{"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 --:--:-- --:--:-- --:--:--   439\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100  664k  100  664k    0     0  1492k      0 --:--:-- --:--:-- --:--:-- 8300k\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 (24.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/rawLog.txt\nCompleted 6.0 KiB/6.0 KiB (80.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/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/BIOMD0000000475_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000475_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\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/514.9 KiB (5.7 MiB/s) with 1 file(s) remaining\rCompleted 512.0 KiB/514.9 KiB (10.4 MiB/s) with 1 file(s) remaining\rCompleted 514.9 KiB/514.9 KiB (4.1 MiB/s) with 1 file(s) remaining \rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/outputs/reports.h5\nCompleted 256.0 KiB/512.2 KiB (5.5 MiB/s) with 4 file(s) remaining\rCompleted 263.3 KiB/512.2 KiB (2.2 MiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/outputs/plots.zip\nCompleted 263.3 KiB/512.2 KiB (2.2 MiB/s) with 3 file(s) remaining\rCompleted 498.8 KiB/512.2 KiB (3.9 MiB/s) with 3 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/output.zip\nCompleted 498.8 KiB/512.2 KiB (3.9 MiB/s) with 2 file(s) remaining\rCompleted 509.4 KiB/512.2 KiB (3.4 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000475_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/outputs/BIOMD0000000475_url.sedml/autogen_plot_for_task1.pdf\nCompleted 509.4 KiB/512.2 KiB (3.4 MiB/s) with 1 file(s) remaining\rCompleted 512.2 KiB/512.2 KiB (3.3 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000475-biopax2.owl  \n  inflating: contents/BIOMD0000000475-biopax3.owl  \n  inflating: contents/BIOMD0000000475-matlab.m  \n  inflating: contents/BIOMD0000000475-octave.m  \n  inflating: contents/BIOMD0000000475.m  \n  inflating: contents/BIOMD0000000475.ode  \n  inflating: contents/BIOMD0000000475.pdf  \n  inflating: contents/BIOMD0000000475.png  \n  inflating: contents/BIOMD0000000475.svg  \n  inflating: contents/BIOMD0000000475_url.sedml  \n  inflating: contents/BIOMD0000000475_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 82.9 KiB/1.2 MiB (989.7 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000475-biopax3.owl to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/contents/BIOMD0000000475-biopax3.owl\nCompleted 82.9 KiB/1.2 MiB (989.7 KiB/s) with 14 file(s) remaining\rCompleted 95.2 KiB/1.2 MiB (671.8 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000475-matlab.m to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/contents/BIOMD0000000475-matlab.m\nCompleted 95.2 KiB/1.2 MiB (671.8 KiB/s) with 13 file(s) remaining\rCompleted 126.9 KiB/1.2 MiB (816.4 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000475_url.sedml to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/contents/BIOMD0000000475_url.sedml\nCompleted 126.9 KiB/1.2 MiB (816.4 KiB/s) with 12 file(s) remaining\rCompleted 177.3 KiB/1.2 MiB (1.1 MiB/s) with 12 file(s) remaining  \rupload: contents/BIOMD0000000475-biopax2.owl to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/contents/BIOMD0000000475-biopax2.owl\nCompleted 177.3 KiB/1.2 MiB (1.1 MiB/s) with 11 file(s) remaining\rCompleted 270.0 KiB/1.2 MiB (1.6 MiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000475.svg to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/contents/BIOMD0000000475.svg\nCompleted 270.0 KiB/1.2 MiB (1.6 MiB/s) with 10 file(s) remaining\rCompleted 272.7 KiB/1.2 MiB (1.5 MiB/s) with 10 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/contents/metadata.rdf\nCompleted 272.7 KiB/1.2 MiB (1.5 MiB/s) with 9 file(s) remaining\rCompleted 285.0 KiB/1.2 MiB (1.6 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000475-octave.m to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/contents/BIOMD0000000475-octave.m\nCompleted 285.0 KiB/1.2 MiB (1.6 MiB/s) with 8 file(s) remaining\rCompleted 355.4 KiB/1.2 MiB (1.9 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000475_url.xml to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/contents/BIOMD0000000475_url.xml\nCompleted 355.4 KiB/1.2 MiB (1.9 MiB/s) with 7 file(s) remaining\rCompleted 392.8 KiB/1.2 MiB (2.1 MiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/contents/curation_image.png\nCompleted 392.8 KiB/1.2 MiB (2.1 MiB/s) with 6 file(s) remaining\rCompleted 648.8 KiB/1.2 MiB (3.4 MiB/s) with 6 file(s) remaining\rCompleted 904.8 KiB/1.2 MiB (4.6 MiB/s) with 6 file(s) remaining\rCompleted 906.6 KiB/1.2 MiB (4.6 MiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/contents/manifest.xml\nCompleted 906.6 KiB/1.2 MiB (4.6 MiB/s) with 5 file(s) remaining\rCompleted 907.2 KiB/1.2 MiB (4.5 MiB/s) with 5 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/contents/curation_notes.txt\nCompleted 907.2 KiB/1.2 MiB (4.5 MiB/s) with 4 file(s) remaining\rCompleted 919.6 KiB/1.2 MiB (3.8 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000475.m to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/contents/BIOMD0000000475.m\nCompleted 919.6 KiB/1.2 MiB (3.8 MiB/s) with 3 file(s) remaining\rCompleted 928.7 KiB/1.2 MiB (3.8 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000475.ode to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/contents/BIOMD0000000475.ode\nCompleted 928.7 KiB/1.2 MiB (3.8 MiB/s) with 2 file(s) remaining\rCompleted 961.6 KiB/1.2 MiB (3.8 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000475.pdf to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/contents/BIOMD0000000475.pdf\nCompleted 961.6 KiB/1.2 MiB (3.8 MiB/s) with 1 file(s) remaining\rCompleted 1.2 MiB/1.2 MiB (4.2 MiB/s) with 1 file(s) remaining  \rupload: contents/BIOMD0000000475.png to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/contents/BIOMD0000000475.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.8 KiB/8.8 KiB (77.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f14ada4ff2037f59be9b/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000475_url.sedml\ncreating dataset /BIOMD0000000475_url.sedml/autogen_plot_for_task1, shape: (24, 1001), type: float64\ndataset created, uuid: d-da702b24-b182789b-96dc-c22f53-f5f395, chunk_size: (24, 1001)\ncreating dataset /BIOMD0000000475_url.sedml/autogen_report_for_task1, shape: (51, 1001), type: float64\ndataset created, uuid: d-da702b24-b182789b-4a3b-ee95f5-7579bd, chunk_size: (51, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000475_url.sedml\ncreating attribute uri in /BIOMD0000000475_url.sedml\ncreating attribute _type in /BIOMD0000000475_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000475_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000475_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000475_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000475_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000475_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000475_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000475_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000475_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000475_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000475_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000475_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000475_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000475_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000475_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000475_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000475_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000475_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000475_url.sedml\ncreate_links: /BIOMD0000000475_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000475_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000475_url.sedml/autogen_plot_for_task1, shape: (24, 1001), type: float64\niterating over chunks for /BIOMD0000000475_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 24, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000475_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000475_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000475_url.sedml/autogen_report_for_task1, shape: (51, 1001), type: float64\niterating over chunks for /BIOMD0000000475_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 51, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000475_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6488f14ada4ff2037f59be9b\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 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.\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":2.041734,"sedDocuments":[{"location":"BIOMD0000000475_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  BIOMD0000000475_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 51 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 23 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000475_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":1.601939,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.226567,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"deterministic"},{"key":"methodCode","value":22},{"key":"parameters"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.426033,"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_parameter_1","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_1","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_task1_reaction_22","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_23","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_24","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_25","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.77655,"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"}]}]}]}