{"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    437      0 --:--:-- --:--:-- --:--:--   437\n\r100  135k  100  135k    0     0   317k      0 --:--:-- --:--:-- --:--:--  317k\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 (26.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/rawLog.txt\nCompleted 3.6 KiB/3.6 KiB (51.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 77%)\n  adding: outputs/BIOMD0000000642_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000642_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 31%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 72.9 KiB/72.9 KiB (859.1 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/outputs/reports.h5\nCompleted 59.3 KiB/77.2 KiB (704.4 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/output.zip\nCompleted 59.3 KiB/77.2 KiB (704.4 KiB/s) with 3 file(s) remaining\rCompleted 65.5 KiB/77.2 KiB (662.4 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/outputs/plots.zip\nCompleted 65.5 KiB/77.2 KiB (662.4 KiB/s) with 2 file(s) remaining\rCompleted 74.5 KiB/77.2 KiB (728.0 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000642_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/outputs/BIOMD0000000642_url.sedml/autogen_plot_for_task1.pdf\nCompleted 74.5 KiB/77.2 KiB (728.0 KiB/s) with 1 file(s) remaining\rCompleted 77.2 KiB/77.2 KiB (659.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000642-biopax2.owl  \n  inflating: contents/BIOMD0000000642-biopax3.owl  \n  inflating: contents/BIOMD0000000642-matlab.m  \n  inflating: contents/BIOMD0000000642-octave.m  \n  inflating: contents/BIOMD0000000642.ode  \n  inflating: contents/BIOMD0000000642_url.sedml  \n  inflating: contents/BIOMD0000000642_url.xml  \n  inflating: contents/MODEL1304190001-biopax2.owl  \n  inflating: contents/MODEL1304190001-biopax3.owl  \n  inflating: contents/MODEL1304190001.m  \n  inflating: contents/MODEL1304190001.ode  \n  inflating: contents/MODEL1304190001.pdf  \n  inflating: contents/MODEL1304190001.png  \n  inflating: contents/MODEL1304190001.sci  \n  inflating: contents/MODEL1304190001.svg  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 6.0 KiB/226.7 KiB (88.8 KiB/s) with 19 file(s) remaining\rupload: contents/BIOMD0000000642-biopax3.owl to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/contents/BIOMD0000000642-biopax3.owl\nCompleted 6.0 KiB/226.7 KiB (88.8 KiB/s) with 18 file(s) remaining\rCompleted 10.3 KiB/226.7 KiB (96.1 KiB/s) with 18 file(s) remaining\rupload: contents/BIOMD0000000642-matlab.m to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/contents/BIOMD0000000642-matlab.m\nCompleted 10.3 KiB/226.7 KiB (96.1 KiB/s) with 17 file(s) remaining\rCompleted 15.8 KiB/226.7 KiB (129.9 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000642-biopax2.owl to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/contents/BIOMD0000000642-biopax2.owl\nCompleted 15.8 KiB/226.7 KiB (129.9 KiB/s) with 16 file(s) remaining\rCompleted 19.3 KiB/226.7 KiB (154.3 KiB/s) with 16 file(s) remaining\rupload: contents/MODEL1304190001.m to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/contents/MODEL1304190001.m\nCompleted 19.3 KiB/226.7 KiB (154.3 KiB/s) with 15 file(s) remaining\rCompleted 23.6 KiB/226.7 KiB (184.3 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000642-octave.m to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/contents/BIOMD0000000642-octave.m\nCompleted 23.6 KiB/226.7 KiB (184.3 KiB/s) with 14 file(s) remaining\rCompleted 25.9 KiB/226.7 KiB (198.7 KiB/s) with 14 file(s) remaining\rupload: contents/MODEL1304190001-biopax3.owl to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/contents/MODEL1304190001-biopax3.owl\nCompleted 25.9 KiB/226.7 KiB (198.7 KiB/s) with 13 file(s) remaining\rCompleted 26.7 KiB/226.7 KiB (193.6 KiB/s) with 13 file(s) remaining\rupload: contents/MODEL1304190001.svg to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/contents/MODEL1304190001.svg\nCompleted 26.7 KiB/226.7 KiB (193.6 KiB/s) with 12 file(s) remaining\rCompleted 29.0 KiB/226.7 KiB (202.7 KiB/s) with 12 file(s) remaining\rupload: contents/MODEL1304190001.ode to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/contents/MODEL1304190001.ode\nCompleted 29.0 KiB/226.7 KiB (202.7 KiB/s) with 11 file(s) remaining\rCompleted 34.0 KiB/226.7 KiB (207.9 KiB/s) with 11 file(s) remaining\rupload: contents/MODEL1304190001.png to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/contents/MODEL1304190001.png\nCompleted 34.0 KiB/226.7 KiB (207.9 KiB/s) with 10 file(s) remaining\rCompleted 160.0 KiB/226.7 KiB (966.7 KiB/s) with 10 file(s) remaining\rupload: contents/MODEL1304190001.pdf to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/contents/MODEL1304190001.pdf\nCompleted 160.0 KiB/226.7 KiB (966.7 KiB/s) with 9 file(s) remaining\rCompleted 175.5 KiB/226.7 KiB (994.3 KiB/s) with 9 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/contents/curation_image.png\nCompleted 175.5 KiB/226.7 KiB (994.3 KiB/s) with 8 file(s) remaining\rCompleted 177.4 KiB/226.7 KiB (933.3 KiB/s) with 8 file(s) remaining\rupload: contents/MODEL1304190001-biopax2.owl to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/contents/MODEL1304190001-biopax2.owl\nCompleted 177.4 KiB/226.7 KiB (933.3 KiB/s) with 7 file(s) remaining\rCompleted 179.6 KiB/226.7 KiB (929.8 KiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/contents/manifest.xml\nCompleted 179.6 KiB/226.7 KiB (929.8 KiB/s) with 6 file(s) remaining\rCompleted 179.8 KiB/226.7 KiB (907.1 KiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/contents/curation_notes.txt\nCompleted 179.8 KiB/226.7 KiB (907.1 KiB/s) with 5 file(s) remaining\rCompleted 181.7 KiB/226.7 KiB (899.1 KiB/s) with 5 file(s) remaining\rupload: contents/MODEL1304190001.sci to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/contents/MODEL1304190001.sci\nCompleted 181.7 KiB/226.7 KiB (899.1 KiB/s) with 4 file(s) remaining\rCompleted 185.8 KiB/226.7 KiB (894.5 KiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/contents/metadata.rdf\nCompleted 185.8 KiB/226.7 KiB (894.5 KiB/s) with 3 file(s) remaining\rCompleted 211.0 KiB/226.7 KiB (1003.6 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000642_url.xml to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/contents/BIOMD0000000642_url.xml\nCompleted 211.0 KiB/226.7 KiB (1003.6 KiB/s) with 2 file(s) remaining\rCompleted 224.3 KiB/226.7 KiB (1007.4 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000642_url.sedml to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/contents/BIOMD0000000642_url.sedml\nCompleted 224.3 KiB/226.7 KiB (1007.4 KiB/s) with 1 file(s) remaining\rCompleted 226.7 KiB/226.7 KiB (971.4 KiB/s) with 1 file(s) remaining \rupload: contents/BIOMD0000000642.ode to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/contents/BIOMD0000000642.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.9 KiB/9.9 KiB (147.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711ba149c0d898ffdf151c/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000642_url.sedml\ncreating dataset /BIOMD0000000642_url.sedml/autogen_plot_for_task1, shape: (5, 1001), type: float64\ndataset created, uuid: d-3865064d-710c410b-7dad-99c67a-8fca14, chunk_size: (5, 1001)\ncreating dataset /BIOMD0000000642_url.sedml/autogen_report_for_task1, shape: (24, 1001), type: float64\ndataset created, uuid: d-3865064d-710c410b-bf27-ac6549-3ad156, chunk_size: (24, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000642_url.sedml\ncreating attribute uri in /BIOMD0000000642_url.sedml\ncreating attribute _type in /BIOMD0000000642_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000642_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000642_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000642_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000642_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000642_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000642_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000642_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000642_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000642_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000642_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000642_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000642_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000642_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000642_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000642_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000642_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000642_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000642_url.sedml\ncreate_links: /BIOMD0000000642_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000642_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000642_url.sedml/autogen_plot_for_task1, shape: (5, 1001), type: float64\niterating over chunks for /BIOMD0000000642_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000642_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000642_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000642_url.sedml/autogen_report_for_task1, shape: (24, 1001), type: float64\niterating over chunks for /BIOMD0000000642_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 24, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000642_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711ba149c0d898ffdf151c\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.\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.\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 SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.277185,"sedDocuments":[{"location":"BIOMD0000000642_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  BIOMD0000000642_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 24 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 4 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000642_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":0.900198,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.194355,"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":0.202547,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_H","status":"SUCCEEDED"},{"id":"autogen_task1_T","status":"SUCCEEDED"},{"id":"autogen_task1_I","status":"SUCCEEDED"},{"id":"autogen_task1_E","status":"SUCCEEDED"},{"id":"autogen_task1_alpha1","status":"SUCCEEDED"},{"id":"autogen_task1_alpha2","status":"SUCCEEDED"},{"id":"autogen_task1_beta1","status":"SUCCEEDED"},{"id":"autogen_task1_beta2","status":"SUCCEEDED"},{"id":"autogen_task1_delta1","status":"SUCCEEDED"},{"id":"autogen_task1_gamma2","status":"SUCCEEDED"},{"id":"autogen_task1_s","status":"SUCCEEDED"},{"id":"autogen_task1_rho","status":"SUCCEEDED"},{"id":"autogen_task1_omega","status":"SUCCEEDED"},{"id":"autogen_task1_mu","status":"SUCCEEDED"},{"id":"autogen_task1_alpha3","status":"SUCCEEDED"},{"id":"autogen_task1_gamma3","status":"SUCCEEDED"},{"id":"autogen_task1_sigma1","status":"SUCCEEDED"},{"id":"autogen_task1_sigma2","status":"SUCCEEDED"},{"id":"autogen_task1_sigma3","status":"SUCCEEDED"},{"id":"autogen_task1_v","status":"SUCCEEDED"},{"id":"autogen_task1_theta","status":"SUCCEEDED"},{"id":"autogen_task1_pi","status":"SUCCEEDED"},{"id":"autogen_task1_Tissue","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.386027,"curves":[{"id":"autogen_curve_task1_H","status":"SUCCEEDED"},{"id":"autogen_curve_task1_T","status":"SUCCEEDED"},{"id":"autogen_curve_task1_I","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E","status":"SUCCEEDED"}]}]}]}