{"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    485      0 --:--:-- --:--:-- --:--:--   486\n\r100  235k  100  235k    0     0   602k      0 --:--:-- --:--:-- --:--:--  602k\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 (26.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/rawLog.txt\nCompleted 3.0 KiB/3.0 KiB (47.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/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/BIOMD0000000487_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000487_url.sedml/autogen_plot_for_task1.pdf (deflated 33%)\n  adding: outputs/reports.h5 (deflated 79%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 28.0 KiB/28.0 KiB (400.3 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/outputs/reports.h5\nCompleted 14.0 KiB/31.0 KiB (206.1 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/output.zip\nCompleted 14.0 KiB/31.0 KiB (206.1 KiB/s) with 3 file(s) remaining\rCompleted 22.7 KiB/31.0 KiB (222.4 KiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000487_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/outputs/BIOMD0000000487_url.sedml/autogen_plot_for_task1.pdf\nCompleted 22.7 KiB/31.0 KiB (222.4 KiB/s) with 2 file(s) remaining\rCompleted 28.4 KiB/31.0 KiB (242.1 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/outputs/plots.zip\nCompleted 28.4 KiB/31.0 KiB (242.1 KiB/s) with 1 file(s) remaining\rCompleted 31.0 KiB/31.0 KiB (213.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000487-biopax2.owl  \n  inflating: contents/BIOMD0000000487-biopax3.owl  \n  inflating: contents/BIOMD0000000487-matlab.m  \n  inflating: contents/BIOMD0000000487-octave.m  \n  inflating: contents/BIOMD0000000487.m  \n  inflating: contents/BIOMD0000000487.ode  \n  inflating: contents/BIOMD0000000487.pdf  \n  inflating: contents/BIOMD0000000487.png  \n  inflating: contents/BIOMD0000000487.sci  \n  inflating: contents/BIOMD0000000487.svg  \n  inflating: contents/BIOMD0000000487.vcml  \n  inflating: contents/BIOMD0000000487_url.sedml  \n  inflating: contents/BIOMD0000000487_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 13.3 KiB/389.1 KiB (174.1 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000487-biopax2.owl to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/contents/BIOMD0000000487-biopax2.owl\nCompleted 13.3 KiB/389.1 KiB (174.1 KiB/s) with 16 file(s) remaining\rCompleted 15.3 KiB/389.1 KiB (140.4 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000487.ode to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/contents/BIOMD0000000487.ode\nCompleted 15.3 KiB/389.1 KiB (140.4 KiB/s) with 15 file(s) remaining\rCompleted 19.2 KiB/389.1 KiB (151.6 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000487.m to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/contents/BIOMD0000000487.m\nCompleted 19.2 KiB/389.1 KiB (151.6 KiB/s) with 14 file(s) remaining\rCompleted 37.2 KiB/389.1 KiB (288.0 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000487.svg to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/contents/BIOMD0000000487.svg\nCompleted 37.2 KiB/389.1 KiB (288.0 KiB/s) with 13 file(s) remaining\rCompleted 197.3 KiB/389.1 KiB (1.4 MiB/s) with 13 file(s) remaining \rupload: contents/BIOMD0000000487.pdf to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/contents/BIOMD0000000487.pdf\nCompleted 197.3 KiB/389.1 KiB (1.4 MiB/s) with 12 file(s) remaining\rCompleted 210.1 KiB/389.1 KiB (1.5 MiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000487_url.xml to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/contents/BIOMD0000000487_url.xml\nCompleted 210.1 KiB/389.1 KiB (1.5 MiB/s) with 11 file(s) remaining\rCompleted 221.6 KiB/389.1 KiB (1.5 MiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000487_url.sedml to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/contents/BIOMD0000000487_url.sedml\nCompleted 221.6 KiB/389.1 KiB (1.5 MiB/s) with 10 file(s) remaining\rCompleted 223.3 KiB/389.1 KiB (1.5 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000487.sci to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/contents/BIOMD0000000487.sci\nCompleted 223.3 KiB/389.1 KiB (1.5 MiB/s) with 9 file(s) remaining\rCompleted 243.7 KiB/389.1 KiB (1.6 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000487.vcml to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/contents/BIOMD0000000487.vcml\nCompleted 243.7 KiB/389.1 KiB (1.6 MiB/s) with 8 file(s) remaining\rCompleted 330.8 KiB/389.1 KiB (2.2 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000487.png to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/contents/BIOMD0000000487.png\nCompleted 330.8 KiB/389.1 KiB (2.2 MiB/s) with 7 file(s) remaining\rCompleted 356.7 KiB/389.1 KiB (2.1 MiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/contents/curation_image.png\nCompleted 356.7 KiB/389.1 KiB (2.1 MiB/s) with 6 file(s) remaining\rCompleted 376.8 KiB/389.1 KiB (2.1 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000487-biopax3.owl to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/contents/BIOMD0000000487-biopax3.owl\nCompleted 376.8 KiB/389.1 KiB (2.1 MiB/s) with 5 file(s) remaining\rCompleted 377.4 KiB/389.1 KiB (1.9 MiB/s) with 5 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/contents/curation_notes.txt\nCompleted 377.4 KiB/389.1 KiB (1.9 MiB/s) with 4 file(s) remaining\rCompleted 379.4 KiB/389.1 KiB (1.9 MiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/contents/manifest.xml\nCompleted 379.4 KiB/389.1 KiB (1.9 MiB/s) with 3 file(s) remaining\rCompleted 383.3 KiB/389.1 KiB (1.9 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000487-octave.m to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/contents/BIOMD0000000487-octave.m\nCompleted 383.3 KiB/389.1 KiB (1.9 MiB/s) with 2 file(s) remaining\rCompleted 385.2 KiB/389.1 KiB (1.8 MiB/s) with 2 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/contents/metadata.rdf\nCompleted 385.2 KiB/389.1 KiB (1.8 MiB/s) with 1 file(s) remaining\rCompleted 389.1 KiB/389.1 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000487-matlab.m to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/contents/BIOMD0000000487-matlab.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.1 KiB/9.1 KiB (139.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710d7649c0d898ffde64a3/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000487_url.sedml\ncreating dataset /BIOMD0000000487_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\ndataset created, uuid: d-f5e90718-36d25b4b-b439-3161ac-ee5234, chunk_size: (7, 1001)\ncreating dataset /BIOMD0000000487_url.sedml/autogen_report_for_task1, shape: (20, 1001), type: float64\ndataset created, uuid: d-f5e90718-36d25b4b-51e3-5121a0-9ab003, chunk_size: (20, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000487_url.sedml\ncreating attribute uri in /BIOMD0000000487_url.sedml\ncreating attribute _type in /BIOMD0000000487_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000487_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000487_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000487_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000487_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000487_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000487_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000487_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000487_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000487_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000487_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000487_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000487_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000487_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000487_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000487_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000487_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000487_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000487_url.sedml\ncreate_links: /BIOMD0000000487_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000487_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000487_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\niterating over chunks for /BIOMD0000000487_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000487_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000487_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000487_url.sedml/autogen_report_for_task1, shape: (20, 1001), type: float64\niterating over chunks for /BIOMD0000000487_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 20, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000487_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710d7649c0d898ffde64a3\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 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 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.\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":1.188093,"sedDocuments":[{"location":"BIOMD0000000487_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  BIOMD0000000487_url.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      autogen_plot_for_task1: 6 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000487_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":0.841479,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.124459,"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":0.201446,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_S1","status":"SUCCEEDED"},{"id":"autogen_task1_S2","status":"SUCCEEDED"},{"id":"autogen_task1_S3","status":"SUCCEEDED"},{"id":"autogen_task1_S4","status":"SUCCEEDED"},{"id":"autogen_task1_S5","status":"SUCCEEDED"},{"id":"autogen_task1_S6","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_default","status":"SUCCEEDED"},{"id":"autogen_task1_re1","status":"SUCCEEDED"},{"id":"autogen_task1_re2","status":"SUCCEEDED"},{"id":"autogen_task1_re3","status":"SUCCEEDED"},{"id":"autogen_task1_re4","status":"SUCCEEDED"},{"id":"autogen_task1_re5","status":"SUCCEEDED"},{"id":"autogen_task1_re6","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.411962,"curves":[{"id":"autogen_curve_task1_S1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_S2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_S3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_S4","status":"SUCCEEDED"},{"id":"autogen_curve_task1_S5","status":"SUCCEEDED"},{"id":"autogen_curve_task1_S6","status":"SUCCEEDED"}]}]}]}