{"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    429      0 --:--:-- --:--:-- --:--:--   430\n\r100  313k  100  313k    0     0   718k      0 --:--:-- --:--:-- --:--:--  718k\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 (27.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/rawLog.txt\nCompleted 5.3 KiB/5.3 KiB (85.5 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 83%)\n  adding: outputs/BIOMD0000000042.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000042.sedml/plot_1_task1.pdf (deflated 23%)\n  adding: outputs/reports.h5 (deflated 14%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 218.7 KiB/218.7 KiB (2.2 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/outputs/reports.h5\nCompleted 200.9 KiB/226.8 KiB (2.1 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/output.zip\nCompleted 200.9 KiB/226.8 KiB (2.1 MiB/s) with 3 file(s) remaining\rCompleted 214.2 KiB/226.8 KiB (1.9 MiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000042.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/outputs/BIOMD0000000042.sedml/plot_1_task1.pdf\nCompleted 214.2 KiB/226.8 KiB (1.9 MiB/s) with 2 file(s) remaining\rCompleted 216.8 KiB/226.8 KiB (1.8 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/rawLog.txt\nCompleted 216.8 KiB/226.8 KiB (1.8 MiB/s) with 1 file(s) remaining\rCompleted 226.8 KiB/226.8 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000042-biopax2.owl  \n  inflating: contents/BIOMD0000000042-biopax3.owl  \n  inflating: contents/BIOMD0000000042-matlab.m  \n  inflating: contents/BIOMD0000000042-octave.m  \n  inflating: contents/BIOMD0000000042.cps  \n  inflating: contents/BIOMD0000000042.m  \n  inflating: contents/BIOMD0000000042.ode  \n  inflating: contents/BIOMD0000000042.pdf  \n  inflating: contents/BIOMD0000000042.png  \n  inflating: contents/BIOMD0000000042.sci  \n  inflating: contents/BIOMD0000000042.sedml  \n  inflating: contents/BIOMD0000000042.svg  \n  inflating: contents/BIOMD0000000042.vcml  \n  inflating: contents/BIOMD0000000042_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 52.5 KiB/809.0 KiB (685.7 KiB/s) with 18 file(s) remaining\rupload: contents/BIOMD0000000042-biopax2.owl to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/contents/BIOMD0000000042-biopax2.owl\nCompleted 52.5 KiB/809.0 KiB (685.7 KiB/s) with 17 file(s) remaining\rCompleted 62.0 KiB/809.0 KiB (524.0 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000042-octave.m to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/contents/BIOMD0000000042-octave.m\nCompleted 62.0 KiB/809.0 KiB (524.0 KiB/s) with 16 file(s) remaining\rCompleted 71.6 KiB/809.0 KiB (575.9 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000042-matlab.m to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/contents/BIOMD0000000042-matlab.m\nCompleted 71.6 KiB/809.0 KiB (575.9 KiB/s) with 15 file(s) remaining\rCompleted 93.0 KiB/809.0 KiB (693.3 KiB/s) with 15 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/contents/curation_image.png\nCompleted 93.0 KiB/809.0 KiB (693.3 KiB/s) with 14 file(s) remaining\rCompleted 314.1 KiB/809.0 KiB (2.1 MiB/s) with 14 file(s) remaining \rupload: contents/BIOMD0000000042.pdf to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/contents/BIOMD0000000042.pdf\nCompleted 314.1 KiB/809.0 KiB (2.1 MiB/s) with 13 file(s) remaining\rCompleted 321.4 KiB/809.0 KiB (2.1 MiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000042.sci to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/contents/BIOMD0000000042.sci\nCompleted 321.4 KiB/809.0 KiB (2.1 MiB/s) with 12 file(s) remaining\rCompleted 435.6 KiB/809.0 KiB (2.6 MiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000042.png to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/contents/BIOMD0000000042.png\nCompleted 435.6 KiB/809.0 KiB (2.6 MiB/s) with 11 file(s) remaining\rCompleted 435.6 KiB/809.0 KiB (2.5 MiB/s) with 11 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/contents/curation_notes.txt\nCompleted 435.6 KiB/809.0 KiB (2.5 MiB/s) with 10 file(s) remaining\rCompleted 480.4 KiB/809.0 KiB (2.6 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000042.svg to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/contents/BIOMD0000000042.svg\nCompleted 480.4 KiB/809.0 KiB (2.6 MiB/s) with 9 file(s) remaining\rCompleted 482.5 KiB/809.0 KiB (2.6 MiB/s) with 9 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/contents/manifest.xml\nCompleted 482.5 KiB/809.0 KiB (2.6 MiB/s) with 8 file(s) remaining\rCompleted 554.1 KiB/809.0 KiB (2.8 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000042.vcml to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/contents/BIOMD0000000042.vcml\nCompleted 554.1 KiB/809.0 KiB (2.8 MiB/s) with 7 file(s) remaining\rCompleted 588.5 KiB/809.0 KiB (2.9 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000042.sedml to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/contents/BIOMD0000000042.sedml\nCompleted 588.5 KiB/809.0 KiB (2.9 MiB/s) with 6 file(s) remaining\rCompleted 591.5 KiB/809.0 KiB (2.9 MiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/contents/metadata.rdf\nCompleted 591.5 KiB/809.0 KiB (2.9 MiB/s) with 5 file(s) remaining\rCompleted 637.2 KiB/809.0 KiB (3.1 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000042_url.xml to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/contents/BIOMD0000000042_url.xml\nCompleted 637.2 KiB/809.0 KiB (3.1 MiB/s) with 4 file(s) remaining\rCompleted 643.5 KiB/809.0 KiB (3.1 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000042.ode to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/contents/BIOMD0000000042.ode\nCompleted 643.5 KiB/809.0 KiB (3.1 MiB/s) with 3 file(s) remaining\rCompleted 715.7 KiB/809.0 KiB (3.1 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000042-biopax3.owl to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/contents/BIOMD0000000042-biopax3.owl\nCompleted 715.7 KiB/809.0 KiB (3.1 MiB/s) with 2 file(s) remaining\rCompleted 799.5 KiB/809.0 KiB (3.4 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000042.cps to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/contents/BIOMD0000000042.cps\nCompleted 799.5 KiB/809.0 KiB (3.4 MiB/s) with 1 file(s) remaining\rCompleted 809.0 KiB/809.0 KiB (3.2 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000042.m to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/contents/BIOMD0000000042.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.3 KiB/9.3 KiB (142.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471077a49c0d898ffdd9898/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000042.sedml\ncreating dataset /BIOMD0000000042.sedml/autogen_report_for_task1, shape: (67, 601), type: float64\ndataset created, uuid: d-6493cdce-2e3a9613-fa63-462ff9-b0767b, chunk_size: (67, 601)\ncreating dataset /BIOMD0000000042.sedml/plot_1_task1, shape: (2, 601), type: float64\ndataset created, uuid: d-6493cdce-2e3a9613-681b-30294c-e0d7fe, chunk_size: (2, 601)\ncreating attribute combineArchiveLocation in /BIOMD0000000042.sedml\ncreating attribute uri in /BIOMD0000000042.sedml\ncreating attribute _type in /BIOMD0000000042.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000042.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000042.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000042.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000042.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000042.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000042.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000042.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000042.sedml/autogen_report_for_task1\ncreating attribute _type in /BIOMD0000000042.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000042.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000042.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000042.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000042.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000042.sedml/plot_1_task1\ncreating attribute sedmlId in /BIOMD0000000042.sedml/plot_1_task1\ncreating attribute sedmlName in /BIOMD0000000042.sedml/plot_1_task1\ncreating attribute uri in /BIOMD0000000042.sedml/plot_1_task1\ncreate_links: /\ngot link: BIOMD0000000042.sedml\ncreate_links: /BIOMD0000000042.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /BIOMD0000000042.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000042.sedml/autogen_report_for_task1, shape: (67, 601), type: float64\niterating over chunks for /BIOMD0000000042.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 67, 1), slice(0, 601, 1))\ndone with dataload for /BIOMD0000000042.sedml/autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000042.sedml/plot_1_task1 to tgt: /BIOMD0000000042.sedml/plot_1_task1, shape: (2, 601), type: float64\niterating over chunks for /BIOMD0000000042.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 601, 1))\ndone with dataload for /BIOMD0000000042.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471077a49c0d898ffdd9898\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 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.\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 SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.556405,"sedDocuments":[{"location":"BIOMD0000000042.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  BIOMD0000000042.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 67 data sets\r\n    Plots (1):\r\n      plot_1_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000042.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":1.07981,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.226672,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"deterministic"},{"key":"methodCode","value":22},{"key":"parameters","value":{"Absolute Tolerance":1e-12,"Integrate Reduced Model":false,"Max Internal Steps":10000,"Relative Tolerance":0.000001}}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.35007,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.326347,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_NADH","status":"SUCCEEDED"},{"id":"autogen_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_task1_ADP","status":"SUCCEEDED"},{"id":"autogen_task1_AMP","status":"SUCCEEDED"},{"id":"autogen_task1_GLC","status":"SUCCEEDED"},{"id":"autogen_task1_F6P","status":"SUCCEEDED"},{"id":"autogen_task1_FBP","status":"SUCCEEDED"},{"id":"autogen_task1_GAP","status":"SUCCEEDED"},{"id":"autogen_task1_NAD","status":"SUCCEEDED"},{"id":"autogen_task1_DPG","status":"SUCCEEDED"},{"id":"autogen_task1_PEP","status":"SUCCEEDED"},{"id":"autogen_task1_PYR","status":"SUCCEEDED"},{"id":"autogen_task1_ACA","status":"SUCCEEDED"},{"id":"autogen_task1_EtOH","status":"SUCCEEDED"},{"id":"autogen_task1_P","status":"SUCCEEDED"},{"id":"autogen_task1_V1","status":"SUCCEEDED"},{"id":"autogen_task1_K1GLC","status":"SUCCEEDED"},{"id":"autogen_task1_K1ATP","status":"SUCCEEDED"},{"id":"autogen_task1_V2","status":"SUCCEEDED"},{"id":"autogen_task1_K2","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_K2ATP","status":"SUCCEEDED"},{"id":"autogen_task1_k3f","status":"SUCCEEDED"},{"id":"autogen_task1_k3b","status":"SUCCEEDED"},{"id":"autogen_task1_V4","status":"SUCCEEDED"},{"id":"autogen_task1_K4GAP","status":"SUCCEEDED"},{"id":"autogen_task1_K4NAD","status":"SUCCEEDED"},{"id":"autogen_task1_k5f","status":"SUCCEEDED"},{"id":"autogen_task1_k5b","status":"SUCCEEDED"},{"id":"autogen_task1_V6","status":"SUCCEEDED"},{"id":"autogen_task1_K6PEP","status":"SUCCEEDED"},{"id":"autogen_task1_K6ADP","status":"SUCCEEDED"},{"id":"autogen_task1_V7","status":"SUCCEEDED"},{"id":"autogen_task1_K7PYR","status":"SUCCEEDED"},{"id":"autogen_task1_k8f","status":"SUCCEEDED"},{"id":"autogen_task1_k8b","status":"SUCCEEDED"},{"id":"autogen_task1_k9f","status":"SUCCEEDED"},{"id":"autogen_task1_k9b","status":"SUCCEEDED"},{"id":"autogen_task1_k10","status":"SUCCEEDED"},{"id":"autogen_task1_flow","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_ATPflow","status":"SUCCEEDED"},{"id":"autogen_task1_ADPflow","status":"SUCCEEDED"},{"id":"autogen_task1_NADHflow","status":"SUCCEEDED"},{"id":"autogen_task1_NADflow","status":"SUCCEEDED"},{"id":"autogen_task1_GLCflow","status":"SUCCEEDED"},{"id":"autogen_task1_F6Pflow","status":"SUCCEEDED"},{"id":"autogen_task1_FBPflow","status":"SUCCEEDED"},{"id":"autogen_task1_GAPflow","status":"SUCCEEDED"},{"id":"autogen_task1_DPGflow","status":"SUCCEEDED"},{"id":"autogen_task1_PEPflow","status":"SUCCEEDED"},{"id":"autogen_task1_PYRflow","status":"SUCCEEDED"},{"id":"autogen_task1_ACAflow","status":"SUCCEEDED"},{"id":"autogen_task1_EtOHflow","status":"SUCCEEDED"},{"id":"autogen_task1_AMPflow","status":"SUCCEEDED"},{"id":"autogen_task1_Pflow","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_1","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_2","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_3","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_4","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_5","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_6","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_7","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_8","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_9","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_10","status":"SUCCEEDED"}]}]}]}