{"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    220      0 --:--:-- --:--:-- --:--:--   220\n\r  8  200k    8 16536    0     0  22697      0  0:00:09 --:--:--  0:00:09 22697\r100  200k  100  200k    0     0   267k      0 --:--:-- --:--:-- --:--:-- 9688k\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 (22.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/rawLog.txt\nCompleted 4.8 KiB/4.8 KiB (76.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/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/reports.h5 (deflated 11%)\n  adding: outputs/BIOMD0000000026_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000026_url.sedml/autogen_plot_for_task1.pdf (deflated 28%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/266.7 KiB (5.9 MiB/s) with 1 file(s) remaining\rCompleted 266.7 KiB/266.7 KiB (2.9 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/outputs/reports.h5\nCompleted 248.2 KiB/269.9 KiB (2.6 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/output.zip\nCompleted 248.2 KiB/269.9 KiB (2.6 MiB/s) with 3 file(s) remaining\rCompleted 256.0 KiB/269.9 KiB (2.3 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/outputs/plots.zip\nCompleted 256.0 KiB/269.9 KiB (2.3 MiB/s) with 2 file(s) remaining\rCompleted 267.2 KiB/269.9 KiB (2.2 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000026_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/outputs/BIOMD0000000026_url.sedml/autogen_plot_for_task1.pdf\nCompleted 267.2 KiB/269.9 KiB (2.2 MiB/s) with 1 file(s) remaining\rCompleted 269.9 KiB/269.9 KiB (2.2 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000026-biopax2.owl  \n  inflating: contents/BIOMD0000000026-biopax3.owl  \n  inflating: contents/BIOMD0000000026-matlab.m  \n  inflating: contents/BIOMD0000000026-octave.m  \n  inflating: contents/BIOMD0000000026.m  \n  inflating: contents/BIOMD0000000026.ode  \n  inflating: contents/BIOMD0000000026.pdf  \n  inflating: contents/BIOMD0000000026.png  \n  inflating: contents/BIOMD0000000026.sci  \n  inflating: contents/BIOMD0000000026.svg  \n  inflating: contents/BIOMD0000000026.vcml  \n  inflating: contents/BIOMD0000000026_url.sedml  \n  inflating: contents/BIOMD0000000026_url.xml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 35.7 KiB/439.5 KiB (534.6 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000026-biopax3.owl to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/contents/BIOMD0000000026-biopax3.owl\nCompleted 35.7 KiB/439.5 KiB (534.6 KiB/s) with 14 file(s) remaining\rCompleted 41.7 KiB/439.5 KiB (420.4 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000026-matlab.m to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/contents/BIOMD0000000026-matlab.m\nCompleted 41.7 KiB/439.5 KiB (420.4 KiB/s) with 13 file(s) remaining\rCompleted 65.2 KiB/439.5 KiB (556.2 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000026-biopax2.owl to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/contents/BIOMD0000000026-biopax2.owl\nCompleted 65.2 KiB/439.5 KiB (556.2 KiB/s) with 12 file(s) remaining\rCompleted 71.3 KiB/439.5 KiB (568.7 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000026-octave.m to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/contents/BIOMD0000000026-octave.m\nCompleted 71.3 KiB/439.5 KiB (568.7 KiB/s) with 11 file(s) remaining\rCompleted 73.0 KiB/439.5 KiB (576.2 KiB/s) with 11 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/contents/manifest.xml\nCompleted 73.0 KiB/439.5 KiB (576.2 KiB/s) with 10 file(s) remaining\rCompleted 76.7 KiB/439.5 KiB (567.7 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000026.sci to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/contents/BIOMD0000000026.sci\nCompleted 76.7 KiB/439.5 KiB (567.7 KiB/s) with 9 file(s) remaining\rCompleted 103.8 KiB/439.5 KiB (707.7 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000026.svg to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/contents/BIOMD0000000026.svg\nCompleted 103.8 KiB/439.5 KiB (707.7 KiB/s) with 8 file(s) remaining\rCompleted 125.2 KiB/439.5 KiB (741.4 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000026_url.sedml to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/contents/BIOMD0000000026_url.sedml\nCompleted 125.2 KiB/439.5 KiB (741.4 KiB/s) with 7 file(s) remaining\rCompleted 166.2 KiB/439.5 KiB (965.3 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000026.vcml to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/contents/BIOMD0000000026.vcml\nCompleted 166.2 KiB/439.5 KiB (965.3 KiB/s) with 6 file(s) remaining\rCompleted 228.4 KiB/439.5 KiB (1.2 MiB/s) with 6 file(s) remaining  \rupload: contents/BIOMD0000000026.png to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/contents/BIOMD0000000026.png\nCompleted 228.4 KiB/439.5 KiB (1.2 MiB/s) with 5 file(s) remaining\rCompleted 234.4 KiB/439.5 KiB (1.2 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000026.m to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/contents/BIOMD0000000026.m\nCompleted 234.4 KiB/439.5 KiB (1.2 MiB/s) with 4 file(s) remaining\rCompleted 408.0 KiB/439.5 KiB (2.1 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000026.pdf to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/contents/BIOMD0000000026.pdf\nCompleted 408.0 KiB/439.5 KiB (2.1 MiB/s) with 3 file(s) remaining\rCompleted 433.6 KiB/439.5 KiB (2.2 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000026_url.xml to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/contents/BIOMD0000000026_url.xml\nCompleted 433.6 KiB/439.5 KiB (2.2 MiB/s) with 2 file(s) remaining\rCompleted 437.5 KiB/439.5 KiB (2.1 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000026.ode to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/contents/BIOMD0000000026.ode\nCompleted 437.5 KiB/439.5 KiB (2.1 MiB/s) with 1 file(s) remaining\rCompleted 439.5 KiB/439.5 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/contents/metadata.rdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (124.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107470dcacb55678b3b9a/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000026_url.sedml\ncreating dataset /BIOMD0000000026_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\ndataset created, uuid: d-d022fad3-4261311c-7041-355a1f-b965f0, chunk_size: (12, 1001)\ncreating dataset /BIOMD0000000026_url.sedml/autogen_report_for_task1, shape: (39, 1001), type: float64\ndataset created, uuid: d-d022fad3-4261311c-1222-1b06fc-077b76, chunk_size: (39, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000026_url.sedml\ncreating attribute uri in /BIOMD0000000026_url.sedml\ncreating attribute _type in /BIOMD0000000026_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000026_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000026_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000026_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000026_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000026_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000026_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000026_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000026_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000026_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000026_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000026_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000026_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000026_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000026_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000026_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000026_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000026_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000026_url.sedml\ncreate_links: /BIOMD0000000026_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000026_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000026_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\niterating over chunks for /BIOMD0000000026_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 12, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000026_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000026_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000026_url.sedml/autogen_report_for_task1, shape: (39, 1001), type: float64\niterating over chunks for /BIOMD0000000026_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 39, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000026_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647107470dcacb55678b3b9a\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.\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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.7816,"sedDocuments":[{"location":"BIOMD0000000026_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  BIOMD0000000026_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 39 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 11 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000026_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":1.293199,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.245791,"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":0.321737,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_M","status":"SUCCEEDED"},{"id":"autogen_task1_Mp","status":"SUCCEEDED"},{"id":"autogen_task1_Mpp","status":"SUCCEEDED"},{"id":"autogen_task1_MAPKK","status":"SUCCEEDED"},{"id":"autogen_task1_MKP3","status":"SUCCEEDED"},{"id":"autogen_task1_M_MAPKK","status":"SUCCEEDED"},{"id":"autogen_task1_Mp_MAPKK","status":"SUCCEEDED"},{"id":"autogen_task1_Mpp_MKP3","status":"SUCCEEDED"},{"id":"autogen_task1_Mp_MKP3_dep","status":"SUCCEEDED"},{"id":"autogen_task1_Mp_MKP3","status":"SUCCEEDED"},{"id":"autogen_task1_M_MKP3","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k_1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_k_3","status":"SUCCEEDED"},{"id":"autogen_task1_k4","status":"SUCCEEDED"},{"id":"autogen_task1_h1","status":"SUCCEEDED"},{"id":"autogen_task1_h_1","status":"SUCCEEDED"},{"id":"autogen_task1_h2","status":"SUCCEEDED"},{"id":"autogen_task1_h3","status":"SUCCEEDED"},{"id":"autogen_task1_h_3","status":"SUCCEEDED"},{"id":"autogen_task1_h4","status":"SUCCEEDED"},{"id":"autogen_task1_h_4","status":"SUCCEEDED"},{"id":"autogen_task1_h5","status":"SUCCEEDED"},{"id":"autogen_task1_h6","status":"SUCCEEDED"},{"id":"autogen_task1_h_6","status":"SUCCEEDED"},{"id":"autogen_task1_uVol","status":"SUCCEEDED"},{"id":"autogen_task1_v1a","status":"SUCCEEDED"},{"id":"autogen_task1_v1b","status":"SUCCEEDED"},{"id":"autogen_task1_v2a","status":"SUCCEEDED"},{"id":"autogen_task1_v2b","status":"SUCCEEDED"},{"id":"autogen_task1_v3a","status":"SUCCEEDED"},{"id":"autogen_task1_v3b","status":"SUCCEEDED"},{"id":"autogen_task1_v3c","status":"SUCCEEDED"},{"id":"autogen_task1_v4a","status":"SUCCEEDED"},{"id":"autogen_task1_v4b","status":"SUCCEEDED"},{"id":"autogen_task1_v4c","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.585247,"curves":[{"id":"autogen_curve_task1_M","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Mp","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Mpp","status":"SUCCEEDED"},{"id":"autogen_curve_task1_MAPKK","status":"SUCCEEDED"},{"id":"autogen_curve_task1_MKP3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_M_MAPKK","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Mp_MAPKK","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Mpp_MKP3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Mp_MKP3_dep","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Mp_MKP3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_M_MKP3","status":"SUCCEEDED"}]}]}]}