{"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    455      0 --:--:-- --:--:-- --:--:--   457\n\r100  147k  100  147k    0     0   365k      0 --:--:-- --:--:-- --:--:--  365k\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 (21.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/rawLog.txt\nCompleted 5.2 KiB/5.2 KiB (70.5 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 82%)\n  adding: outputs/BIOMD0000000020_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000020_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 15%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 199.2 KiB/199.2 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/outputs/reports.h5\nCompleted 180.3 KiB/204.8 KiB (1.9 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/output.zip\nCompleted 180.3 KiB/204.8 KiB (1.9 MiB/s) with 3 file(s) remaining\rCompleted 189.1 KiB/204.8 KiB (1.6 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/outputs/plots.zip\nCompleted 189.1 KiB/204.8 KiB (1.6 MiB/s) with 2 file(s) remaining\rCompleted 191.7 KiB/204.8 KiB (1.5 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/rawLog.txt\nCompleted 191.7 KiB/204.8 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 204.8 KiB/204.8 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000020_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/outputs/BIOMD0000000020_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/BIOMD0000000020-biopax2.owl  \n  inflating: contents/BIOMD0000000020-biopax3.owl  \n  inflating: contents/BIOMD0000000020-matlab.m  \n  inflating: contents/BIOMD0000000020-octave.m  \n  inflating: contents/BIOMD0000000020.m  \n  inflating: contents/BIOMD0000000020.ode  \n  inflating: contents/BIOMD0000000020.pdf  \n  inflating: contents/BIOMD0000000020.png  \n  inflating: contents/BIOMD0000000020.svg  \n  inflating: contents/BIOMD0000000020_url.sedml  \n  inflating: contents/BIOMD0000000020_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 4.2 KiB/250.6 KiB (55.9 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000020-biopax2.owl to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/contents/BIOMD0000000020-biopax2.owl\nCompleted 4.2 KiB/250.6 KiB (55.9 KiB/s) with 14 file(s) remaining\rCompleted 9.3 KiB/250.6 KiB (78.5 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000020.png to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/contents/BIOMD0000000020.png\nCompleted 9.3 KiB/250.6 KiB (78.5 KiB/s) with 13 file(s) remaining\rCompleted 12.7 KiB/250.6 KiB (91.6 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000020.ode to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/contents/BIOMD0000000020.ode\nCompleted 12.7 KiB/250.6 KiB (91.6 KiB/s) with 12 file(s) remaining\rCompleted 13.5 KiB/250.6 KiB (95.0 KiB/s) with 12 file(s) remaining\rCompleted 18.8 KiB/250.6 KiB (129.7 KiB/s) with 12 file(s) remaining\rCompleted 24.0 KiB/250.6 KiB (164.7 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000020.svg to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/contents/BIOMD0000000020.svg\nCompleted 24.0 KiB/250.6 KiB (164.7 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000020-octave.m to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/contents/BIOMD0000000020-octave.m\nCompleted 24.0 KiB/250.6 KiB (164.7 KiB/s) with 10 file(s) remaining\rCompleted 28.3 KiB/250.6 KiB (191.6 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000020-matlab.m to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/contents/BIOMD0000000020-matlab.m\nCompleted 28.3 KiB/250.6 KiB (191.6 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000020-biopax3.owl to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/contents/BIOMD0000000020-biopax3.owl\nCompleted 28.3 KiB/250.6 KiB (191.6 KiB/s) with 8 file(s) remaining\rCompleted 176.8 KiB/250.6 KiB (1.1 MiB/s) with 8 file(s) remaining \rupload: contents/BIOMD0000000020.pdf to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/contents/BIOMD0000000020.pdf\nCompleted 176.8 KiB/250.6 KiB (1.1 MiB/s) with 7 file(s) remaining\rCompleted 196.2 KiB/250.6 KiB (1.1 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000020_url.sedml to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/contents/BIOMD0000000020_url.sedml\nCompleted 196.2 KiB/250.6 KiB (1.1 MiB/s) with 6 file(s) remaining\rCompleted 197.9 KiB/250.6 KiB (1.1 MiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/contents/manifest.xml\nCompleted 197.9 KiB/250.6 KiB (1.1 MiB/s) with 5 file(s) remaining\rCompleted 203.6 KiB/250.6 KiB (1.1 MiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/contents/metadata.rdf\nCompleted 203.6 KiB/250.6 KiB (1.1 MiB/s) with 4 file(s) remaining\rCompleted 208.9 KiB/250.6 KiB (986.3 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000020.m to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/contents/BIOMD0000000020.m\nCompleted 208.9 KiB/250.6 KiB (986.3 KiB/s) with 3 file(s) remaining\rCompleted 238.8 KiB/250.6 KiB (1021.6 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000020_url.xml to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/contents/BIOMD0000000020_url.xml\nCompleted 238.8 KiB/250.6 KiB (1021.6 KiB/s) with 2 file(s) remaining\rCompleted 238.9 KiB/250.6 KiB (985.2 KiB/s) with 2 file(s) remaining \rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/contents/curation_notes.txt\nCompleted 238.9 KiB/250.6 KiB (985.2 KiB/s) with 1 file(s) remaining\rCompleted 250.6 KiB/250.6 KiB (977.1 KiB/s) with 1 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/contents/curation_image.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (119.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c3f1195afd5df17687b6/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000020_url.sedml\ncreating dataset /BIOMD0000000020_url.sedml/autogen_plot_for_task1, shape: (28, 1001), type: float64\ndataset created, uuid: d-699482b4-ac641550-1338-52ce1d-45fe4c, chunk_size: (28, 1001)\ncreating dataset /BIOMD0000000020_url.sedml/autogen_report_for_task1, shape: (29, 1001), type: float64\ndataset created, uuid: d-699482b4-ac641550-bae1-d36d01-457da6, chunk_size: (29, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000020_url.sedml\ncreating attribute uri in /BIOMD0000000020_url.sedml\ncreating attribute _type in /BIOMD0000000020_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000020_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000020_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000020_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000020_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000020_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000020_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000020_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000020_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000020_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000020_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000020_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000020_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000020_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000020_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000020_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000020_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000020_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000020_url.sedml\ncreate_links: /BIOMD0000000020_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000020_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000020_url.sedml/autogen_plot_for_task1, shape: (28, 1001), type: float64\niterating over chunks for /BIOMD0000000020_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 28, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000020_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000020_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000020_url.sedml/autogen_report_for_task1, shape: (29, 1001), type: float64\niterating over chunks for /BIOMD0000000020_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 29, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000020_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6480c3f1195afd5df17687b6\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 SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file 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.\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.\nProcess and upload the outputs of the simulation run ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.962973,"sedDocuments":[{"location":"BIOMD0000000020_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  BIOMD0000000020_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 29 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 27 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000020_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":1.496516,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.201652,"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":0.261127,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_V","status":"SUCCEEDED"},{"id":"autogen_task1_V_neg","status":"SUCCEEDED"},{"id":"autogen_task1_E","status":"SUCCEEDED"},{"id":"autogen_task1_I","status":"SUCCEEDED"},{"id":"autogen_task1_i_Na","status":"SUCCEEDED"},{"id":"autogen_task1_i_K","status":"SUCCEEDED"},{"id":"autogen_task1_i_L","status":"SUCCEEDED"},{"id":"autogen_task1_m","status":"SUCCEEDED"},{"id":"autogen_task1_h","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_E_R","status":"SUCCEEDED"},{"id":"autogen_task1_Cm","status":"SUCCEEDED"},{"id":"autogen_task1_g_Na","status":"SUCCEEDED"},{"id":"autogen_task1_g_K","status":"SUCCEEDED"},{"id":"autogen_task1_g_L","status":"SUCCEEDED"},{"id":"autogen_task1_E_Na","status":"SUCCEEDED"},{"id":"autogen_task1_E_K","status":"SUCCEEDED"},{"id":"autogen_task1_E_L","status":"SUCCEEDED"},{"id":"autogen_task1_V_Na","status":"SUCCEEDED"},{"id":"autogen_task1_V_K","status":"SUCCEEDED"},{"id":"autogen_task1_V_L","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_m","status":"SUCCEEDED"},{"id":"autogen_task1_beta_m","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_h","status":"SUCCEEDED"},{"id":"autogen_task1_beta_h","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_n","status":"SUCCEEDED"},{"id":"autogen_task1_beta_n","status":"SUCCEEDED"},{"id":"autogen_task1_unit_compartment","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.888593,"curves":[{"id":"autogen_curve_task1_V","status":"SUCCEEDED"},{"id":"autogen_curve_task1_V_neg","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E","status":"SUCCEEDED"},{"id":"autogen_curve_task1_I","status":"SUCCEEDED"},{"id":"autogen_curve_task1_i_Na","status":"SUCCEEDED"},{"id":"autogen_curve_task1_i_K","status":"SUCCEEDED"},{"id":"autogen_curve_task1_i_L","status":"SUCCEEDED"},{"id":"autogen_curve_task1_m","status":"SUCCEEDED"},{"id":"autogen_curve_task1_h","status":"SUCCEEDED"},{"id":"autogen_curve_task1_n","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E_R","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Cm","status":"SUCCEEDED"},{"id":"autogen_curve_task1_g_Na","status":"SUCCEEDED"},{"id":"autogen_curve_task1_g_K","status":"SUCCEEDED"},{"id":"autogen_curve_task1_g_L","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E_Na","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E_K","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E_L","status":"SUCCEEDED"},{"id":"autogen_curve_task1_V_Na","status":"SUCCEEDED"},{"id":"autogen_curve_task1_V_K","status":"SUCCEEDED"},{"id":"autogen_curve_task1_V_L","status":"SUCCEEDED"},{"id":"autogen_curve_task1_alpha_m","status":"SUCCEEDED"},{"id":"autogen_curve_task1_beta_m","status":"SUCCEEDED"},{"id":"autogen_curve_task1_alpha_h","status":"SUCCEEDED"},{"id":"autogen_curve_task1_beta_h","status":"SUCCEEDED"},{"id":"autogen_curve_task1_alpha_n","status":"SUCCEEDED"},{"id":"autogen_curve_task1_beta_n","status":"SUCCEEDED"}]}]}]}