{"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    439      0 --:--:-- --:--:-- --:--:--   441\n\r100  274k  100  274k    0     0   632k      0 --:--:-- --:--:-- --:--:--  632k\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 (20.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/rawLog.txt\nCompleted 4.8 KiB/4.8 KiB (70.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/BIOMD0000000099_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000099_url.sedml/autogen_plot_for_task1.pdf (deflated 18%)\n  adding: outputs/log.yml (deflated 81%)\n  adding: outputs/reports.h5 (deflated 12%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 235.7 KiB/235.7 KiB (2.4 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/outputs/reports.h5\nCompleted 224.1 KiB/255.7 KiB (2.4 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/output.zip\nCompleted 224.1 KiB/255.7 KiB (2.4 MiB/s) with 3 file(s) remaining\rCompleted 226.7 KiB/255.7 KiB (2.1 MiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/rawLog.txt\nCompleted 226.7 KiB/255.7 KiB (2.1 MiB/s) with 2 file(s) remaining\rCompleted 242.8 KiB/255.7 KiB (1.9 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000099_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/outputs/BIOMD0000000099_url.sedml/autogen_plot_for_task1.pdf\nCompleted 242.8 KiB/255.7 KiB (1.9 MiB/s) with 1 file(s) remaining\rCompleted 255.7 KiB/255.7 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000099-biopax2.owl  \n  inflating: contents/BIOMD0000000099-biopax3.owl  \n  inflating: contents/BIOMD0000000099-matlab.m  \n  inflating: contents/BIOMD0000000099-octave.m  \n  inflating: contents/BIOMD0000000099.m  \n  inflating: contents/BIOMD0000000099.ode  \n  inflating: contents/BIOMD0000000099.pdf  \n  inflating: contents/BIOMD0000000099.png  \n  inflating: contents/BIOMD0000000099.sci  \n  inflating: contents/BIOMD0000000099.svg  \n  inflating: contents/BIOMD0000000099.vcml  \n  inflating: contents/BIOMD0000000099_url.sedml  \n  inflating: contents/BIOMD0000000099_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 28.1 KiB/510.3 KiB (331.1 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000099-biopax3.owl to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/contents/BIOMD0000000099-biopax3.owl\nCompleted 28.1 KiB/510.3 KiB (331.1 KiB/s) with 16 file(s) remaining\rCompleted 34.3 KiB/510.3 KiB (323.2 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000099-matlab.m to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/contents/BIOMD0000000099-matlab.m\nCompleted 34.3 KiB/510.3 KiB (323.2 KiB/s) with 15 file(s) remaining\rCompleted 55.4 KiB/510.3 KiB (434.8 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000099-biopax2.owl to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/contents/BIOMD0000000099-biopax2.owl\nCompleted 55.4 KiB/510.3 KiB (434.8 KiB/s) with 14 file(s) remaining\rCompleted 61.5 KiB/510.3 KiB (457.0 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000099-octave.m to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/contents/BIOMD0000000099-octave.m\nCompleted 61.5 KiB/510.3 KiB (457.0 KiB/s) with 13 file(s) remaining\rCompleted 64.6 KiB/510.3 KiB (475.2 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000099.sci to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/contents/BIOMD0000000099.sci\nCompleted 64.6 KiB/510.3 KiB (475.2 KiB/s) with 12 file(s) remaining\rCompleted 91.0 KiB/510.3 KiB (632.8 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000099_url.xml to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/contents/BIOMD0000000099_url.xml\nCompleted 91.0 KiB/510.3 KiB (632.8 KiB/s) with 11 file(s) remaining\rCompleted 92.9 KiB/510.3 KiB (570.4 KiB/s) with 11 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/contents/manifest.xml\nCompleted 92.9 KiB/510.3 KiB (570.4 KiB/s) with 10 file(s) remaining\rCompleted 125.8 KiB/510.3 KiB (749.5 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000099.svg to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/contents/BIOMD0000000099.svg\nCompleted 125.8 KiB/510.3 KiB (749.5 KiB/s) with 9 file(s) remaining\rCompleted 164.0 KiB/510.3 KiB (939.4 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000099.vcml to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/contents/BIOMD0000000099.vcml\nCompleted 164.0 KiB/510.3 KiB (939.4 KiB/s) with 8 file(s) remaining\rCompleted 186.3 KiB/510.3 KiB (1.0 MiB/s) with 8 file(s) remaining  \rupload: contents/BIOMD0000000099_url.sedml to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/contents/BIOMD0000000099_url.sedml\nCompleted 186.3 KiB/510.3 KiB (1.0 MiB/s) with 7 file(s) remaining\rCompleted 233.5 KiB/510.3 KiB (1.2 MiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/contents/curation_image.png\nCompleted 233.5 KiB/510.3 KiB (1.2 MiB/s) with 6 file(s) remaining\rCompleted 236.3 KiB/510.3 KiB (1.2 MiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/contents/metadata.rdf\nCompleted 236.3 KiB/510.3 KiB (1.2 MiB/s) with 5 file(s) remaining\rCompleted 236.3 KiB/510.3 KiB (1.2 MiB/s) with 5 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/contents/curation_notes.txt\nCompleted 236.3 KiB/510.3 KiB (1.2 MiB/s) with 4 file(s) remaining\rCompleted 242.4 KiB/510.3 KiB (1.2 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000099.m to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/contents/BIOMD0000000099.m\nCompleted 242.4 KiB/510.3 KiB (1.2 MiB/s) with 3 file(s) remaining\rCompleted 421.6 KiB/510.3 KiB (1.9 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000099.pdf to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/contents/BIOMD0000000099.pdf\nCompleted 421.6 KiB/510.3 KiB (1.9 MiB/s) with 2 file(s) remaining\rCompleted 425.5 KiB/510.3 KiB (1.9 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000099.ode to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/contents/BIOMD0000000099.ode\nCompleted 425.5 KiB/510.3 KiB (1.9 MiB/s) with 1 file(s) remaining\rCompleted 510.3 KiB/510.3 KiB (2.3 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000099.png to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/contents/BIOMD0000000099.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.1 KiB/9.1 KiB (144.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471083e0dcacb55678b5884/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000099_url.sedml\ncreating dataset /BIOMD0000000099_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\ndataset created, uuid: d-f8369350-ee29bdd8-acf2-fb187a-4c4bb4, chunk_size: (8, 1001)\ncreating dataset /BIOMD0000000099_url.sedml/autogen_report_for_task1, shape: (38, 1001), type: float64\ndataset created, uuid: d-f8369350-ee29bdd8-1e7b-efe581-b6ec09, chunk_size: (38, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000099_url.sedml\ncreating attribute uri in /BIOMD0000000099_url.sedml\ncreating attribute _type in /BIOMD0000000099_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000099_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000099_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000099_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000099_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000099_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000099_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000099_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000099_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000099_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000099_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000099_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000099_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000099_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000099_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000099_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000099_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000099_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000099_url.sedml\ncreate_links: /BIOMD0000000099_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000099_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000099_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\niterating over chunks for /BIOMD0000000099_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 8, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000099_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000099_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000099_url.sedml/autogen_report_for_task1, shape: (38, 1001), type: float64\niterating over chunks for /BIOMD0000000099_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 38, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000099_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471083e0dcacb55678b5884\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.\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.\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":1.70977,"sedDocuments":[{"location":"BIOMD0000000099_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  BIOMD0000000099_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: 7 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000099_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":1.222576,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.232357,"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":0.312134,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_species_0","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_parameter_0","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_compartment_0","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_1","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0","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_task1_reaction_11","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_12","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_13","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.521778,"curves":[{"id":"autogen_curve_task1_species_0","status":"SUCCEEDED"},{"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"}]}]}]}