{"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    475      0 --:--:-- --:--:-- --:--:--   477\n\r100  278k  100  278k    0     0   661k      0 --:--:-- --:--:-- --:--:--  661k\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 (25.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/rawLog.txt\nCompleted 3.7 KiB/3.7 KiB (56.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 80%)\n  adding: outputs/BIOMD0000000023_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000023_url.sedml/autogen_plot_for_task1.pdf (deflated 29%)\n  adding: outputs/reports.h5 (deflated 13%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 180.4 KiB/180.4 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/outputs/reports.h5\nCompleted 170.3 KiB/198.4 KiB (1.9 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/output.zip\nCompleted 170.3 KiB/198.4 KiB (1.9 MiB/s) with 3 file(s) remaining\rCompleted 180.7 KiB/198.4 KiB (1.6 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/outputs/plots.zip\nCompleted 180.7 KiB/198.4 KiB (1.6 MiB/s) with 2 file(s) remaining\rCompleted 195.8 KiB/198.4 KiB (1.7 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000023_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/outputs/BIOMD0000000023_url.sedml/autogen_plot_for_task1.pdf\nCompleted 195.8 KiB/198.4 KiB (1.7 MiB/s) with 1 file(s) remaining\rCompleted 198.4 KiB/198.4 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000023-biopax2.owl  \n  inflating: contents/BIOMD0000000023-biopax3.owl  \n  inflating: contents/BIOMD0000000023-matlab.m  \n  inflating: contents/BIOMD0000000023-octave.m  \n  inflating: contents/BIOMD0000000023.m  \n  inflating: contents/BIOMD0000000023.ode  \n  inflating: contents/BIOMD0000000023.pdf  \n  inflating: contents/BIOMD0000000023.png  \n  inflating: contents/BIOMD0000000023.sci  \n  inflating: contents/BIOMD0000000023.svg  \n  inflating: contents/BIOMD0000000023.vcml  \n  inflating: contents/BIOMD0000000023_url.sedml  \n  inflating: contents/BIOMD0000000023_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 46.4 KiB/599.7 KiB (552.9 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000023-biopax3.owl to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/contents/BIOMD0000000023-biopax3.owl\nCompleted 46.4 KiB/599.7 KiB (552.9 KiB/s) with 16 file(s) remaining\rCompleted 57.7 KiB/599.7 KiB (542.3 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000023-octave.m to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/contents/BIOMD0000000023-octave.m\nCompleted 57.7 KiB/599.7 KiB (542.3 KiB/s) with 15 file(s) remaining\rCompleted 67.4 KiB/599.7 KiB (473.5 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000023.sci to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/contents/BIOMD0000000023.sci\nCompleted 67.4 KiB/599.7 KiB (473.5 KiB/s) with 14 file(s) remaining\rCompleted 67.7 KiB/599.7 KiB (451.3 KiB/s) with 14 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/contents/curation_notes.txt\nCompleted 67.7 KiB/599.7 KiB (451.3 KiB/s) with 13 file(s) remaining\rCompleted 166.4 KiB/599.7 KiB (1.1 MiB/s) with 13 file(s) remaining \rupload: contents/BIOMD0000000023.png to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/contents/BIOMD0000000023.png\nCompleted 166.4 KiB/599.7 KiB (1.1 MiB/s) with 12 file(s) remaining\rCompleted 192.0 KiB/599.7 KiB (1.2 MiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000023.svg to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/contents/BIOMD0000000023.svg\nCompleted 192.0 KiB/599.7 KiB (1.2 MiB/s) with 11 file(s) remaining\rCompleted 203.3 KiB/599.7 KiB (1.2 MiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000023-matlab.m to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/contents/BIOMD0000000023-matlab.m\nCompleted 203.3 KiB/599.7 KiB (1.2 MiB/s) with 10 file(s) remaining\rCompleted 257.9 KiB/599.7 KiB (1.5 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000023.vcml to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/contents/BIOMD0000000023.vcml\nCompleted 257.9 KiB/599.7 KiB (1.5 MiB/s) with 9 file(s) remaining\rCompleted 259.9 KiB/599.7 KiB (1.5 MiB/s) with 9 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/contents/manifest.xml\nCompleted 259.9 KiB/599.7 KiB (1.5 MiB/s) with 8 file(s) remaining\rCompleted 275.5 KiB/599.7 KiB (1.5 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000023_url.sedml to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/contents/BIOMD0000000023_url.sedml\nCompleted 275.5 KiB/599.7 KiB (1.5 MiB/s) with 7 file(s) remaining\rCompleted 330.0 KiB/599.7 KiB (1.7 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000023_url.xml to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/contents/BIOMD0000000023_url.xml\nCompleted 330.0 KiB/599.7 KiB (1.7 MiB/s) with 6 file(s) remaining\rCompleted 333.7 KiB/599.7 KiB (1.5 MiB/s) with 6 file(s) remaining\rCompleted 352.7 KiB/599.7 KiB (1.6 MiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/contents/curation_image.png\nCompleted 352.7 KiB/599.7 KiB (1.6 MiB/s) with 5 file(s) remaining\rCompleted 386.5 KiB/599.7 KiB (1.8 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000023-biopax2.owl to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/contents/BIOMD0000000023-biopax2.owl\nCompleted 386.5 KiB/599.7 KiB (1.8 MiB/s) with 4 file(s) remaining\rCompleted 397.9 KiB/599.7 KiB (1.8 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000023.m to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/contents/BIOMD0000000023.m\nCompleted 397.9 KiB/599.7 KiB (1.8 MiB/s) with 3 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/contents/metadata.rdf\nCompleted 397.9 KiB/599.7 KiB (1.8 MiB/s) with 2 file(s) remaining\rCompleted 405.7 KiB/599.7 KiB (1.7 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000023.ode to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/contents/BIOMD0000000023.ode\nCompleted 405.7 KiB/599.7 KiB (1.7 MiB/s) with 1 file(s) remaining\rCompleted 599.7 KiB/599.7 KiB (2.5 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000023.pdf to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/contents/BIOMD0000000023.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.1 KiB/9.1 KiB (101.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471073f0dcacb55678b3b21/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000023_url.sedml\ncreating dataset /BIOMD0000000023_url.sedml/autogen_plot_for_task1, shape: (14, 1001), type: float64\ndataset created, uuid: d-a628daad-8c91cd5a-0ca5-47ee19-c41298, chunk_size: (14, 1001)\ncreating dataset /BIOMD0000000023_url.sedml/autogen_report_for_task1, shape: (26, 1001), type: float64\ndataset created, uuid: d-a628daad-8c91cd5a-7a01-93f47a-1e068c, chunk_size: (26, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000023_url.sedml\ncreating attribute uri in /BIOMD0000000023_url.sedml\ncreating attribute _type in /BIOMD0000000023_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000023_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000023_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000023_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000023_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000023_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000023_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000023_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000023_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000023_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000023_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000023_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000023_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000023_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000023_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000023_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000023_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000023_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000023_url.sedml\ncreate_links: /BIOMD0000000023_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000023_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000023_url.sedml/autogen_plot_for_task1, shape: (14, 1001), type: float64\niterating over chunks for /BIOMD0000000023_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 14, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000023_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000023_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000023_url.sedml/autogen_report_for_task1, shape: (26, 1001), type: float64\niterating over chunks for /BIOMD0000000023_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 26, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000023_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471073f0dcacb55678b3b21\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":1.714645,"sedDocuments":[{"location":"BIOMD0000000023_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  BIOMD0000000023_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 26 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 13 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000023_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":1.269926,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.210577,"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":0.275159,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Fru","status":"SUCCEEDED"},{"id":"autogen_task1_Glc","status":"SUCCEEDED"},{"id":"autogen_task1_HexP","status":"SUCCEEDED"},{"id":"autogen_task1_Suc6P","status":"SUCCEEDED"},{"id":"autogen_task1_Suc","status":"SUCCEEDED"},{"id":"autogen_task1_Sucvac","status":"SUCCEEDED"},{"id":"autogen_task1_glycolysis","status":"SUCCEEDED"},{"id":"autogen_task1_phos","status":"SUCCEEDED"},{"id":"autogen_task1_UDP","status":"SUCCEEDED"},{"id":"autogen_task1_ADP","status":"SUCCEEDED"},{"id":"autogen_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_task1_Glcex","status":"SUCCEEDED"},{"id":"autogen_task1_Fruex","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_task1_v11","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.634789,"curves":[{"id":"autogen_curve_task1_Fru","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Glc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_HexP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Suc6P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Suc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Sucvac","status":"SUCCEEDED"},{"id":"autogen_curve_task1_glycolysis","status":"SUCCEEDED"},{"id":"autogen_curve_task1_phos","status":"SUCCEEDED"},{"id":"autogen_curve_task1_UDP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ADP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Glcex","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Fruex","status":"SUCCEEDED"}]}]}]}