{"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    420      0 --:--:-- --:--:-- --:--:--   421\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100  174k  100  174k    0     0   396k      0 --:--:-- --:--:-- --:--:-- 2272k\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 (25.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/rawLog.txt\nCompleted 2.9 KiB/2.9 KiB (44.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/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/BIOMD0000000036_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000036_url.sedml/autogen_plot_for_task1.pdf (deflated 29%)\n  adding: outputs/reports.h5 (deflated 26%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 97.9 KiB/97.9 KiB (1.0 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/outputs/reports.h5\nCompleted 82.9 KiB/103.8 KiB (881.3 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/output.zip\nCompleted 82.9 KiB/103.8 KiB (881.3 KiB/s) with 3 file(s) remaining\rCompleted 90.3 KiB/103.8 KiB (827.1 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/outputs/plots.zip\nCompleted 90.3 KiB/103.8 KiB (827.1 KiB/s) with 2 file(s) remaining\rCompleted 101.1 KiB/103.8 KiB (855.1 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000036_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/outputs/BIOMD0000000036_url.sedml/autogen_plot_for_task1.pdf\nCompleted 101.1 KiB/103.8 KiB (855.1 KiB/s) with 1 file(s) remaining\rCompleted 103.8 KiB/103.8 KiB (806.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000036-biopax2.owl  \n  inflating: contents/BIOMD0000000036-biopax3.owl  \n  inflating: contents/BIOMD0000000036-matlab.m  \n  inflating: contents/BIOMD0000000036-octave.m  \n  inflating: contents/BIOMD0000000036.m  \n  inflating: contents/BIOMD0000000036.ode  \n  inflating: contents/BIOMD0000000036.pdf  \n  inflating: contents/BIOMD0000000036.png  \n  inflating: contents/BIOMD0000000036.sci  \n  inflating: contents/BIOMD0000000036.svg  \n  inflating: contents/BIOMD0000000036_url.sedml  \n  inflating: contents/BIOMD0000000036_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 15.4 KiB/279.3 KiB (217.7 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000036-biopax3.owl to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/contents/BIOMD0000000036-biopax3.owl\nCompleted 15.4 KiB/279.3 KiB (217.7 KiB/s) with 15 file(s) remaining\rCompleted 19.4 KiB/279.3 KiB (199.0 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000036-matlab.m to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/contents/BIOMD0000000036-matlab.m\nCompleted 19.4 KiB/279.3 KiB (199.0 KiB/s) with 14 file(s) remaining\rCompleted 30.7 KiB/279.3 KiB (263.2 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000036-biopax2.owl to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/contents/BIOMD0000000036-biopax2.owl\nCompleted 30.7 KiB/279.3 KiB (263.2 KiB/s) with 13 file(s) remaining\rCompleted 32.5 KiB/279.3 KiB (254.3 KiB/s) with 13 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/contents/manifest.xml\nCompleted 32.5 KiB/279.3 KiB (254.3 KiB/s) with 12 file(s) remaining\rCompleted 34.3 KiB/279.3 KiB (264.8 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000036.sci to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/contents/BIOMD0000000036.sci\nCompleted 34.3 KiB/279.3 KiB (264.8 KiB/s) with 11 file(s) remaining\rCompleted 41.7 KiB/279.3 KiB (282.5 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000036_url.sedml to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/contents/BIOMD0000000036_url.sedml\nCompleted 41.7 KiB/279.3 KiB (282.5 KiB/s) with 10 file(s) remaining\rCompleted 44.2 KiB/279.3 KiB (288.3 KiB/s) with 10 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/contents/metadata.rdf\nCompleted 44.2 KiB/279.3 KiB (288.3 KiB/s) with 9 file(s) remaining\rCompleted 48.2 KiB/279.3 KiB (312.1 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000036-octave.m to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/contents/BIOMD0000000036-octave.m\nCompleted 48.2 KiB/279.3 KiB (312.1 KiB/s) with 8 file(s) remaining\rCompleted 59.6 KiB/279.3 KiB (367.6 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000036.svg to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/contents/BIOMD0000000036.svg\nCompleted 59.6 KiB/279.3 KiB (367.6 KiB/s) with 7 file(s) remaining\rCompleted 74.2 KiB/279.3 KiB (450.4 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000036_url.xml to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/contents/BIOMD0000000036_url.xml\nCompleted 74.2 KiB/279.3 KiB (450.4 KiB/s) with 6 file(s) remaining\rCompleted 74.3 KiB/279.3 KiB (398.5 KiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/contents/curation_notes.txt\nCompleted 74.3 KiB/279.3 KiB (398.5 KiB/s) with 5 file(s) remaining\rCompleted 78.2 KiB/279.3 KiB (407.5 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000036.m to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/contents/BIOMD0000000036.m\nCompleted 78.2 KiB/279.3 KiB (407.5 KiB/s) with 4 file(s) remaining\rCompleted 104.4 KiB/279.3 KiB (537.1 KiB/s) with 4 file(s) remaining\rCompleted 122.7 KiB/279.3 KiB (624.3 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000036.png to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/contents/BIOMD0000000036.png\nCompleted 122.7 KiB/279.3 KiB (624.3 KiB/s) with 3 file(s) remaining\rCompleted 277.3 KiB/279.3 KiB (1.4 MiB/s) with 3 file(s) remaining  \rupload: contents/BIOMD0000000036.pdf to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/contents/BIOMD0000000036.pdf\nCompleted 277.3 KiB/279.3 KiB (1.4 MiB/s) with 2 file(s) remaining\rCompleted 279.3 KiB/279.3 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000036.ode to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/contents/BIOMD0000000036.ode\nCompleted 279.3 KiB/279.3 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/contents/curation_image.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (124.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107679a62a8be53f73e4b/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000036_url.sedml\ncreating dataset /BIOMD0000000036_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-1c5e0f34-64dbdc47-cc0d-203d34-362fa3, chunk_size: (4, 1001)\ncreating dataset /BIOMD0000000036_url.sedml/autogen_report_for_task1, shape: (12, 1001), type: float64\ndataset created, uuid: d-1c5e0f34-64dbdc47-5d19-40b106-e32449, chunk_size: (12, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000036_url.sedml\ncreating attribute uri in /BIOMD0000000036_url.sedml\ncreating attribute _type in /BIOMD0000000036_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000036_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000036_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000036_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000036_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000036_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000036_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000036_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000036_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000036_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000036_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000036_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000036_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000036_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000036_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000036_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000036_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000036_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000036_url.sedml\ncreate_links: /BIOMD0000000036_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000036_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000036_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\niterating over chunks for /BIOMD0000000036_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000036_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000036_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000036_url.sedml/autogen_report_for_task1, shape: (12, 1001), type: float64\niterating over chunks for /BIOMD0000000036_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 12, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000036_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647107679a62a8be53f73e4b\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 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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.321282,"sedDocuments":[{"location":"BIOMD0000000036_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  BIOMD0000000036_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 12 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000036_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":0.88815,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.201326,"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":0.143486,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_EmptySet","status":"SUCCEEDED"},{"id":"autogen_task1_M","status":"SUCCEEDED"},{"id":"autogen_task1_P","status":"SUCCEEDED"},{"id":"autogen_task1_N_A","status":"SUCCEEDED"},{"id":"autogen_task1_default","status":"SUCCEEDED"},{"id":"autogen_task1_CYTOPLASM","status":"SUCCEEDED"},{"id":"autogen_task1_TC","status":"SUCCEEDED"},{"id":"autogen_task1_TL","status":"SUCCEEDED"},{"id":"autogen_task1_mRNAD","status":"SUCCEEDED"},{"id":"autogen_task1_ProteinD","status":"SUCCEEDED"},{"id":"autogen_task1_DBT","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.42561,"curves":[{"id":"autogen_curve_task1_EmptySet","status":"SUCCEEDED"},{"id":"autogen_curve_task1_M","status":"SUCCEEDED"},{"id":"autogen_curve_task1_P","status":"SUCCEEDED"}]}]}]}