{"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    426      0 --:--:-- --:--:-- --:--:--   427\n\r100  172k  100  172k    0     0   390k      0 --:--:-- --:--:-- --:--:--  390k\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 (23.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/rawLog.txt\nCompleted 4.5 KiB/4.5 KiB (50.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/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/BIOMD0000000304_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000304_url.sedml/autogen_plot_for_task1.pdf (deflated 33%)\n  adding: outputs/reports.h5 (deflated 14%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 199.0 KiB/199.0 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/outputs/reports.h5\nCompleted 181.0 KiB/201.3 KiB (2.0 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/output.zip\nCompleted 181.0 KiB/201.3 KiB (2.0 MiB/s) with 3 file(s) remaining\rCompleted 188.0 KiB/201.3 KiB (1.8 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/outputs/plots.zip\nCompleted 188.0 KiB/201.3 KiB (1.8 MiB/s) with 2 file(s) remaining\rCompleted 190.6 KiB/201.3 KiB (1.5 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/rawLog.txt\nCompleted 190.6 KiB/201.3 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 201.3 KiB/201.3 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000304_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/outputs/BIOMD0000000304_url.sedml/autogen_plot_for_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000304-biopax2.owl  \n  inflating: contents/BIOMD0000000304-biopax3.owl  \n  inflating: contents/BIOMD0000000304-matlab.m  \n  inflating: contents/BIOMD0000000304-octave.m  \n  inflating: contents/BIOMD0000000304.m  \n  inflating: contents/BIOMD0000000304.ode  \n  inflating: contents/BIOMD0000000304.pdf  \n  inflating: contents/BIOMD0000000304.png  \n  inflating: contents/BIOMD0000000304.sci  \n  inflating: contents/BIOMD0000000304.svg  \n  inflating: contents/BIOMD0000000304_url.sedml  \n  inflating: contents/BIOMD0000000304_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 6.8 KiB/~284.5 KiB (121.6 KiB/s) with ~14 file(s) remaining (calculating...)\rupload: contents/BIOMD0000000304-biopax2.owl to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/contents/BIOMD0000000304-biopax2.owl\nCompleted 6.8 KiB/~284.5 KiB (121.6 KiB/s) with ~13 file(s) remaining (calculating...)\rCompleted 13.6 KiB/289.8 KiB (120.2 KiB/s) with 15 file(s) remaining                  \rupload: contents/BIOMD0000000304-octave.m to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/contents/BIOMD0000000304-octave.m\nCompleted 13.6 KiB/289.8 KiB (120.2 KiB/s) with 14 file(s) remaining\rCompleted 20.5 KiB/289.8 KiB (169.4 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000304-matlab.m to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/contents/BIOMD0000000304-matlab.m\nCompleted 20.5 KiB/289.8 KiB (169.4 KiB/s) with 13 file(s) remaining\rCompleted 56.2 KiB/289.8 KiB (441.2 KiB/s) with 13 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/contents/curation_image.png\nCompleted 56.2 KiB/289.8 KiB (441.2 KiB/s) with 12 file(s) remaining\rCompleted 61.2 KiB/289.8 KiB (452.0 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000304.png to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/contents/BIOMD0000000304.png\nCompleted 61.2 KiB/289.8 KiB (452.0 KiB/s) with 11 file(s) remaining\rCompleted 65.1 KiB/289.8 KiB (415.9 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000304.sci to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/contents/BIOMD0000000304.sci\nCompleted 65.1 KiB/289.8 KiB (415.9 KiB/s) with 10 file(s) remaining\rCompleted 86.9 KiB/289.8 KiB (546.9 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000304_url.sedml to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/contents/BIOMD0000000304_url.sedml\nCompleted 86.9 KiB/289.8 KiB (546.9 KiB/s) with 9 file(s) remaining\rCompleted 109.2 KiB/289.8 KiB (660.0 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000304_url.xml to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/contents/BIOMD0000000304_url.xml\nCompleted 109.2 KiB/289.8 KiB (660.0 KiB/s) with 8 file(s) remaining\rCompleted 109.5 KiB/289.8 KiB (617.9 KiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/contents/curation_notes.txt\nCompleted 109.5 KiB/289.8 KiB (617.9 KiB/s) with 7 file(s) remaining\rCompleted 111.3 KiB/289.8 KiB (612.9 KiB/s) with 7 file(s) remaining\rCompleted 114.8 KiB/289.8 KiB (623.1 KiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/contents/metadata.rdf\nCompleted 114.8 KiB/289.8 KiB (623.1 KiB/s) with 6 file(s) remaining\rCompleted 122.1 KiB/289.8 KiB (652.6 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000304-biopax3.owl to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/contents/BIOMD0000000304-biopax3.owl\nCompleted 122.1 KiB/289.8 KiB (652.6 KiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/contents/manifest.xml\nCompleted 122.1 KiB/289.8 KiB (652.6 KiB/s) with 4 file(s) remaining\rCompleted 129.0 KiB/289.8 KiB (656.9 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000304.m to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/contents/BIOMD0000000304.m\nCompleted 129.0 KiB/289.8 KiB (656.9 KiB/s) with 3 file(s) remaining\rCompleted 284.0 KiB/289.8 KiB (1.4 MiB/s) with 3 file(s) remaining  \rupload: contents/BIOMD0000000304.pdf to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/contents/BIOMD0000000304.pdf\nCompleted 284.0 KiB/289.8 KiB (1.4 MiB/s) with 2 file(s) remaining\rCompleted 284.9 KiB/289.8 KiB (1.2 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000304.svg to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/contents/BIOMD0000000304.svg\nCompleted 284.9 KiB/289.8 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 289.8 KiB/289.8 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000304.ode to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/contents/BIOMD0000000304.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (132.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710af20dcacb55678ba5f2/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000304_url.sedml\ncreating dataset /BIOMD0000000304_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\ndataset created, uuid: d-339c8d00-441e4852-5c10-dd07c4-21bb2d, chunk_size: (6, 1001)\ncreating dataset /BIOMD0000000304_url.sedml/autogen_report_for_task1, shape: (41, 1001), type: float64\ndataset created, uuid: d-339c8d00-441e4852-9f2e-02bfb9-92dae1, chunk_size: (41, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000304_url.sedml\ncreating attribute uri in /BIOMD0000000304_url.sedml\ncreating attribute _type in /BIOMD0000000304_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000304_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000304_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000304_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000304_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000304_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000304_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000304_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000304_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000304_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000304_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000304_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000304_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000304_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000304_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000304_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000304_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000304_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000304_url.sedml\ncreate_links: /BIOMD0000000304_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000304_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000304_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\niterating over chunks for /BIOMD0000000304_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000304_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000304_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000304_url.sedml/autogen_report_for_task1, shape: (41, 1001), type: float64\niterating over chunks for /BIOMD0000000304_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 41, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000304_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710af20dcacb55678ba5f2\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 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.\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":1.742548,"sedDocuments":[{"location":"BIOMD0000000304_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  BIOMD0000000304_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 41 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 5 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000304_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":1.264121,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.272926,"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":0.348279,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_V_membrane","status":"SUCCEEDED"},{"id":"autogen_task1_h1","status":"SUCCEEDED"},{"id":"autogen_task1_x1","status":"SUCCEEDED"},{"id":"autogen_task1_n1","status":"SUCCEEDED"},{"id":"autogen_task1_c","status":"SUCCEEDED"},{"id":"autogen_task1_i_Na","status":"SUCCEEDED"},{"id":"autogen_task1_V_I","status":"SUCCEEDED"},{"id":"autogen_task1_V_K","status":"SUCCEEDED"},{"id":"autogen_task1_V_L","status":"SUCCEEDED"},{"id":"autogen_task1_V_Ca","status":"SUCCEEDED"},{"id":"autogen_task1_g_I","status":"SUCCEEDED"},{"id":"autogen_task1_g_K","status":"SUCCEEDED"},{"id":"autogen_task1_g_T","status":"SUCCEEDED"},{"id":"autogen_task1_g_K_Ca","status":"SUCCEEDED"},{"id":"autogen_task1_g_L","status":"SUCCEEDED"},{"id":"autogen_task1_K_p","status":"SUCCEEDED"},{"id":"autogen_task1_K_c","status":"SUCCEEDED"},{"id":"autogen_task1_f","status":"SUCCEEDED"},{"id":"autogen_task1_tau_x","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_Vs","status":"SUCCEEDED"},{"id":"autogen_task1_m_infinity","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_m","status":"SUCCEEDED"},{"id":"autogen_task1_beta_m","status":"SUCCEEDED"},{"id":"autogen_task1_h_infinity","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_h","status":"SUCCEEDED"},{"id":"autogen_task1_beta_h","status":"SUCCEEDED"},{"id":"autogen_task1_tau_h","status":"SUCCEEDED"},{"id":"autogen_task1_g_Ca","status":"SUCCEEDED"},{"id":"autogen_task1_x_infinity","status":"SUCCEEDED"},{"id":"autogen_task1_i_Ca","status":"SUCCEEDED"},{"id":"autogen_task1_n_infinity","status":"SUCCEEDED"},{"id":"autogen_task1_i_K","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_n","status":"SUCCEEDED"},{"id":"autogen_task1_beta_n","status":"SUCCEEDED"},{"id":"autogen_task1_tau_n","status":"SUCCEEDED"},{"id":"autogen_task1_i_K_Ca","status":"SUCCEEDED"},{"id":"autogen_task1_i_L","status":"SUCCEEDED"},{"id":"autogen_task1_COMpartment","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.483026,"curves":[{"id":"autogen_curve_task1_V_membrane","status":"SUCCEEDED"},{"id":"autogen_curve_task1_h1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_x1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_n1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_c","status":"SUCCEEDED"}]}]}]}