{"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    448      0 --:--:-- --:--:-- --:--:--   448\n\r100  205k  100  205k    0     0   482k      0 --:--:-- --:--:-- --:--:--  482k\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 (18.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/rawLog.txt\nCompleted 2.6 KiB/2.6 KiB (25.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 75%)\n  adding: outputs/BIOMD0000000040_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000040_url.sedml/autogen_plot_for_task1.pdf (deflated 29%)\n  adding: outputs/reports.h5 (deflated 25%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 104.2 KiB/104.2 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/outputs/reports.h5\nCompleted 88.5 KiB/109.2 KiB (1.0 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/output.zip\nCompleted 88.5 KiB/109.2 KiB (1.0 MiB/s) with 3 file(s) remaining\rCompleted 95.9 KiB/109.2 KiB (985.6 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/outputs/plots.zip\nCompleted 95.9 KiB/109.2 KiB (985.6 KiB/s) with 2 file(s) remaining\rCompleted 106.6 KiB/109.2 KiB (939.1 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000040_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/outputs/BIOMD0000000040_url.sedml/autogen_plot_for_task1.pdf\nCompleted 106.6 KiB/109.2 KiB (939.1 KiB/s) with 1 file(s) remaining\rCompleted 109.2 KiB/109.2 KiB (933.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000040-biopax2.owl  \n  inflating: contents/BIOMD0000000040-biopax3.owl  \n  inflating: contents/BIOMD0000000040-matlab.m  \n  inflating: contents/BIOMD0000000040-octave.m  \n  inflating: contents/BIOMD0000000040.m  \n  inflating: contents/BIOMD0000000040.ode  \n  inflating: contents/BIOMD0000000040.pdf  \n  inflating: contents/BIOMD0000000040.png  \n  inflating: contents/BIOMD0000000040.sci  \n  inflating: contents/BIOMD0000000040.svg  \n  inflating: contents/BIOMD0000000040.vcml  \n  inflating: contents/BIOMD0000000040_url.sedml  \n  inflating: contents/BIOMD0000000040_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 10.9 KiB/333.3 KiB (167.8 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000040-biopax2.owl to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/contents/BIOMD0000000040-biopax2.owl\nCompleted 10.9 KiB/333.3 KiB (167.8 KiB/s) with 16 file(s) remaining\rCompleted 14.7 KiB/333.3 KiB (128.2 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000040-matlab.m to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/contents/BIOMD0000000040-matlab.m\nCompleted 14.7 KiB/333.3 KiB (128.2 KiB/s) with 15 file(s) remaining\rCompleted 46.5 KiB/333.3 KiB (342.3 KiB/s) with 15 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/contents/curation_image.png\nCompleted 46.5 KiB/333.3 KiB (342.3 KiB/s) with 14 file(s) remaining\rCompleted 50.2 KiB/333.3 KiB (356.4 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000040-octave.m to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/contents/BIOMD0000000040-octave.m\nCompleted 50.2 KiB/333.3 KiB (356.4 KiB/s) with 13 file(s) remaining\rCompleted 96.0 KiB/333.3 KiB (655.6 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000040.png to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/contents/BIOMD0000000040.png\nCompleted 96.0 KiB/333.3 KiB (655.6 KiB/s) with 12 file(s) remaining\rCompleted 107.7 KiB/333.3 KiB (723.8 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000040.svg to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/contents/BIOMD0000000040.svg\nCompleted 107.7 KiB/333.3 KiB (723.8 KiB/s) with 11 file(s) remaining\rCompleted 109.4 KiB/333.3 KiB (715.4 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000040.sci to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/contents/BIOMD0000000040.sci\nCompleted 109.4 KiB/333.3 KiB (715.4 KiB/s) with 10 file(s) remaining\rCompleted 129.5 KiB/333.3 KiB (788.5 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000040.vcml to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/contents/BIOMD0000000040.vcml\nCompleted 129.5 KiB/333.3 KiB (788.5 KiB/s) with 9 file(s) remaining\rCompleted 137.8 KiB/333.3 KiB (819.2 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000040_url.sedml to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/contents/BIOMD0000000040_url.sedml\nCompleted 137.8 KiB/333.3 KiB (819.2 KiB/s) with 8 file(s) remaining\rCompleted 139.7 KiB/333.3 KiB (816.9 KiB/s) with 8 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/contents/manifest.xml\nCompleted 139.7 KiB/333.3 KiB (816.9 KiB/s) with 7 file(s) remaining\rCompleted 139.8 KiB/333.3 KiB (799.2 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/contents/curation_notes.txt\nCompleted 139.8 KiB/333.3 KiB (799.2 KiB/s) with 6 file(s) remaining\rCompleted 150.9 KiB/333.3 KiB (845.0 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000040_url.xml to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/contents/BIOMD0000000040_url.xml\nCompleted 150.9 KiB/333.3 KiB (845.0 KiB/s) with 5 file(s) remaining\rCompleted 154.6 KiB/333.3 KiB (779.2 KiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/contents/metadata.rdf\nCompleted 154.6 KiB/333.3 KiB (779.2 KiB/s) with 4 file(s) remaining\rCompleted 158.4 KiB/333.3 KiB (732.7 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000040.m to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/contents/BIOMD0000000040.m\nCompleted 158.4 KiB/333.3 KiB (732.7 KiB/s) with 3 file(s) remaining\rCompleted 160.2 KiB/333.3 KiB (720.9 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000040.ode to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/contents/BIOMD0000000040.ode\nCompleted 160.2 KiB/333.3 KiB (720.9 KiB/s) with 2 file(s) remaining\rCompleted 177.5 KiB/333.3 KiB (787.9 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000040-biopax3.owl to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/contents/BIOMD0000000040-biopax3.owl\nCompleted 177.5 KiB/333.3 KiB (787.9 KiB/s) with 1 file(s) remaining\rCompleted 333.3 KiB/333.3 KiB (1.3 MiB/s) with 1 file(s) remaining  \rupload: contents/BIOMD0000000040.pdf to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/contents/BIOMD0000000040.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.1 KiB/9.1 KiB (149.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107740dcacb55678b412f/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000040_url.sedml\ncreating dataset /BIOMD0000000040_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\ndataset created, uuid: d-da2bd8a5-a596c464-deb7-b74df1-e56f5c, chunk_size: (6, 1001)\ncreating dataset /BIOMD0000000040_url.sedml/autogen_report_for_task1, shape: (13, 1001), type: float64\ndataset created, uuid: d-da2bd8a5-a596c464-296c-d90aab-181339, chunk_size: (13, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000040_url.sedml\ncreating attribute uri in /BIOMD0000000040_url.sedml\ncreating attribute _type in /BIOMD0000000040_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000040_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000040_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000040_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000040_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000040_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000040_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000040_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000040_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000040_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000040_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000040_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000040_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000040_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000040_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000040_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000040_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000040_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000040_url.sedml\ncreate_links: /BIOMD0000000040_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000040_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000040_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\niterating over chunks for /BIOMD0000000040_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000040_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000040_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000040_url.sedml/autogen_report_for_task1, shape: (13, 1001), type: float64\niterating over chunks for /BIOMD0000000040_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 13, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000040_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647107740dcacb55678b412f\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 and upload the outputs of the simulation run ... 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.135605,"sedDocuments":[{"location":"BIOMD0000000040_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  BIOMD0000000040_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 13 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 5 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000040_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":0.748079,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.104394,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"deterministic"},{"key":"methodCode","value":22},{"key":"parameters"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.1377,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Br","status":"SUCCEEDED"},{"id":"autogen_task1_BrO3","status":"SUCCEEDED"},{"id":"autogen_task1_Ce","status":"SUCCEEDED"},{"id":"autogen_task1_HBrO2","status":"SUCCEEDED"},{"id":"autogen_task1_HOBr","status":"SUCCEEDED"},{"id":"autogen_task1_f","status":"SUCCEEDED"},{"id":"autogen_task1_BZ","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction1","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction2","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction3","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction4","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction5","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.398339,"curves":[{"id":"autogen_curve_task1_Br","status":"SUCCEEDED"},{"id":"autogen_curve_task1_BrO3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ce","status":"SUCCEEDED"},{"id":"autogen_curve_task1_HBrO2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_HOBr","status":"SUCCEEDED"}]}]}]}