{"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    435      0 --:--:-- --:--:-- --:--:--   437\n\r100  230k  100  230k    0     0   526k      0 --:--:-- --:--:-- --:--:--  526k\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 (21.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/rawLog.txt\nCompleted 3.8 KiB/3.8 KiB (54.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 79%)\n  adding: outputs/BIOMD0000000306_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000306_url.sedml/autogen_plot_for_task1.pdf (deflated 34%)\n  adding: outputs/reports.h5 (deflated 78%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 28.7 KiB/28.7 KiB (390.5 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/outputs/reports.h5\nCompleted 5.7 KiB/31.5 KiB (53.0 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/outputs/plots.zip\nCompleted 5.7 KiB/31.5 KiB (53.0 KiB/s) with 3 file(s) remaining\rCompleted 20.2 KiB/31.5 KiB (164.5 KiB/s) with 3 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/output.zip\nCompleted 20.2 KiB/31.5 KiB (164.5 KiB/s) with 2 file(s) remaining\rCompleted 28.9 KiB/31.5 KiB (230.1 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000306_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/outputs/BIOMD0000000306_url.sedml/autogen_plot_for_task1.pdf\nCompleted 28.9 KiB/31.5 KiB (230.1 KiB/s) with 1 file(s) remaining\rCompleted 31.5 KiB/31.5 KiB (234.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000306-biopax2.owl  \n  inflating: contents/BIOMD0000000306-biopax3.owl  \n  inflating: contents/BIOMD0000000306-matlab.m  \n  inflating: contents/BIOMD0000000306-octave.m  \n  inflating: contents/BIOMD0000000306.m  \n  inflating: contents/BIOMD0000000306.ode  \n  inflating: contents/BIOMD0000000306.pdf  \n  inflating: contents/BIOMD0000000306.png  \n  inflating: contents/BIOMD0000000306.svg  \n  inflating: contents/BIOMD0000000306.vcml  \n  inflating: contents/BIOMD0000000306_url.sedml  \n  inflating: contents/BIOMD0000000306_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 15.7 KiB/391.5 KiB (197.0 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000306-biopax3.owl to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/contents/BIOMD0000000306-biopax3.owl\nCompleted 15.7 KiB/391.5 KiB (197.0 KiB/s) with 15 file(s) remaining\rCompleted 20.2 KiB/391.5 KiB (189.9 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000306-matlab.m to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/contents/BIOMD0000000306-matlab.m\nCompleted 20.2 KiB/391.5 KiB (189.9 KiB/s) with 14 file(s) remaining\rCompleted 31.5 KiB/391.5 KiB (264.8 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000306-biopax2.owl to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/contents/BIOMD0000000306-biopax2.owl\nCompleted 31.5 KiB/391.5 KiB (264.8 KiB/s) with 13 file(s) remaining\rCompleted 47.6 KiB/391.5 KiB (349.6 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000306.svg to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/contents/BIOMD0000000306.svg\nCompleted 47.6 KiB/391.5 KiB (349.6 KiB/s) with 12 file(s) remaining\rCompleted 47.9 KiB/391.5 KiB (338.9 KiB/s) with 12 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/contents/curation_notes.txt\nCompleted 47.9 KiB/391.5 KiB (338.9 KiB/s) with 11 file(s) remaining\rCompleted 73.8 KiB/391.5 KiB (484.4 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000306.vcml to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/contents/BIOMD0000000306.vcml\nCompleted 73.8 KiB/391.5 KiB (484.4 KiB/s) with 10 file(s) remaining\rCompleted 78.4 KiB/391.5 KiB (507.2 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000306-octave.m to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/contents/BIOMD0000000306-octave.m\nCompleted 78.4 KiB/391.5 KiB (507.2 KiB/s) with 9 file(s) remaining\rCompleted 81.7 KiB/391.5 KiB (494.0 KiB/s) with 9 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/contents/metadata.rdf\nCompleted 81.7 KiB/391.5 KiB (494.0 KiB/s) with 8 file(s) remaining\rCompleted 96.8 KiB/391.5 KiB (574.8 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000306_url.sedml to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/contents/BIOMD0000000306_url.sedml\nCompleted 96.8 KiB/391.5 KiB (574.8 KiB/s) with 7 file(s) remaining\rCompleted 119.8 KiB/391.5 KiB (704.5 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000306_url.xml to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/contents/BIOMD0000000306_url.xml\nCompleted 119.8 KiB/391.5 KiB (704.5 KiB/s) with 6 file(s) remaining\rCompleted 296.7 KiB/391.5 KiB (1.4 MiB/s) with 6 file(s) remaining  \rupload: contents/BIOMD0000000306.pdf to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/contents/BIOMD0000000306.pdf\nCompleted 296.7 KiB/391.5 KiB (1.4 MiB/s) with 5 file(s) remaining\rCompleted 336.1 KiB/391.5 KiB (1.6 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000306.png to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/contents/BIOMD0000000306.png\nCompleted 336.1 KiB/391.5 KiB (1.6 MiB/s) with 4 file(s) remaining\rCompleted 340.7 KiB/391.5 KiB (1.6 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000306.m to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/contents/BIOMD0000000306.m\nCompleted 340.7 KiB/391.5 KiB (1.6 MiB/s) with 3 file(s) remaining\rCompleted 342.5 KiB/391.5 KiB (1.6 MiB/s) with 3 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/contents/manifest.xml\nCompleted 342.5 KiB/391.5 KiB (1.6 MiB/s) with 2 file(s) remaining\rCompleted 345.0 KiB/391.5 KiB (1.5 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000306.ode to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/contents/BIOMD0000000306.ode\nCompleted 345.0 KiB/391.5 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 391.5 KiB/391.5 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/contents/curation_image.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.8 KiB/8.8 KiB (98.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710af79a62a8be53f7ae2d/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000306_url.sedml\ncreating dataset /BIOMD0000000306_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\ndataset created, uuid: d-53f5531c-0ee8c04a-79fd-1d3491-17542b, chunk_size: (6, 1001)\ncreating dataset /BIOMD0000000306_url.sedml/autogen_report_for_task1, shape: (28, 1001), type: float64\ndataset created, uuid: d-53f5531c-0ee8c04a-0e0d-7c6b62-b9a26a, chunk_size: (28, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000306_url.sedml\ncreating attribute uri in /BIOMD0000000306_url.sedml\ncreating attribute _type in /BIOMD0000000306_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000306_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000306_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000306_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000306_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000306_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000306_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000306_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000306_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000306_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000306_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000306_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000306_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000306_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000306_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000306_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000306_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000306_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000306_url.sedml\ncreate_links: /BIOMD0000000306_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000306_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000306_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\niterating over chunks for /BIOMD0000000306_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000306_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000306_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000306_url.sedml/autogen_report_for_task1, shape: (28, 1001), type: float64\niterating over chunks for /BIOMD0000000306_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 28, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000306_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710af79a62a8be53f7ae2d\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 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.\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.\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":1.618725,"sedDocuments":[{"location":"BIOMD0000000306_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  BIOMD0000000306_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 28 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 5 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000306_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":1.136123,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.252043,"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":0.234537,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_R","status":"SUCCEEDED"},{"id":"autogen_task1_X","status":"SUCCEEDED"},{"id":"autogen_task1_S","status":"SUCCEEDED"},{"id":"autogen_task1_E","status":"SUCCEEDED"},{"id":"autogen_task1_Ep","status":"SUCCEEDED"},{"id":"autogen_task1_k0","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k2_prime","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_J3","status":"SUCCEEDED"},{"id":"autogen_task1_k4","status":"SUCCEEDED"},{"id":"autogen_task1_J4","status":"SUCCEEDED"},{"id":"autogen_task1_k5","status":"SUCCEEDED"},{"id":"autogen_task1_k6","status":"SUCCEEDED"},{"id":"autogen_task1_Et","status":"SUCCEEDED"},{"id":"autogen_task1_Km3","status":"SUCCEEDED"},{"id":"autogen_task1_Km4","status":"SUCCEEDED"},{"id":"autogen_task1_env","status":"SUCCEEDED"},{"id":"autogen_task1_r0","status":"SUCCEEDED"},{"id":"autogen_task1_r1","status":"SUCCEEDED"},{"id":"autogen_task1_r2","status":"SUCCEEDED"},{"id":"autogen_task1_r2_prime","status":"SUCCEEDED"},{"id":"autogen_task1_r3","status":"SUCCEEDED"},{"id":"autogen_task1_r4","status":"SUCCEEDED"},{"id":"autogen_task1_r5","status":"SUCCEEDED"},{"id":"autogen_task1_r6","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.469871,"curves":[{"id":"autogen_curve_task1_R","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X","status":"SUCCEEDED"},{"id":"autogen_curve_task1_S","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ep","status":"SUCCEEDED"}]}]}]}