{"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 --:--:-- --:--:-- --:--:--   444\n\r100  265k  100  265k    0     0   617k      0 --:--:-- --:--:-- --:--:--  617k\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 (23.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/rawLog.txt\nCompleted 4.5 KiB/4.5 KiB (63.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 81%)\n  adding: outputs/BIOMD0000000050_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000050_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 7%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/349.6 KiB (5.7 MiB/s) with 1 file(s) remaining\rCompleted 349.6 KiB/349.6 KiB (3.5 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/outputs/reports.h5\nCompleted 256.0 KiB/357.6 KiB (5.9 MiB/s) with 4 file(s) remaining\rCompleted 335.3 KiB/357.6 KiB (3.2 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/output.zip\nCompleted 335.3 KiB/357.6 KiB (3.2 MiB/s) with 3 file(s) remaining\rCompleted 343.2 KiB/357.6 KiB (3.2 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/outputs/plots.zip\nCompleted 343.2 KiB/357.6 KiB (3.2 MiB/s) with 2 file(s) remaining\rCompleted 354.9 KiB/357.6 KiB (2.8 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000050_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/outputs/BIOMD0000000050_url.sedml/autogen_plot_for_task1.pdf\nCompleted 354.9 KiB/357.6 KiB (2.8 MiB/s) with 1 file(s) remaining\rCompleted 357.6 KiB/357.6 KiB (2.5 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000050-biopax2.owl  \n  inflating: contents/BIOMD0000000050-biopax3.owl  \n  inflating: contents/BIOMD0000000050-matlab.m  \n  inflating: contents/BIOMD0000000050-octave.m  \n  inflating: contents/BIOMD0000000050.m  \n  inflating: contents/BIOMD0000000050.ode  \n  inflating: contents/BIOMD0000000050.pdf  \n  inflating: contents/BIOMD0000000050.png  \n  inflating: contents/BIOMD0000000050.sci  \n  inflating: contents/BIOMD0000000050.svg  \n  inflating: contents/BIOMD0000000050.vcml  \n  inflating: contents/BIOMD0000000050_url.sedml  \n  inflating: contents/BIOMD0000000050_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 41.7 KiB/522.8 KiB (467.1 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000050-biopax3.owl to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/contents/BIOMD0000000050-biopax3.owl\nCompleted 41.7 KiB/522.8 KiB (467.1 KiB/s) with 16 file(s) remaining\rCompleted 67.9 KiB/522.8 KiB (564.4 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000050-biopax2.owl to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/contents/BIOMD0000000050-biopax2.owl\nCompleted 67.9 KiB/522.8 KiB (564.4 KiB/s) with 15 file(s) remaining\rCompleted 74.5 KiB/522.8 KiB (612.6 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000050-octave.m to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/contents/BIOMD0000000050-octave.m\nCompleted 74.5 KiB/522.8 KiB (612.6 KiB/s) with 14 file(s) remaining\rCompleted 74.7 KiB/522.8 KiB (512.2 KiB/s) with 14 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/contents/curation_notes.txt\nCompleted 74.7 KiB/522.8 KiB (512.2 KiB/s) with 13 file(s) remaining\rCompleted 78.7 KiB/522.8 KiB (530.2 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000050.sci to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/contents/BIOMD0000000050.sci\nCompleted 78.7 KiB/522.8 KiB (530.2 KiB/s) with 12 file(s) remaining\rCompleted 85.3 KiB/522.8 KiB (546.1 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000050-matlab.m to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/contents/BIOMD0000000050-matlab.m\nCompleted 85.3 KiB/522.8 KiB (546.1 KiB/s) with 11 file(s) remaining\rCompleted 123.3 KiB/522.8 KiB (743.0 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000050.vcml to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/contents/BIOMD0000000050.vcml\nCompleted 123.3 KiB/522.8 KiB (743.0 KiB/s) with 10 file(s) remaining\rCompleted 153.9 KiB/522.8 KiB (918.7 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000050.svg to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/contents/BIOMD0000000050.svg\nCompleted 153.9 KiB/522.8 KiB (918.7 KiB/s) with 9 file(s) remaining\rCompleted 158.8 KiB/522.8 KiB (907.9 KiB/s) with 9 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/contents/metadata.rdf\nCompleted 158.8 KiB/522.8 KiB (907.9 KiB/s) with 8 file(s) remaining\rCompleted 160.8 KiB/522.8 KiB (875.9 KiB/s) with 8 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/contents/manifest.xml\nCompleted 160.8 KiB/522.8 KiB (875.9 KiB/s) with 7 file(s) remaining\rCompleted 179.1 KiB/522.8 KiB (938.4 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000050_url.sedml to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/contents/BIOMD0000000050_url.sedml\nCompleted 179.1 KiB/522.8 KiB (938.4 KiB/s) with 6 file(s) remaining\rCompleted 203.9 KiB/522.8 KiB (1.0 MiB/s) with 6 file(s) remaining  \rupload: contents/BIOMD0000000050_url.xml to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/contents/BIOMD0000000050_url.xml\nCompleted 203.9 KiB/522.8 KiB (1.0 MiB/s) with 5 file(s) remaining\rCompleted 236.0 KiB/522.8 KiB (1.1 MiB/s) with 5 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/contents/curation_image.png\nCompleted 236.0 KiB/522.8 KiB (1.1 MiB/s) with 4 file(s) remaining\rCompleted 305.8 KiB/522.8 KiB (1.3 MiB/s) with 4 file(s) remaining\rCompleted 512.3 KiB/522.8 KiB (2.2 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000050.png to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/contents/BIOMD0000000050.png\nCompleted 512.3 KiB/522.8 KiB (2.2 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000050.pdf to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/contents/BIOMD0000000050.pdf\nCompleted 512.3 KiB/522.8 KiB (2.2 MiB/s) with 2 file(s) remaining\rCompleted 516.2 KiB/522.8 KiB (2.1 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000050.ode to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/contents/BIOMD0000000050.ode\nCompleted 516.2 KiB/522.8 KiB (2.1 MiB/s) with 1 file(s) remaining\rCompleted 522.8 KiB/522.8 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000050.m to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/contents/BIOMD0000000050.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.2 KiB/9.2 KiB (143.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471079649c0d898ffdd9b98/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000050_url.sedml\ncreating dataset /BIOMD0000000050_url.sedml/autogen_plot_for_task1, shape: (15, 1001), type: float64\ndataset created, uuid: d-34454079-a5b12c97-68cd-60f129-6d3a1f, chunk_size: (15, 1001)\ncreating dataset /BIOMD0000000050_url.sedml/autogen_report_for_task1, shape: (32, 1001), type: float64\ndataset created, uuid: d-34454079-a5b12c97-c2e9-5f5f8e-5792b3, chunk_size: (32, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000050_url.sedml\ncreating attribute uri in /BIOMD0000000050_url.sedml\ncreating attribute _type in /BIOMD0000000050_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000050_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000050_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000050_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000050_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000050_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000050_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000050_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000050_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000050_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000050_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000050_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000050_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000050_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000050_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000050_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000050_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000050_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000050_url.sedml\ncreate_links: /BIOMD0000000050_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000050_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000050_url.sedml/autogen_plot_for_task1, shape: (15, 1001), type: float64\niterating over chunks for /BIOMD0000000050_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 15, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000050_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000050_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000050_url.sedml/autogen_report_for_task1, shape: (32, 1001), type: float64\niterating over chunks for /BIOMD0000000050_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 32, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000050_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471079649c0d898ffdd9b98\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mRetrieve 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 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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.743526,"sedDocuments":[{"location":"BIOMD0000000050_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  BIOMD0000000050_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 32 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 14 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000050_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":1.256283,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.227604,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"simulate"},{"key":"solver","value":"cvode"},{"key":"relative_tolerance","value":0.000001},{"key":"absolute_tolerance","value":1e-12},{"key":"stiff","value":true},{"key":"maximum_bdf_order","value":5},{"key":"maximum_adams_order","value":12},{"key":"maximum_num_steps","value":20000},{"key":"maximum_time_step","value":0},{"key":"minimum_time_step","value":0},{"key":"initial_time_step","value":0},{"key":"multiple_steps","value":false},{"key":"variable_step_size","value":false},{"key":"max_output_rows","value":100000}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.271387,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_DFG","status":"SUCCEEDED"},{"id":"autogen_task1_E1","status":"SUCCEEDED"},{"id":"autogen_task1_E2","status":"SUCCEEDED"},{"id":"autogen_task1_Cn","status":"SUCCEEDED"},{"id":"autogen_task1_Gly","status":"SUCCEEDED"},{"id":"autogen_task1__3DG","status":"SUCCEEDED"},{"id":"autogen_task1_FA","status":"SUCCEEDED"},{"id":"autogen_task1__1DG","status":"SUCCEEDED"},{"id":"autogen_task1_AA","status":"SUCCEEDED"},{"id":"autogen_task1_Man","status":"SUCCEEDED"},{"id":"autogen_task1_Glu","status":"SUCCEEDED"},{"id":"autogen_task1_MG","status":"SUCCEEDED"},{"id":"autogen_task1_Mel","status":"SUCCEEDED"},{"id":"autogen_task1_Fru","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","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_v5","status":"SUCCEEDED"},{"id":"autogen_task1_v6","status":"SUCCEEDED"},{"id":"autogen_task1_v7","status":"SUCCEEDED"},{"id":"autogen_task1_v8","status":"SUCCEEDED"},{"id":"autogen_task1_v9","status":"SUCCEEDED"},{"id":"autogen_task1_v10","status":"SUCCEEDED"},{"id":"autogen_task1_v11","status":"SUCCEEDED"},{"id":"autogen_task1_v12","status":"SUCCEEDED"},{"id":"autogen_task1_v13","status":"SUCCEEDED"},{"id":"autogen_task1_v14","status":"SUCCEEDED"},{"id":"autogen_task1_v15","status":"SUCCEEDED"},{"id":"autogen_task1_v16","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.619351,"curves":[{"id":"autogen_curve_task1_DFG","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Cn","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Gly","status":"SUCCEEDED"},{"id":"autogen_curve_task1__3DG","status":"SUCCEEDED"},{"id":"autogen_curve_task1_FA","status":"SUCCEEDED"},{"id":"autogen_curve_task1__1DG","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Man","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Glu","status":"SUCCEEDED"},{"id":"autogen_curve_task1_MG","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Mel","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Fru","status":"SUCCEEDED"}]}]}]}