{"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 --:--:-- --:--:-- --:--:--   431\r100   139  100   139    0     0    425      0 --:--:-- --:--:-- --:--:--   425\n\r100  172k  100  172k    0     0   382k      0 --:--:-- --:--:-- --:--:--  382k\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 (22.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/rawLog.txt\nCompleted 2.3 KiB/2.3 KiB (20.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 71%)\n  adding: outputs/BIOMD0000000414_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000414_url.sedml/autogen_plot_for_task1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 38%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 56.2 KiB/56.2 KiB (473.8 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/outputs/reports.h5\nCompleted 45.5 KiB/68.8 KiB (411.2 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/output.zip\nCompleted 45.5 KiB/68.8 KiB (411.2 KiB/s) with 3 file(s) remaining\rCompleted 48.2 KiB/68.8 KiB (365.4 KiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/rawLog.txt\nCompleted 48.2 KiB/68.8 KiB (365.4 KiB/s) with 2 file(s) remaining\rCompleted 60.6 KiB/68.8 KiB (411.6 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000414_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/outputs/BIOMD0000000414_url.sedml/autogen_plot_for_task1.pdf\nCompleted 60.6 KiB/68.8 KiB (411.6 KiB/s) with 1 file(s) remaining\rCompleted 68.8 KiB/68.8 KiB (458.0 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000414-biopax2.owl  \n  inflating: contents/BIOMD0000000414-biopax3.owl  \n  inflating: contents/BIOMD0000000414-matlab.m  \n  inflating: contents/BIOMD0000000414-octave.m  \n  inflating: contents/BIOMD0000000414.m  \n  inflating: contents/BIOMD0000000414.ode  \n  inflating: contents/BIOMD0000000414.pdf  \n  inflating: contents/BIOMD0000000414.png  \n  inflating: contents/BIOMD0000000414.sci  \n  inflating: contents/BIOMD0000000414.svg  \n  inflating: contents/BIOMD0000000414.vcml  \n  inflating: contents/BIOMD0000000414_url.sedml  \n  inflating: contents/BIOMD0000000414_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 9.6 KiB/260.8 KiB (119.3 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000414-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/contents/BIOMD0000000414-biopax3.owl\nCompleted 9.6 KiB/260.8 KiB (119.3 KiB/s) with 16 file(s) remaining\rCompleted 10.4 KiB/260.8 KiB (79.9 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000414.sci to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/contents/BIOMD0000000414.sci\nCompleted 10.4 KiB/260.8 KiB (79.9 KiB/s) with 15 file(s) remaining\rCompleted 13.4 KiB/260.8 KiB (99.6 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000414-octave.m to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/contents/BIOMD0000000414-octave.m\nCompleted 13.4 KiB/260.8 KiB (99.6 KiB/s) with 14 file(s) remaining\rCompleted 19.2 KiB/260.8 KiB (141.6 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000414.svg to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/contents/BIOMD0000000414.svg\nCompleted 19.2 KiB/260.8 KiB (141.6 KiB/s) with 13 file(s) remaining\rCompleted 22.1 KiB/260.8 KiB (150.6 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000414-matlab.m to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/contents/BIOMD0000000414-matlab.m\nCompleted 22.1 KiB/260.8 KiB (150.6 KiB/s) with 12 file(s) remaining\rCompleted 22.6 KiB/260.8 KiB (150.4 KiB/s) with 12 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/contents/curation_notes.txt\nCompleted 22.6 KiB/260.8 KiB (150.4 KiB/s) with 11 file(s) remaining\rCompleted 30.2 KiB/260.8 KiB (193.7 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000414-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/contents/BIOMD0000000414-biopax2.owl\nCompleted 30.2 KiB/260.8 KiB (193.7 KiB/s) with 10 file(s) remaining\rCompleted 46.8 KiB/260.8 KiB (280.4 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000414.vcml to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/contents/BIOMD0000000414.vcml\nCompleted 46.8 KiB/260.8 KiB (280.4 KiB/s) with 9 file(s) remaining\rCompleted 53.4 KiB/260.8 KiB (283.6 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000414_url.sedml to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/contents/BIOMD0000000414_url.sedml\nCompleted 53.4 KiB/260.8 KiB (283.6 KiB/s) with 8 file(s) remaining\rCompleted 56.3 KiB/260.8 KiB (281.6 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000414.m to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/contents/BIOMD0000000414.m\nCompleted 56.3 KiB/260.8 KiB (281.6 KiB/s) with 7 file(s) remaining\rCompleted 95.0 KiB/260.8 KiB (469.5 KiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/contents/curation_image.png\nCompleted 95.0 KiB/260.8 KiB (469.5 KiB/s) with 6 file(s) remaining\rCompleted 99.9 KiB/260.8 KiB (484.6 KiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/contents/metadata.rdf\nCompleted 99.9 KiB/260.8 KiB (484.6 KiB/s) with 5 file(s) remaining\rCompleted 107.3 KiB/260.8 KiB (514.9 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000414.png to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/contents/BIOMD0000000414.png\nCompleted 107.3 KiB/260.8 KiB (514.9 KiB/s) with 4 file(s) remaining\rCompleted 109.3 KiB/260.8 KiB (509.0 KiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/contents/manifest.xml\nCompleted 109.3 KiB/260.8 KiB (509.0 KiB/s) with 3 file(s) remaining\rCompleted 119.3 KiB/260.8 KiB (545.2 KiB/s) with 3 file(s) remaining\rCompleted 259.6 KiB/260.8 KiB (1.2 MiB/s) with 3 file(s) remaining  \rupload: contents/BIOMD0000000414.pdf to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/contents/BIOMD0000000414.pdf\nCompleted 259.6 KiB/260.8 KiB (1.2 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000414_url.xml to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/contents/BIOMD0000000414_url.xml\nCompleted 259.6 KiB/260.8 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 260.8 KiB/260.8 KiB (1.0 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000414.ode to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/contents/BIOMD0000000414.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.2 KiB/9.2 KiB (149.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b2477b6669655060d01/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000414_url.sedml\ncreating dataset /BIOMD0000000414_url.sedml/autogen_plot_for_task1, shape: (2, 1001), type: float64\ndataset created, uuid: d-efa16165-cdaa4672-43c1-26029e-0583b0, chunk_size: (2, 1001)\ncreating dataset /BIOMD0000000414_url.sedml/autogen_report_for_task1, shape: (10, 1001), type: float64\ndataset created, uuid: d-efa16165-cdaa4672-4643-ad8871-a32caa, chunk_size: (10, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000414_url.sedml\ncreating attribute uri in /BIOMD0000000414_url.sedml\ncreating attribute _type in /BIOMD0000000414_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000414_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000414_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000414_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000414_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000414_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000414_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000414_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000414_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000414_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000414_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000414_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000414_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000414_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000414_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000414_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000414_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000414_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000414_url.sedml\ncreate_links: /BIOMD0000000414_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000414_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000414_url.sedml/autogen_plot_for_task1, shape: (2, 1001), type: float64\niterating over chunks for /BIOMD0000000414_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000414_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000414_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000414_url.sedml/autogen_report_for_task1, shape: (10, 1001), type: float64\niterating over chunks for /BIOMD0000000414_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 10, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000414_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b2477b6669655060d01\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... 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 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":16.625537,"sedDocuments":[{"location":"BIOMD0000000414_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  BIOMD0000000414_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 10 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000414_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":16.34772,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":15.915778,"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":0.130175,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_VENUS","status":"SUCCEEDED"},{"id":"autogen_task1_p1_star","status":"SUCCEEDED"},{"id":"autogen_task1_p2","status":"SUCCEEDED"},{"id":"autogen_task1_lambda_star","status":"SUCCEEDED"},{"id":"autogen_task1_qj_star","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_VENUSproduction","status":"SUCCEEDED"},{"id":"autogen_task1_VENUSdecayduetophotobleaching","status":"SUCCEEDED"},{"id":"autogen_task1_VENUSdecayduetoauxin","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.207919,"curves":[{"id":"autogen_curve_task1_VENUS","status":"SUCCEEDED"}]}]}]}