{"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    454      0 --:--:-- --:--:-- --:--:--   454\n\r100  160k  100  160k    0     0   368k      0 --:--:-- --:--:-- --:--:--  368k\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 (23.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/rawLog.txt\nCompleted 2.9 KiB/2.9 KiB (48.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 74%)\n  adding: outputs/BIOMD0000000549_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000549_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 37%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 67.5 KiB/67.5 KiB (782.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/outputs/reports.h5\nCompleted 51.5 KiB/70.5 KiB (648.6 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/output.zip\nCompleted 51.5 KiB/70.5 KiB (648.6 KiB/s) with 3 file(s) remaining\rCompleted 58.1 KiB/70.5 KiB (597.1 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/outputs/plots.zip\nCompleted 58.1 KiB/70.5 KiB (597.1 KiB/s) with 2 file(s) remaining\rCompleted 67.8 KiB/70.5 KiB (577.8 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000549_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/outputs/BIOMD0000000549_url.sedml/autogen_plot_for_task1.pdf\nCompleted 67.8 KiB/70.5 KiB (577.8 KiB/s) with 1 file(s) remaining\rCompleted 70.5 KiB/70.5 KiB (516.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000549-biopax2.owl  \n  inflating: contents/BIOMD0000000549-biopax3.owl  \n  inflating: contents/BIOMD0000000549-matlab.m  \n  inflating: contents/BIOMD0000000549-octave.m  \n  inflating: contents/BIOMD0000000549.m  \n  inflating: contents/BIOMD0000000549.ode  \n  inflating: contents/BIOMD0000000549.pdf  \n  inflating: contents/BIOMD0000000549.png  \n  inflating: contents/BIOMD0000000549.svg  \n  inflating: contents/BIOMD0000000549_url.sedml  \n  inflating: contents/BIOMD0000000549_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 5.8 KiB/240.5 KiB (56.9 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000549-biopax3.owl to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/contents/BIOMD0000000549-biopax3.owl\nCompleted 5.8 KiB/240.5 KiB (56.9 KiB/s) with 14 file(s) remaining\rCompleted 9.3 KiB/240.5 KiB (80.6 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000549-matlab.m to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/contents/BIOMD0000000549-matlab.m\nCompleted 9.3 KiB/240.5 KiB (80.6 KiB/s) with 13 file(s) remaining\rCompleted 14.8 KiB/240.5 KiB (120.9 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000549-biopax2.owl to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/contents/BIOMD0000000549-biopax2.owl\nCompleted 14.8 KiB/240.5 KiB (120.9 KiB/s) with 12 file(s) remaining\rCompleted 15.6 KiB/240.5 KiB (107.4 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000549.svg to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/contents/BIOMD0000000549.svg\nCompleted 15.6 KiB/240.5 KiB (107.4 KiB/s) with 11 file(s) remaining\rCompleted 23.4 KiB/240.5 KiB (158.5 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000549_url.sedml to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/contents/BIOMD0000000549_url.sedml\nCompleted 23.4 KiB/240.5 KiB (158.5 KiB/s) with 10 file(s) remaining\rCompleted 26.9 KiB/240.5 KiB (179.9 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000549-octave.m to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/contents/BIOMD0000000549-octave.m\nCompleted 26.9 KiB/240.5 KiB (179.9 KiB/s) with 9 file(s) remaining\rCompleted 49.0 KiB/240.5 KiB (306.7 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000549_url.xml to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/contents/BIOMD0000000549_url.xml\nCompleted 49.0 KiB/240.5 KiB (306.7 KiB/s) with 8 file(s) remaining\rCompleted 54.2 KiB/240.5 KiB (324.2 KiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/contents/metadata.rdf\nCompleted 54.2 KiB/240.5 KiB (324.2 KiB/s) with 7 file(s) remaining\rCompleted 54.6 KiB/240.5 KiB (313.5 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/contents/curation_notes.txt\nCompleted 54.6 KiB/240.5 KiB (313.5 KiB/s) with 6 file(s) remaining\rCompleted 94.8 KiB/240.5 KiB (535.7 KiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/contents/curation_image.png\nCompleted 94.8 KiB/240.5 KiB (535.7 KiB/s) with 5 file(s) remaining\rCompleted 96.6 KiB/240.5 KiB (535.2 KiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/contents/manifest.xml\nCompleted 96.6 KiB/240.5 KiB (535.2 KiB/s) with 4 file(s) remaining\rCompleted 230.9 KiB/240.5 KiB (1.1 MiB/s) with 4 file(s) remaining \rupload: contents/BIOMD0000000549.pdf to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/contents/BIOMD0000000549.pdf\nCompleted 230.9 KiB/240.5 KiB (1.1 MiB/s) with 3 file(s) remaining\rCompleted 235.2 KiB/240.5 KiB (1.1 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000549.png to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/contents/BIOMD0000000549.png\nCompleted 235.2 KiB/240.5 KiB (1.1 MiB/s) with 2 file(s) remaining\rCompleted 237.0 KiB/240.5 KiB (1.1 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000549.ode to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/contents/BIOMD0000000549.ode\nCompleted 237.0 KiB/240.5 KiB (1.1 MiB/s) with 1 file(s) remaining\rCompleted 240.5 KiB/240.5 KiB (995.0 KiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000549.m to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/contents/BIOMD0000000549.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (119.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647111740dcacb55678c8d8d/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000549_url.sedml\ncreating dataset /BIOMD0000000549_url.sedml/autogen_plot_for_task1, shape: (3, 1001), type: float64\ndataset created, uuid: d-39834e5a-49cba153-678a-434274-4c586d, chunk_size: (3, 1001)\ncreating dataset /BIOMD0000000549_url.sedml/autogen_report_for_task1, shape: (12, 1001), type: float64\ndataset created, uuid: d-39834e5a-49cba153-6025-4a3f8f-7cbbe4, chunk_size: (12, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000549_url.sedml\ncreating attribute uri in /BIOMD0000000549_url.sedml\ncreating attribute _type in /BIOMD0000000549_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000549_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000549_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000549_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000549_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000549_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000549_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000549_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000549_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000549_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000549_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000549_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000549_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000549_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000549_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000549_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000549_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000549_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000549_url.sedml\ncreate_links: /BIOMD0000000549_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000549_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000549_url.sedml/autogen_plot_for_task1, shape: (3, 1001), type: float64\niterating over chunks for /BIOMD0000000549_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000549_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000549_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000549_url.sedml/autogen_report_for_task1, shape: (12, 1001), type: float64\niterating over chunks for /BIOMD0000000549_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 12, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000549_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647111740dcacb55678c8d8d\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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.292647,"sedDocuments":[{"location":"BIOMD0000000549_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  BIOMD0000000549_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 12 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 2 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000549_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":0.845578,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.20074,"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":0.147863,"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_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_compartment_1","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.403386,"curves":[{"id":"autogen_curve_task1_species_1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_2","status":"SUCCEEDED"}]}]}]}