{"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    433      0 --:--:-- --:--:-- --:--:--   434\n\r100  240k  100  240k    0     0   532k      0 --:--:-- --:--:-- --:--:--  532k\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 (15.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/rawLog.txt\nCompleted 3.2 KiB/3.2 KiB (29.8 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 76%)\n  adding: outputs/BIOMD0000000005.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000005.sedml/plot1.pdf (deflated 24%)\n  adding: outputs/reports.h5 (deflated 15%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 140.2 KiB/140.2 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/outputs/reports.h5\nCompleted 131.5 KiB/155.7 KiB (1019.0 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/output.zip\nCompleted 131.5 KiB/155.7 KiB (1019.0 KiB/s) with 3 file(s) remaining\rCompleted 140.7 KiB/155.7 KiB (991.4 KiB/s) with 3 file(s) remaining \rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/outputs/plots.zip\nCompleted 140.7 KiB/155.7 KiB (991.4 KiB/s) with 2 file(s) remaining\rCompleted 153.1 KiB/155.7 KiB (940.0 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000005.sedml/plot1.pdf to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/outputs/BIOMD0000000005.sedml/plot1.pdf\nCompleted 153.1 KiB/155.7 KiB (940.0 KiB/s) with 1 file(s) remaining\rCompleted 155.7 KiB/155.7 KiB (881.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000005-biopax2.owl  \n  inflating: contents/BIOMD0000000005-biopax3.owl  \n  inflating: contents/BIOMD0000000005-matlab.m  \n  inflating: contents/BIOMD0000000005-octave.m  \n  inflating: contents/BIOMD0000000005.m  \n  inflating: contents/BIOMD0000000005.ode  \n  inflating: contents/BIOMD0000000005.pdf  \n  inflating: contents/BIOMD0000000005.png  \n  inflating: contents/BIOMD0000000005.sci  \n  inflating: contents/BIOMD0000000005.sedml  \n  inflating: contents/BIOMD0000000005.svg  \n  inflating: contents/BIOMD0000000005.vcml  \n  inflating: contents/BIOMD0000000005_manual.png  \n  inflating: contents/BIOMD0000000005_manual.svg  \n  inflating: contents/BIOMD0000000005_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 29.5 KiB/465.2 KiB (330.7 KiB/s) with 19 file(s) remaining\rupload: contents/BIOMD0000000005-biopax3.owl to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/contents/BIOMD0000000005-biopax3.owl\nCompleted 29.5 KiB/465.2 KiB (330.7 KiB/s) with 18 file(s) remaining\rCompleted 35.1 KiB/465.2 KiB (321.0 KiB/s) with 18 file(s) remaining\rupload: contents/BIOMD0000000005-matlab.m to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/contents/BIOMD0000000005-matlab.m\nCompleted 35.1 KiB/465.2 KiB (321.0 KiB/s) with 17 file(s) remaining\rCompleted 55.8 KiB/465.2 KiB (349.3 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000005-biopax2.owl to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/contents/BIOMD0000000005-biopax2.owl\nCompleted 55.8 KiB/465.2 KiB (349.3 KiB/s) with 16 file(s) remaining\rCompleted 61.5 KiB/465.2 KiB (370.1 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000005-octave.m to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/contents/BIOMD0000000005-octave.m\nCompleted 61.5 KiB/465.2 KiB (370.1 KiB/s) with 15 file(s) remaining\rCompleted 72.3 KiB/465.2 KiB (392.2 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000005.sedml to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/contents/BIOMD0000000005.sedml\nCompleted 72.3 KiB/465.2 KiB (392.2 KiB/s) with 14 file(s) remaining\rCompleted 98.3 KiB/465.2 KiB (523.8 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000005_url.xml to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/contents/BIOMD0000000005_url.xml\nCompleted 98.3 KiB/465.2 KiB (523.8 KiB/s) with 13 file(s) remaining\rCompleted 101.3 KiB/465.2 KiB (532.7 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000005.sci to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/contents/BIOMD0000000005.sci\nCompleted 101.3 KiB/465.2 KiB (532.7 KiB/s) with 12 file(s) remaining\rCompleted 133.8 KiB/465.2 KiB (627.4 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000005_manual.png to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/contents/BIOMD0000000005_manual.png\nCompleted 133.8 KiB/465.2 KiB (627.4 KiB/s) with 11 file(s) remaining\rCompleted 155.4 KiB/465.2 KiB (721.9 KiB/s) with 11 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/contents/curation_image.png\nCompleted 155.4 KiB/465.2 KiB (721.9 KiB/s) with 10 file(s) remaining\rCompleted 179.2 KiB/465.2 KiB (811.7 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000005.svg to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/contents/BIOMD0000000005.svg\nCompleted 179.2 KiB/465.2 KiB (811.7 KiB/s) with 9 file(s) remaining\rCompleted 216.3 KiB/465.2 KiB (925.4 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000005.vcml to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/contents/BIOMD0000000005.vcml\nCompleted 216.3 KiB/465.2 KiB (925.4 KiB/s) with 8 file(s) remaining\rCompleted 240.0 KiB/465.2 KiB (1002.3 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000005_manual.svg to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/contents/BIOMD0000000005_manual.svg\nCompleted 240.0 KiB/465.2 KiB (1002.3 KiB/s) with 7 file(s) remaining\rCompleted 240.1 KiB/465.2 KiB (922.5 KiB/s) with 7 file(s) remaining \rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/contents/curation_notes.txt\nCompleted 240.1 KiB/465.2 KiB (922.5 KiB/s) with 6 file(s) remaining\rCompleted 242.3 KiB/465.2 KiB (848.0 KiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/contents/manifest.xml\nCompleted 242.3 KiB/465.2 KiB (848.0 KiB/s) with 5 file(s) remaining\rCompleted 274.9 KiB/465.2 KiB (905.1 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000005.png to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/contents/BIOMD0000000005.png\nCompleted 274.9 KiB/465.2 KiB (905.1 KiB/s) with 4 file(s) remaining\rCompleted 280.6 KiB/465.2 KiB (916.8 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000005.m to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/contents/BIOMD0000000005.m\nCompleted 280.6 KiB/465.2 KiB (916.8 KiB/s) with 3 file(s) remaining\rCompleted 284.5 KiB/465.2 KiB (923.1 KiB/s) with 3 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/contents/metadata.rdf\nCompleted 284.5 KiB/465.2 KiB (923.1 KiB/s) with 2 file(s) remaining\rCompleted 287.8 KiB/465.2 KiB (927.9 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000005.ode to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/contents/BIOMD0000000005.ode\nCompleted 287.8 KiB/465.2 KiB (927.9 KiB/s) with 1 file(s) remaining\rCompleted 465.2 KiB/465.2 KiB (1.4 MiB/s) with 1 file(s) remaining  \rupload: contents/BIOMD0000000005.pdf to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/contents/BIOMD0000000005.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.7 KiB/9.7 KiB (139.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647106fc9a62a8be53f734d7/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000005.sedml\ncreating dataset /BIOMD0000000005.sedml/autogen_report_for_task1, shape: (20, 1001), type: float64\ndataset created, uuid: d-58c73119-780fd036-c0fe-d26698-b2182c, chunk_size: (20, 1001)\ncreating dataset /BIOMD0000000005.sedml/plot1, shape: (3, 1001), type: float64\ndataset created, uuid: d-58c73119-780fd036-61b5-2d5552-ff10bc, chunk_size: (3, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000005.sedml\ncreating attribute uri in /BIOMD0000000005.sedml\ncreating attribute _type in /BIOMD0000000005.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000005.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000005.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000005.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000005.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000005.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000005.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000005.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000005.sedml/autogen_report_for_task1\ncreating attribute _type in /BIOMD0000000005.sedml/plot1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000005.sedml/plot1\ncreating attribute sedmlDataSetIds in /BIOMD0000000005.sedml/plot1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000005.sedml/plot1\ncreating attribute sedmlDataSetNames in /BIOMD0000000005.sedml/plot1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000005.sedml/plot1\ncreating attribute sedmlId in /BIOMD0000000005.sedml/plot1\ncreating attribute sedmlName in /BIOMD0000000005.sedml/plot1\ncreating attribute uri in /BIOMD0000000005.sedml/plot1\ncreate_links: /\ngot link: BIOMD0000000005.sedml\ncreate_links: /BIOMD0000000005.sedml\ngot link: autogen_report_for_task1\ngot link: plot1\nwrite_dataset src: /BIOMD0000000005.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000005.sedml/autogen_report_for_task1, shape: (20, 1001), type: float64\niterating over chunks for /BIOMD0000000005.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 20, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000005.sedml/autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000005.sedml/plot1 to tgt: /BIOMD0000000005.sedml/plot1, shape: (3, 1001), type: float64\niterating over chunks for /BIOMD0000000005.sedml/plot1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000005.sedml/plot1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647106fc9a62a8be53f734d7\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 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.\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":1.419859,"sedDocuments":[{"location":"BIOMD0000000005.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  BIOMD0000000005.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 20 data sets\r\n    Plots (1):\r\n      plot1: 2 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000005.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_report_for_task1`\r\n      `plot1`\r\n  Executing task 1: `task1`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `plot1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_report_for_task1` ...","duration":0.970228,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.218466,"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":"plot1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.406834,"curves":[{"id":"curve_0","status":"SUCCEEDED"},{"id":"curve_1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.205429,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_YT","status":"SUCCEEDED"},{"id":"autogen_task1_M","status":"SUCCEEDED"},{"id":"autogen_task1_EmptySet","status":"SUCCEEDED"},{"id":"autogen_task1_C2","status":"SUCCEEDED"},{"id":"autogen_task1_CP","status":"SUCCEEDED"},{"id":"autogen_task1_pM","status":"SUCCEEDED"},{"id":"autogen_task1_Y","status":"SUCCEEDED"},{"id":"autogen_task1_YP","status":"SUCCEEDED"},{"id":"autogen_task1_CT","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction1","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction2","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction3","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction4","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction5","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction6","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction7","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction8","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction9","status":"SUCCEEDED"}]}]}]}