{"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    460      0 --:--:-- --:--:-- --:--:--   461\n\r100  214k  100  214k    0     0   529k      0 --:--:-- --:--:-- --:--:--  529k\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 (24.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/rawLog.txt\nCompleted 2.9 KiB/2.9 KiB (47.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/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/BIOMD0000000043_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000043_url.sedml/autogen_plot_for_task1.pdf (deflated 13%)\n  adding: outputs/reports.h5 (deflated 15%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 144.6 KiB/144.6 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/outputs/reports.h5\nCompleted 153.4 KiB/217.3 KiB (1.7 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/output.zip\nCompleted 153.4 KiB/217.3 KiB (1.7 MiB/s) with 3 file(s) remaining\rCompleted 186.2 KiB/217.3 KiB (1.4 MiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000043_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/outputs/BIOMD0000000043_url.sedml/autogen_plot_for_task1.pdf\nCompleted 186.2 KiB/217.3 KiB (1.4 MiB/s) with 2 file(s) remaining\rCompleted 188.8 KiB/217.3 KiB (1.3 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/rawLog.txt\nCompleted 188.8 KiB/217.3 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 217.3 KiB/217.3 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000043-biopax2.owl  \n  inflating: contents/BIOMD0000000043-biopax3.owl  \n  inflating: contents/BIOMD0000000043-matlab.m  \n  inflating: contents/BIOMD0000000043-octave.m  \n  inflating: contents/BIOMD0000000043.m  \n  inflating: contents/BIOMD0000000043.ode  \n  inflating: contents/BIOMD0000000043.pdf  \n  inflating: contents/BIOMD0000000043.png  \n  inflating: contents/BIOMD0000000043.sci  \n  inflating: contents/BIOMD0000000043.svg  \n  inflating: contents/BIOMD0000000043.vcml  \n  inflating: contents/BIOMD0000000043_url.sedml  \n  inflating: contents/BIOMD0000000043_url.xml  \n  inflating: contents/curation_image.jpeg  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 15.3 KiB/389.9 KiB (177.1 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000043-biopax2.owl to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/contents/BIOMD0000000043-biopax2.owl\nCompleted 15.3 KiB/389.9 KiB (177.1 KiB/s) with 16 file(s) remaining\rCompleted 17.8 KiB/389.9 KiB (161.9 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000043.ode to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/contents/BIOMD0000000043.ode\nCompleted 17.8 KiB/389.9 KiB (161.9 KiB/s) with 15 file(s) remaining\rCompleted 22.5 KiB/389.9 KiB (154.9 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000043-octave.m to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/contents/BIOMD0000000043-octave.m\nCompleted 22.5 KiB/389.9 KiB (154.9 KiB/s) with 14 file(s) remaining\rCompleted 25.5 KiB/389.9 KiB (161.0 KiB/s) with 14 file(s) remaining\rCompleted 46.4 KiB/389.9 KiB (290.7 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000043-biopax3.owl to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/contents/BIOMD0000000043-biopax3.owl\nCompleted 46.4 KiB/389.9 KiB (290.7 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000043.sci to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/contents/BIOMD0000000043.sci\nCompleted 46.4 KiB/389.9 KiB (290.7 KiB/s) with 12 file(s) remaining\rCompleted 51.1 KiB/389.9 KiB (315.2 KiB/s) with 12 file(s) remaining\rCompleted 84.4 KiB/389.9 KiB (518.7 KiB/s) with 12 file(s) remaining\rCompleted 95.6 KiB/389.9 KiB (581.2 KiB/s) with 12 file(s) remaining\rCompleted 141.3 KiB/389.9 KiB (847.0 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000043.png to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/contents/BIOMD0000000043.png\nCompleted 141.3 KiB/389.9 KiB (847.0 KiB/s) with 11 file(s) remaining\rCompleted 156.1 KiB/389.9 KiB (923.9 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000043_url.sedml to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/contents/BIOMD0000000043_url.sedml\nCompleted 156.1 KiB/389.9 KiB (923.9 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000043.vcml to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/contents/BIOMD0000000043.vcml\nCompleted 156.1 KiB/389.9 KiB (923.9 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000043-matlab.m to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/contents/BIOMD0000000043-matlab.m\nCompleted 156.1 KiB/389.9 KiB (923.9 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000043.svg to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/contents/BIOMD0000000043.svg\nCompleted 156.1 KiB/389.9 KiB (923.9 KiB/s) with 7 file(s) remaining\rCompleted 160.8 KiB/389.9 KiB (849.3 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000043.m to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/contents/BIOMD0000000043.m\nCompleted 160.8 KiB/389.9 KiB (849.3 KiB/s) with 6 file(s) remaining\rCompleted 165.8 KiB/389.9 KiB (817.6 KiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/contents/metadata.rdf\nCompleted 165.8 KiB/389.9 KiB (817.6 KiB/s) with 5 file(s) remaining\rCompleted 332.5 KiB/389.9 KiB (1.5 MiB/s) with 5 file(s) remaining  \rupload: contents/BIOMD0000000043.pdf to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/contents/BIOMD0000000043.pdf\nCompleted 332.5 KiB/389.9 KiB (1.5 MiB/s) with 4 file(s) remaining\rCompleted 332.7 KiB/389.9 KiB (1.5 MiB/s) with 4 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/contents/curation_notes.txt\nCompleted 332.7 KiB/389.9 KiB (1.5 MiB/s) with 3 file(s) remaining\rCompleted 363.5 KiB/389.9 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/contents/curation_image.jpeg\nCompleted 363.5 KiB/389.9 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 365.5 KiB/389.9 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 389.9 KiB/389.9 KiB (1.6 MiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/contents/manifest.xml\nCompleted 389.9 KiB/389.9 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000043_url.xml to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/contents/BIOMD0000000043_url.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.1 KiB/9.1 KiB (130.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c3ff195afd5df1768855/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000043_url.sedml\ncreating dataset /BIOMD0000000043_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\ndataset created, uuid: d-77a287fb-2b475d10-a186-47e9fa-b538a3, chunk_size: (6, 1001)\ncreating dataset /BIOMD0000000043_url.sedml/autogen_report_for_task1, shape: (19, 1001), type: float64\ndataset created, uuid: d-77a287fb-2b475d10-5259-458de4-710581, chunk_size: (19, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000043_url.sedml\ncreating attribute uri in /BIOMD0000000043_url.sedml\ncreating attribute _type in /BIOMD0000000043_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000043_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000043_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000043_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000043_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000043_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000043_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000043_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000043_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000043_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000043_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000043_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000043_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000043_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000043_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000043_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000043_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000043_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000043_url.sedml\ncreate_links: /BIOMD0000000043_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000043_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000043_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\niterating over chunks for /BIOMD0000000043_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000043_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000043_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000043_url.sedml/autogen_report_for_task1, shape: (19, 1001), type: float64\niterating over chunks for /BIOMD0000000043_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 19, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000043_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6480c3ff195afd5df1768855\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 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.\nProcess 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.\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":14.801986,"sedDocuments":[{"location":"BIOMD0000000043_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  BIOMD0000000043_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 19 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 5 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000043_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":14.504825,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":13.891921,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.194579,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_EC","status":"SUCCEEDED"},{"id":"autogen_task1_Z","status":"SUCCEEDED"},{"id":"autogen_task1_Rho","status":"SUCCEEDED"},{"id":"autogen_task1_Y","status":"SUCCEEDED"},{"id":"autogen_task1_Fraction_Inactive_Channels","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_d","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_extracellular","status":"SUCCEEDED"},{"id":"autogen_task1_cytosol","status":"SUCCEEDED"},{"id":"autogen_task1_intravesicular","status":"SUCCEEDED"},{"id":"autogen_task1_vin","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_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.301164,"curves":[{"id":"autogen_curve_task1_EC","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Z","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Rho","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Y","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Fraction_Inactive_Channels","status":"SUCCEEDED"}]}]}]}