{"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    452      0 --:--:-- --:--:-- --:--:--   452\n\r100  269k  100  269k    0     0   625k      0 --:--:-- --:--:-- --:--:--  625k\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 (25.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/rawLog.txt\nCompleted 4.2 KiB/4.2 KiB (61.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 80%)\n  adding: outputs/BIOMD0000000415_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000415_url.sedml/autogen_plot_for_task1.pdf (deflated 28%)\n  adding: outputs/reports.h5 (deflated 10%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 214.0 KiB/214.0 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/outputs/reports.h5\nCompleted 8.1 KiB/225.6 KiB (64.2 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/outputs/plots.zip\nCompleted 8.1 KiB/225.6 KiB (64.2 KiB/s) with 3 file(s) remaining\rCompleted 19.6 KiB/225.6 KiB (151.0 KiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000415_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/outputs/BIOMD0000000415_url.sedml/autogen_plot_for_task1.pdf\nCompleted 19.6 KiB/225.6 KiB (151.0 KiB/s) with 2 file(s) remaining\rCompleted 22.2 KiB/225.6 KiB (154.5 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/rawLog.txt\nCompleted 22.2 KiB/225.6 KiB (154.5 KiB/s) with 1 file(s) remaining\rCompleted 225.6 KiB/225.6 KiB (1.5 MiB/s) with 1 file(s) remaining \rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/output.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000415-biopax2.owl  \n  inflating: contents/BIOMD0000000415-biopax3.owl  \n  inflating: contents/BIOMD0000000415-matlab.m  \n  inflating: contents/BIOMD0000000415-octave.m  \n  inflating: contents/BIOMD0000000415.m  \n  inflating: contents/BIOMD0000000415.ode  \n  inflating: contents/BIOMD0000000415.pdf  \n  inflating: contents/BIOMD0000000415.png  \n  inflating: contents/BIOMD0000000415.svg  \n  inflating: contents/BIOMD0000000415_url.sedml  \n  inflating: contents/BIOMD0000000415_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 32.0 KiB/445.8 KiB (333.3 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000415-biopax3.owl to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/contents/BIOMD0000000415-biopax3.owl\nCompleted 32.0 KiB/445.8 KiB (333.3 KiB/s) with 14 file(s) remaining\rCompleted 38.0 KiB/445.8 KiB (352.2 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000415-matlab.m to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/contents/BIOMD0000000415-matlab.m\nCompleted 38.0 KiB/445.8 KiB (352.2 KiB/s) with 13 file(s) remaining\rCompleted 44.0 KiB/445.8 KiB (350.8 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000415-octave.m to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/contents/BIOMD0000000415-octave.m\nCompleted 44.0 KiB/445.8 KiB (350.8 KiB/s) with 12 file(s) remaining\rCompleted 63.3 KiB/445.8 KiB (498.5 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000415-biopax2.owl to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/contents/BIOMD0000000415-biopax2.owl\nCompleted 63.3 KiB/445.8 KiB (498.5 KiB/s) with 11 file(s) remaining\rCompleted 83.0 KiB/445.8 KiB (585.0 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000415.svg to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/contents/BIOMD0000000415.svg\nCompleted 83.0 KiB/445.8 KiB (585.0 KiB/s) with 10 file(s) remaining\rCompleted 86.5 KiB/445.8 KiB (583.6 KiB/s) with 10 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/contents/metadata.rdf\nCompleted 86.5 KiB/445.8 KiB (583.6 KiB/s) with 9 file(s) remaining\rCompleted 109.3 KiB/445.8 KiB (678.2 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000415_url.xml to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/contents/BIOMD0000000415_url.xml\nCompleted 109.3 KiB/445.8 KiB (678.2 KiB/s) with 8 file(s) remaining\rCompleted 125.7 KiB/445.8 KiB (772.8 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000415_url.sedml to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/contents/BIOMD0000000415_url.sedml\nCompleted 125.7 KiB/445.8 KiB (772.8 KiB/s) with 7 file(s) remaining\rCompleted 183.8 KiB/445.8 KiB (1.0 MiB/s) with 7 file(s) remaining  \rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/contents/curation_image.png\nCompleted 183.8 KiB/445.8 KiB (1.0 MiB/s) with 6 file(s) remaining\rCompleted 358.9 KiB/445.8 KiB (1.9 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000415.pdf to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/contents/BIOMD0000000415.pdf\nCompleted 358.9 KiB/445.8 KiB (1.9 MiB/s) with 5 file(s) remaining\rCompleted 364.9 KiB/445.8 KiB (1.9 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000415.m to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/contents/BIOMD0000000415.m\nCompleted 364.9 KiB/445.8 KiB (1.9 MiB/s) with 4 file(s) remaining\rCompleted 365.5 KiB/445.8 KiB (1.9 MiB/s) with 4 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/contents/curation_notes.txt\nCompleted 365.5 KiB/445.8 KiB (1.9 MiB/s) with 3 file(s) remaining\rCompleted 367.2 KiB/445.8 KiB (1.8 MiB/s) with 3 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/contents/manifest.xml\nCompleted 367.2 KiB/445.8 KiB (1.8 MiB/s) with 2 file(s) remaining\rCompleted 441.7 KiB/445.8 KiB (2.1 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000415.png to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/contents/BIOMD0000000415.png\nCompleted 441.7 KiB/445.8 KiB (2.1 MiB/s) with 1 file(s) remaining\rCompleted 445.8 KiB/445.8 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000415.ode to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/contents/BIOMD0000000415.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (121.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710c5c0dcacb55678bd3e0/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000415_url.sedml\ncreating dataset /BIOMD0000000415_url.sedml/autogen_plot_for_task1, shape: (11, 1001), type: float64\ndataset created, uuid: d-78254689-6d19bb17-f661-7e5421-cb3d3f, chunk_size: (11, 1001)\ncreating dataset /BIOMD0000000415_url.sedml/autogen_report_for_task1, shape: (26, 1001), type: float64\ndataset created, uuid: d-78254689-6d19bb17-ebf8-f1e57f-403a4f, chunk_size: (26, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000415_url.sedml\ncreating attribute uri in /BIOMD0000000415_url.sedml\ncreating attribute _type in /BIOMD0000000415_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000415_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000415_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000415_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000415_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000415_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000415_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000415_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000415_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000415_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000415_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000415_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000415_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000415_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000415_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000415_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000415_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000415_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000415_url.sedml\ncreate_links: /BIOMD0000000415_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000415_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000415_url.sedml/autogen_plot_for_task1, shape: (11, 1001), type: float64\niterating over chunks for /BIOMD0000000415_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 11, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000415_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000415_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000415_url.sedml/autogen_report_for_task1, shape: (26, 1001), type: float64\niterating over chunks for /BIOMD0000000415_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 26, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000415_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710c5c0dcacb55678bd3e0\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 metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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":1.615998,"sedDocuments":[{"location":"BIOMD0000000415_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  BIOMD0000000415_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 26 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 10 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000415_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":1.146684,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.227364,"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":0.221237,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_species_1","status":"SUCCEEDED"},{"id":"autogen_task1_species_7","status":"SUCCEEDED"},{"id":"autogen_task1_species_8","status":"SUCCEEDED"},{"id":"autogen_task1_species_9","status":"SUCCEEDED"},{"id":"autogen_task1_species_10","status":"SUCCEEDED"},{"id":"autogen_task1_species_11","status":"SUCCEEDED"},{"id":"autogen_task1_species_12","status":"SUCCEEDED"},{"id":"autogen_task1_species_13","status":"SUCCEEDED"},{"id":"autogen_task1_species_14","status":"SUCCEEDED"},{"id":"autogen_task1_species_15","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_1","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_2","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_3","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_4","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_5","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_6","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_7","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_8","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_9","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_1","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":0.563619,"curves":[{"id":"autogen_curve_task1_species_1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_7","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_8","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_9","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_10","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_11","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_12","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_13","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_14","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_15","status":"SUCCEEDED"}]}]}]}