{"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    446      0 --:--:-- --:--:-- --:--:--   445\n\r100  210k  100  210k    0     0   467k      0 --:--:-- --:--:-- --:--:--  467k\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 (26.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/rawLog.txt\nCompleted 4.1 KiB/4.1 KiB (56.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 81%)\n  adding: outputs/BIOMD0000000038_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000038_url.sedml/autogen_plot_for_task1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 60%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 32.9 KiB/32.9 KiB (423.4 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/outputs/reports.h5\nCompleted 23.1 KiB/44.1 KiB (323.4 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/output.zip\nCompleted 23.1 KiB/44.1 KiB (323.4 KiB/s) with 3 file(s) remaining\rCompleted 34.1 KiB/44.1 KiB (323.8 KiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000038_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/outputs/BIOMD0000000038_url.sedml/autogen_plot_for_task1.pdf\nCompleted 34.1 KiB/44.1 KiB (323.8 KiB/s) with 2 file(s) remaining\rCompleted 41.4 KiB/44.1 KiB (382.5 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/outputs/plots.zip\nCompleted 41.4 KiB/44.1 KiB (382.5 KiB/s) with 1 file(s) remaining\rCompleted 44.1 KiB/44.1 KiB (367.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000038-biopax2.owl  \n  inflating: contents/BIOMD0000000038-biopax3.owl  \n  inflating: contents/BIOMD0000000038-matlab.m  \n  inflating: contents/BIOMD0000000038-octave.m  \n  inflating: contents/BIOMD0000000038.m  \n  inflating: contents/BIOMD0000000038.ode  \n  inflating: contents/BIOMD0000000038.pdf  \n  inflating: contents/BIOMD0000000038.png  \n  inflating: contents/BIOMD0000000038.sci  \n  inflating: contents/BIOMD0000000038.svg  \n  inflating: contents/BIOMD0000000038.vcml  \n  inflating: contents/BIOMD0000000038_url.sedml  \n  inflating: contents/BIOMD0000000038_url.xml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 41.0 KiB/479.2 KiB (490.7 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000038-biopax3.owl to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/contents/BIOMD0000000038-biopax3.owl\nCompleted 41.0 KiB/479.2 KiB (490.7 KiB/s) with 14 file(s) remaining\rCompleted 48.5 KiB/479.2 KiB (483.0 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000038-matlab.m to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/contents/BIOMD0000000038-matlab.m\nCompleted 48.5 KiB/479.2 KiB (483.0 KiB/s) with 13 file(s) remaining\rCompleted 55.9 KiB/479.2 KiB (418.7 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000038-octave.m to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/contents/BIOMD0000000038-octave.m\nCompleted 55.9 KiB/479.2 KiB (418.7 KiB/s) with 12 file(s) remaining\rCompleted 58.2 KiB/479.2 KiB (416.1 KiB/s) with 12 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/contents/metadata.rdf\nCompleted 58.2 KiB/479.2 KiB (416.1 KiB/s) with 11 file(s) remaining\rCompleted 63.7 KiB/479.2 KiB (449.8 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000038.sci to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/contents/BIOMD0000000038.sci\nCompleted 63.7 KiB/479.2 KiB (449.8 KiB/s) with 10 file(s) remaining\rCompleted 87.5 KiB/479.2 KiB (611.8 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000038.svg to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/contents/BIOMD0000000038.svg\nCompleted 87.5 KiB/479.2 KiB (611.8 KiB/s) with 9 file(s) remaining\rCompleted 115.7 KiB/479.2 KiB (781.2 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000038-biopax2.owl to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/contents/BIOMD0000000038-biopax2.owl\nCompleted 115.7 KiB/479.2 KiB (781.2 KiB/s) with 8 file(s) remaining\rCompleted 133.4 KiB/479.2 KiB (796.1 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000038_url.sedml to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/contents/BIOMD0000000038_url.sedml\nCompleted 133.4 KiB/479.2 KiB (796.1 KiB/s) with 7 file(s) remaining\rCompleted 183.3 KiB/479.2 KiB (1.1 MiB/s) with 7 file(s) remaining  \rupload: contents/BIOMD0000000038.vcml to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/contents/BIOMD0000000038.vcml\nCompleted 183.3 KiB/479.2 KiB (1.1 MiB/s) with 6 file(s) remaining\rCompleted 372.8 KiB/479.2 KiB (2.0 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000038.pdf to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/contents/BIOMD0000000038.pdf\nCompleted 372.8 KiB/479.2 KiB (2.0 MiB/s) with 5 file(s) remaining\rCompleted 411.8 KiB/479.2 KiB (2.2 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000038_url.xml to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/contents/BIOMD0000000038_url.xml\nCompleted 411.8 KiB/479.2 KiB (2.2 MiB/s) with 4 file(s) remaining\rCompleted 465.2 KiB/479.2 KiB (2.3 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000038.png to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/contents/BIOMD0000000038.png\nCompleted 465.2 KiB/479.2 KiB (2.3 MiB/s) with 3 file(s) remaining\rCompleted 470.0 KiB/479.2 KiB (2.3 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000038.ode to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/contents/BIOMD0000000038.ode\nCompleted 470.0 KiB/479.2 KiB (2.3 MiB/s) with 2 file(s) remaining\rCompleted 477.5 KiB/479.2 KiB (2.3 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000038.m to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/contents/BIOMD0000000038.m\nCompleted 477.5 KiB/479.2 KiB (2.3 MiB/s) with 1 file(s) remaining\rCompleted 479.2 KiB/479.2 KiB (2.3 MiB/s) with 1 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/contents/manifest.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (121.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471076e9a62a8be53f73f08/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000038_url.sedml\ncreating dataset /BIOMD0000000038_url.sedml/autogen_plot_for_task1, shape: (18, 1001), type: float64\ndataset created, uuid: d-7a18f920-56ce4ac6-fec1-80e2d8-0e28e8, chunk_size: (18, 1001)\ncreating dataset /BIOMD0000000038_url.sedml/autogen_report_for_task1, shape: (29, 1001), type: float64\ndataset created, uuid: d-7a18f920-56ce4ac6-4ee3-582fd2-4e88d1, chunk_size: (29, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000038_url.sedml\ncreating attribute uri in /BIOMD0000000038_url.sedml\ncreating attribute _type in /BIOMD0000000038_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000038_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000038_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000038_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000038_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000038_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000038_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000038_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000038_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000038_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000038_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000038_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000038_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000038_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000038_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000038_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000038_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000038_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000038_url.sedml\ncreate_links: /BIOMD0000000038_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000038_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000038_url.sedml/autogen_plot_for_task1, shape: (18, 1001), type: float64\niterating over chunks for /BIOMD0000000038_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 18, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000038_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000038_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000038_url.sedml/autogen_report_for_task1, shape: (29, 1001), type: float64\niterating over chunks for /BIOMD0000000038_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 29, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000038_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471076e9a62a8be53f73f08\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 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 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 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":1.64025,"sedDocuments":[{"location":"BIOMD0000000038_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  BIOMD0000000038_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 29 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 17 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000038_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":1.226819,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.172519,"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":0.256719,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_EI","status":"SUCCEEDED"},{"id":"autogen_task1_PyrPI","status":"SUCCEEDED"},{"id":"autogen_task1_EIP","status":"SUCCEEDED"},{"id":"autogen_task1_HPr","status":"SUCCEEDED"},{"id":"autogen_task1_EIPHPr","status":"SUCCEEDED"},{"id":"autogen_task1_HPrP","status":"SUCCEEDED"},{"id":"autogen_task1_EIIA","status":"SUCCEEDED"},{"id":"autogen_task1_HPrPIIA","status":"SUCCEEDED"},{"id":"autogen_task1_EIIAP","status":"SUCCEEDED"},{"id":"autogen_task1_EIICB","status":"SUCCEEDED"},{"id":"autogen_task1_EIIAPIICB","status":"SUCCEEDED"},{"id":"autogen_task1_EIICBP","status":"SUCCEEDED"},{"id":"autogen_task1_EIICBPGlc","status":"SUCCEEDED"},{"id":"autogen_task1_PEP","status":"SUCCEEDED"},{"id":"autogen_task1_Pyr","status":"SUCCEEDED"},{"id":"autogen_task1_GlcP","status":"SUCCEEDED"},{"id":"autogen_task1_Glc","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_v1","status":"SUCCEEDED"},{"id":"autogen_task1_v2","status":"SUCCEEDED"},{"id":"autogen_task1_v3","status":"SUCCEEDED"},{"id":"autogen_task1_v4","status":"SUCCEEDED"},{"id":"autogen_task1_v5","status":"SUCCEEDED"},{"id":"autogen_task1_v6","status":"SUCCEEDED"},{"id":"autogen_task1_v7","status":"SUCCEEDED"},{"id":"autogen_task1_v8","status":"SUCCEEDED"},{"id":"autogen_task1_v9","status":"SUCCEEDED"},{"id":"autogen_task1_v10","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.664966,"curves":[{"id":"autogen_curve_task1_EI","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PyrPI","status":"SUCCEEDED"},{"id":"autogen_curve_task1_EIP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_HPr","status":"SUCCEEDED"},{"id":"autogen_curve_task1_EIPHPr","status":"SUCCEEDED"},{"id":"autogen_curve_task1_HPrP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_EIIA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_HPrPIIA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_EIIAP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_EIICB","status":"SUCCEEDED"},{"id":"autogen_curve_task1_EIIAPIICB","status":"SUCCEEDED"},{"id":"autogen_curve_task1_EIICBP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_EIICBPGlc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PEP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Pyr","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GlcP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Glc","status":"SUCCEEDED"}]}]}]}