{"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    447      0 --:--:-- --:--:-- --:--:--   448\n\r100  161k  100  161k    0     0   263k      0 --:--:-- --:--:-- --:--:--  263k\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 (23.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/rawLog.txt\nCompleted 2.7 KiB/2.7 KiB (37.8 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 75%)\n  adding: outputs/BIOMD0000000156_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000156_url.sedml/autogen_plot_for_task1.pdf (deflated 23%)\n  adding: outputs/reports.h5 (deflated 20%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 110.1 KiB/110.1 KiB (962.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/outputs/reports.h5\nCompleted 99.5 KiB/122.1 KiB (1.1 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/output.zip\nCompleted 99.5 KiB/122.1 KiB (1.1 MiB/s) with 3 file(s) remaining\rCompleted 108.1 KiB/122.1 KiB (1.1 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/outputs/plots.zip\nCompleted 108.1 KiB/122.1 KiB (1.1 MiB/s) with 2 file(s) remaining\rCompleted 119.5 KiB/122.1 KiB (1.1 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000156_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/outputs/BIOMD0000000156_url.sedml/autogen_plot_for_task1.pdf\nCompleted 119.5 KiB/122.1 KiB (1.1 MiB/s) with 1 file(s) remaining\rCompleted 122.1 KiB/122.1 KiB (929.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000156-biopax2.owl  \n  inflating: contents/BIOMD0000000156-biopax3.owl  \n  inflating: contents/BIOMD0000000156-matlab.m  \n  inflating: contents/BIOMD0000000156-octave.m  \n  inflating: contents/BIOMD0000000156.m  \n  inflating: contents/BIOMD0000000156.ode  \n  inflating: contents/BIOMD0000000156.pdf  \n  inflating: contents/BIOMD0000000156.png  \n  inflating: contents/BIOMD0000000156.sci  \n  inflating: contents/BIOMD0000000156.svg  \n  inflating: contents/BIOMD0000000156_url.sedml  \n  inflating: contents/BIOMD0000000156_url.xml  \n  inflating: contents/curation_image.jpeg  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 12.5 KiB/259.8 KiB (173.0 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000156-biopax3.owl to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/contents/BIOMD0000000156-biopax3.owl\nCompleted 12.5 KiB/259.8 KiB (173.0 KiB/s) with 15 file(s) remaining\rCompleted 16.2 KiB/259.8 KiB (138.1 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000156-matlab.m to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/contents/BIOMD0000000156-matlab.m\nCompleted 16.2 KiB/259.8 KiB (138.1 KiB/s) with 14 file(s) remaining\rCompleted 26.0 KiB/259.8 KiB (219.1 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000156-biopax2.owl to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/contents/BIOMD0000000156-biopax2.owl\nCompleted 26.0 KiB/259.8 KiB (219.1 KiB/s) with 13 file(s) remaining\rCompleted 29.7 KiB/259.8 KiB (247.2 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000156-octave.m to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/contents/BIOMD0000000156-octave.m\nCompleted 29.7 KiB/259.8 KiB (247.2 KiB/s) with 12 file(s) remaining\rCompleted 29.7 KiB/259.8 KiB (224.2 KiB/s) with 12 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/contents/curation_notes.txt\nCompleted 29.7 KiB/259.8 KiB (224.2 KiB/s) with 11 file(s) remaining\rCompleted 31.2 KiB/259.8 KiB (204.4 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000156.sci to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/contents/BIOMD0000000156.sci\nCompleted 31.2 KiB/259.8 KiB (204.4 KiB/s) with 10 file(s) remaining\rCompleted 43.3 KiB/259.8 KiB (263.3 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000156_url.xml to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/contents/BIOMD0000000156_url.xml\nCompleted 43.3 KiB/259.8 KiB (263.3 KiB/s) with 9 file(s) remaining\rCompleted 53.1 KiB/259.8 KiB (314.5 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000156_url.sedml to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/contents/BIOMD0000000156_url.sedml\nCompleted 53.1 KiB/259.8 KiB (314.5 KiB/s) with 8 file(s) remaining\rCompleted 56.2 KiB/259.8 KiB (311.8 KiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/contents/metadata.rdf\nCompleted 56.2 KiB/259.8 KiB (311.8 KiB/s) with 7 file(s) remaining\rCompleted 77.5 KiB/259.8 KiB (427.3 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000156.png to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/contents/BIOMD0000000156.png\nCompleted 77.5 KiB/259.8 KiB (427.3 KiB/s) with 6 file(s) remaining\rCompleted 96.3 KiB/259.8 KiB (517.7 KiB/s) with 6 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/contents/curation_image.jpeg\nCompleted 96.3 KiB/259.8 KiB (517.7 KiB/s) with 5 file(s) remaining\rCompleted 100.0 KiB/259.8 KiB (525.3 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000156.m to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/contents/BIOMD0000000156.m\nCompleted 100.0 KiB/259.8 KiB (525.3 KiB/s) with 4 file(s) remaining\rCompleted 101.9 KiB/259.8 KiB (529.0 KiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/contents/manifest.xml\nCompleted 101.9 KiB/259.8 KiB (529.0 KiB/s) with 3 file(s) remaining\rCompleted 247.7 KiB/259.8 KiB (1.2 MiB/s) with 3 file(s) remaining  \rupload: contents/BIOMD0000000156.pdf to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/contents/BIOMD0000000156.pdf\nCompleted 247.7 KiB/259.8 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 249.6 KiB/259.8 KiB (1.0 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000156.ode to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/contents/BIOMD0000000156.ode\nCompleted 249.6 KiB/259.8 KiB (1.0 MiB/s) with 1 file(s) remaining\rCompleted 259.8 KiB/259.8 KiB (1.0 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000156.svg to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/contents/BIOMD0000000156.svg\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.8 KiB/8.8 KiB (138.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108f549c0d898ffddc8b7/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000156_url.sedml\ncreating dataset /BIOMD0000000156_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-34c4f97d-f797c5e9-c71c-13e8dc-89bf91, chunk_size: (4, 1001)\ncreating dataset /BIOMD0000000156_url.sedml/autogen_report_for_task1, shape: (17, 1001), type: float64\ndataset created, uuid: d-34c4f97d-f797c5e9-1f38-7af918-85a7de, chunk_size: (17, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000156_url.sedml\ncreating attribute uri in /BIOMD0000000156_url.sedml\ncreating attribute _type in /BIOMD0000000156_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000156_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000156_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000156_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000156_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000156_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000156_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000156_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000156_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000156_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000156_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000156_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000156_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000156_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000156_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000156_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000156_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000156_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000156_url.sedml\ncreate_links: /BIOMD0000000156_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000156_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000156_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\niterating over chunks for /BIOMD0000000156_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000156_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000156_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000156_url.sedml/autogen_report_for_task1, shape: (17, 1001), type: float64\niterating over chunks for /BIOMD0000000156_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 17, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000156_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647108f549c0d898ffddc8b7\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 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 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 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":1.273472,"sedDocuments":[{"location":"BIOMD0000000156_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  BIOMD0000000156_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 17 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000156_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":0.873169,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.120333,"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":0.203544,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_x","status":"SUCCEEDED"},{"id":"autogen_task1_y","status":"SUCCEEDED"},{"id":"autogen_task1_y0","status":"SUCCEEDED"},{"id":"autogen_task1_psi","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_x","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_xy","status":"SUCCEEDED"},{"id":"autogen_task1_beta_y","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_y","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_0","status":"SUCCEEDED"},{"id":"autogen_task1_Theta","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_R1","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_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.438994,"curves":[{"id":"autogen_curve_task1_x","status":"SUCCEEDED"},{"id":"autogen_curve_task1_y","status":"SUCCEEDED"},{"id":"autogen_curve_task1_y0","status":"SUCCEEDED"}]}]}]}