{"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    454      0 --:--:-- --:--:-- --:--:--   455\n\r100  154k  100  154k    0     0   366k      0 --:--:-- --:--:-- --:--:--  366k\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/6488f159da4ff2037f59bf41/rawLog.txt\nCompleted 3.9 KiB/3.9 KiB (49.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 79%)\n  adding: outputs/BIOMD0000000617_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000617_url.sedml/autogen_plot_for_task1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 56%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 48.0 KiB/48.0 KiB (549.5 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/outputs/reports.h5\nCompleted 30.7 KiB/51.3 KiB (453.3 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/output.zip\nCompleted 30.7 KiB/51.3 KiB (453.3 KiB/s) with 3 file(s) remaining\rCompleted 37.9 KiB/51.3 KiB (392.4 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/outputs/plots.zip\nCompleted 37.9 KiB/51.3 KiB (392.4 KiB/s) with 2 file(s) remaining\rCompleted 48.7 KiB/51.3 KiB (478.4 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000617_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/outputs/BIOMD0000000617_url.sedml/autogen_plot_for_task1.pdf\nCompleted 48.7 KiB/51.3 KiB (478.4 KiB/s) with 1 file(s) remaining\rCompleted 51.3 KiB/51.3 KiB (447.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000617-biopax2.owl  \n  inflating: contents/BIOMD0000000617-biopax3.owl  \n  inflating: contents/BIOMD0000000617-matlab.m  \n  inflating: contents/BIOMD0000000617-octave.m  \n  inflating: contents/BIOMD0000000617.m  \n  inflating: contents/BIOMD0000000617.ode  \n  inflating: contents/BIOMD0000000617.pdf  \n  inflating: contents/BIOMD0000000617.png  \n  inflating: contents/BIOMD0000000617.sci  \n  inflating: contents/BIOMD0000000617.svg  \n  inflating: contents/BIOMD0000000617_url.sedml  \n  inflating: contents/BIOMD0000000617_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 6.5 KiB/~287.2 KiB (98.5 KiB/s) with ~14 file(s) remaining (calculating...)\rupload: contents/BIOMD0000000617-biopax2.owl to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/contents/BIOMD0000000617-biopax2.owl\nCompleted 6.5 KiB/~287.2 KiB (98.5 KiB/s) with ~13 file(s) remaining (calculating...)\rCompleted 15.1 KiB/293.9 KiB (126.2 KiB/s) with 15 file(s) remaining                 \rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/contents/curation_image.png\nCompleted 15.1 KiB/293.9 KiB (126.2 KiB/s) with 14 file(s) remaining\rCompleted 15.5 KiB/293.9 KiB (109.7 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000617.sci to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/contents/BIOMD0000000617.sci\nCompleted 15.5 KiB/293.9 KiB (109.7 KiB/s) with 13 file(s) remaining\rCompleted 21.6 KiB/293.9 KiB (150.7 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000617-octave.m to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/contents/BIOMD0000000617-octave.m\nCompleted 21.6 KiB/293.9 KiB (150.7 KiB/s) with 12 file(s) remaining\rCompleted 31.2 KiB/293.9 KiB (209.6 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000617.png to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/contents/BIOMD0000000617.png\nCompleted 31.2 KiB/293.9 KiB (209.6 KiB/s) with 11 file(s) remaining\rCompleted 37.3 KiB/293.9 KiB (236.7 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000617-matlab.m to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/contents/BIOMD0000000617-matlab.m\nCompleted 37.3 KiB/293.9 KiB (236.7 KiB/s) with 10 file(s) remaining\rCompleted 43.6 KiB/293.9 KiB (261.3 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000617.svg to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/contents/BIOMD0000000617.svg\nCompleted 43.6 KiB/293.9 KiB (261.3 KiB/s) with 9 file(s) remaining\rCompleted 43.9 KiB/293.9 KiB (255.8 KiB/s) with 9 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/contents/curation_notes.txt\nCompleted 43.9 KiB/293.9 KiB (255.8 KiB/s) with 8 file(s) remaining\rCompleted 61.4 KiB/293.9 KiB (334.0 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000617_url.sedml to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/contents/BIOMD0000000617_url.sedml\nCompleted 61.4 KiB/293.9 KiB (334.0 KiB/s) with 7 file(s) remaining\rCompleted 63.2 KiB/293.9 KiB (325.5 KiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/contents/manifest.xml\nCompleted 63.2 KiB/293.9 KiB (325.5 KiB/s) with 6 file(s) remaining\rCompleted 116.0 KiB/293.9 KiB (588.1 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000617_url.xml to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/contents/BIOMD0000000617_url.xml\nCompleted 116.0 KiB/293.9 KiB (588.1 KiB/s) with 5 file(s) remaining\rCompleted 120.9 KiB/293.9 KiB (584.2 KiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/contents/metadata.rdf\nCompleted 120.9 KiB/293.9 KiB (584.2 KiB/s) with 4 file(s) remaining\rCompleted 127.0 KiB/293.9 KiB (568.2 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000617.m to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/contents/BIOMD0000000617.m\nCompleted 127.0 KiB/293.9 KiB (568.2 KiB/s) with 3 file(s) remaining\rCompleted 135.2 KiB/293.9 KiB (588.6 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000617-biopax3.owl to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/contents/BIOMD0000000617-biopax3.owl\nCompleted 135.2 KiB/293.9 KiB (588.6 KiB/s) with 2 file(s) remaining\rCompleted 139.0 KiB/293.9 KiB (562.0 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000617.ode to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/contents/BIOMD0000000617.ode\nCompleted 139.0 KiB/293.9 KiB (562.0 KiB/s) with 1 file(s) remaining\rCompleted 293.9 KiB/293.9 KiB (1.1 MiB/s) with 1 file(s) remaining  \rupload: contents/BIOMD0000000617.pdf to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/contents/BIOMD0000000617.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (135.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f159da4ff2037f59bf41/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000617_url.sedml\ncreating dataset /BIOMD0000000617_url.sedml/autogen_plot_for_task1, shape: (2, 1001), type: float64\ndataset created, uuid: d-606638eb-8cb7507f-23c3-40ed0a-34178f, chunk_size: (2, 1001)\ncreating dataset /BIOMD0000000617_url.sedml/autogen_report_for_task1, shape: (34, 1001), type: float64\ndataset created, uuid: d-606638eb-8cb7507f-5144-dbc0f2-d97c25, chunk_size: (34, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000617_url.sedml\ncreating attribute uri in /BIOMD0000000617_url.sedml\ncreating attribute _type in /BIOMD0000000617_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000617_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000617_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000617_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000617_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000617_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000617_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000617_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000617_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000617_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000617_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000617_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000617_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000617_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000617_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000617_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000617_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000617_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000617_url.sedml\ncreate_links: /BIOMD0000000617_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000617_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000617_url.sedml/autogen_plot_for_task1, shape: (2, 1001), type: float64\niterating over chunks for /BIOMD0000000617_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000617_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000617_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000617_url.sedml/autogen_report_for_task1, shape: (34, 1001), type: float64\niterating over chunks for /BIOMD0000000617_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 34, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000617_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6488f159da4ff2037f59bf41\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 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.\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 metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.5063,"sedDocuments":[{"location":"BIOMD0000000617_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  BIOMD0000000617_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 34 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000617_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":1.03849,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.265199,"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":0.27874,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_v","status":"SUCCEEDED"},{"id":"autogen_task1_V1s","status":"SUCCEEDED"},{"id":"autogen_task1_S","status":"SUCCEEDED"},{"id":"autogen_task1_K1s","status":"SUCCEEDED"},{"id":"autogen_task1_V2s","status":"SUCCEEDED"},{"id":"autogen_task1_H1","status":"SUCCEEDED"},{"id":"autogen_task1_K2s","status":"SUCCEEDED"},{"id":"autogen_task1_H2","status":"SUCCEEDED"},{"id":"autogen_task1_K3s","status":"SUCCEEDED"},{"id":"autogen_task1_V2","status":"SUCCEEDED"},{"id":"autogen_task1_V2i","status":"SUCCEEDED"},{"id":"autogen_task1_Ii","status":"SUCCEEDED"},{"id":"autogen_task1_Hxx","status":"SUCCEEDED"},{"id":"autogen_task1_Kxx1","status":"SUCCEEDED"},{"id":"autogen_task1_K2","status":"SUCCEEDED"},{"id":"autogen_task1_K2i","status":"SUCCEEDED"},{"id":"autogen_task1_V1","status":"SUCCEEDED"},{"id":"autogen_task1_V1is","status":"SUCCEEDED"},{"id":"autogen_task1_Hx1","status":"SUCCEEDED"},{"id":"autogen_task1_Kx1","status":"SUCCEEDED"},{"id":"autogen_task1_Hx2","status":"SUCCEEDED"},{"id":"autogen_task1_Kx2","status":"SUCCEEDED"},{"id":"autogen_task1_V1ii","status":"SUCCEEDED"},{"id":"autogen_task1_K1","status":"SUCCEEDED"},{"id":"autogen_task1_K1is","status":"SUCCEEDED"},{"id":"autogen_task1_K1ii","status":"SUCCEEDED"},{"id":"autogen_task1_V3","status":"SUCCEEDED"},{"id":"autogen_task1_default_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_Compartment_","status":"SUCCEEDED"},{"id":"autogen_task1_R1","status":"SUCCEEDED"},{"id":"autogen_task1_R2","status":"SUCCEEDED"},{"id":"autogen_task1_R3","status":"SUCCEEDED"},{"id":"autogen_task1_R4","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.350898,"curves":[{"id":"autogen_curve_task1_v","status":"SUCCEEDED"}]}]}]}