{"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    298      0 --:--:-- --:--:-- --:--:--   298\n\r100  170k  100  170k    0     0   292k      0 --:--:-- --:--:-- --:--:--  292k\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 4 SED documents:\n  SED documents (4):\n    Succeeded: 4\n    Skipped: 0\n    Failed: 0\n  Tasks (4):\n    Succeeded: 4\n    Skipped: 0\n    Failed: 0\n  Outputs (8):\n    Succeeded: 8\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 1.6 KiB/1.6 KiB (23.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a303877b6669655052088/rawLog.txt\nCompleted 21.7 KiB/21.7 KiB (309.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a303877b6669655052088/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 94%)\n  adding: outputs/Linke2017_figure1d.sedml/ (stored 0%)\n  adding: outputs/Linke2017_figure1d.sedml/plot_1_task1.pdf (deflated 27%)\n  adding: outputs/Linke2017f1b.sedml/ (stored 0%)\n  adding: outputs/Linke2017f1b.sedml/plot_1_task1.pdf (deflated 27%)\n  adding: outputs/Linke2017_figure1e.sedml/ (stored 0%)\n  adding: outputs/Linke2017_figure1e.sedml/plot_1_task1.pdf (deflated 27%)\n  adding: outputs/Linke2017_figure1c.sedml/ (stored 0%)\n  adding: outputs/Linke2017_figure1c.sedml/plot_1_task1.pdf (deflated 27%)\n  adding: outputs/reports.h5 (deflated 48%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 253.5 KiB/253.5 KiB (2.9 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a303877b6669655052088/outputs/reports.h5\nCompleted 13.2 KiB/268.1 KiB (124.5 KiB/s) with 7 file(s) remaining\rupload: outputs/Linke2017_figure1c.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a303877b6669655052088/outputs/Linke2017_figure1c.sedml/plot_1_task1.pdf\nCompleted 13.2 KiB/268.1 KiB (124.5 KiB/s) with 6 file(s) remaining\rCompleted 187.5 KiB/268.1 KiB (1.5 MiB/s) with 6 file(s) remaining \rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a303877b6669655052088/output.zip\nCompleted 187.5 KiB/268.1 KiB (1.5 MiB/s) with 5 file(s) remaining\rCompleted 225.3 KiB/268.1 KiB (1.5 MiB/s) with 5 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a303877b6669655052088/outputs/plots.zip\nCompleted 225.3 KiB/268.1 KiB (1.5 MiB/s) with 4 file(s) remaining\rCompleted 238.5 KiB/268.1 KiB (1.5 MiB/s) with 4 file(s) remaining\rupload: outputs/Linke2017_figure1e.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a303877b6669655052088/outputs/Linke2017_figure1e.sedml/plot_1_task1.pdf\nCompleted 238.5 KiB/268.1 KiB (1.5 MiB/s) with 3 file(s) remaining\rCompleted 251.8 KiB/268.1 KiB (1.6 MiB/s) with 3 file(s) remaining\rupload: outputs/Linke2017f1b.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a303877b6669655052088/outputs/Linke2017f1b.sedml/plot_1_task1.pdf\nCompleted 251.8 KiB/268.1 KiB (1.6 MiB/s) with 2 file(s) remaining\rCompleted 254.8 KiB/268.1 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a303877b6669655052088/rawLog.txt\nCompleted 254.8 KiB/268.1 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 268.1 KiB/268.1 KiB (639.5 KiB/s) with 1 file(s) remaining\rupload: outputs/Linke2017_figure1d.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a303877b6669655052088/outputs/Linke2017_figure1d.sedml/plot_1_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Linke2017-biopax2.owl  \n  inflating: contents/Linke2017-biopax3.owl  \n  inflating: contents/Linke2017-matlab.m  \n  inflating: contents/Linke2017-octave.m  \n  inflating: contents/Linke2017.ode  \n  inflating: contents/Linke2017.xml  \n  inflating: contents/Linke2017_figure1b.cps  \n  inflating: contents/Linke2017_figure1c.cps  \n  inflating: contents/Linke2017_figure1c.sedml  \n  inflating: contents/Linke2017_figure1d.cps  \n  inflating: contents/Linke2017_figure1d.sedml  \n  inflating: contents/Linke2017_figure1e.cps  \n  inflating: contents/Linke2017_figure1e.sedml  \n  inflating: contents/Linke2017f1b.sedml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 34.3 KiB/978.2 KiB (359.8 KiB/s) with 18 file(s) remaining\rupload: contents/Linke2017-biopax2.owl to s3://files.biosimulations.org/simulations/647a303877b6669655052088/contents/Linke2017-biopax2.owl\nCompleted 34.3 KiB/978.2 KiB (359.8 KiB/s) with 17 file(s) remaining\rCompleted 165.6 KiB/978.2 KiB (1.2 MiB/s) with 17 file(s) remaining \rCompleted 246.4 KiB/978.2 KiB (1.7 MiB/s) with 17 file(s) remaining \rupload: contents/Linke2017_figure1b.cps to s3://files.biosimulations.org/simulations/647a303877b6669655052088/contents/Linke2017_figure1b.cps\nCompleted 246.4 KiB/978.2 KiB (1.7 MiB/s) with 16 file(s) remaining\rupload: contents/Linke2017.xml to s3://files.biosimulations.org/simulations/647a303877b6669655052088/contents/Linke2017.xml\nCompleted 246.4 KiB/978.2 KiB (1.7 MiB/s) with 15 file(s) remaining\rCompleted 255.1 KiB/978.2 KiB (1.7 MiB/s) with 15 file(s) remaining\rupload: contents/Linke2017.ode to s3://files.biosimulations.org/simulations/647a303877b6669655052088/contents/Linke2017.ode\nCompleted 255.1 KiB/978.2 KiB (1.7 MiB/s) with 14 file(s) remaining\rCompleted 289.7 KiB/978.2 KiB (1.8 MiB/s) with 14 file(s) remaining\rupload: contents/Linke2017_figure1d.sedml to s3://files.biosimulations.org/simulations/647a303877b6669655052088/contents/Linke2017_figure1d.sedml\nCompleted 289.7 KiB/978.2 KiB (1.8 MiB/s) with 13 file(s) remaining\rCompleted 421.1 KiB/978.2 KiB (2.5 MiB/s) with 13 file(s) remaining\rupload: contents/Linke2017_figure1c.cps to s3://files.biosimulations.org/simulations/647a303877b6669655052088/contents/Linke2017_figure1c.cps\nCompleted 421.1 KiB/978.2 KiB (2.5 MiB/s) with 12 file(s) remaining\rCompleted 552.4 KiB/978.2 KiB (3.2 MiB/s) with 12 file(s) remaining\rupload: contents/Linke2017_figure1e.cps to s3://files.biosimulations.org/simulations/647a303877b6669655052088/contents/Linke2017_figure1e.cps\nCompleted 552.4 KiB/978.2 KiB (3.2 MiB/s) with 11 file(s) remaining\rCompleted 587.1 KiB/978.2 KiB (3.3 MiB/s) with 11 file(s) remaining\rCompleted 643.9 KiB/978.2 KiB (3.6 MiB/s) with 11 file(s) remaining\rCompleted 775.3 KiB/978.2 KiB (4.3 MiB/s) with 11 file(s) remaining\rupload: contents/Linke2017_figure1c.sedml to s3://files.biosimulations.org/simulations/647a303877b6669655052088/contents/Linke2017_figure1c.sedml\nCompleted 775.3 KiB/978.2 KiB (4.3 MiB/s) with 10 file(s) remaining\rupload: contents/Linke2017-biopax3.owl to s3://files.biosimulations.org/simulations/647a303877b6669655052088/contents/Linke2017-biopax3.owl\nCompleted 775.3 KiB/978.2 KiB (4.3 MiB/s) with 9 file(s) remaining\rupload: contents/Linke2017_figure1d.cps to s3://files.biosimulations.org/simulations/647a303877b6669655052088/contents/Linke2017_figure1d.cps\nCompleted 775.3 KiB/978.2 KiB (4.3 MiB/s) with 8 file(s) remaining\rCompleted 786.7 KiB/978.2 KiB (4.2 MiB/s) with 8 file(s) remaining\rupload: contents/Linke2017-matlab.m to s3://files.biosimulations.org/simulations/647a303877b6669655052088/contents/Linke2017-matlab.m\nCompleted 786.7 KiB/978.2 KiB (4.2 MiB/s) with 7 file(s) remaining\rCompleted 798.2 KiB/978.2 KiB (3.8 MiB/s) with 7 file(s) remaining\rupload: contents/Linke2017-octave.m to s3://files.biosimulations.org/simulations/647a303877b6669655052088/contents/Linke2017-octave.m\nCompleted 798.2 KiB/978.2 KiB (3.8 MiB/s) with 6 file(s) remaining\rCompleted 832.9 KiB/978.2 KiB (3.7 MiB/s) with 6 file(s) remaining\rupload: contents/Linke2017_figure1e.sedml to s3://files.biosimulations.org/simulations/647a303877b6669655052088/contents/Linke2017_figure1e.sedml\nCompleted 832.9 KiB/978.2 KiB (3.7 MiB/s) with 5 file(s) remaining\rCompleted 867.5 KiB/978.2 KiB (3.8 MiB/s) with 5 file(s) remaining\rupload: contents/Linke2017f1b.sedml to s3://files.biosimulations.org/simulations/647a303877b6669655052088/contents/Linke2017f1b.sedml\nCompleted 867.5 KiB/978.2 KiB (3.8 MiB/s) with 4 file(s) remaining\rCompleted 867.7 KiB/978.2 KiB (3.7 MiB/s) with 4 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a303877b6669655052088/contents/curation_notes.txt\nCompleted 867.7 KiB/978.2 KiB (3.7 MiB/s) with 3 file(s) remaining\rCompleted 869.5 KiB/978.2 KiB (3.6 MiB/s) with 3 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a303877b6669655052088/contents/metadata.rdf\nCompleted 869.5 KiB/978.2 KiB (3.6 MiB/s) with 2 file(s) remaining\rCompleted 976.1 KiB/978.2 KiB (4.0 MiB/s) with 2 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a303877b6669655052088/contents/curation_image.png\nCompleted 976.1 KiB/978.2 KiB (4.0 MiB/s) with 1 file(s) remaining\rCompleted 978.2 KiB/978.2 KiB (3.9 MiB/s) with 1 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a303877b6669655052088/contents/manifest.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 10.7 KiB/10.7 KiB (153.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a303877b6669655052088/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Linke2017_figure1c.sedml\ncreating dataset /Linke2017_figure1c.sedml/autogen_report_for_task1, shape: (60, 101), type: float64\ndataset created, uuid: d-e0c11f60-216e4eb7-3447-06bb69-a69197, chunk_size: (60, 101)\ncreating dataset /Linke2017_figure1c.sedml/plot_1_task1, shape: (4, 101), type: float64\ndataset created, uuid: d-e0c11f60-216e4eb7-7b7e-302f04-a363e7, chunk_size: (4, 101)\ncreating group /Linke2017_figure1d.sedml\ncreating dataset /Linke2017_figure1d.sedml/autogen_report_for_task1, shape: (60, 101), type: float64\ndataset created, uuid: d-e0c11f60-216e4eb7-15d1-2e0b2e-ef2503, chunk_size: (60, 101)\ncreating dataset /Linke2017_figure1d.sedml/plot_1_task1, shape: (4, 101), type: float64\ndataset created, uuid: d-e0c11f60-216e4eb7-c7a6-45220d-c059cf, chunk_size: (4, 101)\ncreating group /Linke2017_figure1e.sedml\ncreating dataset /Linke2017_figure1e.sedml/autogen_report_for_task1, shape: (60, 101), type: float64\ndataset created, uuid: d-e0c11f60-216e4eb7-e0b4-f800db-28aab7, chunk_size: (60, 101)\ncreating dataset /Linke2017_figure1e.sedml/plot_1_task1, shape: (4, 101), type: float64\ndataset created, uuid: d-e0c11f60-216e4eb7-ae3e-92d83c-e586bf, chunk_size: (4, 101)\ncreating group /Linke2017f1b.sedml\ncreating dataset /Linke2017f1b.sedml/autogen_report_for_task1, shape: (60, 101), type: float64\ndataset created, uuid: d-e0c11f60-216e4eb7-2c7f-d51de3-d10b71, chunk_size: (60, 101)\ncreating dataset /Linke2017f1b.sedml/plot_1_task1, shape: (4, 101), type: float64\ndataset created, uuid: d-e0c11f60-216e4eb7-6264-9e58db-71dcc3, chunk_size: (4, 101)\ncreating attribute combineArchiveLocation in /Linke2017_figure1c.sedml\ncreating attribute uri in /Linke2017_figure1c.sedml\ncreating attribute _type in /Linke2017_figure1c.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Linke2017_figure1c.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Linke2017_figure1c.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Linke2017_figure1c.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Linke2017_figure1c.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Linke2017_figure1c.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Linke2017_figure1c.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Linke2017_figure1c.sedml/autogen_report_for_task1\ncreating attribute uri in /Linke2017_figure1c.sedml/autogen_report_for_task1\ncreating attribute _type in /Linke2017_figure1c.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Linke2017_figure1c.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Linke2017_figure1c.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Linke2017_figure1c.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Linke2017_figure1c.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Linke2017_figure1c.sedml/plot_1_task1\ncreating attribute sedmlId in /Linke2017_figure1c.sedml/plot_1_task1\ncreating attribute sedmlName in /Linke2017_figure1c.sedml/plot_1_task1\ncreating attribute uri in /Linke2017_figure1c.sedml/plot_1_task1\ncreating attribute combineArchiveLocation in /Linke2017_figure1d.sedml\ncreating attribute uri in /Linke2017_figure1d.sedml\ncreating attribute _type in /Linke2017_figure1d.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Linke2017_figure1d.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Linke2017_figure1d.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Linke2017_figure1d.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Linke2017_figure1d.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Linke2017_figure1d.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Linke2017_figure1d.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Linke2017_figure1d.sedml/autogen_report_for_task1\ncreating attribute uri in /Linke2017_figure1d.sedml/autogen_report_for_task1\ncreating attribute _type in /Linke2017_figure1d.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Linke2017_figure1d.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Linke2017_figure1d.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Linke2017_figure1d.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Linke2017_figure1d.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Linke2017_figure1d.sedml/plot_1_task1\ncreating attribute sedmlId in /Linke2017_figure1d.sedml/plot_1_task1\ncreating attribute sedmlName in /Linke2017_figure1d.sedml/plot_1_task1\ncreating attribute uri in /Linke2017_figure1d.sedml/plot_1_task1\ncreating attribute combineArchiveLocation in /Linke2017_figure1e.sedml\ncreating attribute uri in /Linke2017_figure1e.sedml\ncreating attribute _type in /Linke2017_figure1e.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Linke2017_figure1e.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Linke2017_figure1e.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Linke2017_figure1e.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Linke2017_figure1e.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Linke2017_figure1e.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Linke2017_figure1e.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Linke2017_figure1e.sedml/autogen_report_for_task1\ncreating attribute uri in /Linke2017_figure1e.sedml/autogen_report_for_task1\ncreating attribute _type in /Linke2017_figure1e.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Linke2017_figure1e.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Linke2017_figure1e.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Linke2017_figure1e.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Linke2017_figure1e.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Linke2017_figure1e.sedml/plot_1_task1\ncreating attribute sedmlId in /Linke2017_figure1e.sedml/plot_1_task1\ncreating attribute sedmlName in /Linke2017_figure1e.sedml/plot_1_task1\ncreating attribute uri in /Linke2017_figure1e.sedml/plot_1_task1\ncreating attribute combineArchiveLocation in /Linke2017f1b.sedml\ncreating attribute uri in /Linke2017f1b.sedml\ncreating attribute _type in /Linke2017f1b.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Linke2017f1b.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Linke2017f1b.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Linke2017f1b.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Linke2017f1b.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Linke2017f1b.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Linke2017f1b.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Linke2017f1b.sedml/autogen_report_for_task1\ncreating attribute uri in /Linke2017f1b.sedml/autogen_report_for_task1\ncreating attribute _type in /Linke2017f1b.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Linke2017f1b.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Linke2017f1b.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Linke2017f1b.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Linke2017f1b.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Linke2017f1b.sedml/plot_1_task1\ncreating attribute sedmlId in /Linke2017f1b.sedml/plot_1_task1\ncreating attribute sedmlName in /Linke2017f1b.sedml/plot_1_task1\ncreating attribute uri in /Linke2017f1b.sedml/plot_1_task1\ncreate_links: /\ngot link: Linke2017_figure1c.sedml\ngot link: Linke2017_figure1d.sedml\ngot link: Linke2017_figure1e.sedml\ngot link: Linke2017f1b.sedml\ncreate_links: /Linke2017_figure1c.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\ncreate_links: /Linke2017_figure1d.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\ncreate_links: /Linke2017_figure1e.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\ncreate_links: /Linke2017f1b.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Linke2017_figure1c.sedml/autogen_report_for_task1 to tgt: /Linke2017_figure1c.sedml/autogen_report_for_task1, shape: (60, 101), type: float64\niterating over chunks for /Linke2017_figure1c.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 60, 1), slice(0, 101, 1))\ndone with dataload for /Linke2017_figure1c.sedml/autogen_report_for_task1\nwrite_dataset src: /Linke2017_figure1c.sedml/plot_1_task1 to tgt: /Linke2017_figure1c.sedml/plot_1_task1, shape: (4, 101), type: float64\niterating over chunks for /Linke2017_figure1c.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 101, 1))\ndone with dataload for /Linke2017_figure1c.sedml/plot_1_task1\nwrite_dataset src: /Linke2017_figure1d.sedml/autogen_report_for_task1 to tgt: /Linke2017_figure1d.sedml/autogen_report_for_task1, shape: (60, 101), type: float64\niterating over chunks for /Linke2017_figure1d.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 60, 1), slice(0, 101, 1))\ndone with dataload for /Linke2017_figure1d.sedml/autogen_report_for_task1\nwrite_dataset src: /Linke2017_figure1d.sedml/plot_1_task1 to tgt: /Linke2017_figure1d.sedml/plot_1_task1, shape: (4, 101), type: float64\niterating over chunks for /Linke2017_figure1d.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 101, 1))\ndone with dataload for /Linke2017_figure1d.sedml/plot_1_task1\nwrite_dataset src: /Linke2017_figure1e.sedml/autogen_report_for_task1 to tgt: /Linke2017_figure1e.sedml/autogen_report_for_task1, shape: (60, 101), type: float64\niterating over chunks for /Linke2017_figure1e.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 60, 1), slice(0, 101, 1))\ndone with dataload for /Linke2017_figure1e.sedml/autogen_report_for_task1\nwrite_dataset src: /Linke2017_figure1e.sedml/plot_1_task1 to tgt: /Linke2017_figure1e.sedml/plot_1_task1, shape: (4, 101), type: float64\niterating over chunks for /Linke2017_figure1e.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 101, 1))\ndone with dataload for /Linke2017_figure1e.sedml/plot_1_task1\nwrite_dataset src: /Linke2017f1b.sedml/autogen_report_for_task1 to tgt: /Linke2017f1b.sedml/autogen_report_for_task1, shape: (60, 101), type: float64\niterating over chunks for /Linke2017f1b.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 60, 1), slice(0, 101, 1))\ndone with dataload for /Linke2017f1b.sedml/autogen_report_for_task1\nwrite_dataset src: /Linke2017f1b.sedml/plot_1_task1 to tgt: /Linke2017f1b.sedml/plot_1_task1, shape: (4, 101), type: float64\niterating over chunks for /Linke2017f1b.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 101, 1))\ndone with dataload for /Linke2017f1b.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a303877b6669655052088\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 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.\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":64.851768,"sedDocuments":[{"location":"Linke2017_figure1c.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Archive contains 4 SED-ML documents with 4 models, 4 simulations, 4 tasks, 4 reports, and 4 plots:\r\n  Linke2017_figure1c.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 60 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n  Linke2017_figure1d.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 60 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n  Linke2017_figure1e.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 60 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n  Linke2017f1b.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 60 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Linke2017_figure1c.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":17.485564,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":16.88613,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.201052,"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":0.102889,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Clb12_total","status":"SUCCEEDED"},{"id":"autogen_task1_Clb34_total","status":"SUCCEEDED"},{"id":"autogen_task1_Clb56_total","status":"SUCCEEDED"},{"id":"autogen_task1_Sic1","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb5or6","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb5or6_Sic1","status":"SUCCEEDED"},{"id":"autogen_task1_Clb5or6_degraded","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb3or4","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb3or4_Sic1","status":"SUCCEEDED"},{"id":"autogen_task1_Clb3or4_degraded","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb1or2","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb1or2_Sic1","status":"SUCCEEDED"},{"id":"autogen_task1_Clb1or2_degraded","status":"SUCCEEDED"},{"id":"autogen_task1_Sic1_degraded_re14","status":"SUCCEEDED"},{"id":"autogen_task1_Sic1_degraded_re18","status":"SUCCEEDED"},{"id":"autogen_task1_Sic1_degraded_re5","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_k4","status":"SUCCEEDED"},{"id":"autogen_task1_k5","status":"SUCCEEDED"},{"id":"autogen_task1_k6","status":"SUCCEEDED"},{"id":"autogen_task1_k7","status":"SUCCEEDED"},{"id":"autogen_task1_k8","status":"SUCCEEDED"},{"id":"autogen_task1_k9","status":"SUCCEEDED"},{"id":"autogen_task1_k10","status":"SUCCEEDED"},{"id":"autogen_task1_k11","status":"SUCCEEDED"},{"id":"autogen_task1_k12","status":"SUCCEEDED"},{"id":"autogen_task1_k13","status":"SUCCEEDED"},{"id":"autogen_task1_k14","status":"SUCCEEDED"},{"id":"autogen_task1_k15","status":"SUCCEEDED"},{"id":"autogen_task1_k16","status":"SUCCEEDED"},{"id":"autogen_task1_k17","status":"SUCCEEDED"},{"id":"autogen_task1_k18","status":"SUCCEEDED"},{"id":"autogen_task1_k26","status":"SUCCEEDED"},{"id":"autogen_task1_kA","status":"SUCCEEDED"},{"id":"autogen_task1_kB","status":"SUCCEEDED"},{"id":"autogen_task1_kC","status":"SUCCEEDED"},{"id":"autogen_task1_kD","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb5_6_production","status":"SUCCEEDED"},{"id":"autogen_task1_Sic1_binding_to_Cdk1_Clb5_6","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb5_6_Sic1_dissociation","status":"SUCCEEDED"},{"id":"autogen_task1_Clb5_6_degradation__ternary","status":"SUCCEEDED"},{"id":"autogen_task1_Sic1_degradation__Clb_regulated","status":"SUCCEEDED"},{"id":"autogen_task1_Clb5_6_degradation__binary","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb3_4_production","status":"SUCCEEDED"},{"id":"autogen_task1_Clb3_4_degradation__binary","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb1_2_production","status":"SUCCEEDED"},{"id":"autogen_task1_Clb1_2_degradation__binary","status":"SUCCEEDED"},{"id":"autogen_task1_Sic1_binding_to_Cdk1_Clb1_2","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb1_2_Sic1_dissociation","status":"SUCCEEDED"},{"id":"autogen_task1_Clb1_2_degradation__ternary","status":"SUCCEEDED"},{"id":"autogen_task1_Sic1_degradation__Clb_regulated__1","status":"SUCCEEDED"},{"id":"autogen_task1_Sic1_binding_to_Cdk1_Clb3_4","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb3_4_Sic1_dissociation","status":"SUCCEEDED"},{"id":"autogen_task1_Clb3_4_degradation__ternary","status":"SUCCEEDED"},{"id":"autogen_task1_Sic1_degradation__Clb_regulated__2","status":"SUCCEEDED"},{"id":"autogen_task1_Sic1_degradation__basal","status":"SUCCEEDED"}]}]},{"location":"Linke2017_figure1d.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: Linke2017_figure1d.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":15.846284,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":15.105962,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.166657,"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":0.106466,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Clb12_total","status":"SUCCEEDED"},{"id":"autogen_task1_Clb34_total","status":"SUCCEEDED"},{"id":"autogen_task1_Clb56_total","status":"SUCCEEDED"},{"id":"autogen_task1_Sic1","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb5or6","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb5or6_Sic1","status":"SUCCEEDED"},{"id":"autogen_task1_Clb5or6_degraded","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb3or4","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb3or4_Sic1","status":"SUCCEEDED"},{"id":"autogen_task1_Clb3or4_degraded","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb1or2","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb1or2_Sic1","status":"SUCCEEDED"},{"id":"autogen_task1_Clb1or2_degraded","status":"SUCCEEDED"},{"id":"autogen_task1_Sic1_degraded_re14","status":"SUCCEEDED"},{"id":"autogen_task1_Sic1_degraded_re18","status":"SUCCEEDED"},{"id":"autogen_task1_Sic1_degraded_re5","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_k4","status":"SUCCEEDED"},{"id":"autogen_task1_k5","status":"SUCCEEDED"},{"id":"autogen_task1_k6","status":"SUCCEEDED"},{"id":"autogen_task1_k7","status":"SUCCEEDED"},{"id":"autogen_task1_k8","status":"SUCCEEDED"},{"id":"autogen_task1_k9","status":"SUCCEEDED"},{"id":"autogen_task1_k10","status":"SUCCEEDED"},{"id":"autogen_task1_k11","status":"SUCCEEDED"},{"id":"autogen_task1_k12","status":"SUCCEEDED"},{"id":"autogen_task1_k13","status":"SUCCEEDED"},{"id":"autogen_task1_k14","status":"SUCCEEDED"},{"id":"autogen_task1_k15","status":"SUCCEEDED"},{"id":"autogen_task1_k16","status":"SUCCEEDED"},{"id":"autogen_task1_k17","status":"SUCCEEDED"},{"id":"autogen_task1_k18","status":"SUCCEEDED"},{"id":"autogen_task1_k26","status":"SUCCEEDED"},{"id":"autogen_task1_kA","status":"SUCCEEDED"},{"id":"autogen_task1_kB","status":"SUCCEEDED"},{"id":"autogen_task1_kC","status":"SUCCEEDED"},{"id":"autogen_task1_kD","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb5_6_production","status":"SUCCEEDED"},{"id":"autogen_task1_Sic1_binding_to_Cdk1_Clb5_6","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb5_6_Sic1_dissociation","status":"SUCCEEDED"},{"id":"autogen_task1_Clb5_6_degradation__ternary","status":"SUCCEEDED"},{"id":"autogen_task1_Sic1_degradation__Clb_regulated","status":"SUCCEEDED"},{"id":"autogen_task1_Clb5_6_degradation__binary","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb3_4_production","status":"SUCCEEDED"},{"id":"autogen_task1_Clb3_4_degradation__binary","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb1_2_production","status":"SUCCEEDED"},{"id":"autogen_task1_Clb1_2_degradation__binary","status":"SUCCEEDED"},{"id":"autogen_task1_Sic1_binding_to_Cdk1_Clb1_2","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb1_2_Sic1_dissociation","status":"SUCCEEDED"},{"id":"autogen_task1_Clb1_2_degradation__ternary","status":"SUCCEEDED"},{"id":"autogen_task1_Sic1_degradation__Clb_regulated__1","status":"SUCCEEDED"},{"id":"autogen_task1_Sic1_binding_to_Cdk1_Clb3_4","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk1_Clb3_4_Sic1_dissociation","status":"SUCCEEDED"},{"id":"autogen_task1_Clb3_4_degradation__ternary","status":"SUCCEEDED"},{"id":"autogen_task1_Sic1_degradation__Clb_regulated__2","status":"SUCCEEDED"},{"id":"autogen_task1_Sic1_degradation__basal","status":"SUCCEEDED"}]}]},{"location":"Linke2017_figure1e.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: Linke2017_figure1e.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` 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