{"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    438      0 --:--:-- --:--:-- --:--:--   438\n\r100  188k  100  188k    0     0   402k      0 --:--:-- --:--:-- --:--:--  402k\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 (22.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/rawLog.txt\nCompleted 4.0 KiB/4.0 KiB (38.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 81%)\n  adding: outputs/BIOMD0000000331_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000331_url.sedml/autogen_plot_for_task1.pdf (deflated 24%)\n  adding: outputs/reports.h5 (deflated 20%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 140.2 KiB/140.2 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/outputs/reports.h5\nCompleted 127.5 KiB/159.6 KiB (1.4 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/output.zip\nCompleted 127.5 KiB/159.6 KiB (1.4 MiB/s) with 3 file(s) remaining\rCompleted 144.4 KiB/159.6 KiB (1.2 MiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000331_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/outputs/BIOMD0000000331_url.sedml/autogen_plot_for_task1.pdf\nCompleted 144.4 KiB/159.6 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 157.0 KiB/159.6 KiB (1.2 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/outputs/plots.zip\nCompleted 157.0 KiB/159.6 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 159.6 KiB/159.6 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000331-biopax2.owl  \n  inflating: contents/BIOMD0000000331-biopax3.owl  \n  inflating: contents/BIOMD0000000331-matlab.m  \n  inflating: contents/BIOMD0000000331-octave.m  \n  inflating: contents/BIOMD0000000331.m  \n  inflating: contents/BIOMD0000000331.ode  \n  inflating: contents/BIOMD0000000331.pdf  \n  inflating: contents/BIOMD0000000331.png  \n  inflating: contents/BIOMD0000000331.sci  \n  inflating: contents/BIOMD0000000331.svg  \n  inflating: contents/BIOMD0000000331_url.sedml  \n  inflating: contents/BIOMD0000000331_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/293.3 KiB (102.0 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000331-biopax2.owl to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/contents/BIOMD0000000331-biopax2.owl\nCompleted 6.5 KiB/293.3 KiB (102.0 KiB/s) with 15 file(s) remaining\rCompleted 12.4 KiB/293.3 KiB (107.4 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000331-matlab.m to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/contents/BIOMD0000000331-matlab.m\nCompleted 12.4 KiB/293.3 KiB (107.4 KiB/s) with 14 file(s) remaining\rCompleted 15.5 KiB/293.3 KiB (128.4 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000331.sci to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/contents/BIOMD0000000331.sci\nCompleted 15.5 KiB/293.3 KiB (128.4 KiB/s) with 13 file(s) remaining\rCompleted 19.8 KiB/293.3 KiB (152.8 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000331.png to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/contents/BIOMD0000000331.png\nCompleted 19.8 KiB/293.3 KiB (152.8 KiB/s) with 12 file(s) remaining\rCompleted 20.0 KiB/293.3 KiB (140.8 KiB/s) with 12 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/contents/curation_notes.txt\nCompleted 20.0 KiB/293.3 KiB (140.8 KiB/s) with 11 file(s) remaining\rCompleted 26.0 KiB/293.3 KiB (179.6 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000331-octave.m to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/contents/BIOMD0000000331-octave.m\nCompleted 26.0 KiB/293.3 KiB (179.6 KiB/s) with 10 file(s) remaining\rCompleted 26.8 KiB/293.3 KiB (178.2 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000331.svg to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/contents/BIOMD0000000331.svg\nCompleted 26.8 KiB/293.3 KiB (178.2 KiB/s) with 9 file(s) remaining\rCompleted 47.2 KiB/293.3 KiB (287.4 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000331_url.sedml to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/contents/BIOMD0000000331_url.sedml\nCompleted 47.2 KiB/293.3 KiB (287.4 KiB/s) with 8 file(s) remaining\rCompleted 51.0 KiB/293.3 KiB (295.6 KiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/contents/metadata.rdf\nCompleted 51.0 KiB/293.3 KiB (295.6 KiB/s) with 7 file(s) remaining\rCompleted 52.9 KiB/293.3 KiB (301.4 KiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/contents/manifest.xml\nCompleted 52.9 KiB/293.3 KiB (301.4 KiB/s) with 6 file(s) remaining\rCompleted 107.5 KiB/293.3 KiB (579.0 KiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/contents/curation_image.png\nCompleted 107.5 KiB/293.3 KiB (579.0 KiB/s) with 5 file(s) remaining\rCompleted 129.1 KiB/293.3 KiB (660.3 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000331_url.xml to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/contents/BIOMD0000000331_url.xml\nCompleted 129.1 KiB/293.3 KiB (660.3 KiB/s) with 4 file(s) remaining\rCompleted 132.8 KiB/293.3 KiB (669.0 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000331.ode to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/contents/BIOMD0000000331.ode\nCompleted 132.8 KiB/293.3 KiB (669.0 KiB/s) with 3 file(s) remaining\rCompleted 280.1 KiB/293.3 KiB (1.3 MiB/s) with 3 file(s) remaining  \rupload: contents/BIOMD0000000331.pdf to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/contents/BIOMD0000000331.pdf\nCompleted 280.1 KiB/293.3 KiB (1.3 MiB/s) with 2 file(s) remaining\rCompleted 286.0 KiB/293.3 KiB (1.3 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000331.m to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/contents/BIOMD0000000331.m\nCompleted 286.0 KiB/293.3 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 293.3 KiB/293.3 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000331-biopax3.owl to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/contents/BIOMD0000000331-biopax3.owl\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.8 KiB/8.8 KiB (91.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a280d0fb37cdb9ae4db00/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000331_url.sedml\ncreating dataset /BIOMD0000000331_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\ndataset created, uuid: d-7c8b2da2-b2d1c1e4-0c6c-78b06c-9b89b0, chunk_size: (8, 1001)\ncreating dataset /BIOMD0000000331_url.sedml/autogen_report_for_task1, shape: (38, 1001), type: float64\ndataset created, uuid: d-7c8b2da2-b2d1c1e4-5e08-97ae3d-99f770, chunk_size: (38, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000331_url.sedml\ncreating attribute uri in /BIOMD0000000331_url.sedml\ncreating attribute _type in /BIOMD0000000331_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000331_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000331_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000331_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000331_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000331_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000331_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000331_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000331_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000331_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000331_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000331_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000331_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000331_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000331_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000331_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000331_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000331_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000331_url.sedml\ncreate_links: /BIOMD0000000331_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000331_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000331_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\niterating over chunks for /BIOMD0000000331_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 8, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000331_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000331_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000331_url.sedml/autogen_report_for_task1, shape: (38, 1001), type: float64\niterating over chunks for /BIOMD0000000331_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 38, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000331_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a280d0fb37cdb9ae4db00\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 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 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":1.618445,"sedDocuments":[{"location":"BIOMD0000000331_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  BIOMD0000000331_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 38 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 7 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000331_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":1.129989,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.178826,"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":0.324599,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_G_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_PLC","status":"SUCCEEDED"},{"id":"autogen_task1_Ca_cyt","status":"SUCCEEDED"},{"id":"autogen_task1_Ca_ER","status":"SUCCEEDED"},{"id":"autogen_task1_Ca_mit","status":"SUCCEEDED"},{"id":"autogen_task1_Enz","status":"SUCCEEDED"},{"id":"autogen_task1_Product","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_K4","status":"SUCCEEDED"},{"id":"autogen_task1_k5","status":"SUCCEEDED"},{"id":"autogen_task1_K6","status":"SUCCEEDED"},{"id":"autogen_task1_k7","status":"SUCCEEDED"},{"id":"autogen_task1_k8","status":"SUCCEEDED"},{"id":"autogen_task1_K9","status":"SUCCEEDED"},{"id":"autogen_task1_k10","status":"SUCCEEDED"},{"id":"autogen_task1_K11","status":"SUCCEEDED"},{"id":"autogen_task1_k12","status":"SUCCEEDED"},{"id":"autogen_task1_k13","status":"SUCCEEDED"},{"id":"autogen_task1_k14","status":"SUCCEEDED"},{"id":"autogen_task1_K15","status":"SUCCEEDED"},{"id":"autogen_task1_k16","status":"SUCCEEDED"},{"id":"autogen_task1_K17","status":"SUCCEEDED"},{"id":"autogen_task1_k18","status":"SUCCEEDED"},{"id":"autogen_task1_K19","status":"SUCCEEDED"},{"id":"autogen_task1_k20","status":"SUCCEEDED"},{"id":"autogen_task1_K21","status":"SUCCEEDED"},{"id":"autogen_task1_k_act","status":"SUCCEEDED"},{"id":"autogen_task1_KM","status":"SUCCEEDED"},{"id":"autogen_task1_k_inact","status":"SUCCEEDED"},{"id":"autogen_task1_p","status":"SUCCEEDED"},{"id":"autogen_task1_k_enz","status":"SUCCEEDED"},{"id":"autogen_task1_k_rem","status":"SUCCEEDED"},{"id":"autogen_task1_cytoplasm","status":"SUCCEEDED"},{"id":"autogen_task1_ER","status":"SUCCEEDED"},{"id":"autogen_task1_mit","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.46696,"curves":[{"id":"autogen_curve_task1_G_alpha","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PLC","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ca_cyt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ca_ER","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ca_mit","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Enz","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Product","status":"SUCCEEDED"}]}]}]}