{"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    507      0 --:--:-- --:--:-- --:--:--   507\r100   139  100   139    0     0    507      0 --:--:-- --:--:-- --:--:--   507\n\r100  163k  100  163k    0     0   442k      0 --:--:-- --:--:-- --:--:--  442k\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 (24.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/rawLog.txt\nCompleted 2.4 KiB/2.4 KiB (41.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 73%)\n  adding: outputs/BIOMD0000000337_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000337_url.sedml/autogen_plot_for_task1.pdf (deflated 34%)\n  adding: outputs/reports.h5 (deflated 68%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 38.6 KiB/38.6 KiB (536.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/outputs/reports.h5\nCompleted 7.6 KiB/35.0 KiB (83.2 KiB/s) with 4 file(s) remaining\rupload: outputs/BIOMD0000000337_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/outputs/BIOMD0000000337_url.sedml/autogen_plot_for_task1.pdf\nCompleted 7.6 KiB/35.0 KiB (83.2 KiB/s) with 3 file(s) remaining\rCompleted 12.6 KiB/35.0 KiB (113.6 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/outputs/plots.zip\nCompleted 12.6 KiB/35.0 KiB (113.6 KiB/s) with 2 file(s) remaining\rCompleted 32.3 KiB/35.0 KiB (285.5 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/output.zip\nCompleted 32.3 KiB/35.0 KiB (285.5 KiB/s) with 1 file(s) remaining\rCompleted 35.0 KiB/35.0 KiB (286.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000337-biopax2.owl  \n  inflating: contents/BIOMD0000000337-biopax3.owl  \n  inflating: contents/BIOMD0000000337-matlab.m  \n  inflating: contents/BIOMD0000000337-octave.m  \n  inflating: contents/BIOMD0000000337.m  \n  inflating: contents/BIOMD0000000337.ode  \n  inflating: contents/BIOMD0000000337.pdf  \n  inflating: contents/BIOMD0000000337.png  \n  inflating: contents/BIOMD0000000337.svg  \n  inflating: contents/BIOMD0000000337_url.sedml  \n  inflating: contents/BIOMD0000000337_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 8.5 KiB/252.5 KiB (119.9 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000337-biopax2.owl to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/contents/BIOMD0000000337-biopax2.owl\nCompleted 8.5 KiB/252.5 KiB (119.9 KiB/s) with 14 file(s) remaining\rCompleted 23.4 KiB/252.5 KiB (199.5 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000337.png to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/contents/BIOMD0000000337.png\nCompleted 23.4 KiB/252.5 KiB (199.5 KiB/s) with 13 file(s) remaining\rCompleted 36.3 KiB/252.5 KiB (289.0 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000337_url.xml to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/contents/BIOMD0000000337_url.xml\nCompleted 36.3 KiB/252.5 KiB (289.0 KiB/s) with 12 file(s) remaining\rCompleted 37.8 KiB/252.5 KiB (294.9 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000337.ode to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/contents/BIOMD0000000337.ode\nCompleted 37.8 KiB/252.5 KiB (294.9 KiB/s) with 11 file(s) remaining\rCompleted 187.8 KiB/252.5 KiB (1.3 MiB/s) with 11 file(s) remaining \rupload: contents/BIOMD0000000337.pdf to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/contents/BIOMD0000000337.pdf\nCompleted 187.8 KiB/252.5 KiB (1.3 MiB/s) with 10 file(s) remaining\rCompleted 195.0 KiB/252.5 KiB (1.4 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000337_url.sedml to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/contents/BIOMD0000000337_url.sedml\nCompleted 195.0 KiB/252.5 KiB (1.4 MiB/s) with 9 file(s) remaining\rCompleted 198.3 KiB/252.5 KiB (1.2 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000337-matlab.m to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/contents/BIOMD0000000337-matlab.m\nCompleted 198.3 KiB/252.5 KiB (1.2 MiB/s) with 8 file(s) remaining\rCompleted 206.4 KiB/252.5 KiB (1.3 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000337.svg to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/contents/BIOMD0000000337.svg\nCompleted 206.4 KiB/252.5 KiB (1.3 MiB/s) with 7 file(s) remaining\rCompleted 230.0 KiB/252.5 KiB (1.4 MiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/contents/curation_image.png\nCompleted 230.0 KiB/252.5 KiB (1.4 MiB/s) with 6 file(s) remaining\rCompleted 233.2 KiB/252.5 KiB (1.4 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000337.m to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/contents/BIOMD0000000337.m\nCompleted 233.2 KiB/252.5 KiB (1.4 MiB/s) with 5 file(s) remaining\rCompleted 244.7 KiB/252.5 KiB (1.3 MiB/s) with 5 file(s) remaining\rCompleted 244.9 KiB/252.5 KiB (1.3 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000337-biopax3.owl to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/contents/BIOMD0000000337-biopax3.owl\nCompleted 244.9 KiB/252.5 KiB (1.3 MiB/s) with 4 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/contents/curation_notes.txt\nCompleted 244.9 KiB/252.5 KiB (1.3 MiB/s) with 3 file(s) remaining\rCompleted 248.1 KiB/252.5 KiB (1.2 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000337-octave.m to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/contents/BIOMD0000000337-octave.m\nCompleted 248.1 KiB/252.5 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 249.8 KiB/252.5 KiB (1.2 MiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/contents/manifest.xml\nCompleted 249.8 KiB/252.5 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 252.5 KiB/252.5 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/contents/metadata.rdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (130.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710b5b9a62a8be53f7b9bb/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000337_url.sedml\ncreating dataset /BIOMD0000000337_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-7a87834e-73c275c5-cd93-68eb3e-8552dc, chunk_size: (4, 1001)\ncreating dataset /BIOMD0000000337_url.sedml/autogen_report_for_task1, shape: (12, 1001), type: float64\ndataset created, uuid: d-7a87834e-73c275c5-c5ac-6b9b0d-e2caa9, chunk_size: (12, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000337_url.sedml\ncreating attribute uri in /BIOMD0000000337_url.sedml\ncreating attribute _type in /BIOMD0000000337_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000337_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000337_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000337_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000337_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000337_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000337_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000337_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000337_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000337_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000337_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000337_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000337_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000337_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000337_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000337_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000337_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000337_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000337_url.sedml\ncreate_links: /BIOMD0000000337_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000337_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000337_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\niterating over chunks for /BIOMD0000000337_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000337_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000337_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000337_url.sedml/autogen_report_for_task1, shape: (12, 1001), type: float64\niterating over chunks for /BIOMD0000000337_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 12, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000337_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710b5b9a62a8be53f7b9bb\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 and upload the outputs of the simulation run ... 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 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":1.186046,"sedDocuments":[{"location":"BIOMD0000000337_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  BIOMD0000000337_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 12 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000337_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":0.786689,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.116987,"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":0.170683,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_S","status":"SUCCEEDED"},{"id":"autogen_task1_N1","status":"SUCCEEDED"},{"id":"autogen_task1_N2","status":"SUCCEEDED"},{"id":"autogen_task1_v","status":"SUCCEEDED"},{"id":"autogen_task1_d","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","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_task1_r5","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.397774,"curves":[{"id":"autogen_curve_task1_S","status":"SUCCEEDED"},{"id":"autogen_curve_task1_N1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_N2","status":"SUCCEEDED"}]}]}]}