{"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    448      0 --:--:-- --:--:-- --:--:--   448\n\r100  331k  100  331k    0     0   752k      0 --:--:-- --:--:-- --:--:--  752k\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 (23.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/rawLog.txt\nCompleted 4.3 KiB/4.3 KiB (66.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 82%)\n  adding: outputs/BIOMD0000000046_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000046_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 8%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/298.9 KiB (5.7 MiB/s) with 1 file(s) remaining\rCompleted 298.9 KiB/298.9 KiB (3.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/outputs/reports.h5\nCompleted 256.0 KiB/309.2 KiB (6.1 MiB/s) with 4 file(s) remaining\rCompleted 285.0 KiB/309.2 KiB (2.9 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/output.zip\nCompleted 285.0 KiB/309.2 KiB (2.9 MiB/s) with 3 file(s) remaining\rCompleted 293.7 KiB/309.2 KiB (2.7 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/outputs/plots.zip\nCompleted 293.7 KiB/309.2 KiB (2.7 MiB/s) with 2 file(s) remaining\rCompleted 306.4 KiB/309.2 KiB (2.7 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000046_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/outputs/BIOMD0000000046_url.sedml/autogen_plot_for_task1.pdf\nCompleted 306.4 KiB/309.2 KiB (2.7 MiB/s) with 1 file(s) remaining\rCompleted 309.2 KiB/309.2 KiB (2.6 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000046-biopax2.owl  \n  inflating: contents/BIOMD0000000046-biopax3.owl  \n  inflating: contents/BIOMD0000000046-matlab.m  \n  inflating: contents/BIOMD0000000046-octave.m  \n  inflating: contents/BIOMD0000000046.m  \n  inflating: contents/BIOMD0000000046.ode  \n  inflating: contents/BIOMD0000000046.pdf  \n  inflating: contents/BIOMD0000000046.png  \n  inflating: contents/BIOMD0000000046.sci  \n  inflating: contents/BIOMD0000000046.svg  \n  inflating: contents/BIOMD0000000046.vcml  \n  inflating: contents/BIOMD0000000046_url.sedml  \n  inflating: contents/BIOMD0000000046_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 32.4 KiB/645.4 KiB (434.3 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000046-biopax2.owl to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/contents/BIOMD0000000046-biopax2.owl\nCompleted 32.4 KiB/645.4 KiB (434.3 KiB/s) with 16 file(s) remaining\rCompleted 39.8 KiB/645.4 KiB (333.6 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000046-octave.m to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/contents/BIOMD0000000046-octave.m\nCompleted 39.8 KiB/645.4 KiB (333.6 KiB/s) with 15 file(s) remaining\rCompleted 90.4 KiB/645.4 KiB (738.8 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000046-biopax3.owl to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/contents/BIOMD0000000046-biopax3.owl\nCompleted 90.4 KiB/645.4 KiB (738.8 KiB/s) with 14 file(s) remaining\rCompleted 97.8 KiB/645.4 KiB (776.6 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000046-matlab.m to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/contents/BIOMD0000000046-matlab.m\nCompleted 97.8 KiB/645.4 KiB (776.6 KiB/s) with 13 file(s) remaining\rCompleted 105.3 KiB/645.4 KiB (816.0 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000046.m to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/contents/BIOMD0000000046.m\nCompleted 105.3 KiB/645.4 KiB (816.0 KiB/s) with 12 file(s) remaining\rCompleted 122.3 KiB/645.4 KiB (928.0 KiB/s) with 12 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/contents/curation_image.png\nCompleted 122.3 KiB/645.4 KiB (928.0 KiB/s) with 11 file(s) remaining\rCompleted 157.6 KiB/645.4 KiB (917.7 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000046.svg to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/contents/BIOMD0000000046.svg\nCompleted 157.6 KiB/645.4 KiB (917.7 KiB/s) with 10 file(s) remaining\rCompleted 176.9 KiB/645.4 KiB (1013.8 KiB/s) with 10 file(s) remaining\rCompleted 178.9 KiB/645.4 KiB (997.1 KiB/s) with 10 file(s) remaining \rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/contents/manifest.xml\nCompleted 178.9 KiB/645.4 KiB (997.1 KiB/s) with 9 file(s) remaining\rCompleted 225.0 KiB/645.4 KiB (1.2 MiB/s) with 9 file(s) remaining  \rupload: contents/BIOMD0000000046.vcml to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/contents/BIOMD0000000046.vcml\nCompleted 225.0 KiB/645.4 KiB (1.2 MiB/s) with 8 file(s) remaining\rCompleted 230.3 KiB/645.4 KiB (1.2 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000046.sci to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/contents/BIOMD0000000046.sci\nCompleted 230.3 KiB/645.4 KiB (1.2 MiB/s) with 7 file(s) remaining\rCompleted 234.5 KiB/645.4 KiB (1.2 MiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/contents/metadata.rdf\nCompleted 234.5 KiB/645.4 KiB (1.2 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000046_url.sedml to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/contents/BIOMD0000000046_url.sedml\nCompleted 234.5 KiB/645.4 KiB (1.2 MiB/s) with 5 file(s) remaining\rCompleted 234.6 KiB/645.4 KiB (1.2 MiB/s) with 5 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/contents/curation_notes.txt\nCompleted 234.6 KiB/645.4 KiB (1.2 MiB/s) with 4 file(s) remaining\rCompleted 262.8 KiB/645.4 KiB (1.3 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000046_url.xml to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/contents/BIOMD0000000046_url.xml\nCompleted 262.8 KiB/645.4 KiB (1.3 MiB/s) with 3 file(s) remaining\rCompleted 472.1 KiB/645.4 KiB (2.3 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000046.pdf to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/contents/BIOMD0000000046.pdf\nCompleted 472.1 KiB/645.4 KiB (2.3 MiB/s) with 2 file(s) remaining\rCompleted 640.7 KiB/645.4 KiB (3.0 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000046.png to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/contents/BIOMD0000000046.png\nCompleted 640.7 KiB/645.4 KiB (3.0 MiB/s) with 1 file(s) remaining\rCompleted 645.4 KiB/645.4 KiB (2.7 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000046.ode to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/contents/BIOMD0000000046.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.3 KiB/9.3 KiB (119.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471078649c0d898ffdd99f8/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000046_url.sedml\ncreating dataset /BIOMD0000000046_url.sedml/autogen_plot_for_task1, shape: (17, 1001), type: float64\ndataset created, uuid: d-f2a3fc2b-e55f9958-f0e8-2c89e5-76040b, chunk_size: (17, 1001)\ncreating dataset /BIOMD0000000046_url.sedml/autogen_report_for_task1, shape: (33, 1001), type: float64\ndataset created, uuid: d-f2a3fc2b-e55f9958-5611-1bd018-0dac09, chunk_size: (33, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000046_url.sedml\ncreating attribute uri in /BIOMD0000000046_url.sedml\ncreating attribute _type in /BIOMD0000000046_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000046_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000046_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000046_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000046_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000046_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000046_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000046_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000046_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000046_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000046_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000046_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000046_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000046_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000046_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000046_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000046_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000046_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000046_url.sedml\ncreate_links: /BIOMD0000000046_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000046_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000046_url.sedml/autogen_plot_for_task1, shape: (17, 1001), type: float64\niterating over chunks for /BIOMD0000000046_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 17, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000046_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000046_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000046_url.sedml/autogen_report_for_task1, shape: (33, 1001), type: float64\niterating over chunks for /BIOMD0000000046_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 33, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000046_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471078649c0d898ffdd99f8\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 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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":20.888064,"sedDocuments":[{"location":"BIOMD0000000046_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  BIOMD0000000046_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 33 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 16 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000046_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":20.557756,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":19.605654,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.322915,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_NADH","status":"SUCCEEDED"},{"id":"autogen_task1_O2","status":"SUCCEEDED"},{"id":"autogen_task1_H2O2","status":"SUCCEEDED"},{"id":"autogen_task1_per3","status":"SUCCEEDED"},{"id":"autogen_task1_coI","status":"SUCCEEDED"},{"id":"autogen_task1_ArH","status":"SUCCEEDED"},{"id":"autogen_task1_coII","status":"SUCCEEDED"},{"id":"autogen_task1_Ar","status":"SUCCEEDED"},{"id":"autogen_task1_NADrad","status":"SUCCEEDED"},{"id":"autogen_task1_super","status":"SUCCEEDED"},{"id":"autogen_task1_coIII","status":"SUCCEEDED"},{"id":"autogen_task1_per2","status":"SUCCEEDED"},{"id":"autogen_task1_NAD2","status":"SUCCEEDED"},{"id":"autogen_task1_NAD","status":"SUCCEEDED"},{"id":"autogen_task1_O2g","status":"SUCCEEDED"},{"id":"autogen_task1_NADHres","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_v1","status":"SUCCEEDED"},{"id":"autogen_task1_v2","status":"SUCCEEDED"},{"id":"autogen_task1_v3","status":"SUCCEEDED"},{"id":"autogen_task1_v4","status":"SUCCEEDED"},{"id":"autogen_task1_v5","status":"SUCCEEDED"},{"id":"autogen_task1_v6","status":"SUCCEEDED"},{"id":"autogen_task1_v7","status":"SUCCEEDED"},{"id":"autogen_task1_v8","status":"SUCCEEDED"},{"id":"autogen_task1_v9","status":"SUCCEEDED"},{"id":"autogen_task1_v10","status":"SUCCEEDED"},{"id":"autogen_task1_v11","status":"SUCCEEDED"},{"id":"autogen_task1_v12","status":"SUCCEEDED"},{"id":"autogen_task1_v131","status":"SUCCEEDED"},{"id":"autogen_task1_v132","status":"SUCCEEDED"},{"id":"autogen_task1_v14","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.492368,"curves":[{"id":"autogen_curve_task1_NADH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_O2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_H2O2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_per3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_coI","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ArH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_coII","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ar","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADrad","status":"SUCCEEDED"},{"id":"autogen_curve_task1_super","status":"SUCCEEDED"},{"id":"autogen_curve_task1_coIII","status":"SUCCEEDED"},{"id":"autogen_curve_task1_per2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NAD2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NAD","status":"SUCCEEDED"},{"id":"autogen_curve_task1_O2g","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADHres","status":"SUCCEEDED"}]}]}]}