{"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    464      0 --:--:-- --:--:-- --:--:--   464\n\r100  242k  100  242k    0     0   575k      0 --:--:-- --:--:-- --:--:--  575k\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 (16.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/rawLog.txt\nCompleted 4.9 KiB/4.9 KiB (73.8 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 81%)\n  adding: outputs/reports.h5 (deflated 12%)\n  adding: outputs/BIOMD0000000240_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000240_url.sedml/autogen_plot_for_task1.pdf (deflated 32%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 227.1 KiB/227.1 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/outputs/reports.h5\nCompleted 6.3 KiB/227.0 KiB (56.3 KiB/s) with 4 file(s) remaining\rCompleted 214.9 KiB/227.0 KiB (1.9 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/output.zip\nCompleted 214.9 KiB/227.0 KiB (1.9 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/outputs/plots.zip\nCompleted 214.9 KiB/227.0 KiB (1.9 MiB/s) with 2 file(s) remaining\rCompleted 224.4 KiB/227.0 KiB (1.9 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000240_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/outputs/BIOMD0000000240_url.sedml/autogen_plot_for_task1.pdf\nCompleted 224.4 KiB/227.0 KiB (1.9 MiB/s) with 1 file(s) remaining\rCompleted 227.0 KiB/227.0 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000240-biopax2.owl  \n  inflating: contents/BIOMD0000000240-biopax3.owl  \n  inflating: contents/BIOMD0000000240-matlab.m  \n  inflating: contents/BIOMD0000000240-octave.m  \n  inflating: contents/BIOMD0000000240.m  \n  inflating: contents/BIOMD0000000240.ode  \n  inflating: contents/BIOMD0000000240.pdf  \n  inflating: contents/BIOMD0000000240.png  \n  inflating: contents/BIOMD0000000240.svg  \n  inflating: contents/BIOMD0000000240_url.sedml  \n  inflating: contents/BIOMD0000000240_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 26.3 KiB/443.6 KiB (280.9 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000240-biopax3.owl to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/contents/BIOMD0000000240-biopax3.owl\nCompleted 26.3 KiB/443.6 KiB (280.9 KiB/s) with 14 file(s) remaining\rCompleted 44.3 KiB/443.6 KiB (371.9 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000240-biopax2.owl to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/contents/BIOMD0000000240-biopax2.owl\nCompleted 44.3 KiB/443.6 KiB (371.9 KiB/s) with 13 file(s) remaining\rCompleted 72.4 KiB/443.6 KiB (488.8 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000240.svg to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/contents/BIOMD0000000240.svg\nCompleted 72.4 KiB/443.6 KiB (488.8 KiB/s) with 12 file(s) remaining\rCompleted 105.2 KiB/443.6 KiB (696.8 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000240_url.xml to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/contents/BIOMD0000000240_url.xml\nCompleted 105.2 KiB/443.6 KiB (696.8 KiB/s) with 11 file(s) remaining\rCompleted 129.6 KiB/443.6 KiB (842.7 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000240_url.sedml to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/contents/BIOMD0000000240_url.sedml\nCompleted 129.6 KiB/443.6 KiB (842.7 KiB/s) with 10 file(s) remaining\rCompleted 133.7 KiB/443.6 KiB (850.5 KiB/s) with 10 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/contents/metadata.rdf\nCompleted 133.7 KiB/443.6 KiB (850.5 KiB/s) with 9 file(s) remaining\rCompleted 140.2 KiB/443.6 KiB (880.1 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000240-octave.m to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/contents/BIOMD0000000240-octave.m\nCompleted 140.2 KiB/443.6 KiB (880.1 KiB/s) with 8 file(s) remaining\rCompleted 176.2 KiB/443.6 KiB (1.0 MiB/s) with 8 file(s) remaining  \rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/contents/curation_image.png\nCompleted 176.2 KiB/443.6 KiB (1.0 MiB/s) with 7 file(s) remaining\rCompleted 176.7 KiB/443.6 KiB (1002.3 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/contents/curation_notes.txt\nCompleted 176.7 KiB/443.6 KiB (1002.3 KiB/s) with 6 file(s) remaining\rCompleted 178.4 KiB/443.6 KiB (975.0 KiB/s) with 6 file(s) remaining \rCompleted 184.9 KiB/443.6 KiB (1001.9 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000240-matlab.m to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/contents/BIOMD0000000240-matlab.m\nCompleted 184.9 KiB/443.6 KiB (1001.9 KiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/contents/manifest.xml\nCompleted 184.9 KiB/443.6 KiB (1001.9 KiB/s) with 4 file(s) remaining\rCompleted 376.4 KiB/443.6 KiB (1.8 MiB/s) with 4 file(s) remaining   \rupload: contents/BIOMD0000000240.pdf to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/contents/BIOMD0000000240.pdf\nCompleted 376.4 KiB/443.6 KiB (1.8 MiB/s) with 3 file(s) remaining\rCompleted 382.9 KiB/443.6 KiB (1.7 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000240.m to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/contents/BIOMD0000000240.m\nCompleted 382.9 KiB/443.6 KiB (1.7 MiB/s) with 2 file(s) remaining\rCompleted 386.9 KiB/443.6 KiB (1.7 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000240.ode to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/contents/BIOMD0000000240.ode\nCompleted 386.9 KiB/443.6 KiB (1.7 MiB/s) with 1 file(s) remaining\rCompleted 443.6 KiB/443.6 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000240.png to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/contents/BIOMD0000000240.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (112.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a100dcacb55678b8c76/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000240_url.sedml\ncreating dataset /BIOMD0000000240_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\ndataset created, uuid: d-db0742ee-45520d75-ec63-54c448-8d1c82, chunk_size: (7, 1001)\ncreating dataset /BIOMD0000000240_url.sedml/autogen_report_for_task1, shape: (45, 1001), type: float64\ndataset created, uuid: d-db0742ee-45520d75-3301-3d962a-7eb34c, chunk_size: (45, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000240_url.sedml\ncreating attribute uri in /BIOMD0000000240_url.sedml\ncreating attribute _type in /BIOMD0000000240_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000240_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000240_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000240_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000240_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000240_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000240_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000240_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000240_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000240_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000240_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000240_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000240_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000240_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000240_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000240_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000240_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000240_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000240_url.sedml\ncreate_links: /BIOMD0000000240_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000240_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000240_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\niterating over chunks for /BIOMD0000000240_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000240_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000240_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000240_url.sedml/autogen_report_for_task1, shape: (45, 1001), type: float64\niterating over chunks for /BIOMD0000000240_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 45, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000240_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710a100dcacb55678b8c76\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 metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.806528,"sedDocuments":[{"location":"BIOMD0000000240_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  BIOMD0000000240_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 45 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 6 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000240_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":1.291589,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.24541,"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":0.368503,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_AprE","status":"SUCCEEDED"},{"id":"autogen_task1_DegU","status":"SUCCEEDED"},{"id":"autogen_task1_DegUP","status":"SUCCEEDED"},{"id":"autogen_task1_Dim","status":"SUCCEEDED"},{"id":"autogen_task1_mAprE","status":"SUCCEEDED"},{"id":"autogen_task1_mDegU","status":"SUCCEEDED"},{"id":"autogen_task1_Imax","status":"SUCCEEDED"},{"id":"autogen_task1_Io","status":"SUCCEEDED"},{"id":"autogen_task1_Irmax","status":"SUCCEEDED"},{"id":"autogen_task1_Iro","status":"SUCCEEDED"},{"id":"autogen_task1_K","status":"SUCCEEDED"},{"id":"autogen_task1_Kdim","status":"SUCCEEDED"},{"id":"autogen_task1_Kr","status":"SUCCEEDED"},{"id":"autogen_task1_Kr1","status":"SUCCEEDED"},{"id":"autogen_task1_R","status":"SUCCEEDED"},{"id":"autogen_task1_V","status":"SUCCEEDED"},{"id":"autogen_task1_ka","status":"SUCCEEDED"},{"id":"autogen_task1_kd","status":"SUCCEEDED"},{"id":"autogen_task1_kdeg","status":"SUCCEEDED"},{"id":"autogen_task1_kdegA","status":"SUCCEEDED"},{"id":"autogen_task1_kdegm","status":"SUCCEEDED"},{"id":"autogen_task1_kdephos","status":"SUCCEEDED"},{"id":"autogen_task1_kphos","status":"SUCCEEDED"},{"id":"autogen_task1_ksyn","status":"SUCCEEDED"},{"id":"autogen_task1_ksyn1","status":"SUCCEEDED"},{"id":"autogen_task1_p","status":"SUCCEEDED"},{"id":"autogen_task1_q","status":"SUCCEEDED"},{"id":"autogen_task1_ratio","status":"SUCCEEDED"},{"id":"autogen_task1_DegU_Total","status":"SUCCEEDED"},{"id":"autogen_task1_univ","status":"SUCCEEDED"},{"id":"autogen_task1_AprEdeg","status":"SUCCEEDED"},{"id":"autogen_task1_AprEsyn","status":"SUCCEEDED"},{"id":"autogen_task1_DimerAss","status":"SUCCEEDED"},{"id":"autogen_task1_DimerDis","status":"SUCCEEDED"},{"id":"autogen_task1_degradation1","status":"SUCCEEDED"},{"id":"autogen_task1_degradation2","status":"SUCCEEDED"},{"id":"autogen_task1_degradation3","status":"SUCCEEDED"},{"id":"autogen_task1_degradationmRNA","status":"SUCCEEDED"},{"id":"autogen_task1_dephosphorylation","status":"SUCCEEDED"},{"id":"autogen_task1_mRNAAprEdeg","status":"SUCCEEDED"},{"id":"autogen_task1_mRNAAprEsyn","status":"SUCCEEDED"},{"id":"autogen_task1_phosphorylation","status":"SUCCEEDED"},{"id":"autogen_task1_synthesisDegU","status":"SUCCEEDED"},{"id":"autogen_task1_synthesismRNA","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.502089,"curves":[{"id":"autogen_curve_task1_AprE","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DegU","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DegUP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Dim","status":"SUCCEEDED"},{"id":"autogen_curve_task1_mAprE","status":"SUCCEEDED"},{"id":"autogen_curve_task1_mDegU","status":"SUCCEEDED"}]}]}]}