{"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    462      0 --:--:-- --:--:-- --:--:--   463\n\r100  242k  100  242k    0     0   568k      0 --:--:-- --:--:-- --:--:--  568k\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 (25.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488baf36262268786a279af/rawLog.txt\nCompleted 6.7 KiB/6.7 KiB (93.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6488baf36262268786a279af/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 86%)\n  adding: outputs/BIOMD0000000499_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000499_url.sedml/autogen_plot_for_task1.pdf (deflated 20%)\n  adding: outputs/reports.h5 (deflated 10%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/381.4 KiB (5.6 MiB/s) with 1 file(s) remaining\rCompleted 381.4 KiB/381.4 KiB (3.7 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6488baf36262268786a279af/outputs/reports.h5\nCompleted 256.0 KiB/389.2 KiB (5.9 MiB/s) with 4 file(s) remaining\rCompleted 258.7 KiB/389.2 KiB (2.3 MiB/s) with 4 file(s) remaining\rCompleted 361.6 KiB/389.2 KiB (3.1 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6488baf36262268786a279af/output.zip\nCompleted 361.6 KiB/389.2 KiB (3.1 MiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488baf36262268786a279af/rawLog.txt\nCompleted 361.6 KiB/389.2 KiB (3.1 MiB/s) with 2 file(s) remaining\rCompleted 373.7 KiB/389.2 KiB (3.2 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6488baf36262268786a279af/outputs/plots.zip\nCompleted 373.7 KiB/389.2 KiB (3.2 MiB/s) with 1 file(s) remaining\rCompleted 389.2 KiB/389.2 KiB (3.2 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000499_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6488baf36262268786a279af/outputs/BIOMD0000000499_url.sedml/autogen_plot_for_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000499-biopax2.owl  \n  inflating: contents/BIOMD0000000499-biopax3.owl  \n  inflating: contents/BIOMD0000000499-matlab.m  \n  inflating: contents/BIOMD0000000499.m  \n  inflating: contents/BIOMD0000000499.ode  \n  inflating: contents/BIOMD0000000499.pdf  \n  inflating: contents/BIOMD0000000499.png  \n  inflating: contents/BIOMD0000000499.svg  \n  inflating: contents/BIOMD0000000499_url.sedml  \n  inflating: contents/BIOMD0000000499_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 11.8 KiB/472.6 KiB (185.5 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000499-biopax2.owl to s3://files.biosimulations.org/simulations/6488baf36262268786a279af/contents/BIOMD0000000499-biopax2.owl\nCompleted 11.8 KiB/472.6 KiB (185.5 KiB/s) with 13 file(s) remaining\rCompleted 23.6 KiB/472.6 KiB (203.6 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000499-matlab.m to s3://files.biosimulations.org/simulations/6488baf36262268786a279af/contents/BIOMD0000000499-matlab.m\nCompleted 23.6 KiB/472.6 KiB (203.6 KiB/s) with 12 file(s) remaining\rCompleted 35.3 KiB/472.6 KiB (300.9 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000499.m to s3://files.biosimulations.org/simulations/6488baf36262268786a279af/contents/BIOMD0000000499.m\nCompleted 35.3 KiB/472.6 KiB (300.9 KiB/s) with 11 file(s) remaining\rCompleted 43.8 KiB/472.6 KiB (355.2 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000499.ode to s3://files.biosimulations.org/simulations/6488baf36262268786a279af/contents/BIOMD0000000499.ode\nCompleted 43.8 KiB/472.6 KiB (355.2 KiB/s) with 10 file(s) remaining\rCompleted 44.6 KiB/472.6 KiB (298.1 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000499.svg to s3://files.biosimulations.org/simulations/6488baf36262268786a279af/contents/BIOMD0000000499.svg\nCompleted 44.6 KiB/472.6 KiB (298.1 KiB/s) with 9 file(s) remaining\rCompleted 49.7 KiB/472.6 KiB (326.6 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000499.png to s3://files.biosimulations.org/simulations/6488baf36262268786a279af/contents/BIOMD0000000499.png\nCompleted 49.7 KiB/472.6 KiB (326.6 KiB/s) with 8 file(s) remaining\rCompleted 85.2 KiB/472.6 KiB (540.3 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000499_url.sedml to s3://files.biosimulations.org/simulations/6488baf36262268786a279af/contents/BIOMD0000000499_url.sedml\nCompleted 85.2 KiB/472.6 KiB (540.3 KiB/s) with 7 file(s) remaining\rCompleted 99.6 KiB/472.6 KiB (622.4 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000499-biopax3.owl to s3://files.biosimulations.org/simulations/6488baf36262268786a279af/contents/BIOMD0000000499-biopax3.owl\nCompleted 99.6 KiB/472.6 KiB (622.4 KiB/s) with 6 file(s) remaining\rCompleted 290.7 KiB/472.6 KiB (1.7 MiB/s) with 6 file(s) remaining \rupload: contents/BIOMD0000000499.pdf to s3://files.biosimulations.org/simulations/6488baf36262268786a279af/contents/BIOMD0000000499.pdf\nCompleted 290.7 KiB/472.6 KiB (1.7 MiB/s) with 5 file(s) remaining\rCompleted 291.0 KiB/472.6 KiB (1.5 MiB/s) with 5 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6488baf36262268786a279af/contents/curation_notes.txt\nCompleted 291.0 KiB/472.6 KiB (1.5 MiB/s) with 4 file(s) remaining\rCompleted 292.6 KiB/472.6 KiB (1.5 MiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6488baf36262268786a279af/contents/manifest.xml\nCompleted 292.6 KiB/472.6 KiB (1.5 MiB/s) with 3 file(s) remaining\rCompleted 294.3 KiB/472.6 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6488baf36262268786a279af/contents/metadata.rdf\nCompleted 294.3 KiB/472.6 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 389.2 KiB/472.6 KiB (1.8 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000499_url.xml to s3://files.biosimulations.org/simulations/6488baf36262268786a279af/contents/BIOMD0000000499_url.xml\nCompleted 389.2 KiB/472.6 KiB (1.8 MiB/s) with 1 file(s) remaining\rCompleted 472.6 KiB/472.6 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6488baf36262268786a279af/contents/curation_image.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.3 KiB/8.3 KiB (108.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488baf36262268786a279af/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000499_url.sedml\ncreating dataset /BIOMD0000000499_url.sedml/autogen_plot_for_task1, shape: (27, 1001), type: float64\ndataset created, uuid: d-ee0644f4-818e3855-b6fe-b5eead-5ea84a, chunk_size: (27, 1001)\ncreating dataset /BIOMD0000000499_url.sedml/autogen_report_for_task1, shape: (57, 1001), type: float64\ndataset created, uuid: d-ee0644f4-818e3855-61ff-b37ed8-7a3171, chunk_size: (57, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000499_url.sedml\ncreating attribute uri in /BIOMD0000000499_url.sedml\ncreating attribute _type in /BIOMD0000000499_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000499_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000499_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000499_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000499_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000499_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000499_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000499_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000499_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000499_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000499_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000499_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000499_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000499_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000499_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000499_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000499_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000499_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000499_url.sedml\ncreate_links: /BIOMD0000000499_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000499_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000499_url.sedml/autogen_plot_for_task1, shape: (27, 1001), type: float64\niterating over chunks for /BIOMD0000000499_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 27, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000499_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000499_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000499_url.sedml/autogen_report_for_task1, shape: (57, 1001), type: float64\niterating over chunks for /BIOMD0000000499_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 57, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000499_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6488baf36262268786a279af\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.\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.\nProcess and upload the outputs of the simulation run ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":4.717077,"sedDocuments":[{"location":"BIOMD0000000499_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  BIOMD0000000499_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 57 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 26 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000499_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":4.371662,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":3.246206,"algorithm":"KISAO_0000086","simulatorDetails":[{"key":"method","value":"simulateSBMLFromFile"},{"key":"arguments","value":{"dt":0.0001,"method":51,"print_amount":0,"print_interval":100,"sim_time":10,"use_lazy_method":0}}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.396783,"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_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_species_19","status":"SUCCEEDED"},{"id":"autogen_task1_species_20","status":"SUCCEEDED"},{"id":"autogen_task1_species_21","status":"SUCCEEDED"},{"id":"autogen_task1_species_22","status":"SUCCEEDED"},{"id":"autogen_task1_species_23","status":"SUCCEEDED"},{"id":"autogen_task1_species_24","status":"SUCCEEDED"},{"id":"autogen_task1_species_25","status":"SUCCEEDED"},{"id":"autogen_task1_species_26","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_parameter_15","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_16","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_17","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_18","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_19","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_20","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_21","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_22","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_23","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_24","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_25","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_26","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_27","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_28","status":"SUCCEEDED"},{"id":"autogen_task1_Metabolite_9","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_1","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.546934,"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"},{"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"},{"id":"autogen_curve_task1_species_19","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_20","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_21","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_22","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_23","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_24","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_25","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_26","status":"SUCCEEDED"}]}]}]}