{"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    462      0 --:--:-- --:--:-- --:--:--   461\r100   139  100   139    0     0    454      0 --:--:-- --:--:-- --:--:--   454\n\r100  315k  100  315k    0     0   723k      0 --:--:-- --:--:-- --:--:--  723k\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 (24.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/rawLog.txt\nCompleted 3.2 KiB/3.2 KiB (48.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 78%)\n  adding: outputs/BIOMD0000000456_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000456_url.sedml/autogen_plot_for_task1.pdf (deflated 33%)\n  adding: outputs/reports.h5 (deflated 57%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 42.1 KiB/42.1 KiB (525.1 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/outputs/reports.h5\nCompleted 26.4 KiB/43.6 KiB (363.4 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/output.zip\nCompleted 26.4 KiB/43.6 KiB (363.4 KiB/s) with 3 file(s) remaining\rCompleted 32.2 KiB/43.6 KiB (290.6 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/outputs/plots.zip\nCompleted 32.2 KiB/43.6 KiB (290.6 KiB/s) with 2 file(s) remaining\rCompleted 40.9 KiB/43.6 KiB (359.7 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000456_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/outputs/BIOMD0000000456_url.sedml/autogen_plot_for_task1.pdf\nCompleted 40.9 KiB/43.6 KiB (359.7 KiB/s) with 1 file(s) remaining\rCompleted 43.6 KiB/43.6 KiB (353.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000456-biopax2.owl  \n  inflating: contents/BIOMD0000000456-biopax3.owl  \n  inflating: contents/BIOMD0000000456-matlab.m  \n  inflating: contents/BIOMD0000000456-octave.m  \n  inflating: contents/BIOMD0000000456.m  \n  inflating: contents/BIOMD0000000456.ode  \n  inflating: contents/BIOMD0000000456.pdf  \n  inflating: contents/BIOMD0000000456.png  \n  inflating: contents/BIOMD0000000456.svg  \n  inflating: contents/BIOMD0000000456_url.sedml  \n  inflating: contents/BIOMD0000000456_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 18.1 KiB/457.6 KiB (243.3 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000456-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/contents/BIOMD0000000456-biopax3.owl\nCompleted 18.1 KiB/457.6 KiB (243.3 KiB/s) with 14 file(s) remaining\rCompleted 29.7 KiB/457.6 KiB (259.5 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000456-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/contents/BIOMD0000000456-biopax2.owl\nCompleted 29.7 KiB/457.6 KiB (259.5 KiB/s) with 13 file(s) remaining\rCompleted 34.4 KiB/457.6 KiB (274.4 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000456-matlab.m to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/contents/BIOMD0000000456-matlab.m\nCompleted 34.4 KiB/457.6 KiB (274.4 KiB/s) with 12 file(s) remaining\rCompleted 38.5 KiB/457.6 KiB (286.3 KiB/s) with 12 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/contents/metadata.rdf\nCompleted 38.5 KiB/457.6 KiB (286.3 KiB/s) with 11 file(s) remaining\rCompleted 43.3 KiB/457.6 KiB (315.8 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000456-octave.m to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/contents/BIOMD0000000456-octave.m\nCompleted 43.3 KiB/457.6 KiB (315.8 KiB/s) with 10 file(s) remaining\rCompleted 63.8 KiB/457.6 KiB (418.7 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000456.svg to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/contents/BIOMD0000000456.svg\nCompleted 63.8 KiB/457.6 KiB (418.7 KiB/s) with 9 file(s) remaining\rCompleted 75.5 KiB/457.6 KiB (473.6 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000456_url.sedml to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/contents/BIOMD0000000456_url.sedml\nCompleted 75.5 KiB/457.6 KiB (473.6 KiB/s) with 8 file(s) remaining\rCompleted 75.6 KiB/457.6 KiB (426.3 KiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/contents/curation_notes.txt\nCompleted 75.6 KiB/457.6 KiB (426.3 KiB/s) with 7 file(s) remaining\rCompleted 94.9 KiB/457.6 KiB (512.6 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000456_url.xml to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/contents/BIOMD0000000456_url.xml\nCompleted 94.9 KiB/457.6 KiB (512.6 KiB/s) with 6 file(s) remaining\rCompleted 197.7 KiB/457.6 KiB (1.0 MiB/s) with 6 file(s) remaining \rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/contents/curation_image.png\nCompleted 197.7 KiB/457.6 KiB (1.0 MiB/s) with 5 file(s) remaining\rCompleted 202.4 KiB/457.6 KiB (1.0 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000456.m to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/contents/BIOMD0000000456.m\nCompleted 202.4 KiB/457.6 KiB (1.0 MiB/s) with 4 file(s) remaining\rCompleted 204.2 KiB/457.6 KiB (1018.8 KiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/contents/manifest.xml\nCompleted 204.2 KiB/457.6 KiB (1018.8 KiB/s) with 3 file(s) remaining\rCompleted 283.8 KiB/457.6 KiB (1.3 MiB/s) with 3 file(s) remaining   \rupload: contents/BIOMD0000000456.png to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/contents/BIOMD0000000456.png\nCompleted 283.8 KiB/457.6 KiB (1.3 MiB/s) with 2 file(s) remaining\rCompleted 455.1 KiB/457.6 KiB (2.0 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000456.pdf to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/contents/BIOMD0000000456.pdf\nCompleted 455.1 KiB/457.6 KiB (2.0 MiB/s) with 1 file(s) remaining\rCompleted 457.6 KiB/457.6 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000456.ode to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/contents/BIOMD0000000456.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (123.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b37195afd5df175ec28/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000456_url.sedml\ncreating dataset /BIOMD0000000456_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\ndataset created, uuid: d-f4b41c77-0c9dc24e-2dcc-1031b7-5ef651, chunk_size: (12, 1001)\ncreating dataset /BIOMD0000000456_url.sedml/autogen_report_for_task1, shape: (19, 1001), type: float64\ndataset created, uuid: d-f4b41c77-0c9dc24e-d12e-83acbc-cbdf9e, chunk_size: (19, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000456_url.sedml\ncreating attribute uri in /BIOMD0000000456_url.sedml\ncreating attribute _type in /BIOMD0000000456_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000456_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000456_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000456_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000456_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000456_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000456_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000456_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000456_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000456_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000456_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000456_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000456_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000456_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000456_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000456_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000456_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000456_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000456_url.sedml\ncreate_links: /BIOMD0000000456_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000456_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000456_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\niterating over chunks for /BIOMD0000000456_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 12, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000456_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000456_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000456_url.sedml/autogen_report_for_task1, shape: (19, 1001), type: float64\niterating over chunks for /BIOMD0000000456_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 19, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000456_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b37195afd5df175ec28\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.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... 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.\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":1.400228,"sedDocuments":[{"location":"BIOMD0000000456_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  BIOMD0000000456_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: 11 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000456_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":1.038345,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.147369,"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":0.209972,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_x1","status":"SUCCEEDED"},{"id":"autogen_task1_x2","status":"SUCCEEDED"},{"id":"autogen_task1_x3","status":"SUCCEEDED"},{"id":"autogen_task1_y1","status":"SUCCEEDED"},{"id":"autogen_task1_y2","status":"SUCCEEDED"},{"id":"autogen_task1_y3","status":"SUCCEEDED"},{"id":"autogen_task1_y4","status":"SUCCEEDED"},{"id":"autogen_task1_y5","status":"SUCCEEDED"},{"id":"autogen_task1_y7","status":"SUCCEEDED"},{"id":"autogen_task1_x4","status":"SUCCEEDED"},{"id":"autogen_task1_y8","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_v1","status":"SUCCEEDED"},{"id":"autogen_task1_v2","status":"SUCCEEDED"},{"id":"autogen_task1_v3","status":"SUCCEEDED"},{"id":"autogen_task1_v4","status":"SUCCEEDED"},{"id":"autogen_task1_v6","status":"SUCCEEDED"},{"id":"autogen_task1_v7","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.548082,"curves":[{"id":"autogen_curve_task1_x1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_x2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_x3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_y1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_y2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_y3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_y4","status":"SUCCEEDED"},{"id":"autogen_curve_task1_y5","status":"SUCCEEDED"},{"id":"autogen_curve_task1_y7","status":"SUCCEEDED"},{"id":"autogen_curve_task1_x4","status":"SUCCEEDED"},{"id":"autogen_curve_task1_y8","status":"SUCCEEDED"}]}]}]}