{"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    373      0 --:--:-- --:--:-- --:--:--   373\n\r100  996k  100  996k    0     0  1945k      0 --:--:-- --:--:-- --:--:-- 1945k\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 (25.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/rawLog.txt\nCompleted 5.8 KiB/5.8 KiB (85.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 84%)\n  adding: outputs/BIOMD0000000443_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000443_url.sedml/autogen_plot_for_task1.pdf (deflated 29%)\n  adding: outputs/reports.h5 (deflated 6%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/411.4 KiB (4.8 MiB/s) with 1 file(s) remaining\rCompleted 411.4 KiB/411.4 KiB (3.6 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/outputs/reports.h5\nCompleted 256.0 KiB/416.1 KiB (6.0 MiB/s) with 4 file(s) remaining\rCompleted 258.8 KiB/416.1 KiB (2.3 MiB/s) with 4 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/rawLog.txt\nCompleted 258.8 KiB/416.1 KiB (2.3 MiB/s) with 3 file(s) remaining\rCompleted 266.3 KiB/416.1 KiB (2.3 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/outputs/plots.zip\nCompleted 266.3 KiB/416.1 KiB (2.3 MiB/s) with 2 file(s) remaining\rCompleted 277.1 KiB/416.1 KiB (2.4 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000443_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/outputs/BIOMD0000000443_url.sedml/autogen_plot_for_task1.pdf\nCompleted 277.1 KiB/416.1 KiB (2.4 MiB/s) with 1 file(s) remaining\rCompleted 416.1 KiB/416.1 KiB (3.3 MiB/s) with 1 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/output.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000443-biopax2.owl  \n  inflating: contents/BIOMD0000000443-biopax3.owl  \n  inflating: contents/BIOMD0000000443-matlab.m  \n  inflating: contents/BIOMD0000000443.m  \n  inflating: contents/BIOMD0000000443.ode  \n  inflating: contents/BIOMD0000000443.pdf  \n  inflating: contents/BIOMD0000000443.png  \n  inflating: contents/BIOMD0000000443.svg  \n  inflating: contents/BIOMD0000000443.vcml  \n  inflating: contents/BIOMD0000000443_url.sedml  \n  inflating: contents/BIOMD0000000443_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 60.1 KiB/1.6 MiB (800.1 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000443-biopax3.owl to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/contents/BIOMD0000000443-biopax3.owl\nCompleted 60.1 KiB/1.6 MiB (800.1 KiB/s) with 14 file(s) remaining\rCompleted 74.8 KiB/1.6 MiB (679.0 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000443-matlab.m to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/contents/BIOMD0000000443-matlab.m\nCompleted 74.8 KiB/1.6 MiB (679.0 KiB/s) with 13 file(s) remaining\rCompleted 117.0 KiB/1.6 MiB (919.9 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000443-biopax2.owl to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/contents/BIOMD0000000443-biopax2.owl\nCompleted 117.0 KiB/1.6 MiB (919.9 KiB/s) with 12 file(s) remaining\rCompleted 143.8 KiB/1.6 MiB (1.0 MiB/s) with 12 file(s) remaining  \rupload: contents/BIOMD0000000443_url.sedml to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/contents/BIOMD0000000443_url.sedml\nCompleted 143.8 KiB/1.6 MiB (1.0 MiB/s) with 11 file(s) remaining\rCompleted 150.3 KiB/1.6 MiB (1.1 MiB/s) with 11 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/contents/metadata.rdf\nCompleted 150.3 KiB/1.6 MiB (1.1 MiB/s) with 10 file(s) remaining\rCompleted 254.9 KiB/1.6 MiB (1.8 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000443.vcml to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/contents/BIOMD0000000443.vcml\nCompleted 254.9 KiB/1.6 MiB (1.8 MiB/s) with 9 file(s) remaining\rCompleted 510.9 KiB/1.6 MiB (3.4 MiB/s) with 9 file(s) remaining\rCompleted 766.9 KiB/1.6 MiB (5.0 MiB/s) with 9 file(s) remaining\rCompleted 1022.9 KiB/1.6 MiB (6.5 MiB/s) with 9 file(s) remaining\rCompleted 1.2 MiB/1.6 MiB (7.9 MiB/s) with 9 file(s) remaining   \rCompleted 1.3 MiB/1.6 MiB (7.4 MiB/s) with 9 file(s) remaining   \rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/contents/curation_image.png\nCompleted 1.3 MiB/1.6 MiB (7.4 MiB/s) with 8 file(s) remaining\rCompleted 1.4 MiB/1.6 MiB (7.8 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000443_url.xml to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/contents/BIOMD0000000443_url.xml\nCompleted 1.4 MiB/1.6 MiB (7.8 MiB/s) with 7 file(s) remaining\rCompleted 1.4 MiB/1.6 MiB (7.8 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000443.m to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/contents/BIOMD0000000443.m\nCompleted 1.4 MiB/1.6 MiB (7.8 MiB/s) with 6 file(s) remaining\rCompleted 1.4 MiB/1.6 MiB (7.6 MiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/contents/manifest.xml\nCompleted 1.4 MiB/1.6 MiB (7.6 MiB/s) with 5 file(s) remaining\rCompleted 1.5 MiB/1.6 MiB (7.7 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000443.svg to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/contents/BIOMD0000000443.svg\nCompleted 1.5 MiB/1.6 MiB (7.7 MiB/s) with 4 file(s) remaining\rCompleted 1.5 MiB/1.6 MiB (7.4 MiB/s) with 4 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/contents/curation_notes.txt\nCompleted 1.5 MiB/1.6 MiB (7.4 MiB/s) with 3 file(s) remaining\rCompleted 1.5 MiB/1.6 MiB (7.4 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000443.ode to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/contents/BIOMD0000000443.ode\nCompleted 1.5 MiB/1.6 MiB (7.4 MiB/s) with 2 file(s) remaining\rCompleted 1.6 MiB/1.6 MiB (7.2 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000443.png to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/contents/BIOMD0000000443.png\nCompleted 1.6 MiB/1.6 MiB (7.2 MiB/s) with 1 file(s) remaining\rCompleted 1.6 MiB/1.6 MiB (7.3 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000443.pdf to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/contents/BIOMD0000000443.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.8 KiB/8.8 KiB (136.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c50477b666965506b916/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000443_url.sedml\ncreating dataset /BIOMD0000000443_url.sedml/autogen_plot_for_task1, shape: (20, 1001), type: float64\ndataset created, uuid: d-642f4f89-2817f0b1-c863-f40d4c-0be158, chunk_size: (20, 1001)\ncreating dataset /BIOMD0000000443_url.sedml/autogen_report_for_task1, shape: (43, 1001), type: float64\ndataset created, uuid: d-642f4f89-2817f0b1-c4f9-fdfe86-8d2409, chunk_size: (43, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000443_url.sedml\ncreating attribute uri in /BIOMD0000000443_url.sedml\ncreating attribute _type in /BIOMD0000000443_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000443_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000443_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000443_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000443_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000443_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000443_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000443_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000443_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000443_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000443_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000443_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000443_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000443_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000443_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000443_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000443_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000443_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000443_url.sedml\ncreate_links: /BIOMD0000000443_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000443_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000443_url.sedml/autogen_plot_for_task1, shape: (20, 1001), type: float64\niterating over chunks for /BIOMD0000000443_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 20, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000443_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000443_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000443_url.sedml/autogen_report_for_task1, shape: (43, 1001), type: float64\niterating over chunks for /BIOMD0000000443_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 43, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000443_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6480c50477b666965506b916\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.\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":1.884111,"sedDocuments":[{"location":"BIOMD0000000443_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  BIOMD0000000443_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 43 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 19 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000443_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":1.386716,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.253819,"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":0.295647,"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_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_species_16","status":"SUCCEEDED"},{"id":"autogen_task1_species_17","status":"SUCCEEDED"},{"id":"autogen_task1_species_18","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_0","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_task1_reaction_14","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_15","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_16","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_17","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_18","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_19","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_20","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_21","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.665112,"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"},{"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"},{"id":"autogen_curve_task1_species_16","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_17","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_18","status":"SUCCEEDED"}]}]}]}