{"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    440      0 --:--:-- --:--:-- --:--:--   441\n\r100  143k  100  143k    0     0   337k      0 --:--:-- --:--:-- --:--:--  337k\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 (26.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107ee9a62a8be53f74f95/rawLog.txt\nCompleted 2.6 KiB/2.6 KiB (28.5 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647107ee9a62a8be53f74f95/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 72%)\n  adding: outputs/reports.h5 (deflated 49%)\n  adding: outputs/BIOMD0000000076_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000076_url.sedml/autogen_plot_for_task1.pdf (deflated 34%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 47.9 KiB/47.9 KiB (420.3 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647107ee9a62a8be53f74f95/outputs/reports.h5\nCompleted 32.8 KiB/50.7 KiB (399.4 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647107ee9a62a8be53f74f95/output.zip\nCompleted 32.8 KiB/50.7 KiB (399.4 KiB/s) with 3 file(s) remaining\rCompleted 35.4 KiB/50.7 KiB (328.2 KiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107ee9a62a8be53f74f95/rawLog.txt\nCompleted 35.4 KiB/50.7 KiB (328.2 KiB/s) with 2 file(s) remaining\rCompleted 44.7 KiB/50.7 KiB (403.5 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000076_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647107ee9a62a8be53f74f95/outputs/BIOMD0000000076_url.sedml/autogen_plot_for_task1.pdf\nCompleted 44.7 KiB/50.7 KiB (403.5 KiB/s) with 1 file(s) remaining\rCompleted 50.7 KiB/50.7 KiB (445.7 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647107ee9a62a8be53f74f95/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000076-biopax2.owl  \n  inflating: contents/BIOMD0000000076-biopax3.owl  \n  inflating: contents/BIOMD0000000076-matlab.m  \n  inflating: contents/BIOMD0000000076-octave.m  \n  inflating: contents/BIOMD0000000076.m  \n  inflating: contents/BIOMD0000000076.ode  \n  inflating: contents/BIOMD0000000076.pdf  \n  inflating: contents/BIOMD0000000076.png  \n  inflating: contents/BIOMD0000000076.svg  \n  inflating: contents/BIOMD0000000076.vcml  \n  inflating: contents/BIOMD0000000076_url.sedml  \n  inflating: contents/BIOMD0000000076_url.xml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 11.1 KiB/245.8 KiB (171.3 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000076-biopax3.owl to s3://files.biosimulations.org/simulations/647107ee9a62a8be53f74f95/contents/BIOMD0000000076-biopax3.owl\nCompleted 11.1 KiB/245.8 KiB (171.3 KiB/s) with 13 file(s) remaining\rCompleted 15.7 KiB/245.8 KiB (146.7 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000076-matlab.m to s3://files.biosimulations.org/simulations/647107ee9a62a8be53f74f95/contents/BIOMD0000000076-matlab.m\nCompleted 15.7 KiB/245.8 KiB (146.7 KiB/s) with 12 file(s) remaining\rCompleted 20.4 KiB/245.8 KiB (160.3 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000076-octave.m to s3://files.biosimulations.org/simulations/647107ee9a62a8be53f74f95/contents/BIOMD0000000076-octave.m\nCompleted 20.4 KiB/245.8 KiB (160.3 KiB/s) with 11 file(s) remaining\rCompleted 24.8 KiB/245.8 KiB (187.4 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000076.svg to s3://files.biosimulations.org/simulations/647107ee9a62a8be53f74f95/contents/BIOMD0000000076.svg\nCompleted 24.8 KiB/245.8 KiB (187.4 KiB/s) with 10 file(s) remaining\rCompleted 34.0 KiB/245.8 KiB (249.3 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000076-biopax2.owl to s3://files.biosimulations.org/simulations/647107ee9a62a8be53f74f95/contents/BIOMD0000000076-biopax2.owl\nCompleted 34.0 KiB/245.8 KiB (249.3 KiB/s) with 9 file(s) remaining\rCompleted 35.6 KiB/245.8 KiB (239.3 KiB/s) with 9 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647107ee9a62a8be53f74f95/contents/manifest.xml\nCompleted 35.6 KiB/245.8 KiB (239.3 KiB/s) with 8 file(s) remaining\rCompleted 40.7 KiB/245.8 KiB (268.9 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000076_url.sedml to s3://files.biosimulations.org/simulations/647107ee9a62a8be53f74f95/contents/BIOMD0000000076_url.sedml\nCompleted 40.7 KiB/245.8 KiB (268.9 KiB/s) with 7 file(s) remaining\rCompleted 60.9 KiB/245.8 KiB (397.0 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000076.vcml to s3://files.biosimulations.org/simulations/647107ee9a62a8be53f74f95/contents/BIOMD0000000076.vcml\nCompleted 60.9 KiB/245.8 KiB (397.0 KiB/s) with 6 file(s) remaining\rCompleted 72.4 KiB/245.8 KiB (448.3 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000076.png to s3://files.biosimulations.org/simulations/647107ee9a62a8be53f74f95/contents/BIOMD0000000076.png\nCompleted 72.4 KiB/245.8 KiB (448.3 KiB/s) with 5 file(s) remaining\rCompleted 76.0 KiB/245.8 KiB (409.0 KiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647107ee9a62a8be53f74f95/contents/metadata.rdf\nCompleted 76.0 KiB/245.8 KiB (409.0 KiB/s) with 4 file(s) remaining\rCompleted 80.7 KiB/245.8 KiB (418.0 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000076.m to s3://files.biosimulations.org/simulations/647107ee9a62a8be53f74f95/contents/BIOMD0000000076.m\nCompleted 80.7 KiB/245.8 KiB (418.0 KiB/s) with 3 file(s) remaining\rCompleted 95.9 KiB/245.8 KiB (489.6 KiB/s) with 3 file(s) remaining\rCompleted 98.5 KiB/245.8 KiB (496.7 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000076.ode to s3://files.biosimulations.org/simulations/647107ee9a62a8be53f74f95/contents/BIOMD0000000076.ode\nCompleted 98.5 KiB/245.8 KiB (496.7 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000076_url.xml to s3://files.biosimulations.org/simulations/647107ee9a62a8be53f74f95/contents/BIOMD0000000076_url.xml\nCompleted 98.5 KiB/245.8 KiB (496.7 KiB/s) with 1 file(s) remaining\rCompleted 245.8 KiB/245.8 KiB (1.2 MiB/s) with 1 file(s) remaining \rupload: contents/BIOMD0000000076.pdf to s3://files.biosimulations.org/simulations/647107ee9a62a8be53f74f95/contents/BIOMD0000000076.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.2 KiB/8.2 KiB (119.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107ee9a62a8be53f74f95/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000076_url.sedml\ncreating dataset /BIOMD0000000076_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-28e57cf7-2350bff7-f335-2c7144-0e8125, chunk_size: (4, 1001)\ncreating dataset /BIOMD0000000076_url.sedml/autogen_report_for_task1, shape: (7, 1001), type: float64\ndataset created, uuid: d-28e57cf7-2350bff7-883a-8d9782-00d323, chunk_size: (7, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000076_url.sedml\ncreating attribute uri in /BIOMD0000000076_url.sedml\ncreating attribute _type in /BIOMD0000000076_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000076_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000076_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000076_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000076_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000076_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000076_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000076_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000076_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000076_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000076_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000076_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000076_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000076_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000076_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000076_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000076_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000076_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000076_url.sedml\ncreate_links: /BIOMD0000000076_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000076_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000076_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\niterating over chunks for /BIOMD0000000076_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000076_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000076_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000076_url.sedml/autogen_report_for_task1, shape: (7, 1001), type: float64\niterating over chunks for /BIOMD0000000076_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000076_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647107ee9a62a8be53f74f95\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.\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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.354312,"sedDocuments":[{"location":"BIOMD0000000076_url.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n  BIOMD0000000076_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 7 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000076_url.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_plot_for_task1`\r\n      `autogen_report_for_task1`\r\n  Executing task 1: `task1`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_plot_for_task1` ...","duration":0.904915,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.197722,"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":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.125017,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_G3P","status":"SUCCEEDED"},{"id":"autogen_task1_Gly","status":"SUCCEEDED"},{"id":"autogen_task1_DHAP","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_Gpd_p","status":"SUCCEEDED"},{"id":"autogen_task1_Gpp_p","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.438814,"curves":[{"id":"autogen_curve_task1_G3P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Gly","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DHAP","status":"SUCCEEDED"}]}]}]}