{"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    439      0 --:--:-- --:--:-- --:--:--   441\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100  188k  100  188k    0     0   437k      0 --:--:-- --:--:-- --:--:-- 1779k\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 (22.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/rawLog.txt\nCompleted 3.7 KiB/3.7 KiB (51.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/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/reports.h5 (deflated 38%)\n  adding: outputs/BIOMD0000000276_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000276_url.sedml/autogen_plot_for_task1.pdf (deflated 33%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 60.2 KiB/60.2 KiB (729.8 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/outputs/reports.h5\nCompleted 45.4 KiB/61.5 KiB (575.2 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/output.zip\nCompleted 45.4 KiB/61.5 KiB (575.2 KiB/s) with 3 file(s) remaining\rCompleted 50.7 KiB/61.5 KiB (502.7 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/outputs/plots.zip\nCompleted 50.7 KiB/61.5 KiB (502.7 KiB/s) with 2 file(s) remaining\rCompleted 58.8 KiB/61.5 KiB (525.2 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000276_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/outputs/BIOMD0000000276_url.sedml/autogen_plot_for_task1.pdf\nCompleted 58.8 KiB/61.5 KiB (525.2 KiB/s) with 1 file(s) remaining\rCompleted 61.5 KiB/61.5 KiB (513.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000276-biopax2.owl  \n  inflating: contents/BIOMD0000000276-biopax3.owl  \n  inflating: contents/BIOMD0000000276-matlab.m  \n  inflating: contents/BIOMD0000000276-octave.m  \n  inflating: contents/BIOMD0000000276.m  \n  inflating: contents/BIOMD0000000276.ode  \n  inflating: contents/BIOMD0000000276.pdf  \n  inflating: contents/BIOMD0000000276.png  \n  inflating: contents/BIOMD0000000276.svg  \n  inflating: contents/BIOMD0000000276_url.sedml  \n  inflating: contents/BIOMD0000000276_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 6.0 KiB/~280.6 KiB (86.7 KiB/s) with ~14 file(s) remaining (calculating...)\rupload: contents/BIOMD0000000276-biopax3.owl to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/contents/BIOMD0000000276-biopax3.owl\nCompleted 6.0 KiB/~280.6 KiB (86.7 KiB/s) with ~13 file(s) remaining (calculating...)\rCompleted 11.1 KiB/288.1 KiB (114.8 KiB/s) with 14 file(s) remaining                 \rupload: contents/BIOMD0000000276-matlab.m to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/contents/BIOMD0000000276-matlab.m\nCompleted 11.1 KiB/288.1 KiB (114.8 KiB/s) with 13 file(s) remaining\rCompleted 16.7 KiB/288.1 KiB (144.6 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000276-biopax2.owl to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/contents/BIOMD0000000276-biopax2.owl\nCompleted 16.7 KiB/288.1 KiB (144.6 KiB/s) with 12 file(s) remaining\rCompleted 21.7 KiB/288.1 KiB (178.3 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000276-octave.m to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/contents/BIOMD0000000276-octave.m\nCompleted 21.7 KiB/288.1 KiB (178.3 KiB/s) with 11 file(s) remaining\rCompleted 23.4 KiB/288.1 KiB (184.7 KiB/s) with 11 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/contents/manifest.xml\nCompleted 23.4 KiB/288.1 KiB (184.7 KiB/s) with 10 file(s) remaining\rCompleted 24.3 KiB/288.1 KiB (183.8 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000276.svg to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/contents/BIOMD0000000276.svg\nCompleted 24.3 KiB/288.1 KiB (183.8 KiB/s) with 9 file(s) remaining\rCompleted 38.9 KiB/288.1 KiB (245.7 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000276_url.sedml to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/contents/BIOMD0000000276_url.sedml\nCompleted 38.9 KiB/288.1 KiB (245.7 KiB/s) with 8 file(s) remaining\rCompleted 39.6 KiB/288.1 KiB (236.4 KiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/contents/curation_notes.txt\nCompleted 39.6 KiB/288.1 KiB (236.4 KiB/s) with 7 file(s) remaining\rCompleted 44.6 KiB/288.1 KiB (255.9 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000276.png to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/contents/BIOMD0000000276.png\nCompleted 44.6 KiB/288.1 KiB (255.9 KiB/s) with 6 file(s) remaining\rCompleted 49.6 KiB/288.1 KiB (278.8 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000276.m to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/contents/BIOMD0000000276.m\nCompleted 49.6 KiB/288.1 KiB (278.8 KiB/s) with 5 file(s) remaining\rCompleted 199.5 KiB/288.1 KiB (1.1 MiB/s) with 5 file(s) remaining \rupload: contents/BIOMD0000000276.pdf to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/contents/BIOMD0000000276.pdf\nCompleted 199.5 KiB/288.1 KiB (1.1 MiB/s) with 4 file(s) remaining\rCompleted 207.0 KiB/288.1 KiB (1.1 MiB/s) with 4 file(s) remaining\rCompleted 262.4 KiB/288.1 KiB (1.4 MiB/s) with 4 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/contents/curation_image.png\nCompleted 262.4 KiB/288.1 KiB (1.4 MiB/s) with 3 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/contents/metadata.rdf\nCompleted 262.4 KiB/288.1 KiB (1.4 MiB/s) with 2 file(s) remaining\rCompleted 265.5 KiB/288.1 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000276.ode to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/contents/BIOMD0000000276.ode\nCompleted 265.5 KiB/288.1 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 288.1 KiB/288.1 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000276_url.xml to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/contents/BIOMD0000000276_url.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (129.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a910dcacb55678b9ace/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000276_url.sedml\ncreating dataset /BIOMD0000000276_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-baf4b276-2d728625-cc9b-02e0a6-4b7e4e, chunk_size: (4, 1001)\ncreating dataset /BIOMD0000000276_url.sedml/autogen_report_for_task1, shape: (27, 1001), type: float64\ndataset created, uuid: d-baf4b276-2d728625-6a1d-8a070e-5019d0, chunk_size: (27, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000276_url.sedml\ncreating attribute uri in /BIOMD0000000276_url.sedml\ncreating attribute _type in /BIOMD0000000276_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000276_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000276_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000276_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000276_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000276_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000276_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000276_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000276_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000276_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000276_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000276_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000276_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000276_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000276_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000276_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000276_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000276_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000276_url.sedml\ncreate_links: /BIOMD0000000276_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000276_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000276_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\niterating over chunks for /BIOMD0000000276_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000276_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000276_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000276_url.sedml/autogen_report_for_task1, shape: (27, 1001), type: float64\niterating over chunks for /BIOMD0000000276_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 27, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000276_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710a910dcacb55678b9ace\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 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.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata 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":1.503664,"sedDocuments":[{"location":"BIOMD0000000276_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  BIOMD0000000276_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 27 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000276_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":1.038915,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.266913,"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":0.228917,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_x1","status":"SUCCEEDED"},{"id":"autogen_task1_x2","status":"SUCCEEDED"},{"id":"autogen_task1_Ca","status":"SUCCEEDED"},{"id":"autogen_task1_k","status":"SUCCEEDED"},{"id":"autogen_task1_lambda_Ca","status":"SUCCEEDED"},{"id":"autogen_task1_m_Ca","status":"SUCCEEDED"},{"id":"autogen_task1_m1","status":"SUCCEEDED"},{"id":"autogen_task1_m2","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_R","status":"SUCCEEDED"},{"id":"autogen_task1_lambda_1","status":"SUCCEEDED"},{"id":"autogen_task1_lambda_2","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_B","status":"SUCCEEDED"},{"id":"autogen_task1_S","status":"SUCCEEDED"},{"id":"autogen_task1_Ca0","status":"SUCCEEDED"},{"id":"autogen_task1_Ca1","status":"SUCCEEDED"},{"id":"autogen_task1_t0","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_x1_n","status":"SUCCEEDED"},{"id":"autogen_task1_x2_n","status":"SUCCEEDED"},{"id":"autogen_task1_x2_min","status":"SUCCEEDED"},{"id":"autogen_task1_x2_max","status":"SUCCEEDED"},{"id":"autogen_task1_Ca0_baseline","status":"SUCCEEDED"},{"id":"autogen_task1_PTG_pool","status":"SUCCEEDED"},{"id":"autogen_task1_Plasma_pool","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.413153,"curves":[{"id":"autogen_curve_task1_x1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_x2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ca","status":"SUCCEEDED"}]}]}]}