{"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    443      0 --:--:-- --:--:-- --:--:--   445\n\r100  162k  100  162k    0     0   382k      0 --:--:-- --:--:-- --:--:--  382k\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 (21.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/rawLog.txt\nCompleted 3.0 KiB/3.0 KiB (46.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/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/BIOMD0000000369_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000369_url.sedml/autogen_plot_for_task1.pdf (deflated 27%)\n  adding: outputs/reports.h5 (deflated 17%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 128.5 KiB/128.5 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/outputs/reports.h5\nCompleted 6.8 KiB/135.3 KiB (68.6 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/outputs/plots.zip\nCompleted 6.8 KiB/135.3 KiB (68.6 KiB/s) with 3 file(s) remaining\rCompleted 16.5 KiB/135.3 KiB (155.1 KiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000369_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/outputs/BIOMD0000000369_url.sedml/autogen_plot_for_task1.pdf\nCompleted 16.5 KiB/135.3 KiB (155.1 KiB/s) with 2 file(s) remaining\rCompleted 132.7 KiB/135.3 KiB (1.2 MiB/s) with 2 file(s) remaining \rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/output.zip\nCompleted 132.7 KiB/135.3 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 135.3 KiB/135.3 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000369-biopax2.owl  \n  inflating: contents/BIOMD0000000369-biopax3.owl  \n  inflating: contents/BIOMD0000000369-matlab.m  \n  inflating: contents/BIOMD0000000369-octave.m  \n  inflating: contents/BIOMD0000000369.m  \n  inflating: contents/BIOMD0000000369.ode  \n  inflating: contents/BIOMD0000000369.pdf  \n  inflating: contents/BIOMD0000000369.png  \n  inflating: contents/BIOMD0000000369.sci  \n  inflating: contents/BIOMD0000000369.svg  \n  inflating: contents/BIOMD0000000369_url.sedml  \n  inflating: contents/BIOMD0000000369_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 4.4 KiB/236.6 KiB (62.6 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000369-biopax3.owl to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/contents/BIOMD0000000369-biopax3.owl\nCompleted 4.4 KiB/236.6 KiB (62.6 KiB/s) with 15 file(s) remaining\rCompleted 8.6 KiB/236.6 KiB (84.0 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000369-matlab.m to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/contents/BIOMD0000000369-matlab.m\nCompleted 8.6 KiB/236.6 KiB (84.0 KiB/s) with 14 file(s) remaining\rCompleted 12.2 KiB/236.6 KiB (96.4 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000369-biopax2.owl to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/contents/BIOMD0000000369-biopax2.owl\nCompleted 12.2 KiB/236.6 KiB (96.4 KiB/s) with 13 file(s) remaining\rCompleted 14.1 KiB/236.6 KiB (109.4 KiB/s) with 13 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/contents/manifest.xml\nCompleted 14.1 KiB/236.6 KiB (109.4 KiB/s) with 12 file(s) remaining\rCompleted 14.9 KiB/236.6 KiB (113.7 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000369.svg to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/contents/BIOMD0000000369.svg\nCompleted 14.9 KiB/236.6 KiB (113.7 KiB/s) with 11 file(s) remaining\rCompleted 26.1 KiB/236.6 KiB (170.0 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000369_url.sedml to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/contents/BIOMD0000000369_url.sedml\nCompleted 26.1 KiB/236.6 KiB (170.0 KiB/s) with 10 file(s) remaining\rCompleted 27.9 KiB/236.6 KiB (179.8 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000369.sci to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/contents/BIOMD0000000369.sci\nCompleted 27.9 KiB/236.6 KiB (179.8 KiB/s) with 9 file(s) remaining\rCompleted 32.2 KiB/236.6 KiB (202.4 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000369-octave.m to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/contents/BIOMD0000000369-octave.m\nCompleted 32.2 KiB/236.6 KiB (202.4 KiB/s) with 8 file(s) remaining\rCompleted 41.3 KiB/236.6 KiB (256.8 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000369_url.xml to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/contents/BIOMD0000000369_url.xml\nCompleted 41.3 KiB/236.6 KiB (256.8 KiB/s) with 7 file(s) remaining\rCompleted 46.3 KiB/236.6 KiB (238.6 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000369.png to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/contents/BIOMD0000000369.png\nCompleted 46.3 KiB/236.6 KiB (238.6 KiB/s) with 6 file(s) remaining\rCompleted 46.4 KiB/236.6 KiB (233.6 KiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/contents/curation_notes.txt\nCompleted 46.4 KiB/236.6 KiB (233.6 KiB/s) with 5 file(s) remaining\rCompleted 48.5 KiB/236.6 KiB (227.9 KiB/s) with 5 file(s) remaining\rCompleted 52.7 KiB/236.6 KiB (245.2 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000369.m to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/contents/BIOMD0000000369.m\nCompleted 52.7 KiB/236.6 KiB (245.2 KiB/s) with 4 file(s) remaining\rCompleted 55.0 KiB/236.6 KiB (252.8 KiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/contents/metadata.rdf\nCompleted 55.0 KiB/236.6 KiB (252.8 KiB/s) with 3 file(s) remaining\rCompleted 189.1 KiB/236.6 KiB (858.1 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000369.pdf to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/contents/BIOMD0000000369.pdf\nCompleted 189.1 KiB/236.6 KiB (858.1 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000369.ode to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/contents/BIOMD0000000369.ode\nCompleted 189.1 KiB/236.6 KiB (858.1 KiB/s) with 1 file(s) remaining\rCompleted 236.6 KiB/236.6 KiB (756.2 KiB/s) with 1 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/contents/curation_image.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.8 KiB/8.8 KiB (89.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710bc149c0d898ffde1920/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000369_url.sedml\ncreating dataset /BIOMD0000000369_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\ndataset created, uuid: d-d7ede1e7-0bb870d2-ff4b-e9ab07-a7e995, chunk_size: (8, 1001)\ncreating dataset /BIOMD0000000369_url.sedml/autogen_report_for_task1, shape: (19, 1001), type: float64\ndataset created, uuid: d-d7ede1e7-0bb870d2-f03e-aebaf1-649dfd, chunk_size: (19, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000369_url.sedml\ncreating attribute uri in /BIOMD0000000369_url.sedml\ncreating attribute _type in /BIOMD0000000369_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000369_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000369_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000369_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000369_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000369_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000369_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000369_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000369_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000369_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000369_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000369_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000369_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000369_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000369_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000369_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000369_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000369_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000369_url.sedml\ncreate_links: /BIOMD0000000369_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000369_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000369_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\niterating over chunks for /BIOMD0000000369_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 8, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000369_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000369_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000369_url.sedml/autogen_report_for_task1, shape: (19, 1001), type: float64\niterating over chunks for /BIOMD0000000369_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 19, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000369_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710bc149c0d898ffde1920\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 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 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.\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":1.095423,"sedDocuments":[{"location":"BIOMD0000000369_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  BIOMD0000000369_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: 7 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000369_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":0.746047,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.110243,"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":0.156423,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Z1","status":"SUCCEEDED"},{"id":"autogen_task1_Z2","status":"SUCCEEDED"},{"id":"autogen_task1_Z4","status":"SUCCEEDED"},{"id":"autogen_task1_E1","status":"SUCCEEDED"},{"id":"autogen_task1_E2","status":"SUCCEEDED"},{"id":"autogen_task1_E3","status":"SUCCEEDED"},{"id":"autogen_task1_E4","status":"SUCCEEDED"},{"id":"autogen_task1_mu1","status":"SUCCEEDED"},{"id":"autogen_task1_mu2","status":"SUCCEEDED"},{"id":"autogen_task1_mu3","status":"SUCCEEDED"},{"id":"autogen_task1_mu4","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_mu5","status":"SUCCEEDED"},{"id":"autogen_task1_C","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_1","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.374211,"curves":[{"id":"autogen_curve_task1_Z1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Z2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Z4","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E4","status":"SUCCEEDED"}]}]}]}