{"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    461      0 --:--:-- --:--:-- --:--:--   463\n\r100  310k  100  310k    0     0   722k      0 --:--:-- --:--:-- --:--:--  722k\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 3 SED documents:\n  SED documents (3):\n    Succeeded: 3\n    Skipped: 0\n    Failed: 0\n  Tasks (3):\n    Succeeded: 3\n    Skipped: 0\n    Failed: 0\n  Outputs (6):\n    Succeeded: 6\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/64711fc89a62a8be53f98998/rawLog.txt\nCompleted 10.1 KiB/10.1 KiB (138.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 89%)\n  adding: outputs/Sontag2017 - Fig 1D new constant value simulation.sedml/ (stored 0%)\n  adding: outputs/Sontag2017 - Fig 1D new constant value simulation.sedml/plot_1_task1.pdf (deflated 33%)\n  adding: outputs/Sontag2017 - Fig 1D shifted ramp simulation.sedml/ (stored 0%)\n  adding: outputs/Sontag2017 - Fig 1D shifted ramp simulation.sedml/plot_1_task1.pdf (deflated 33%)\n  adding: outputs/Sontag2017 - Fig 1D shifted exponential simulation.sedml/ (stored 0%)\n  adding: outputs/Sontag2017 - Fig 1D shifted exponential simulation.sedml/plot_1_task1.pdf (deflated 33%)\n  adding: outputs/reports.h5 (deflated 65%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 105.7 KiB/105.7 KiB (1.0 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/outputs/reports.h5\nCompleted 67.0 KiB/134.3 KiB (679.2 KiB/s) with 6 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/output.zip\nCompleted 67.0 KiB/134.3 KiB (679.2 KiB/s) with 5 file(s) remaining\rCompleted 80.2 KiB/134.3 KiB (729.7 KiB/s) with 5 file(s) remaining\rupload: outputs/Sontag2017 - Fig 1D shifted exponential simulation.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/outputs/Sontag2017 - Fig 1D shifted exponential simulation.sedml/plot_1_task1.pdf\nCompleted 80.2 KiB/134.3 KiB (729.7 KiB/s) with 4 file(s) remaining\rCompleted 93.5 KiB/134.3 KiB (835.4 KiB/s) with 4 file(s) remaining\rupload: outputs/Sontag2017 - Fig 1D shifted ramp simulation.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/outputs/Sontag2017 - Fig 1D shifted ramp simulation.sedml/plot_1_task1.pdf\nCompleted 93.5 KiB/134.3 KiB (835.4 KiB/s) with 3 file(s) remaining\rCompleted 106.0 KiB/134.3 KiB (885.3 KiB/s) with 3 file(s) remaining\rupload: outputs/Sontag2017 - Fig 1D new constant value simulation.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/outputs/Sontag2017 - Fig 1D new constant value simulation.sedml/plot_1_task1.pdf\nCompleted 106.0 KiB/134.3 KiB (885.3 KiB/s) with 2 file(s) remaining\rCompleted 109.0 KiB/134.3 KiB (850.6 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/rawLog.txt\nCompleted 109.0 KiB/134.3 KiB (850.6 KiB/s) with 1 file(s) remaining\rCompleted 134.3 KiB/134.3 KiB (885.5 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Sontag2017 - Fig 1D new constant value simulation.sedml  \n  inflating: contents/Sontag2017 - Fig 1D shifted exponential simulation.sedml  \n  inflating: contents/Sontag2017 - Fig 1D shifted ramp simulation.sedml  \n  inflating: contents/Sontag2017-biopax2.owl  \n  inflating: contents/Sontag2017-biopax3.owl  \n  inflating: contents/Sontag2017-matlab.m  \n  inflating: contents/Sontag2017-octave.m  \n  inflating: contents/Sontag2017.cps  \n  inflating: contents/Sontag2017.ode  \n  inflating: contents/Sontag2017.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 11.5 KiB/468.6 KiB (167.3 KiB/s) with 14 file(s) remaining\rupload: contents/Sontag2017 - Fig 1D new constant value simulation.sedml to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/contents/Sontag2017 - Fig 1D new constant value simulation.sedml\nCompleted 11.5 KiB/468.6 KiB (167.3 KiB/s) with 13 file(s) remaining\rCompleted 267.5 KiB/468.6 KiB (2.2 MiB/s) with 13 file(s) remaining \rCompleted 279.0 KiB/468.6 KiB (2.3 MiB/s) with 13 file(s) remaining \rupload: contents/Sontag2017-biopax2.owl to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/contents/Sontag2017-biopax2.owl\nCompleted 279.0 KiB/468.6 KiB (2.3 MiB/s) with 12 file(s) remaining\rCompleted 281.9 KiB/468.6 KiB (2.3 MiB/s) with 12 file(s) remaining\rupload: contents/Sontag2017.ode to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/contents/Sontag2017.ode\nCompleted 281.9 KiB/468.6 KiB (2.3 MiB/s) with 11 file(s) remaining\rCompleted 286.3 KiB/468.6 KiB (2.2 MiB/s) with 11 file(s) remaining\rupload: contents/Sontag2017-octave.m to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/contents/Sontag2017-octave.m\nCompleted 286.3 KiB/468.6 KiB (2.2 MiB/s) with 10 file(s) remaining\rCompleted 343.2 KiB/468.6 KiB (2.5 MiB/s) with 10 file(s) remaining\rupload: contents/Sontag2017.cps to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/contents/Sontag2017.cps\nCompleted 343.2 KiB/468.6 KiB (2.5 MiB/s) with 9 file(s) remaining\rCompleted 373.8 KiB/468.6 KiB (2.6 MiB/s) with 9 file(s) remaining\rupload: contents/Sontag2017.xml to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/contents/Sontag2017.xml\nCompleted 373.8 KiB/468.6 KiB (2.6 MiB/s) with 8 file(s) remaining\rCompleted 373.9 KiB/468.6 KiB (2.5 MiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/contents/curation_notes.txt\nCompleted 373.9 KiB/468.6 KiB (2.5 MiB/s) with 7 file(s) remaining\rCompleted 375.6 KiB/468.6 KiB (2.4 MiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/contents/manifest.xml\nCompleted 375.6 KiB/468.6 KiB (2.4 MiB/s) with 6 file(s) remaining\rCompleted 423.6 KiB/468.6 KiB (2.3 MiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/contents/curation_image.png\nCompleted 423.6 KiB/468.6 KiB (2.3 MiB/s) with 5 file(s) remaining\rCompleted 434.8 KiB/468.6 KiB (2.4 MiB/s) with 5 file(s) remaining\rupload: contents/Sontag2017 - Fig 1D shifted exponential simulation.sedml to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/contents/Sontag2017 - Fig 1D shifted exponential simulation.sedml\nCompleted 434.8 KiB/468.6 KiB (2.4 MiB/s) with 4 file(s) remaining\rCompleted 437.9 KiB/468.6 KiB (2.3 MiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/contents/metadata.rdf\nCompleted 437.9 KiB/468.6 KiB (2.3 MiB/s) with 3 file(s) remaining\rCompleted 453.0 KiB/468.6 KiB (2.4 MiB/s) with 3 file(s) remaining\rupload: contents/Sontag2017-biopax3.owl to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/contents/Sontag2017-biopax3.owl\nCompleted 453.0 KiB/468.6 KiB (2.4 MiB/s) with 2 file(s) remaining\rCompleted 457.4 KiB/468.6 KiB (2.4 MiB/s) with 2 file(s) remaining\rupload: contents/Sontag2017-matlab.m to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/contents/Sontag2017-matlab.m\nCompleted 457.4 KiB/468.6 KiB (2.4 MiB/s) with 1 file(s) remaining\rCompleted 468.6 KiB/468.6 KiB (2.2 MiB/s) with 1 file(s) remaining\rupload: contents/Sontag2017 - Fig 1D shifted ramp simulation.sedml to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/contents/Sontag2017 - Fig 1D shifted ramp simulation.sedml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.6 KiB/9.6 KiB (133.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711fc89a62a8be53f98998/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Sontag2017 - Fig 1D new constant value simulation.sedml\ncreating dataset /Sontag2017 - Fig 1D new constant value simulation.sedml/autogen_report_for_task1, shape: (17, 1001), type: float64\ndataset created, uuid: d-d4acf7f3-5742ba0a-d760-a8297c-6000ab, chunk_size: (17, 1001)\ncreating dataset /Sontag2017 - Fig 1D new constant value simulation.sedml/plot_1_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-d4acf7f3-5742ba0a-471a-52ee62-41eecc, chunk_size: (4, 1001)\ncreating group /Sontag2017 - Fig 1D shifted exponential simulation.sedml\ncreating dataset /Sontag2017 - Fig 1D shifted exponential simulation.sedml/autogen_report_for_task1, shape: (17, 1001), type: float64\ndataset created, uuid: d-d4acf7f3-5742ba0a-fcf1-4d481b-a3990d, chunk_size: (17, 1001)\ncreating dataset /Sontag2017 - Fig 1D shifted exponential simulation.sedml/plot_1_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-d4acf7f3-5742ba0a-8021-2ff8f7-38f597, chunk_size: (4, 1001)\ncreating group /Sontag2017 - Fig 1D shifted ramp simulation.sedml\ncreating dataset /Sontag2017 - Fig 1D shifted ramp simulation.sedml/autogen_report_for_task1, shape: (17, 1001), type: float64\ndataset created, uuid: d-d4acf7f3-5742ba0a-22b7-5e509b-ca25b0, chunk_size: (17, 1001)\ncreating dataset /Sontag2017 - Fig 1D shifted ramp simulation.sedml/plot_1_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-d4acf7f3-5742ba0a-1060-a195ba-76fca3, chunk_size: (4, 1001)\ncreating attribute combineArchiveLocation in /Sontag2017 - Fig 1D new constant value simulation.sedml\ncreating attribute uri in /Sontag2017 - Fig 1D new constant value simulation.sedml\ncreating attribute _type in /Sontag2017 - Fig 1D new constant value simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Sontag2017 - Fig 1D new constant value simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Sontag2017 - Fig 1D new constant value simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Sontag2017 - Fig 1D new constant value simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Sontag2017 - Fig 1D new constant value simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Sontag2017 - Fig 1D new constant value simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Sontag2017 - Fig 1D new constant value simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Sontag2017 - Fig 1D new constant value simulation.sedml/autogen_report_for_task1\ncreating attribute uri in /Sontag2017 - Fig 1D new constant value simulation.sedml/autogen_report_for_task1\ncreating attribute _type in /Sontag2017 - Fig 1D new constant value simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Sontag2017 - Fig 1D new constant value simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Sontag2017 - Fig 1D new constant value simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Sontag2017 - Fig 1D new constant value simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Sontag2017 - Fig 1D new constant value simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Sontag2017 - Fig 1D new constant value simulation.sedml/plot_1_task1\ncreating attribute sedmlId in /Sontag2017 - Fig 1D new constant value simulation.sedml/plot_1_task1\ncreating attribute sedmlName in /Sontag2017 - Fig 1D new constant value simulation.sedml/plot_1_task1\ncreating attribute uri in /Sontag2017 - Fig 1D new constant value simulation.sedml/plot_1_task1\ncreating attribute combineArchiveLocation in /Sontag2017 - Fig 1D shifted exponential simulation.sedml\ncreating attribute uri in /Sontag2017 - Fig 1D shifted exponential simulation.sedml\ncreating attribute _type in /Sontag2017 - Fig 1D shifted exponential simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Sontag2017 - Fig 1D shifted exponential simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Sontag2017 - Fig 1D shifted exponential simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Sontag2017 - Fig 1D shifted exponential simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Sontag2017 - Fig 1D shifted exponential simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Sontag2017 - Fig 1D shifted exponential simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Sontag2017 - Fig 1D shifted exponential simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Sontag2017 - Fig 1D shifted exponential simulation.sedml/autogen_report_for_task1\ncreating attribute uri in /Sontag2017 - Fig 1D shifted exponential simulation.sedml/autogen_report_for_task1\ncreating attribute _type in /Sontag2017 - Fig 1D shifted exponential simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Sontag2017 - Fig 1D shifted exponential simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Sontag2017 - Fig 1D shifted exponential simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Sontag2017 - Fig 1D shifted exponential simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Sontag2017 - Fig 1D shifted exponential simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Sontag2017 - Fig 1D shifted exponential simulation.sedml/plot_1_task1\ncreating attribute sedmlId in /Sontag2017 - Fig 1D shifted exponential simulation.sedml/plot_1_task1\ncreating attribute sedmlName in /Sontag2017 - Fig 1D shifted exponential simulation.sedml/plot_1_task1\ncreating attribute uri in /Sontag2017 - Fig 1D shifted exponential simulation.sedml/plot_1_task1\ncreating attribute combineArchiveLocation in /Sontag2017 - Fig 1D shifted ramp simulation.sedml\ncreating attribute uri in /Sontag2017 - Fig 1D shifted ramp simulation.sedml\ncreating attribute _type in /Sontag2017 - Fig 1D shifted ramp simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Sontag2017 - Fig 1D shifted ramp simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Sontag2017 - Fig 1D shifted ramp simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Sontag2017 - Fig 1D shifted ramp simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Sontag2017 - Fig 1D shifted ramp simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Sontag2017 - Fig 1D shifted ramp simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Sontag2017 - Fig 1D shifted ramp simulation.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Sontag2017 - Fig 1D shifted ramp simulation.sedml/autogen_report_for_task1\ncreating attribute uri in /Sontag2017 - Fig 1D shifted ramp simulation.sedml/autogen_report_for_task1\ncreating attribute _type in /Sontag2017 - Fig 1D shifted ramp simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Sontag2017 - Fig 1D shifted ramp simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Sontag2017 - Fig 1D shifted ramp simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Sontag2017 - Fig 1D shifted ramp simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Sontag2017 - Fig 1D shifted ramp simulation.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Sontag2017 - Fig 1D shifted ramp simulation.sedml/plot_1_task1\ncreating attribute sedmlId in /Sontag2017 - Fig 1D shifted ramp simulation.sedml/plot_1_task1\ncreating attribute sedmlName in /Sontag2017 - Fig 1D shifted ramp simulation.sedml/plot_1_task1\ncreating attribute uri in /Sontag2017 - Fig 1D shifted ramp simulation.sedml/plot_1_task1\ncreate_links: /\ngot link: Sontag2017 - Fig 1D new constant value simulation.sedml\ngot link: Sontag2017 - Fig 1D shifted exponential simulation.sedml\ngot link: Sontag2017 - Fig 1D shifted ramp simulation.sedml\ncreate_links: /Sontag2017 - Fig 1D new constant value simulation.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\ncreate_links: /Sontag2017 - Fig 1D shifted exponential simulation.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\ncreate_links: /Sontag2017 - Fig 1D shifted ramp simulation.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Sontag2017 - Fig 1D new constant value simulation.sedml/autogen_report_for_task1 to tgt: /Sontag2017 - Fig 1D new constant value simulation.sedml/autogen_report_for_task1, shape: (17, 1001), type: float64\niterating over chunks for /Sontag2017 - Fig 1D new constant value simulation.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 17, 1), slice(0, 1001, 1))\ndone with dataload for /Sontag2017 - Fig 1D new constant value simulation.sedml/autogen_report_for_task1\nwrite_dataset src: /Sontag2017 - Fig 1D new constant value simulation.sedml/plot_1_task1 to tgt: /Sontag2017 - Fig 1D new constant value simulation.sedml/plot_1_task1, shape: (4, 1001), type: float64\niterating over chunks for /Sontag2017 - Fig 1D new constant value simulation.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /Sontag2017 - Fig 1D new constant value simulation.sedml/plot_1_task1\nwrite_dataset src: /Sontag2017 - Fig 1D shifted exponential simulation.sedml/autogen_report_for_task1 to tgt: /Sontag2017 - Fig 1D shifted exponential simulation.sedml/autogen_report_for_task1, shape: (17, 1001), type: float64\niterating over chunks for /Sontag2017 - Fig 1D shifted exponential simulation.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 17, 1), slice(0, 1001, 1))\ndone with dataload for /Sontag2017 - Fig 1D shifted exponential simulation.sedml/autogen_report_for_task1\nwrite_dataset src: /Sontag2017 - Fig 1D shifted exponential simulation.sedml/plot_1_task1 to tgt: /Sontag2017 - Fig 1D shifted exponential simulation.sedml/plot_1_task1, shape: (4, 1001), type: float64\niterating over chunks for /Sontag2017 - Fig 1D shifted exponential simulation.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /Sontag2017 - Fig 1D shifted exponential simulation.sedml/plot_1_task1\nwrite_dataset src: /Sontag2017 - Fig 1D shifted ramp simulation.sedml/autogen_report_for_task1 to tgt: /Sontag2017 - Fig 1D shifted ramp simulation.sedml/autogen_report_for_task1, shape: (17, 1001), type: float64\niterating over chunks for /Sontag2017 - Fig 1D shifted ramp simulation.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 17, 1), slice(0, 1001, 1))\ndone with dataload for /Sontag2017 - Fig 1D shifted ramp simulation.sedml/autogen_report_for_task1\nwrite_dataset src: /Sontag2017 - Fig 1D shifted ramp simulation.sedml/plot_1_task1 to tgt: /Sontag2017 - Fig 1D shifted ramp simulation.sedml/plot_1_task1, shape: (4, 1001), type: float64\niterating over chunks for /Sontag2017 - Fig 1D shifted ramp simulation.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /Sontag2017 - Fig 1D shifted ramp simulation.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711fc89a62a8be53f98998\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 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 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":2.913246,"sedDocuments":[{"location":"Sontag2017 - Fig 1D new constant value simulation.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Archive contains 3 SED-ML documents with 3 models, 3 simulations, 3 tasks, 3 reports, and 3 plots:\r\n  Sontag2017 - Fig 1D new constant value simulation.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 17 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n  Sontag2017 - Fig 1D shifted exponential simulation.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 17 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n  Sontag2017 - Fig 1D shifted ramp simulation.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 17 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Sontag2017 - Fig 1D new constant value simulation.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_report_for_task1`\r\n      `plot_1_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: `plot_1_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_report_for_task1` ...","duration":0.823625,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.180198,"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":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.349208,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.135768,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Antigen_expressing_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Regulatory_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Effector_cells","status":"SUCCEEDED"},{"id":"autogen_task1_lambda","status":"SUCCEEDED"},{"id":"autogen_task1_kappa","status":"SUCCEEDED"},{"id":"autogen_task1_delta_x","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_mu","status":"SUCCEEDED"},{"id":"autogen_task1_detla_y","status":"SUCCEEDED"},{"id":"autogen_task1_Whole_organism","status":"SUCCEEDED"},{"id":"autogen_task1_pathogen_tumor_production","status":"SUCCEEDED"},{"id":"autogen_task1_pathogen_tumor_consumption","status":"SUCCEEDED"},{"id":"autogen_task1_regulatory_production","status":"SUCCEEDED"},{"id":"autogen_task1_regulatory_consumption","status":"SUCCEEDED"},{"id":"autogen_task1_effector_production","status":"SUCCEEDED"},{"id":"autogen_task1_effector_consumption","status":"SUCCEEDED"}]}]},{"location":"Sontag2017 - Fig 1D shifted exponential simulation.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":" \u001b[34msucceeded\u001b[0m\r\n\r\n  Executed 1 tasks and 2 outputs:\r\n    Tasks:\r\n      Succeeded: 1\r\n      Skipped: 0\r\n      Failed: 0\r\n    Outputs:\r\n      Succeeded: 2\r\n      Skipped: 0\r\n      Failed: 0\r\nExecuting SED-ML file 2: Sontag2017 - Fig 1D shifted exponential simulation.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_report_for_task1`\r\n      `plot_1_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: `plot_1_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_report_for_task1` ...","duration":0.639528,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.091271,"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":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.184611,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.156475,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Antigen_expressing_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Regulatory_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Effector_cells","status":"SUCCEEDED"},{"id":"autogen_task1_lambda","status":"SUCCEEDED"},{"id":"autogen_task1_kappa","status":"SUCCEEDED"},{"id":"autogen_task1_delta_x","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_mu","status":"SUCCEEDED"},{"id":"autogen_task1_detla_y","status":"SUCCEEDED"},{"id":"autogen_task1_Whole_organism","status":"SUCCEEDED"},{"id":"autogen_task1_pathogen_tumor_production","status":"SUCCEEDED"},{"id":"autogen_task1_pathogen_tumor_consumption","status":"SUCCEEDED"},{"id":"autogen_task1_regulatory_production","status":"SUCCEEDED"},{"id":"autogen_task1_regulatory_consumption","status":"SUCCEEDED"},{"id":"autogen_task1_effector_production","status":"SUCCEEDED"},{"id":"autogen_task1_effector_consumption","status":"SUCCEEDED"}]}]},{"location":"Sontag2017 - Fig 1D shifted ramp simulation.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":" \u001b[34msucceeded\u001b[0m\r\n\r\n  Executed 1 tasks and 2 outputs:\r\n    Tasks:\r\n      Succeeded: 1\r\n      Skipped: 0\r\n      Failed: 0\r\n    Outputs:\r\n      Succeeded: 2\r\n      Skipped: 0\r\n      Failed: 0\r\nExecuting SED-ML file 3: Sontag2017 - Fig 1D shifted ramp simulation.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_report_for_task1`\r\n      `plot_1_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: `plot_1_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_report_for_task1` ...","duration":0.676415,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.091969,"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":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.208851,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.149934,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Antigen_expressing_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Regulatory_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Effector_cells","status":"SUCCEEDED"},{"id":"autogen_task1_lambda","status":"SUCCEEDED"},{"id":"autogen_task1_kappa","status":"SUCCEEDED"},{"id":"autogen_task1_delta_x","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_mu","status":"SUCCEEDED"},{"id":"autogen_task1_detla_y","status":"SUCCEEDED"},{"id":"autogen_task1_Whole_organism","status":"SUCCEEDED"},{"id":"autogen_task1_pathogen_tumor_production","status":"SUCCEEDED"},{"id":"autogen_task1_pathogen_tumor_consumption","status":"SUCCEEDED"},{"id":"autogen_task1_regulatory_production","status":"SUCCEEDED"},{"id":"autogen_task1_regulatory_consumption","status":"SUCCEEDED"},{"id":"autogen_task1_effector_production","status":"SUCCEEDED"},{"id":"autogen_task1_effector_consumption","status":"SUCCEEDED"}]}]}]}