{"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    500      0 --:--:-- --:--:-- --:--:--   501\n\r100  222k  100  222k    0     0   571k      0 --:--:-- --:--:-- --:--:--  571k\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 (21.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/rawLog.txt\nCompleted 2.4 KiB/2.4 KiB (26.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 74%)\n  adding: outputs/BIOMD0000000329_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000329_url.sedml/autogen_plot_for_task1.pdf (deflated 22%)\n  adding: outputs/reports.h5 (deflated 20%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 128.6 KiB/128.6 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/outputs/reports.h5\nCompleted 13.0 KiB/141.2 KiB (158.9 KiB/s) with 4 file(s) remaining\rupload: outputs/BIOMD0000000329_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/outputs/BIOMD0000000329_url.sedml/autogen_plot_for_task1.pdf\nCompleted 13.0 KiB/141.2 KiB (158.9 KiB/s) with 3 file(s) remaining\rCompleted 23.0 KiB/141.2 KiB (196.5 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/outputs/plots.zip\nCompleted 23.0 KiB/141.2 KiB (196.5 KiB/s) with 2 file(s) remaining\rCompleted 138.6 KiB/141.2 KiB (1.1 MiB/s) with 2 file(s) remaining \rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/output.zip\nCompleted 138.6 KiB/141.2 KiB (1.1 MiB/s) with 1 file(s) remaining\rCompleted 141.2 KiB/141.2 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000329-biopax2.owl  \n  inflating: contents/BIOMD0000000329-biopax3.owl  \n  inflating: contents/BIOMD0000000329-matlab.m  \n  inflating: contents/BIOMD0000000329-octave.m  \n  inflating: contents/BIOMD0000000329.m  \n  inflating: contents/BIOMD0000000329.ode  \n  inflating: contents/BIOMD0000000329.pdf  \n  inflating: contents/BIOMD0000000329.png  \n  inflating: contents/BIOMD0000000329.svg  \n  inflating: contents/BIOMD0000000329.vcml  \n  inflating: contents/BIOMD0000000329_url.sedml  \n  inflating: contents/BIOMD0000000329_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 4.6 KiB/363.0 KiB (60.6 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000329-octave.m to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/contents/BIOMD0000000329-octave.m\nCompleted 4.6 KiB/363.0 KiB (60.6 KiB/s) with 15 file(s) remaining\rCompleted 7.4 KiB/363.0 KiB (61.2 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000329.ode to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/contents/BIOMD0000000329.ode\nCompleted 7.4 KiB/363.0 KiB (61.2 KiB/s) with 14 file(s) remaining\rCompleted 16.7 KiB/363.0 KiB (126.5 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000329-biopax2.owl to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/contents/BIOMD0000000329-biopax2.owl\nCompleted 16.7 KiB/363.0 KiB (126.5 KiB/s) with 13 file(s) remaining\rCompleted 18.6 KiB/363.0 KiB (138.0 KiB/s) with 13 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/contents/manifest.xml\nCompleted 18.6 KiB/363.0 KiB (138.0 KiB/s) with 12 file(s) remaining\rCompleted 33.4 KiB/363.0 KiB (223.1 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000329.svg to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/contents/BIOMD0000000329.svg\nCompleted 33.4 KiB/363.0 KiB (223.1 KiB/s) with 11 file(s) remaining\rCompleted 59.4 KiB/363.0 KiB (385.5 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000329.vcml to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/contents/BIOMD0000000329.vcml\nCompleted 59.4 KiB/363.0 KiB (385.5 KiB/s) with 10 file(s) remaining\rCompleted 72.2 KiB/363.0 KiB (443.8 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000329-biopax3.owl to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/contents/BIOMD0000000329-biopax3.owl\nCompleted 72.2 KiB/363.0 KiB (443.8 KiB/s) with 9 file(s) remaining\rCompleted 244.6 KiB/363.0 KiB (1.4 MiB/s) with 9 file(s) remaining \rupload: contents/BIOMD0000000329.pdf to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/contents/BIOMD0000000329.pdf\nCompleted 244.6 KiB/363.0 KiB (1.4 MiB/s) with 8 file(s) remaining\rCompleted 244.8 KiB/363.0 KiB (1.4 MiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/contents/curation_notes.txt\nCompleted 244.8 KiB/363.0 KiB (1.4 MiB/s) with 7 file(s) remaining\rCompleted 278.3 KiB/363.0 KiB (1.5 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000329.png to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/contents/BIOMD0000000329.png\nCompleted 278.3 KiB/363.0 KiB (1.5 MiB/s) with 6 file(s) remaining\rCompleted 286.0 KiB/363.0 KiB (1.6 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000329_url.sedml to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/contents/BIOMD0000000329_url.sedml\nCompleted 286.0 KiB/363.0 KiB (1.6 MiB/s) with 5 file(s) remaining\rCompleted 306.1 KiB/363.0 KiB (1.6 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000329_url.xml to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/contents/BIOMD0000000329_url.xml\nCompleted 306.1 KiB/363.0 KiB (1.6 MiB/s) with 4 file(s) remaining\rCompleted 310.7 KiB/363.0 KiB (1.5 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000329.m to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/contents/BIOMD0000000329.m\nCompleted 310.7 KiB/363.0 KiB (1.5 MiB/s) with 3 file(s) remaining\rCompleted 315.5 KiB/363.0 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/contents/metadata.rdf\nCompleted 315.5 KiB/363.0 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 358.4 KiB/363.0 KiB (1.7 MiB/s) with 2 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/contents/curation_image.png\nCompleted 358.4 KiB/363.0 KiB (1.7 MiB/s) with 1 file(s) remaining\rCompleted 363.0 KiB/363.0 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000329-matlab.m to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/contents/BIOMD0000000329-matlab.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.8 KiB/8.8 KiB (120.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a280b77b666965503b624/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000329_url.sedml\ncreating dataset /BIOMD0000000329_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-c6c73ab3-a2aad4b6-8cbc-2fb426-1c6d9d, chunk_size: (4, 1001)\ncreating dataset /BIOMD0000000329_url.sedml/autogen_report_for_task1, shape: (13, 1001), type: float64\ndataset created, uuid: d-c6c73ab3-a2aad4b6-81c3-d66621-43894b, chunk_size: (13, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000329_url.sedml\ncreating attribute uri in /BIOMD0000000329_url.sedml\ncreating attribute _type in /BIOMD0000000329_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000329_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000329_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000329_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000329_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000329_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000329_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000329_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000329_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000329_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000329_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000329_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000329_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000329_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000329_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000329_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000329_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000329_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000329_url.sedml\ncreate_links: /BIOMD0000000329_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000329_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000329_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\niterating over chunks for /BIOMD0000000329_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000329_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000329_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000329_url.sedml/autogen_report_for_task1, shape: (13, 1001), type: float64\niterating over chunks for /BIOMD0000000329_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 13, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000329_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a280b77b666965503b624\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.\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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.146229,"sedDocuments":[{"location":"BIOMD0000000329_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  BIOMD0000000329_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: 3 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000329_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":0.754252,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.118338,"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":0.143219,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_c","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_R1","status":"SUCCEEDED"},{"id":"autogen_task1_R2","status":"SUCCEEDED"},{"id":"autogen_task1_R3","status":"SUCCEEDED"},{"id":"autogen_task1_R4","status":"SUCCEEDED"},{"id":"autogen_task1_R5","status":"SUCCEEDED"},{"id":"autogen_task1_R6","status":"SUCCEEDED"},{"id":"autogen_task1_R7","status":"SUCCEEDED"},{"id":"autogen_task1_R8","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.382521,"curves":[{"id":"autogen_curve_task1_a","status":"SUCCEEDED"},{"id":"autogen_curve_task1_b","status":"SUCCEEDED"},{"id":"autogen_curve_task1_c","status":"SUCCEEDED"}]}]}]}