{"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    431      0 --:--:-- --:--:-- --:--:--   433\n\r100  200k  100  200k    0     0   464k      0 --:--:-- --:--:-- --:--:--  464k\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 (25.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/rawLog.txt\nCompleted 4.3 KiB/4.3 KiB (68.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/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/reports.h5 (deflated 11%)\n  adding: outputs/BIOMD0000000026_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000026_url.sedml/autogen_plot_for_task1.pdf (deflated 28%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/266.8 KiB (5.6 MiB/s) with 1 file(s) remaining\rCompleted 266.8 KiB/266.8 KiB (2.8 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/outputs/reports.h5\nCompleted 247.9 KiB/269.6 KiB (2.4 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/output.zip\nCompleted 247.9 KiB/269.6 KiB (2.4 MiB/s) with 3 file(s) remaining\rCompleted 259.1 KiB/269.6 KiB (2.5 MiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000026_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/outputs/BIOMD0000000026_url.sedml/autogen_plot_for_task1.pdf\nCompleted 259.1 KiB/269.6 KiB (2.5 MiB/s) with 2 file(s) remaining\rCompleted 266.9 KiB/269.6 KiB (2.2 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/outputs/plots.zip\nCompleted 266.9 KiB/269.6 KiB (2.2 MiB/s) with 1 file(s) remaining\rCompleted 269.6 KiB/269.6 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000026-biopax2.owl  \n  inflating: contents/BIOMD0000000026-biopax3.owl  \n  inflating: contents/BIOMD0000000026-matlab.m  \n  inflating: contents/BIOMD0000000026-octave.m  \n  inflating: contents/BIOMD0000000026.m  \n  inflating: contents/BIOMD0000000026.ode  \n  inflating: contents/BIOMD0000000026.pdf  \n  inflating: contents/BIOMD0000000026.png  \n  inflating: contents/BIOMD0000000026.sci  \n  inflating: contents/BIOMD0000000026.svg  \n  inflating: contents/BIOMD0000000026.vcml  \n  inflating: contents/BIOMD0000000026_url.sedml  \n  inflating: contents/BIOMD0000000026_url.xml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 6.1 KiB/439.5 KiB (54.2 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000026-matlab.m to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/contents/BIOMD0000000026-matlab.m\nCompleted 6.1 KiB/439.5 KiB (54.2 KiB/s) with 14 file(s) remaining\rCompleted 29.5 KiB/439.5 KiB (256.0 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000026-biopax2.owl to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/contents/BIOMD0000000026-biopax2.owl\nCompleted 29.5 KiB/439.5 KiB (256.0 KiB/s) with 13 file(s) remaining\rCompleted 65.2 KiB/439.5 KiB (546.9 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000026-biopax3.owl to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/contents/BIOMD0000000026-biopax3.owl\nCompleted 65.2 KiB/439.5 KiB (546.9 KiB/s) with 12 file(s) remaining\rCompleted 68.9 KiB/439.5 KiB (500.4 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000026.sci to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/contents/BIOMD0000000026.sci\nCompleted 68.9 KiB/439.5 KiB (500.4 KiB/s) with 11 file(s) remaining\rCompleted 131.1 KiB/439.5 KiB (941.1 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000026.png to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/contents/BIOMD0000000026.png\nCompleted 131.1 KiB/439.5 KiB (941.1 KiB/s) with 10 file(s) remaining\rCompleted 158.2 KiB/439.5 KiB (1.0 MiB/s) with 10 file(s) remaining  \rupload: contents/BIOMD0000000026.svg to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/contents/BIOMD0000000026.svg\nCompleted 158.2 KiB/439.5 KiB (1.0 MiB/s) with 9 file(s) remaining\rCompleted 160.1 KiB/439.5 KiB (934.3 KiB/s) with 9 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/contents/metadata.rdf\nCompleted 160.1 KiB/439.5 KiB (934.3 KiB/s) with 8 file(s) remaining\rCompleted 333.7 KiB/439.5 KiB (1.9 MiB/s) with 8 file(s) remaining  \rupload: contents/BIOMD0000000026.pdf to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/contents/BIOMD0000000026.pdf\nCompleted 333.7 KiB/439.5 KiB (1.9 MiB/s) with 7 file(s) remaining\rCompleted 339.8 KiB/439.5 KiB (1.9 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000026-octave.m to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/contents/BIOMD0000000026-octave.m\nCompleted 339.8 KiB/439.5 KiB (1.9 MiB/s) with 6 file(s) remaining\rCompleted 361.2 KiB/439.5 KiB (2.0 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000026_url.sedml to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/contents/BIOMD0000000026_url.sedml\nCompleted 361.2 KiB/439.5 KiB (2.0 MiB/s) with 5 file(s) remaining\rCompleted 386.8 KiB/439.5 KiB (2.1 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000026_url.xml to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/contents/BIOMD0000000026_url.xml\nCompleted 386.8 KiB/439.5 KiB (2.1 MiB/s) with 4 file(s) remaining\rCompleted 388.6 KiB/439.5 KiB (2.0 MiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/contents/manifest.xml\nCompleted 388.6 KiB/439.5 KiB (2.0 MiB/s) with 3 file(s) remaining\rCompleted 394.7 KiB/439.5 KiB (1.9 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000026.m to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/contents/BIOMD0000000026.m\nCompleted 394.7 KiB/439.5 KiB (1.9 MiB/s) with 2 file(s) remaining\rCompleted 398.5 KiB/439.5 KiB (1.9 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000026.ode to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/contents/BIOMD0000000026.ode\nCompleted 398.5 KiB/439.5 KiB (1.9 MiB/s) with 1 file(s) remaining\rCompleted 439.5 KiB/439.5 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000026.vcml to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/contents/BIOMD0000000026.vcml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (132.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471074849c0d898ffdd9332/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000026_url.sedml\ncreating dataset /BIOMD0000000026_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\ndataset created, uuid: d-a34332df-e67180d5-a553-9a2b36-80c1c9, chunk_size: (12, 1001)\ncreating dataset /BIOMD0000000026_url.sedml/autogen_report_for_task1, shape: (39, 1001), type: float64\ndataset created, uuid: d-a34332df-e67180d5-1a1d-acca4d-403c37, chunk_size: (39, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000026_url.sedml\ncreating attribute uri in /BIOMD0000000026_url.sedml\ncreating attribute _type in /BIOMD0000000026_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000026_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000026_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000026_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000026_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000026_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000026_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000026_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000026_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000026_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000026_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000026_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000026_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000026_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000026_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000026_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000026_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000026_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000026_url.sedml\ncreate_links: /BIOMD0000000026_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000026_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000026_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\niterating over chunks for /BIOMD0000000026_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 12, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000026_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000026_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000026_url.sedml/autogen_report_for_task1, shape: (39, 1001), type: float64\niterating over chunks for /BIOMD0000000026_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 39, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000026_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471074849c0d898ffdd9332\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 SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":20.143101,"sedDocuments":[{"location":"BIOMD0000000026_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  BIOMD0000000026_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 39 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 11 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000026_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":19.777292,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":18.891125,"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":0.340803,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_M","status":"SUCCEEDED"},{"id":"autogen_task1_Mp","status":"SUCCEEDED"},{"id":"autogen_task1_Mpp","status":"SUCCEEDED"},{"id":"autogen_task1_MAPKK","status":"SUCCEEDED"},{"id":"autogen_task1_MKP3","status":"SUCCEEDED"},{"id":"autogen_task1_M_MAPKK","status":"SUCCEEDED"},{"id":"autogen_task1_Mp_MAPKK","status":"SUCCEEDED"},{"id":"autogen_task1_Mpp_MKP3","status":"SUCCEEDED"},{"id":"autogen_task1_Mp_MKP3_dep","status":"SUCCEEDED"},{"id":"autogen_task1_Mp_MKP3","status":"SUCCEEDED"},{"id":"autogen_task1_M_MKP3","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k_1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_k_3","status":"SUCCEEDED"},{"id":"autogen_task1_k4","status":"SUCCEEDED"},{"id":"autogen_task1_h1","status":"SUCCEEDED"},{"id":"autogen_task1_h_1","status":"SUCCEEDED"},{"id":"autogen_task1_h2","status":"SUCCEEDED"},{"id":"autogen_task1_h3","status":"SUCCEEDED"},{"id":"autogen_task1_h_3","status":"SUCCEEDED"},{"id":"autogen_task1_h4","status":"SUCCEEDED"},{"id":"autogen_task1_h_4","status":"SUCCEEDED"},{"id":"autogen_task1_h5","status":"SUCCEEDED"},{"id":"autogen_task1_h6","status":"SUCCEEDED"},{"id":"autogen_task1_h_6","status":"SUCCEEDED"},{"id":"autogen_task1_uVol","status":"SUCCEEDED"},{"id":"autogen_task1_v1a","status":"SUCCEEDED"},{"id":"autogen_task1_v1b","status":"SUCCEEDED"},{"id":"autogen_task1_v2a","status":"SUCCEEDED"},{"id":"autogen_task1_v2b","status":"SUCCEEDED"},{"id":"autogen_task1_v3a","status":"SUCCEEDED"},{"id":"autogen_task1_v3b","status":"SUCCEEDED"},{"id":"autogen_task1_v3c","status":"SUCCEEDED"},{"id":"autogen_task1_v4a","status":"SUCCEEDED"},{"id":"autogen_task1_v4b","status":"SUCCEEDED"},{"id":"autogen_task1_v4c","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.405239,"curves":[{"id":"autogen_curve_task1_M","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Mp","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Mpp","status":"SUCCEEDED"},{"id":"autogen_curve_task1_MAPKK","status":"SUCCEEDED"},{"id":"autogen_curve_task1_MKP3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_M_MAPKK","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Mp_MAPKK","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Mpp_MKP3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Mp_MKP3_dep","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Mp_MKP3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_M_MKP3","status":"SUCCEEDED"}]}]}]}