{"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    444      0 --:--:-- --:--:-- --:--:--   445\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100  207k  100  207k    0     0   466k      0 --:--:-- --:--:-- --:--:-- 2504k\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 (26.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710c9649c0d898ffde3d58/rawLog.txt\nCompleted 5.0 KiB/5.0 KiB (69.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710c9649c0d898ffde3d58/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 82%)\n  adding: outputs/BIOMD0000000432_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000432_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 13%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 223.6 KiB/223.6 KiB (2.3 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710c9649c0d898ffde3d58/outputs/reports.h5\nCompleted 204.1 KiB/224.3 KiB (2.1 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710c9649c0d898ffde3d58/output.zip\nCompleted 204.1 KiB/224.3 KiB (2.1 MiB/s) with 3 file(s) remaining\rCompleted 214.5 KiB/224.3 KiB (1.9 MiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000432_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710c9649c0d898ffde3d58/outputs/BIOMD0000000432_url.sedml/autogen_plot_for_task1.pdf\nCompleted 214.5 KiB/224.3 KiB (1.9 MiB/s) with 2 file(s) remaining\rCompleted 221.6 KiB/224.3 KiB (1.8 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710c9649c0d898ffde3d58/outputs/plots.zip\nCompleted 221.6 KiB/224.3 KiB (1.8 MiB/s) with 1 file(s) remaining\rCompleted 224.3 KiB/224.3 KiB (1.7 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710c9649c0d898ffde3d58/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000432-biopax2.owl  \n  inflating: contents/BIOMD0000000432-biopax3.owl  \n  inflating: contents/BIOMD0000000432-matlab.m  \n  inflating: contents/BIOMD0000000432.m  \n  inflating: contents/BIOMD0000000432.pdf  \n  inflating: contents/BIOMD0000000432.svg  \n  inflating: contents/BIOMD0000000432_url.sedml  \n  inflating: contents/BIOMD0000000432_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 25.9 KiB/518.5 KiB (229.1 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000432-biopax2.owl to s3://files.biosimulations.org/simulations/64710c9649c0d898ffde3d58/contents/BIOMD0000000432-biopax2.owl\nCompleted 25.9 KiB/518.5 KiB (229.1 KiB/s) with 11 file(s) remaining\rCompleted 48.8 KiB/518.5 KiB (395.9 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000432_url.sedml to s3://files.biosimulations.org/simulations/64710c9649c0d898ffde3d58/contents/BIOMD0000000432_url.sedml\nCompleted 48.8 KiB/518.5 KiB (395.9 KiB/s) with 10 file(s) remaining\rCompleted 57.8 KiB/518.5 KiB (410.6 KiB/s) with 10 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710c9649c0d898ffde3d58/contents/curation_image.png\nCompleted 57.8 KiB/518.5 KiB (410.6 KiB/s) with 9 file(s) remaining\rCompleted 302.8 KiB/518.5 KiB (2.1 MiB/s) with 9 file(s) remaining \rupload: contents/BIOMD0000000432.pdf to s3://files.biosimulations.org/simulations/64710c9649c0d898ffde3d58/contents/BIOMD0000000432.pdf\nCompleted 302.8 KiB/518.5 KiB (2.1 MiB/s) with 8 file(s) remaining\rCompleted 303.1 KiB/518.5 KiB (2.0 MiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710c9649c0d898ffde3d58/contents/curation_notes.txt\nCompleted 303.1 KiB/518.5 KiB (2.0 MiB/s) with 7 file(s) remaining\rCompleted 304.5 KiB/518.5 KiB (2.0 MiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710c9649c0d898ffde3d58/contents/manifest.xml\nCompleted 304.5 KiB/518.5 KiB (2.0 MiB/s) with 6 file(s) remaining\rCompleted 314.7 KiB/518.5 KiB (2.0 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000432-matlab.m to s3://files.biosimulations.org/simulations/64710c9649c0d898ffde3d58/contents/BIOMD0000000432-matlab.m\nCompleted 314.7 KiB/518.5 KiB (2.0 MiB/s) with 5 file(s) remaining\rCompleted 324.2 KiB/518.5 KiB (1.9 MiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710c9649c0d898ffde3d58/contents/metadata.rdf\nCompleted 324.2 KiB/518.5 KiB (1.9 MiB/s) with 4 file(s) remaining\rCompleted 359.2 KiB/518.5 KiB (2.0 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000432-biopax3.owl to s3://files.biosimulations.org/simulations/64710c9649c0d898ffde3d58/contents/BIOMD0000000432-biopax3.owl\nCompleted 359.2 KiB/518.5 KiB (2.0 MiB/s) with 3 file(s) remaining\rCompleted 369.4 KiB/518.5 KiB (1.9 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000432.m to s3://files.biosimulations.org/simulations/64710c9649c0d898ffde3d58/contents/BIOMD0000000432.m\nCompleted 369.4 KiB/518.5 KiB (1.9 MiB/s) with 2 file(s) remaining\rCompleted 432.8 KiB/518.5 KiB (2.2 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000432.svg to s3://files.biosimulations.org/simulations/64710c9649c0d898ffde3d58/contents/BIOMD0000000432.svg\nCompleted 432.8 KiB/518.5 KiB (2.2 MiB/s) with 1 file(s) remaining\rCompleted 518.5 KiB/518.5 KiB (2.5 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000432_url.xml to s3://files.biosimulations.org/simulations/64710c9649c0d898ffde3d58/contents/BIOMD0000000432_url.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.6 KiB/7.6 KiB (111.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710c9649c0d898ffde3d58/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000432_url.sedml\ncreating dataset /BIOMD0000000432_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\ndataset created, uuid: d-58e1716f-6b5cf26c-dbcc-a8aafc-1f6958, chunk_size: (12, 1001)\ncreating dataset /BIOMD0000000432_url.sedml/autogen_report_for_task1, shape: (38, 1001), type: float64\ndataset created, uuid: d-58e1716f-6b5cf26c-3924-1ae61c-0e73d5, chunk_size: (38, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000432_url.sedml\ncreating attribute uri in /BIOMD0000000432_url.sedml\ncreating attribute _type in /BIOMD0000000432_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000432_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000432_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000432_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000432_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000432_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000432_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000432_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000432_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000432_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000432_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000432_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000432_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000432_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000432_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000432_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000432_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000432_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000432_url.sedml\ncreate_links: /BIOMD0000000432_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000432_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000432_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\niterating over chunks for /BIOMD0000000432_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 12, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000432_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000432_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000432_url.sedml/autogen_report_for_task1, shape: (38, 1001), type: float64\niterating over chunks for /BIOMD0000000432_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 38, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000432_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710c9649c0d898ffde3d58\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 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.517027,"sedDocuments":[{"location":"BIOMD0000000432_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  BIOMD0000000432_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 38 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 11 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000432_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":1.102306,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.225695,"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":0.252562,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_species_1","status":"SUCCEEDED"},{"id":"autogen_task1_species_2","status":"SUCCEEDED"},{"id":"autogen_task1_species_3","status":"SUCCEEDED"},{"id":"autogen_task1_species_4","status":"SUCCEEDED"},{"id":"autogen_task1_species_5","status":"SUCCEEDED"},{"id":"autogen_task1_species_6","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_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_parameter_10","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_11","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_12","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_13","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_14","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_1","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_2","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_task1_reaction_6","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_7","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_8","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_9","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_10","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.474365,"curves":[{"id":"autogen_curve_task1_species_1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_4","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_5","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_6","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"}]}]}]}