{"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    456      0 --:--:-- --:--:-- --:--:--   457\n\r100  293k  100  293k    0     0   690k      0 --:--:-- --:--:-- --:--:--  690k\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 (23.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/rawLog.txt\nCompleted 3.3 KiB/3.3 KiB (37.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 76%)\n  adding: outputs/BIOMD0000000454_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000454_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 32.1 KiB/32.1 KiB (384.9 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/outputs/reports.h5\nCompleted 14.9 KiB/31.6 KiB (179.6 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/output.zip\nCompleted 14.9 KiB/31.6 KiB (179.6 KiB/s) with 3 file(s) remaining\rCompleted 23.4 KiB/31.6 KiB (203.4 KiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000454_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/outputs/BIOMD0000000454_url.sedml/autogen_plot_for_task1.pdf\nCompleted 23.4 KiB/31.6 KiB (203.4 KiB/s) with 2 file(s) remaining\rCompleted 26.0 KiB/31.6 KiB (216.1 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/rawLog.txt\nCompleted 26.0 KiB/31.6 KiB (216.1 KiB/s) with 1 file(s) remaining\rCompleted 31.6 KiB/31.6 KiB (217.5 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000454-biopax2.owl  \n  inflating: contents/BIOMD0000000454-biopax3.owl  \n  inflating: contents/BIOMD0000000454-matlab.m  \n  inflating: contents/BIOMD0000000454-octave.m  \n  inflating: contents/BIOMD0000000454.m  \n  inflating: contents/BIOMD0000000454.ode  \n  inflating: contents/BIOMD0000000454.pdf  \n  inflating: contents/BIOMD0000000454.png  \n  inflating: contents/BIOMD0000000454.svg  \n  inflating: contents/BIOMD0000000454_url.sedml  \n  inflating: contents/BIOMD0000000454_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 14.5 KiB/411.8 KiB (182.2 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000454-biopax3.owl to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/contents/BIOMD0000000454-biopax3.owl\nCompleted 14.5 KiB/411.8 KiB (182.2 KiB/s) with 14 file(s) remaining\rCompleted 24.2 KiB/411.8 KiB (220.0 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000454-biopax2.owl to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/contents/BIOMD0000000454-biopax2.owl\nCompleted 24.2 KiB/411.8 KiB (220.0 KiB/s) with 13 file(s) remaining\rCompleted 28.2 KiB/411.8 KiB (248.7 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000454-octave.m to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/contents/BIOMD0000000454-octave.m\nCompleted 28.2 KiB/411.8 KiB (248.7 KiB/s) with 12 file(s) remaining\rCompleted 32.0 KiB/411.8 KiB (228.5 KiB/s) with 12 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/contents/metadata.rdf\nCompleted 32.0 KiB/411.8 KiB (228.5 KiB/s) with 11 file(s) remaining\rCompleted 40.9 KiB/411.8 KiB (288.5 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000454_url.sedml to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/contents/BIOMD0000000454_url.sedml\nCompleted 40.9 KiB/411.8 KiB (288.5 KiB/s) with 10 file(s) remaining\rCompleted 56.8 KiB/411.8 KiB (393.5 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000454.svg to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/contents/BIOMD0000000454.svg\nCompleted 56.8 KiB/411.8 KiB (393.5 KiB/s) with 9 file(s) remaining\rCompleted 60.8 KiB/411.8 KiB (415.4 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000454-matlab.m to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/contents/BIOMD0000000454-matlab.m\nCompleted 60.8 KiB/411.8 KiB (415.4 KiB/s) with 8 file(s) remaining\rCompleted 77.4 KiB/411.8 KiB (500.7 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000454_url.xml to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/contents/BIOMD0000000454_url.xml\nCompleted 77.4 KiB/411.8 KiB (500.7 KiB/s) with 7 file(s) remaining\rCompleted 79.1 KiB/411.8 KiB (436.0 KiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/contents/manifest.xml\nCompleted 79.1 KiB/411.8 KiB (436.0 KiB/s) with 6 file(s) remaining\rCompleted 176.1 KiB/411.8 KiB (940.7 KiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/contents/curation_image.png\nCompleted 176.1 KiB/411.8 KiB (940.7 KiB/s) with 5 file(s) remaining\rCompleted 247.1 KiB/411.8 KiB (1.2 MiB/s) with 5 file(s) remaining  \rupload: contents/BIOMD0000000454.png to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/contents/BIOMD0000000454.png\nCompleted 247.1 KiB/411.8 KiB (1.2 MiB/s) with 4 file(s) remaining\rCompleted 405.6 KiB/411.8 KiB (1.9 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000454.pdf to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/contents/BIOMD0000000454.pdf\nCompleted 405.6 KiB/411.8 KiB (1.9 MiB/s) with 3 file(s) remaining\rCompleted 409.7 KiB/411.8 KiB (1.9 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000454.m to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/contents/BIOMD0000000454.m\nCompleted 409.7 KiB/411.8 KiB (1.9 MiB/s) with 2 file(s) remaining\rCompleted 411.7 KiB/411.8 KiB (1.9 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000454.ode to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/contents/BIOMD0000000454.ode\nCompleted 411.7 KiB/411.8 KiB (1.9 MiB/s) with 1 file(s) remaining\rCompleted 411.8 KiB/411.8 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/contents/curation_notes.txt\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (96.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710cf449c0d898ffde4db7/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000454_url.sedml\ncreating dataset /BIOMD0000000454_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\ndataset created, uuid: d-43465ed2-3450aae6-81b5-a782e8-92bb59, chunk_size: (9, 1001)\ncreating dataset /BIOMD0000000454_url.sedml/autogen_report_for_task1, shape: (14, 1001), type: float64\ndataset created, uuid: d-43465ed2-3450aae6-b303-caf977-a80e11, chunk_size: (14, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000454_url.sedml\ncreating attribute uri in /BIOMD0000000454_url.sedml\ncreating attribute _type in /BIOMD0000000454_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000454_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000454_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000454_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000454_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000454_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000454_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000454_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000454_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000454_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000454_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000454_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000454_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000454_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000454_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000454_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000454_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000454_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000454_url.sedml\ncreate_links: /BIOMD0000000454_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000454_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000454_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\niterating over chunks for /BIOMD0000000454_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000454_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000454_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000454_url.sedml/autogen_report_for_task1, shape: (14, 1001), type: float64\niterating over chunks for /BIOMD0000000454_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 14, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000454_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710cf449c0d898ffde4db7\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 the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file 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 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":1.324083,"sedDocuments":[{"location":"BIOMD0000000454_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  BIOMD0000000454_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 14 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 8 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000454_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":0.9154,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.183317,"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":0.168945,"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_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_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.435121,"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"}]}]}]}