{"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    465      0 --:--:-- --:--:-- --:--:--   466\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100  213k  100  213k    0     0   513k      0 --:--:-- --:--:-- --:--:-- 3090k\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 (25.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/rawLog.txt\nCompleted 3.7 KiB/3.7 KiB (49.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/BIOMD0000000082_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000082_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/log.yml (deflated 78%)\n  adding: outputs/reports.h5 (deflated 10%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 208.9 KiB/208.9 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/outputs/reports.h5\nCompleted 199.3 KiB/223.2 KiB (2.0 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/output.zip\nCompleted 199.3 KiB/223.2 KiB (2.0 MiB/s) with 3 file(s) remaining\rCompleted 202.0 KiB/223.2 KiB (2.0 MiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/rawLog.txt\nCompleted 202.0 KiB/223.2 KiB (2.0 MiB/s) with 2 file(s) remaining\rCompleted 214.6 KiB/223.2 KiB (2.0 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000082_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/outputs/BIOMD0000000082_url.sedml/autogen_plot_for_task1.pdf\nCompleted 214.6 KiB/223.2 KiB (2.0 MiB/s) with 1 file(s) remaining\rCompleted 223.2 KiB/223.2 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000082-biopax2.owl  \n  inflating: contents/BIOMD0000000082-biopax3.owl  \n  inflating: contents/BIOMD0000000082-matlab.m  \n  inflating: contents/BIOMD0000000082-octave.m  \n  inflating: contents/BIOMD0000000082.m  \n  inflating: contents/BIOMD0000000082.ode  \n  inflating: contents/BIOMD0000000082.pdf  \n  inflating: contents/BIOMD0000000082.png  \n  inflating: contents/BIOMD0000000082.sci  \n  inflating: contents/BIOMD0000000082.svg  \n  inflating: contents/BIOMD0000000082.vcml  \n  inflating: contents/BIOMD0000000082_url.sedml  \n  inflating: contents/BIOMD0000000082_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 26.2 KiB/404.3 KiB (356.9 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000082-biopax3.owl to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/contents/BIOMD0000000082-biopax3.owl\nCompleted 26.2 KiB/404.3 KiB (356.9 KiB/s) with 16 file(s) remaining\rCompleted 31.6 KiB/404.3 KiB (321.7 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000082-matlab.m to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/contents/BIOMD0000000082-matlab.m\nCompleted 31.6 KiB/404.3 KiB (321.7 KiB/s) with 15 file(s) remaining\rCompleted 37.0 KiB/404.3 KiB (289.3 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000082-octave.m to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/contents/BIOMD0000000082-octave.m\nCompleted 37.0 KiB/404.3 KiB (289.3 KiB/s) with 14 file(s) remaining\rCompleted 40.5 KiB/404.3 KiB (308.8 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000082.sci to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/contents/BIOMD0000000082.sci\nCompleted 40.5 KiB/404.3 KiB (308.8 KiB/s) with 13 file(s) remaining\rCompleted 58.9 KiB/404.3 KiB (421.4 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000082-biopax2.owl to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/contents/BIOMD0000000082-biopax2.owl\nCompleted 58.9 KiB/404.3 KiB (421.4 KiB/s) with 12 file(s) remaining\rCompleted 224.7 KiB/404.3 KiB (1.5 MiB/s) with 12 file(s) remaining \rupload: contents/BIOMD0000000082.pdf to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/contents/BIOMD0000000082.pdf\nCompleted 224.7 KiB/404.3 KiB (1.5 MiB/s) with 11 file(s) remaining\rCompleted 226.7 KiB/404.3 KiB (1.5 MiB/s) with 11 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/contents/manifest.xml\nCompleted 226.7 KiB/404.3 KiB (1.5 MiB/s) with 10 file(s) remaining\rCompleted 263.0 KiB/404.3 KiB (1.5 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000082.vcml to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/contents/BIOMD0000000082.vcml\nCompleted 263.0 KiB/404.3 KiB (1.5 MiB/s) with 9 file(s) remaining\rCompleted 305.3 KiB/404.3 KiB (1.6 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000082.png to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/contents/BIOMD0000000082.png\nCompleted 305.3 KiB/404.3 KiB (1.6 MiB/s) with 8 file(s) remaining\rCompleted 308.4 KiB/404.3 KiB (1.6 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000082.ode to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/contents/BIOMD0000000082.ode\nCompleted 308.4 KiB/404.3 KiB (1.6 MiB/s) with 7 file(s) remaining\rCompleted 311.8 KiB/404.3 KiB (1.6 MiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/contents/metadata.rdf\nCompleted 311.8 KiB/404.3 KiB (1.6 MiB/s) with 6 file(s) remaining\rCompleted 317.2 KiB/404.3 KiB (1.6 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000082.m to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/contents/BIOMD0000000082.m\nCompleted 317.2 KiB/404.3 KiB (1.6 MiB/s) with 5 file(s) remaining\rCompleted 334.3 KiB/404.3 KiB (1.7 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000082.svg to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/contents/BIOMD0000000082.svg\nCompleted 334.3 KiB/404.3 KiB (1.7 MiB/s) with 4 file(s) remaining\rCompleted 359.7 KiB/404.3 KiB (1.7 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000082_url.xml to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/contents/BIOMD0000000082_url.xml\nCompleted 359.7 KiB/404.3 KiB (1.7 MiB/s) with 3 file(s) remaining\rCompleted 359.8 KiB/404.3 KiB (1.7 MiB/s) with 3 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/contents/curation_notes.txt\nCompleted 359.8 KiB/404.3 KiB (1.7 MiB/s) with 2 file(s) remaining\rCompleted 392.7 KiB/404.3 KiB (1.7 MiB/s) with 2 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/contents/curation_image.png\nCompleted 392.7 KiB/404.3 KiB (1.7 MiB/s) with 1 file(s) remaining\rCompleted 404.3 KiB/404.3 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000082_url.sedml to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/contents/BIOMD0000000082_url.sedml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.2 KiB/9.2 KiB (128.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108009a62a8be53f750be/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000082_url.sedml\ncreating dataset /BIOMD0000000082_url.sedml/autogen_plot_for_task1, shape: (11, 1001), type: float64\ndataset created, uuid: d-cd573b4b-7fa9ccff-a484-39dbb3-7b6f99, chunk_size: (11, 1001)\ncreating dataset /BIOMD0000000082_url.sedml/autogen_report_for_task1, shape: (18, 1001), type: float64\ndataset created, uuid: d-cd573b4b-7fa9ccff-aac9-5cc454-86238b, chunk_size: (18, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000082_url.sedml\ncreating attribute uri in /BIOMD0000000082_url.sedml\ncreating attribute _type in /BIOMD0000000082_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000082_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000082_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000082_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000082_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000082_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000082_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000082_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000082_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000082_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000082_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000082_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000082_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000082_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000082_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000082_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000082_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000082_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000082_url.sedml\ncreate_links: /BIOMD0000000082_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000082_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000082_url.sedml/autogen_plot_for_task1, shape: (11, 1001), type: float64\niterating over chunks for /BIOMD0000000082_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 11, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000082_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000082_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000082_url.sedml/autogen_report_for_task1, shape: (18, 1001), type: float64\niterating over chunks for /BIOMD0000000082_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 18, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000082_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647108009a62a8be53f750be\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.\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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.494617,"sedDocuments":[{"location":"BIOMD0000000082_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  BIOMD0000000082_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 18 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 10 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000082_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":1.031382,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.200767,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"simulate"},{"key":"solver","value":"cvode"},{"key":"relative_tolerance","value":0.000001},{"key":"absolute_tolerance","value":1e-12},{"key":"stiff","value":true},{"key":"maximum_bdf_order","value":5},{"key":"maximum_adams_order","value":12},{"key":"maximum_num_steps","value":20000},{"key":"maximum_time_step","value":0},{"key":"minimum_time_step","value":0},{"key":"initial_time_step","value":0},{"key":"multiple_steps","value":false},{"key":"variable_step_size","value":false},{"key":"max_output_rows","value":100000}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.164668,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_agonist","status":"SUCCEEDED"},{"id":"autogen_task1_DR","status":"SUCCEEDED"},{"id":"autogen_task1_DRG_GDP","status":"SUCCEEDED"},{"id":"autogen_task1_DRG","status":"SUCCEEDED"},{"id":"autogen_task1_GDP","status":"SUCCEEDED"},{"id":"autogen_task1_DRG_GTP","status":"SUCCEEDED"},{"id":"autogen_task1_GTP","status":"SUCCEEDED"},{"id":"autogen_task1_Recptor","status":"SUCCEEDED"},{"id":"autogen_task1_G_GDP","status":"SUCCEEDED"},{"id":"autogen_task1_G_GTP","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Forming","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_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.53851,"curves":[{"id":"autogen_curve_task1_agonist","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DR","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DRG_GDP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DRG","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GDP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DRG_GTP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GTP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Recptor","status":"SUCCEEDED"},{"id":"autogen_curve_task1_G_GDP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_G_GTP","status":"SUCCEEDED"}]}]}]}