{"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    435      0 --:--:-- --:--:-- --:--:--   435\n\r100  240k  100  240k    0     0   536k      0 --:--:-- --:--:-- --:--:--  536k\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 (14.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/rawLog.txt\nCompleted 2.9 KiB/2.9 KiB (25.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 77%)\n  adding: outputs/BIOMD0000000004_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000004_url.sedml/autogen_plot_for_task1.pdf (deflated 34%)\n  adding: outputs/reports.h5 (deflated 14%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 155.2 KiB/155.2 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/outputs/reports.h5\nCompleted 141.4 KiB/158.0 KiB (1.1 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/output.zip\nCompleted 141.4 KiB/158.0 KiB (1.1 MiB/s) with 3 file(s) remaining\rCompleted 146.9 KiB/158.0 KiB (1.1 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/outputs/plots.zip\nCompleted 146.9 KiB/158.0 KiB (1.1 MiB/s) with 2 file(s) remaining\rCompleted 155.3 KiB/158.0 KiB (1.1 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000004_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/outputs/BIOMD0000000004_url.sedml/autogen_plot_for_task1.pdf\nCompleted 155.3 KiB/158.0 KiB (1.1 MiB/s) with 1 file(s) remaining\rCompleted 158.0 KiB/158.0 KiB (917.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000004-biopax2.owl  \n  inflating: contents/BIOMD0000000004-biopax3.owl  \n  inflating: contents/BIOMD0000000004-matlab.m  \n  inflating: contents/BIOMD0000000004-octave.m  \n  inflating: contents/BIOMD0000000004.m  \n  inflating: contents/BIOMD0000000004.ode  \n  inflating: contents/BIOMD0000000004.pdf  \n  inflating: contents/BIOMD0000000004.png  \n  inflating: contents/BIOMD0000000004.sci  \n  inflating: contents/BIOMD0000000004.svg  \n  inflating: contents/BIOMD0000000004.vcml  \n  inflating: contents/BIOMD0000000004_manual.png  \n  inflating: contents/BIOMD0000000004_manual.svg  \n  inflating: contents/BIOMD0000000004_url.sedml  \n  inflating: contents/BIOMD0000000004_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 13.7 KiB/418.2 KiB (165.8 KiB/s) with 19 file(s) remaining\rupload: contents/BIOMD0000000004-biopax2.owl to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/contents/BIOMD0000000004-biopax2.owl\nCompleted 13.7 KiB/418.2 KiB (165.8 KiB/s) with 18 file(s) remaining\rCompleted 18.9 KiB/418.2 KiB (124.1 KiB/s) with 18 file(s) remaining\rupload: contents/BIOMD0000000004-matlab.m to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/contents/BIOMD0000000004-matlab.m\nCompleted 18.9 KiB/418.2 KiB (124.1 KiB/s) with 17 file(s) remaining\rCompleted 24.1 KiB/418.2 KiB (147.2 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000004-octave.m to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/contents/BIOMD0000000004-octave.m\nCompleted 24.1 KiB/418.2 KiB (147.2 KiB/s) with 16 file(s) remaining\rCompleted 64.7 KiB/418.2 KiB (381.8 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000004.png to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/contents/BIOMD0000000004.png\nCompleted 64.7 KiB/418.2 KiB (381.8 KiB/s) with 15 file(s) remaining\rCompleted 75.8 KiB/418.2 KiB (416.6 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000004_url.sedml to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/contents/BIOMD0000000004_url.sedml\nCompleted 75.8 KiB/418.2 KiB (416.6 KiB/s) with 14 file(s) remaining\rCompleted 78.6 KiB/418.2 KiB (393.8 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000004.sci to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/contents/BIOMD0000000004.sci\nCompleted 78.6 KiB/418.2 KiB (393.8 KiB/s) with 13 file(s) remaining\rCompleted 99.4 KiB/418.2 KiB (487.4 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000004.svg to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/contents/BIOMD0000000004.svg\nCompleted 99.4 KiB/418.2 KiB (487.4 KiB/s) with 12 file(s) remaining\rCompleted 127.3 KiB/418.2 KiB (619.0 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000004.vcml to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/contents/BIOMD0000000004.vcml\nCompleted 127.3 KiB/418.2 KiB (619.0 KiB/s) with 11 file(s) remaining\rCompleted 167.9 KiB/418.2 KiB (748.4 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000004_manual.png to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/contents/BIOMD0000000004_manual.png\nCompleted 167.9 KiB/418.2 KiB (748.4 KiB/s) with 10 file(s) remaining\rCompleted 187.4 KiB/418.2 KiB (787.2 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000004_url.xml to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/contents/BIOMD0000000004_url.xml\nCompleted 187.4 KiB/418.2 KiB (787.2 KiB/s) with 9 file(s) remaining\rCompleted 208.3 KiB/418.2 KiB (852.7 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000004_manual.svg to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/contents/BIOMD0000000004_manual.svg\nCompleted 208.3 KiB/418.2 KiB (852.7 KiB/s) with 8 file(s) remaining\rCompleted 213.7 KiB/418.2 KiB (862.9 KiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/contents/metadata.rdf\nCompleted 213.7 KiB/418.2 KiB (862.9 KiB/s) with 7 file(s) remaining\rCompleted 213.9 KiB/418.2 KiB (838.1 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/contents/curation_notes.txt\nCompleted 213.9 KiB/418.2 KiB (838.1 KiB/s) with 6 file(s) remaining\rCompleted 227.7 KiB/418.2 KiB (830.2 KiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/contents/curation_image.png\nCompleted 227.7 KiB/418.2 KiB (830.2 KiB/s) with 5 file(s) remaining\rCompleted 229.9 KiB/418.2 KiB (830.9 KiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/contents/manifest.xml\nCompleted 229.9 KiB/418.2 KiB (830.9 KiB/s) with 4 file(s) remaining\rCompleted 232.8 KiB/418.2 KiB (782.0 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000004.ode to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/contents/BIOMD0000000004.ode\nCompleted 232.8 KiB/418.2 KiB (782.0 KiB/s) with 3 file(s) remaining\rCompleted 238.0 KiB/418.2 KiB (787.5 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000004.m to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/contents/BIOMD0000000004.m\nCompleted 238.0 KiB/418.2 KiB (787.5 KiB/s) with 2 file(s) remaining\rCompleted 399.5 KiB/418.2 KiB (1.2 MiB/s) with 2 file(s) remaining  \rupload: contents/BIOMD0000000004.pdf to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/contents/BIOMD0000000004.pdf\nCompleted 399.5 KiB/418.2 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 418.2 KiB/418.2 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000004-biopax3.owl to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/contents/BIOMD0000000004-biopax3.owl\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.8 KiB/9.8 KiB (64.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647106f90dcacb55678b35fe/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000004_url.sedml\ncreating dataset /BIOMD0000000004_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\ndataset created, uuid: d-6a47fbbc-19abf4b4-9bf1-1904cc-f8ec8c, chunk_size: (6, 1001)\ncreating dataset /BIOMD0000000004_url.sedml/autogen_report_for_task1, shape: (19, 1001), type: float64\ndataset created, uuid: d-6a47fbbc-19abf4b4-b3d8-9ede69-4b4b82, chunk_size: (19, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000004_url.sedml\ncreating attribute uri in /BIOMD0000000004_url.sedml\ncreating attribute _type in /BIOMD0000000004_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000004_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000004_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000004_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000004_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000004_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000004_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000004_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000004_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000004_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000004_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000004_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000004_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000004_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000004_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000004_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000004_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000004_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000004_url.sedml\ncreate_links: /BIOMD0000000004_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000004_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000004_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\niterating over chunks for /BIOMD0000000004_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000004_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000004_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000004_url.sedml/autogen_report_for_task1, shape: (19, 1001), type: float64\niterating over chunks for /BIOMD0000000004_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 19, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000004_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647106f90dcacb55678b35fe\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 SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata 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":1.240461,"sedDocuments":[{"location":"BIOMD0000000004_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  BIOMD0000000004_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 19 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 5 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000004_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":0.8679,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.137713,"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":0.196379,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_C","status":"SUCCEEDED"},{"id":"autogen_task1_M","status":"SUCCEEDED"},{"id":"autogen_task1_X","status":"SUCCEEDED"},{"id":"autogen_task1_MI","status":"SUCCEEDED"},{"id":"autogen_task1_XI","status":"SUCCEEDED"},{"id":"autogen_task1_V1","status":"SUCCEEDED"},{"id":"autogen_task1_V3","status":"SUCCEEDED"},{"id":"autogen_task1_VM1","status":"SUCCEEDED"},{"id":"autogen_task1_VM3","status":"SUCCEEDED"},{"id":"autogen_task1_Kc","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_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.420318,"curves":[{"id":"autogen_curve_task1_C","status":"SUCCEEDED"},{"id":"autogen_curve_task1_M","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X","status":"SUCCEEDED"},{"id":"autogen_curve_task1_MI","status":"SUCCEEDED"},{"id":"autogen_curve_task1_XI","status":"SUCCEEDED"}]}]}]}