{"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    427      0 --:--:-- --:--:-- --:--:--   427\n\r100  204k  100  204k    0     0   456k      0 --:--:-- --:--:-- --:--:--  456k\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 (23.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b6977b66696550612a9/rawLog.txt\nCompleted 3.2 KiB/3.2 KiB (40.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b6977b66696550612a9/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 73%)\n  adding: outputs/Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/ (stored 0%)\n  adding: outputs/Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/plot_1_task1.pdf (deflated 28%)\n  adding: outputs/reports.h5 (deflated 73%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 32.6 KiB/32.6 KiB (397.8 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b6977b66696550612a9/outputs/reports.h5\nCompleted 20.5 KiB/44.6 KiB (259.2 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b6977b66696550612a9/output.zip\nCompleted 20.5 KiB/44.6 KiB (259.2 KiB/s) with 3 file(s) remaining\rCompleted 33.0 KiB/44.6 KiB (322.0 KiB/s) with 3 file(s) remaining\rupload: outputs/Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b6977b66696550612a9/outputs/Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/plot_1_task1.pdf\nCompleted 33.0 KiB/44.6 KiB (322.0 KiB/s) with 2 file(s) remaining\rCompleted 41.9 KiB/44.6 KiB (389.4 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b6977b66696550612a9/outputs/plots.zip\nCompleted 41.9 KiB/44.6 KiB (389.4 KiB/s) with 1 file(s) remaining\rCompleted 44.6 KiB/44.6 KiB (396.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b6977b66696550612a9/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/FIg1 unbounded growth.png  \n  inflating: contents/Fig1 population collapse.png  \n  inflating: contents/Lewkiewics2019 - effects of aging on naive T cell populations and diversity-biopax2.owl  \n  inflating: contents/Lewkiewics2019 - effects of aging on naive T cell populations and diversity-biopax3.owl  \n  inflating: contents/Lewkiewics2019 - 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effects of aging on naive T cell populations and diversity-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b6977b66696550612a9/contents/Lewkiewics2019 - effects of aging on naive T cell populations and diversity-biopax2.owl\nCompleted 28.5 KiB/290.3 KiB (246.3 KiB/s) with 12 file(s) remaining\rCompleted 37.3 KiB/290.3 KiB (317.4 KiB/s) with 12 file(s) remaining\rupload: contents/Lewkiewics2019 - effects of aging on naive T cell populations and diversity-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b6977b66696550612a9/contents/Lewkiewics2019 - effects of aging on naive T cell populations and diversity-biopax3.owl\nCompleted 37.3 KiB/290.3 KiB (317.4 KiB/s) with 11 file(s) remaining\rCompleted 39.6 KiB/290.3 KiB (325.2 KiB/s) with 11 file(s) remaining\rupload: contents/Lewkiewics2019 - effects of aging on naive T cell populations and diversity.ode to s3://files.biosimulations.org/simulations/647a4b6977b66696550612a9/contents/Lewkiewics2019 - effects of aging on naive T cell populations and diversity.ode\nCompleted 39.6 KiB/290.3 KiB (325.2 KiB/s) with 10 file(s) remaining\rCompleted 80.2 KiB/290.3 KiB (570.2 KiB/s) with 10 file(s) remaining\rupload: contents/Lewkiewics2019 - effects of aging on naive T cell populations and diversity.cps to s3://files.biosimulations.org/simulations/647a4b6977b66696550612a9/contents/Lewkiewics2019 - effects of aging on naive T cell populations and diversity.cps\nCompleted 80.2 KiB/290.3 KiB (570.2 KiB/s) with 9 file(s) remaining\rCompleted 89.6 KiB/290.3 KiB (631.8 KiB/s) with 9 file(s) remaining\rupload: contents/Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml to s3://files.biosimulations.org/simulations/647a4b6977b66696550612a9/contents/Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml\nCompleted 89.6 KiB/290.3 KiB (631.8 KiB/s) with 8 file(s) remaining\rCompleted 110.7 KiB/290.3 KiB (718.5 KiB/s) with 8 file(s) remaining\rupload: contents/Lewkiewics2019 - effects of aging on naive T cell populations and diversity.xml to s3://files.biosimulations.org/simulations/647a4b6977b66696550612a9/contents/Lewkiewics2019 - effects of aging on naive T cell populations and diversity.xml\nCompleted 110.7 KiB/290.3 KiB (718.5 KiB/s) with 7 file(s) remaining\rCompleted 111.0 KiB/290.3 KiB (701.2 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b6977b66696550612a9/contents/curation_notes.txt\nCompleted 111.0 KiB/290.3 KiB (701.2 KiB/s) with 6 file(s) remaining\rCompleted 251.3 KiB/290.3 KiB (1.5 MiB/s) with 6 file(s) remaining  \rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b6977b66696550612a9/contents/curation_image.png\nCompleted 251.3 KiB/290.3 KiB (1.5 MiB/s) with 5 file(s) remaining\rCompleted 253.4 KiB/290.3 KiB (1.4 MiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b6977b66696550612a9/contents/manifest.xml\nCompleted 253.4 KiB/290.3 KiB (1.4 MiB/s) with 4 file(s) remaining\rCompleted 256.6 KiB/290.3 KiB (1.4 MiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b6977b66696550612a9/contents/metadata.rdf\nCompleted 256.6 KiB/290.3 KiB (1.4 MiB/s) with 3 file(s) remaining\rCompleted 260.4 KiB/290.3 KiB (1.4 MiB/s) with 3 file(s) remaining\rupload: contents/Lewkiewics2019 - effects of aging on naive T cell populations and diversity-matlab.m to s3://files.biosimulations.org/simulations/647a4b6977b66696550612a9/contents/Lewkiewics2019 - effects of aging on naive T cell populations and diversity-matlab.m\nCompleted 260.4 KiB/290.3 KiB (1.4 MiB/s) with 2 file(s) remaining\rCompleted 264.1 KiB/290.3 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: contents/Lewkiewics2019 - effects of aging on naive T cell populations and diversity-octave.m to s3://files.biosimulations.org/simulations/647a4b6977b66696550612a9/contents/Lewkiewics2019 - effects of aging on naive T cell populations and diversity-octave.m\nCompleted 264.1 KiB/290.3 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 290.3 KiB/290.3 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: contents/Fig1 population collapse.png to s3://files.biosimulations.org/simulations/647a4b6977b66696550612a9/contents/Fig1 population collapse.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.8 KiB/9.8 KiB (154.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b6977b66696550612a9/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml\ncreating dataset /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/autogen_report_for_task1, shape: (14, 101), type: float64\ndataset created, uuid: d-dce0ea48-071a6636-125b-67a552-373474, chunk_size: (14, 101)\ncreating dataset /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/plot_1_task1, shape: (4, 101), type: float64\ndataset created, uuid: d-dce0ea48-071a6636-8236-6819a6-e912cc, chunk_size: (4, 101)\ncreating attribute combineArchiveLocation in /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml\ncreating attribute uri in /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml\ncreating attribute _type in /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Lewkiewics2019 - 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effects of aging on naive T cell populations and diversity.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/plot_1_task1\ncreating attribute sedmlId in /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/plot_1_task1\ncreating attribute sedmlName in /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/plot_1_task1\ncreating attribute uri in /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/plot_1_task1\ncreate_links: /\ngot link: Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml\ncreate_links: /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/autogen_report_for_task1 to tgt: /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/autogen_report_for_task1, shape: (14, 101), type: float64\niterating over chunks for /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 14, 1), slice(0, 101, 1))\ndone with dataload for /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/autogen_report_for_task1\nwrite_dataset src: /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/plot_1_task1 to tgt: /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/plot_1_task1, shape: (4, 101), type: float64\niterating over chunks for /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 101, 1))\ndone with dataload for /Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b6977b66696550612a9\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":1.100772,"sedDocuments":[{"location":"Lewkiewics2019 - effects of aging on naive T cell populations and diversity.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  Lewkiewics2019 - effects of aging on naive T cell populations and diversity.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 14 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Lewkiewics2019 - effects of aging on naive T cell populations and diversity.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":0.705626,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.187042,"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":0.338736,"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":0.064774,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_myu","status":"SUCCEEDED"},{"id":"autogen_task1_N","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_p","status":"SUCCEEDED"},{"id":"autogen_task1_gamma_0","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_myu_0","status":"SUCCEEDED"},{"id":"autogen_task1_myu_1","status":"SUCCEEDED"},{"id":"autogen_task1_K","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_export_of_mature_naive_T_cells","status":"SUCCEEDED"},{"id":"autogen_task1_peripheral_prolieferation","status":"SUCCEEDED"},{"id":"autogen_task1_cell_removal_due_to_death_or_phenotypic_changes","status":"SUCCEEDED"}]}]}]}