{"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    444      0 --:--:-- --:--:-- --:--:--   445\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100  250k  100  250k    0     0   567k      0 --:--:-- --:--:-- --:--:-- 3524k\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 (20.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/rawLog.txt\nCompleted 4.0 KiB/4.0 KiB (56.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/BIOMD0000000063_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000063_url.sedml/autogen_plot_for_task1.pdf (deflated 32%)\n  adding: outputs/log.yml (deflated 78%)\n  adding: outputs/reports.h5 (deflated 17%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 126.9 KiB/126.9 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/outputs/reports.h5\nCompleted 8.0 KiB/138.9 KiB (77.9 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/outputs/plots.zip\nCompleted 8.0 KiB/138.9 KiB (77.9 KiB/s) with 3 file(s) remaining\rCompleted 124.2 KiB/138.9 KiB (1.1 MiB/s) with 3 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/output.zip\nCompleted 124.2 KiB/138.9 KiB (1.1 MiB/s) with 2 file(s) remaining\rCompleted 136.2 KiB/138.9 KiB (1.1 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000063_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/outputs/BIOMD0000000063_url.sedml/autogen_plot_for_task1.pdf\nCompleted 136.2 KiB/138.9 KiB (1.1 MiB/s) with 1 file(s) remaining\rCompleted 138.9 KiB/138.9 KiB (929.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000063-biopax2.owl  \n  inflating: contents/BIOMD0000000063-biopax3.owl  \n  inflating: contents/BIOMD0000000063-matlab.m  \n  inflating: contents/BIOMD0000000063-octave.m  \n  inflating: contents/BIOMD0000000063.m  \n  inflating: contents/BIOMD0000000063.ode  \n  inflating: contents/BIOMD0000000063.pdf  \n  inflating: contents/BIOMD0000000063.png  \n  inflating: contents/BIOMD0000000063.svg  \n  inflating: contents/BIOMD0000000063_url.sedml  \n  inflating: contents/BIOMD0000000063_url.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 38.6 KiB/~530.8 KiB (547.4 KiB/s) with ~14 file(s) remaining (calculating...)\rupload: contents/BIOMD0000000063-biopax3.owl to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/contents/BIOMD0000000063-biopax3.owl\nCompleted 38.6 KiB/~530.8 KiB (547.4 KiB/s) with ~13 file(s) remaining (calculating...)\rCompleted 69.0 KiB/537.1 KiB (585.5 KiB/s) with 14 file(s) remaining                   \rupload: contents/BIOMD0000000063-biopax2.owl to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/contents/BIOMD0000000063-biopax2.owl\nCompleted 69.0 KiB/537.1 KiB (585.5 KiB/s) with 13 file(s) remaining\rCompleted 82.6 KiB/537.1 KiB (580.8 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000063-octave.m to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/contents/BIOMD0000000063-octave.m\nCompleted 82.6 KiB/537.1 KiB (580.8 KiB/s) with 12 file(s) remaining\rCompleted 101.1 KiB/537.1 KiB (701.5 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000063.svg to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/contents/BIOMD0000000063.svg\nCompleted 101.1 KiB/537.1 KiB (701.5 KiB/s) with 11 file(s) remaining\rCompleted 114.8 KiB/537.1 KiB (776.3 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000063-matlab.m to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/contents/BIOMD0000000063-matlab.m\nCompleted 114.8 KiB/537.1 KiB (776.3 KiB/s) with 10 file(s) remaining\rCompleted 210.9 KiB/537.1 KiB (1.3 MiB/s) with 10 file(s) remaining  \rupload: contents/BIOMD0000000063_url.xml to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/contents/BIOMD0000000063_url.xml\nCompleted 210.9 KiB/537.1 KiB (1.3 MiB/s) with 9 file(s) remaining\rCompleted 211.1 KiB/537.1 KiB (1.2 MiB/s) with 9 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/contents/curation_notes.txt\nCompleted 211.1 KiB/537.1 KiB (1.2 MiB/s) with 8 file(s) remaining\rCompleted 226.5 KiB/537.1 KiB (1.3 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000063_url.sedml to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/contents/BIOMD0000000063_url.sedml\nCompleted 226.5 KiB/537.1 KiB (1.3 MiB/s) with 7 file(s) remaining\rCompleted 231.2 KiB/537.1 KiB (1.3 MiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/contents/curation_image.png\nCompleted 231.2 KiB/537.1 KiB (1.3 MiB/s) with 6 file(s) remaining\rCompleted 237.4 KiB/537.1 KiB (1.3 MiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/contents/metadata.rdf\nCompleted 237.4 KiB/537.1 KiB (1.3 MiB/s) with 5 file(s) remaining\rCompleted 246.4 KiB/537.1 KiB (1.3 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000063.ode to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/contents/BIOMD0000000063.ode\nCompleted 246.4 KiB/537.1 KiB (1.3 MiB/s) with 4 file(s) remaining\rCompleted 450.8 KiB/537.1 KiB (2.2 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000063.pdf to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/contents/BIOMD0000000063.pdf\nCompleted 450.8 KiB/537.1 KiB (2.2 MiB/s) with 3 file(s) remaining\rCompleted 464.4 KiB/537.1 KiB (2.0 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000063.m to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/contents/BIOMD0000000063.m\nCompleted 464.4 KiB/537.1 KiB (2.0 MiB/s) with 2 file(s) remaining\rCompleted 466.1 KiB/537.1 KiB (1.9 MiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/contents/manifest.xml\nCompleted 466.1 KiB/537.1 KiB (1.9 MiB/s) with 1 file(s) remaining\rCompleted 537.1 KiB/537.1 KiB (2.2 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000063.png to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/contents/BIOMD0000000063.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (129.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107c149c0d898ffdda237/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000063_url.sedml\ncreating dataset /BIOMD0000000063_url.sedml/autogen_plot_for_task1, shape: (10, 1001), type: float64\ndataset created, uuid: d-791edeed-47c11051-444a-a8035f-18f26d, chunk_size: (10, 1001)\ncreating dataset /BIOMD0000000063_url.sedml/autogen_report_for_task1, shape: (26, 1001), type: float64\ndataset created, uuid: d-791edeed-47c11051-1852-c7c731-ad71af, chunk_size: (26, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000063_url.sedml\ncreating attribute uri in /BIOMD0000000063_url.sedml\ncreating attribute _type in /BIOMD0000000063_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000063_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000063_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000063_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000063_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000063_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000063_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000063_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000063_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000063_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000063_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000063_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000063_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000063_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000063_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000063_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000063_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000063_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000063_url.sedml\ncreate_links: /BIOMD0000000063_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000063_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000063_url.sedml/autogen_plot_for_task1, shape: (10, 1001), type: float64\niterating over chunks for /BIOMD0000000063_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 10, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000063_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000063_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000063_url.sedml/autogen_report_for_task1, shape: (26, 1001), type: float64\niterating over chunks for /BIOMD0000000063_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 26, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000063_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647107c149c0d898ffdda237\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 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.\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":1.887162,"sedDocuments":[{"location":"BIOMD0000000063_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  BIOMD0000000063_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 26 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 9 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000063_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":1.328125,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.362038,"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":0.231519,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Glci","status":"SUCCEEDED"},{"id":"autogen_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_task1_G6P","status":"SUCCEEDED"},{"id":"autogen_task1_FDP","status":"SUCCEEDED"},{"id":"autogen_task1_PEP","status":"SUCCEEDED"},{"id":"autogen_task1_Gly","status":"SUCCEEDED"},{"id":"autogen_task1_EtOH","status":"SUCCEEDED"},{"id":"autogen_task1_Carbo","status":"SUCCEEDED"},{"id":"autogen_task1_Glco","status":"SUCCEEDED"},{"id":"autogen_task1_VappGly","status":"SUCCEEDED"},{"id":"autogen_task1_VratioVmax","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_4","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_5","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_6","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_7","status":"SUCCEEDED"},{"id":"autogen_task1_extracellular","status":"SUCCEEDED"},{"id":"autogen_task1_cytoplasm","status":"SUCCEEDED"},{"id":"autogen_task1_Vin","status":"SUCCEEDED"},{"id":"autogen_task1_Vhk","status":"SUCCEEDED"},{"id":"autogen_task1_Vpol","status":"SUCCEEDED"},{"id":"autogen_task1_Vpfk","status":"SUCCEEDED"},{"id":"autogen_task1_Vgapd","status":"SUCCEEDED"},{"id":"autogen_task1_Vpk","status":"SUCCEEDED"},{"id":"autogen_task1_Vgol","status":"SUCCEEDED"},{"id":"autogen_task1_Vatpase","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.548027,"curves":[{"id":"autogen_curve_task1_Glci","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_G6P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_FDP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PEP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Gly","status":"SUCCEEDED"},{"id":"autogen_curve_task1_EtOH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Carbo","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Glco","status":"SUCCEEDED"}]}]}]}