{"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100  188k  100  188k    0     0   446k      0 --:--:-- --:--:-- --:--:-- 2775k\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 (19.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/rawLog.txt\nCompleted 2.9 KiB/2.9 KiB (44.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 73%)\n  adding: outputs/reports.h5 (deflated 20%)\n  adding: outputs/BIOMD0000000060_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000060_url.sedml/autogen_plot_for_task1.pdf (deflated 29%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 113.5 KiB/113.5 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/outputs/reports.h5\nCompleted 99.7 KiB/118.7 KiB (1.2 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/output.zip\nCompleted 99.7 KiB/118.7 KiB (1.2 MiB/s) with 3 file(s) remaining\rCompleted 109.3 KiB/118.7 KiB (1.0 MiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000060_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/outputs/BIOMD0000000060_url.sedml/autogen_plot_for_task1.pdf\nCompleted 109.3 KiB/118.7 KiB (1.0 MiB/s) with 2 file(s) remaining\rCompleted 112.0 KiB/118.7 KiB (957.3 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/rawLog.txt\nCompleted 112.0 KiB/118.7 KiB (957.3 KiB/s) with 1 file(s) remaining\rCompleted 118.7 KiB/118.7 KiB (980.5 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000060-biopax2.owl  \n  inflating: contents/BIOMD0000000060-biopax3.owl  \n  inflating: contents/BIOMD0000000060-matlab.m  \n  inflating: contents/BIOMD0000000060-octave.m  \n  inflating: contents/BIOMD0000000060.m  \n  inflating: contents/BIOMD0000000060.ode  \n  inflating: contents/BIOMD0000000060.pdf  \n  inflating: contents/BIOMD0000000060.png  \n  inflating: contents/BIOMD0000000060.svg  \n  inflating: contents/BIOMD0000000060_url.sedml  \n  inflating: contents/BIOMD0000000060_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 8.9 KiB/290.2 KiB (146.2 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000060-biopax2.owl to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/contents/BIOMD0000000060-biopax2.owl\nCompleted 8.9 KiB/290.2 KiB (146.2 KiB/s) with 14 file(s) remaining\rCompleted 20.0 KiB/290.2 KiB (176.7 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000060.svg to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/contents/BIOMD0000000060.svg\nCompleted 20.0 KiB/290.2 KiB (176.7 KiB/s) with 13 file(s) remaining\rCompleted 24.1 KiB/290.2 KiB (204.6 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000060-matlab.m to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/contents/BIOMD0000000060-matlab.m\nCompleted 24.1 KiB/290.2 KiB (204.6 KiB/s) with 12 file(s) remaining\rCompleted 28.2 KiB/290.2 KiB (236.2 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000060-octave.m to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/contents/BIOMD0000000060-octave.m\nCompleted 28.2 KiB/290.2 KiB (236.2 KiB/s) with 11 file(s) remaining\rCompleted 30.9 KiB/290.2 KiB (255.1 KiB/s) with 11 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/contents/metadata.rdf\nCompleted 30.9 KiB/290.2 KiB (255.1 KiB/s) with 10 file(s) remaining\rCompleted 37.8 KiB/290.2 KiB (297.8 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000060_url.sedml to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/contents/BIOMD0000000060_url.sedml\nCompleted 37.8 KiB/290.2 KiB (297.8 KiB/s) with 9 file(s) remaining\rCompleted 57.7 KiB/290.2 KiB (450.7 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000060.png to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/contents/BIOMD0000000060.png\nCompleted 57.7 KiB/290.2 KiB (450.7 KiB/s) with 8 file(s) remaining\rCompleted 73.3 KiB/290.2 KiB (494.4 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000060_url.xml to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/contents/BIOMD0000000060_url.xml\nCompleted 73.3 KiB/290.2 KiB (494.4 KiB/s) with 7 file(s) remaining\rCompleted 73.4 KiB/290.2 KiB (469.1 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/contents/curation_notes.txt\nCompleted 73.4 KiB/290.2 KiB (469.1 KiB/s) with 6 file(s) remaining\rCompleted 120.9 KiB/290.2 KiB (758.3 KiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/contents/curation_image.png\nCompleted 120.9 KiB/290.2 KiB (758.3 KiB/s) with 5 file(s) remaining\rCompleted 122.6 KiB/290.2 KiB (763.6 KiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/contents/manifest.xml\nCompleted 122.6 KiB/290.2 KiB (763.6 KiB/s) with 4 file(s) remaining\rCompleted 134.3 KiB/290.2 KiB (770.6 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000060-biopax3.owl to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/contents/BIOMD0000000060-biopax3.owl\nCompleted 134.3 KiB/290.2 KiB (770.6 KiB/s) with 3 file(s) remaining\rCompleted 136.4 KiB/290.2 KiB (762.1 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000060.ode to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/contents/BIOMD0000000060.ode\nCompleted 136.4 KiB/290.2 KiB (762.1 KiB/s) with 2 file(s) remaining\rCompleted 140.5 KiB/290.2 KiB (752.0 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000060.m to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/contents/BIOMD0000000060.m\nCompleted 140.5 KiB/290.2 KiB (752.0 KiB/s) with 1 file(s) remaining\rCompleted 290.2 KiB/290.2 KiB (1.4 MiB/s) with 1 file(s) remaining  \rupload: contents/BIOMD0000000060.pdf to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/contents/BIOMD0000000060.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (131.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107b749c0d898ffdda0f6/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000060_url.sedml\ncreating dataset /BIOMD0000000060_url.sedml/autogen_plot_for_task1, shape: (5, 1001), type: float64\ndataset created, uuid: d-6f90601e-6482e3dd-4aa8-88aac8-f1ca00, chunk_size: (5, 1001)\ncreating dataset /BIOMD0000000060_url.sedml/autogen_report_for_task1, shape: (10, 1001), type: float64\ndataset created, uuid: d-6f90601e-6482e3dd-81b7-04a74e-718b1c, chunk_size: (10, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000060_url.sedml\ncreating attribute uri in /BIOMD0000000060_url.sedml\ncreating attribute _type in /BIOMD0000000060_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000060_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000060_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000060_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000060_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000060_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000060_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000060_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000060_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000060_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000060_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000060_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000060_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000060_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000060_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000060_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000060_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000060_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000060_url.sedml\ncreate_links: /BIOMD0000000060_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000060_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000060_url.sedml/autogen_plot_for_task1, shape: (5, 1001), type: float64\niterating over chunks for /BIOMD0000000060_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000060_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000060_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000060_url.sedml/autogen_report_for_task1, shape: (10, 1001), type: float64\niterating over chunks for /BIOMD0000000060_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 10, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000060_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647107b749c0d898ffdda0f6\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 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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.207966,"sedDocuments":[{"location":"BIOMD0000000060_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  BIOMD0000000060_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 10 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 4 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000060_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":0.793149,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.164076,"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":0.112231,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Pc1","status":"SUCCEEDED"},{"id":"autogen_task1_Po2","status":"SUCCEEDED"},{"id":"autogen_task1_Po1","status":"SUCCEEDED"},{"id":"autogen_task1_Pc2","status":"SUCCEEDED"},{"id":"autogen_task1_Open_probability","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_Closed_state_1","status":"SUCCEEDED"},{"id":"autogen_task1_Open_state_2","status":"SUCCEEDED"},{"id":"autogen_task1_Closed_State_2","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.377934,"curves":[{"id":"autogen_curve_task1_Pc1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Po2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Po1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Pc2","status":"SUCCEEDED"}]}]}]}