{"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    528      0 --:--:-- --:--:-- --:--:--   528\n\r100 23087  100 23087    0     0  65398      0 --:--:-- --:--:-- --:--:-- 65398\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 (27.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647120029a62a8be53f998ee/rawLog.txt\nCompleted 3.5 KiB/3.5 KiB (54.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647120029a62a8be53f998ee/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 76%)\n  adding: outputs/Garde2020.sedml/ (stored 0%)\n  adding: outputs/Garde2020.sedml/plot_1_task1.pdf (deflated 11%)\n  adding: outputs/reports.h5 (deflated 11%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 192.3 KiB/192.3 KiB (2.3 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647120029a62a8be53f998ee/outputs/reports.h5\nCompleted 194.8 KiB/240.2 KiB (2.3 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647120029a62a8be53f998ee/output.zip\nCompleted 194.8 KiB/240.2 KiB (2.3 MiB/s) with 3 file(s) remaining\rCompleted 214.8 KiB/240.2 KiB (2.2 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647120029a62a8be53f998ee/outputs/plots.zip\nCompleted 214.8 KiB/240.2 KiB (2.2 MiB/s) with 2 file(s) remaining\rCompleted 217.4 KiB/240.2 KiB (2.0 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647120029a62a8be53f998ee/rawLog.txt\nCompleted 217.4 KiB/240.2 KiB (2.0 MiB/s) with 1 file(s) remaining\rCompleted 240.2 KiB/240.2 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: outputs/Garde2020.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647120029a62a8be53f998ee/outputs/Garde2020.sedml/plot_1_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Garde2020-biopax2.owl  \n  inflating: contents/Garde2020-biopax3.owl  \n  inflating: contents/Garde2020-matlab.m  \n  inflating: contents/Garde2020-octave.m  \n  inflating: contents/Garde2020.cps  \n  inflating: contents/Garde2020.ode  \n  inflating: contents/Garde2020.sedml  \n  inflating: contents/Garde2020.xml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 16.4 KiB/200.1 KiB (262.4 KiB/s) with 10 file(s) remaining\rupload: contents/Garde2020-biopax2.owl to s3://files.biosimulations.org/simulations/647120029a62a8be53f998ee/contents/Garde2020-biopax2.owl\nCompleted 16.4 KiB/200.1 KiB (262.4 KiB/s) with 9 file(s) remaining\rCompleted 24.2 KiB/200.1 KiB (226.4 KiB/s) with 9 file(s) remaining\rupload: contents/Garde2020-matlab.m to s3://files.biosimulations.org/simulations/647120029a62a8be53f998ee/contents/Garde2020-matlab.m\nCompleted 24.2 KiB/200.1 KiB (226.4 KiB/s) with 8 file(s) remaining\rCompleted 49.5 KiB/200.1 KiB (444.9 KiB/s) with 8 file(s) remaining\rupload: contents/Garde2020-biopax3.owl to s3://files.biosimulations.org/simulations/647120029a62a8be53f998ee/contents/Garde2020-biopax3.owl\nCompleted 49.5 KiB/200.1 KiB (444.9 KiB/s) with 7 file(s) remaining\rCompleted 50.7 KiB/200.1 KiB (452.8 KiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647120029a62a8be53f998ee/contents/metadata.rdf\nCompleted 50.7 KiB/200.1 KiB (452.8 KiB/s) with 6 file(s) remaining\rCompleted 51.9 KiB/200.1 KiB (455.7 KiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647120029a62a8be53f998ee/contents/manifest.xml\nCompleted 51.9 KiB/200.1 KiB (455.7 KiB/s) with 5 file(s) remaining\rCompleted 59.6 KiB/200.1 KiB (471.7 KiB/s) with 5 file(s) remaining\rupload: contents/Garde2020-octave.m to s3://files.biosimulations.org/simulations/647120029a62a8be53f998ee/contents/Garde2020-octave.m\nCompleted 59.6 KiB/200.1 KiB (471.7 KiB/s) with 4 file(s) remaining\rCompleted 107.5 KiB/200.1 KiB (844.9 KiB/s) with 4 file(s) remaining\rupload: contents/Garde2020.xml to s3://files.biosimulations.org/simulations/647120029a62a8be53f998ee/contents/Garde2020.xml\nCompleted 107.5 KiB/200.1 KiB (844.9 KiB/s) with 3 file(s) remaining\rCompleted 124.1 KiB/200.1 KiB (944.5 KiB/s) with 3 file(s) remaining\rupload: contents/Garde2020.sedml to s3://files.biosimulations.org/simulations/647120029a62a8be53f998ee/contents/Garde2020.sedml\nCompleted 124.1 KiB/200.1 KiB (944.5 KiB/s) with 2 file(s) remaining\rCompleted 129.2 KiB/200.1 KiB (919.6 KiB/s) with 2 file(s) remaining\rupload: contents/Garde2020.ode to s3://files.biosimulations.org/simulations/647120029a62a8be53f998ee/contents/Garde2020.ode\nCompleted 129.2 KiB/200.1 KiB (919.6 KiB/s) with 1 file(s) remaining\rCompleted 200.1 KiB/200.1 KiB (1.1 MiB/s) with 1 file(s) remaining  \rupload: contents/Garde2020.cps to s3://files.biosimulations.org/simulations/647120029a62a8be53f998ee/contents/Garde2020.cps\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 6.7 KiB/6.7 KiB (62.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647120029a62a8be53f998ee/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Garde2020.sedml\ncreating dataset /Garde2020.sedml/autogen_report_for_task1, shape: (24, 1001), type: float64\ndataset created, uuid: d-fd2fa1ed-09fa5913-9095-502168-7d4f1e, chunk_size: (24, 1001)\ncreating dataset /Garde2020.sedml/plot_1_task1, shape: (7, 1001), type: float64\ndataset created, uuid: d-fd2fa1ed-09fa5913-9952-b2b0f8-7d561e, chunk_size: (7, 1001)\ncreating attribute combineArchiveLocation in /Garde2020.sedml\ncreating attribute uri in /Garde2020.sedml\ncreating attribute _type in /Garde2020.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Garde2020.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Garde2020.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Garde2020.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Garde2020.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Garde2020.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Garde2020.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Garde2020.sedml/autogen_report_for_task1\ncreating attribute uri in /Garde2020.sedml/autogen_report_for_task1\ncreating attribute _type in /Garde2020.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Garde2020.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Garde2020.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Garde2020.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Garde2020.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Garde2020.sedml/plot_1_task1\ncreating attribute sedmlId in /Garde2020.sedml/plot_1_task1\ncreating attribute sedmlName in /Garde2020.sedml/plot_1_task1\ncreating attribute uri in /Garde2020.sedml/plot_1_task1\ncreate_links: /\ngot link: Garde2020.sedml\ncreate_links: /Garde2020.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Garde2020.sedml/autogen_report_for_task1 to tgt: /Garde2020.sedml/autogen_report_for_task1, shape: (24, 1001), type: float64\niterating over chunks for /Garde2020.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 24, 1), slice(0, 1001, 1))\ndone with dataload for /Garde2020.sedml/autogen_report_for_task1\nwrite_dataset src: /Garde2020.sedml/plot_1_task1 to tgt: /Garde2020.sedml/plot_1_task1, shape: (7, 1001), type: float64\niterating over chunks for /Garde2020.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 1001, 1))\ndone with dataload for /Garde2020.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647120029a62a8be53f998ee\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 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.\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":14.191557,"sedDocuments":[{"location":"Garde2020.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  Garde2020.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 24 data sets\r\n    Plots (1):\r\n      plot_1_task1: 6 curves\r\n\r\nExecuting SED-ML file 1: Garde2020.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":13.917009,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":13.222248,"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":0.384711,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"},{"id":"p1_curve_4_task1","status":"SUCCEEDED"},{"id":"p1_curve_5_task1","status":"SUCCEEDED"},{"id":"p1_curve_6_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.2144,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Gp","status":"SUCCEEDED"},{"id":"autogen_task1_Ai","status":"SUCCEEDED"},{"id":"autogen_task1_Am","status":"SUCCEEDED"},{"id":"autogen_task1_Ap","status":"SUCCEEDED"},{"id":"autogen_task1_Gm","status":"SUCCEEDED"},{"id":"autogen_task1_Gi","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_Ge","status":"SUCCEEDED"},{"id":"autogen_task1_Biofilm","status":"SUCCEEDED"},{"id":"autogen_task1_Positive_feedback_of_Gp_on_itself","status":"SUCCEEDED"},{"id":"autogen_task1_Gp_diffusion_to_the_interior_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Biomass_production","status":"SUCCEEDED"},{"id":"autogen_task1_Diffusion_of_Ammonia_from_interior_to_middle_layer","status":"SUCCEEDED"},{"id":"autogen_task1_Production_of_Ammonia_using_Glutamate_by_inner_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Ammonia_diffusion_from_middle_layer_to_periphery","status":"SUCCEEDED"},{"id":"autogen_task1_loss_of_Ammonia_du_to_diffusion_to_the_environment","status":"SUCCEEDED"},{"id":"autogen_task1_Diffusion_of_Glutamate_from_middle_to_interior_layer","status":"SUCCEEDED"},{"id":"autogen_task1_Production_of_Ammonia_in_middle_layer_using_glutamate","status":"SUCCEEDED"},{"id":"autogen_task1_Use_of_glutamate_in_middle_layer_for_biomass_production","status":"SUCCEEDED"}]}]}]}