{"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    446      0 --:--:-- --:--:-- --:--:--   448\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100  211k  100  211k    0     0   497k      0 --:--:-- --:--:-- --:--:-- 2324k\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 (23.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/rawLog.txt\nCompleted 2.2 KiB/2.2 KiB (31.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 72%)\n  adding: outputs/BIOMD0000000319_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000319_url.sedml/autogen_plot_for_task1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 25%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 92.8 KiB/92.8 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/outputs/reports.h5\nCompleted 2.7 KiB/97.3 KiB (36.2 KiB/s) with 4 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/rawLog.txt\nCompleted 2.7 KiB/97.3 KiB (36.2 KiB/s) with 3 file(s) remaining\rCompleted 12.6 KiB/97.3 KiB (109.7 KiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000319_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/outputs/BIOMD0000000319_url.sedml/autogen_plot_for_task1.pdf\nCompleted 12.6 KiB/97.3 KiB (109.7 KiB/s) with 2 file(s) remaining\rCompleted 90.8 KiB/97.3 KiB (759.5 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/output.zip\nCompleted 90.8 KiB/97.3 KiB (759.5 KiB/s) with 1 file(s) remaining\rCompleted 97.3 KiB/97.3 KiB (794.0 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000319-biopax2.owl  \n  inflating: contents/BIOMD0000000319-biopax3.owl  \n  inflating: contents/BIOMD0000000319-matlab.m  \n  inflating: contents/BIOMD0000000319-octave.m  \n  inflating: contents/BIOMD0000000319.m  \n  inflating: contents/BIOMD0000000319.ode  \n  inflating: contents/BIOMD0000000319.pdf  \n  inflating: contents/BIOMD0000000319.png  \n  inflating: contents/BIOMD0000000319.svg  \n  inflating: contents/BIOMD0000000319_url.sedml  \n  inflating: contents/BIOMD0000000319_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 9.5 KiB/293.6 KiB (137.6 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000319-biopax3.owl to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/contents/BIOMD0000000319-biopax3.owl\nCompleted 9.5 KiB/293.6 KiB (137.6 KiB/s) with 14 file(s) remaining\rCompleted 12.8 KiB/293.6 KiB (111.8 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000319-matlab.m to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/contents/BIOMD0000000319-matlab.m\nCompleted 12.8 KiB/293.6 KiB (111.8 KiB/s) with 13 file(s) remaining\rCompleted 16.2 KiB/293.6 KiB (136.9 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000319-octave.m to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/contents/BIOMD0000000319-octave.m\nCompleted 16.2 KiB/293.6 KiB (136.9 KiB/s) with 12 file(s) remaining\rCompleted 22.7 KiB/293.6 KiB (188.7 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000319.svg to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/contents/BIOMD0000000319.svg\nCompleted 22.7 KiB/293.6 KiB (188.7 KiB/s) with 11 file(s) remaining\rCompleted 29.5 KiB/293.6 KiB (230.4 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000319-biopax2.owl to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/contents/BIOMD0000000319-biopax2.owl\nCompleted 29.5 KiB/293.6 KiB (230.4 KiB/s) with 10 file(s) remaining\rCompleted 31.2 KiB/293.6 KiB (241.5 KiB/s) with 10 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/contents/manifest.xml\nCompleted 31.2 KiB/293.6 KiB (241.5 KiB/s) with 9 file(s) remaining\rCompleted 37.2 KiB/293.6 KiB (279.5 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000319_url.sedml to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/contents/BIOMD0000000319_url.sedml\nCompleted 37.2 KiB/293.6 KiB (279.5 KiB/s) with 8 file(s) remaining\rCompleted 49.8 KiB/293.6 KiB (315.3 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000319_url.xml to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/contents/BIOMD0000000319_url.xml\nCompleted 49.8 KiB/293.6 KiB (315.3 KiB/s) with 7 file(s) remaining\rCompleted 60.2 KiB/293.6 KiB (348.4 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000319.png to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/contents/BIOMD0000000319.png\nCompleted 60.2 KiB/293.6 KiB (348.4 KiB/s) with 6 file(s) remaining\rCompleted 136.4 KiB/293.6 KiB (767.1 KiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/contents/curation_image.png\nCompleted 136.4 KiB/293.6 KiB (767.1 KiB/s) with 5 file(s) remaining\rCompleted 138.1 KiB/293.6 KiB (753.9 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000319.ode to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/contents/BIOMD0000000319.ode\nCompleted 138.1 KiB/293.6 KiB (753.9 KiB/s) with 4 file(s) remaining\rCompleted 138.6 KiB/293.6 KiB (745.2 KiB/s) with 4 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/contents/curation_notes.txt\nCompleted 138.6 KiB/293.6 KiB (745.2 KiB/s) with 3 file(s) remaining\rCompleted 141.7 KiB/293.6 KiB (749.8 KiB/s) with 3 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/contents/metadata.rdf\nCompleted 141.7 KiB/293.6 KiB (749.8 KiB/s) with 2 file(s) remaining\rCompleted 290.2 KiB/293.6 KiB (1.5 MiB/s) with 2 file(s) remaining  \rupload: contents/BIOMD0000000319.pdf to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/contents/BIOMD0000000319.pdf\nCompleted 290.2 KiB/293.6 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 293.6 KiB/293.6 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000319.m to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/contents/BIOMD0000000319.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (130.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710b200dcacb55678baad7/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000319_url.sedml\ncreating dataset /BIOMD0000000319_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-10c89aa8-edf3305c-d130-8709b7-96761e, chunk_size: (4, 1001)\ncreating dataset /BIOMD0000000319_url.sedml/autogen_report_for_task1, shape: (9, 1001), type: float64\ndataset created, uuid: d-10c89aa8-edf3305c-e523-40d7f4-93cc73, chunk_size: (9, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000319_url.sedml\ncreating attribute uri in /BIOMD0000000319_url.sedml\ncreating attribute _type in /BIOMD0000000319_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000319_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000319_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000319_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000319_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000319_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000319_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000319_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000319_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000319_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000319_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000319_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000319_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000319_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000319_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000319_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000319_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000319_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000319_url.sedml\ncreate_links: /BIOMD0000000319_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000319_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000319_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\niterating over chunks for /BIOMD0000000319_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000319_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000319_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000319_url.sedml/autogen_report_for_task1, shape: (9, 1001), type: float64\niterating over chunks for /BIOMD0000000319_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000319_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710b200dcacb55678baad7\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 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.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.059294,"sedDocuments":[{"location":"BIOMD0000000319_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  BIOMD0000000319_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 9 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000319_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":0.712658,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.120487,"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":0.123014,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_cell","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":0.368639,"curves":[{"id":"autogen_curve_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_curve_task1_beta","status":"SUCCEEDED"},{"id":"autogen_curve_task1_gamma","status":"SUCCEEDED"}]}]}]}