float64\niterating over chunks for /BIOMD0000000017_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 35, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000017_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471072949c0d898ffdd8f3d\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 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.\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":1.892134,"sedDocuments":[{"location":"BIOMD0000000017_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  BIOMD0000000017_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 35 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 19 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000017_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":1.420616,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.241379,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"deterministic"},{"key":"methodCode","value":22},{"key":"parameters"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.309865,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_ADP","status":"SUCCEEDED"},{"id":"autogen_task1_NAD","status":"SUCCEEDED"},{"id":"autogen_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_task1_NADH","status":"SUCCEEDED"},{"id":"autogen_task1_pyruvate","status":"SUCCEEDED"},{"id":"autogen_task1_lactate","status":"SUCCEEDED"},{"id":"autogen_task1_CoA","status":"SUCCEEDED"},{"id":"autogen_task1_halfglucose","status":"SUCCEEDED"},{"id":"autogen_task1_AcCoA","status":"SUCCEEDED"},{"id":"autogen_task1_AcP","status":"SUCCEEDED"},{"id":"autogen_task1_Ac","status":"SUCCEEDED"},{"id":"autogen_task1_AcO","status":"SUCCEEDED"},{"id":"autogen_task1_EtOH","status":"SUCCEEDED"},{"id":"autogen_task1_AcLac","status":"SUCCEEDED"},{"id":"autogen_task1_AcetoinIn","status":"SUCCEEDED"},{"id":"autogen_task1_AcetoinOut","status":"SUCCEEDED"},{"id":"autogen_task1_Butanediol","status":"SUCCEEDED"},{"id":"autogen_task1_O2","status":"SUCCEEDED"},{"id":"autogen_task1_PO4","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","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_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.711176,"curves":[{"id":"autogen_curve_task1_ADP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NAD","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_pyruvate","status":"SUCCEEDED"},{"id":"autogen_curve_task1_lactate","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CoA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_halfglucose","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AcCoA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AcP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ac","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AcO","status":"SUCCEEDED"},{"id":"autogen_curve_task1_EtOH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AcLac","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AcetoinIn","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AcetoinOut","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Butanediol","status":"SUCCEEDED"},{"id":"autogen_curve_task1_O2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PO4","status":"SUCCEEDED"}]}]}]}