{"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    438      0 --:--:-- --:--:-- --:--:--   438\r100   139  100   139    0     0    434      0 --:--:-- --:--:-- --:--:--   433\n\r100  229k  100  229k    0     0   514k      0 --:--:-- --:--:-- --:--:--  514k\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 (26.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/rawLog.txt\nCompleted 3.2 KiB/3.2 KiB (42.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 74%)\n  adding: outputs/proctor2017_model4.sedml/ (stored 0%)\n  adding: outputs/proctor2017_model4.sedml/plot_1_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 30%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 65.6 KiB/65.6 KiB (718.3 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/outputs/reports.h5\nCompleted 56.6 KiB/79.1 KiB (680.9 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/output.zip\nCompleted 56.6 KiB/79.1 KiB (680.9 KiB/s) with 3 file(s) remaining\rCompleted 64.7 KiB/79.1 KiB (631.0 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/outputs/plots.zip\nCompleted 64.7 KiB/79.1 KiB (631.0 KiB/s) with 2 file(s) remaining\rCompleted 76.4 KiB/79.1 KiB (726.6 KiB/s) with 2 file(s) remaining\rupload: outputs/proctor2017_model4.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/outputs/proctor2017_model4.sedml/plot_1_task1.pdf\nCompleted 76.4 KiB/79.1 KiB (726.6 KiB/s) with 1 file(s) remaining\rCompleted 79.1 KiB/79.1 KiB (637.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/MODEL1610100004-biopax2.owl  \n  inflating: contents/MODEL1610100004-biopax3.owl  \n  inflating: contents/MODEL1610100004-matlab.m  \n  inflating: contents/MODEL1610100004-octave.m  \n  inflating: contents/MODEL1610100004.m  \n  inflating: contents/MODEL1610100004.ode  \n  inflating: contents/MODEL1610100004.png  \n  inflating: contents/MODEL1610100004.svg  \n  inflating: contents/MODEL1610100004.vcml  \n  inflating: contents/MODEL1610100004_url.xml  \n  inflating: contents/Proctor2017_model4.cps  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/proctor2017_model4-biopax2.owl  \n  inflating: contents/proctor2017_model4-biopax3.owl  \n  inflating: contents/proctor2017_model4-matlab.m  \n  inflating: contents/proctor2017_model4-octave.m  \n  inflating: contents/proctor2017_model4.ode  \n  inflating: contents/proctor2017_model4.sedml  \n  inflating: contents/proctor2017_model4.xml  \n  inflating: contents/manifest.xml   \nCompleted 15.1 KiB/476.2 KiB (199.0 KiB/s) with 22 file(s) remaining\rupload: contents/MODEL1610100004-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/contents/MODEL1610100004-biopax3.owl\nCompleted 15.1 KiB/476.2 KiB (199.0 KiB/s) with 21 file(s) remaining\rCompleted 19.0 KiB/476.2 KiB (161.1 KiB/s) with 21 file(s) remaining\rupload: contents/MODEL1610100004-matlab.m to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/contents/MODEL1610100004-matlab.m\nCompleted 19.0 KiB/476.2 KiB (161.1 KiB/s) with 20 file(s) remaining\rCompleted 21.6 KiB/476.2 KiB (163.7 KiB/s) with 20 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/contents/manifest.xml\nCompleted 21.6 KiB/476.2 KiB (163.7 KiB/s) with 19 file(s) remaining\rCompleted 30.4 KiB/476.2 KiB (223.3 KiB/s) with 19 file(s) remaining\rupload: contents/MODEL1610100004-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/contents/MODEL1610100004-biopax2.owl\nCompleted 30.4 KiB/476.2 KiB (223.3 KiB/s) with 18 file(s) remaining\rCompleted 34.3 KiB/476.2 KiB (249.3 KiB/s) with 18 file(s) remaining\rupload: contents/MODEL1610100004-octave.m to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/contents/MODEL1610100004-octave.m\nCompleted 34.3 KiB/476.2 KiB (249.3 KiB/s) with 17 file(s) remaining\rCompleted 50.1 KiB/476.2 KiB (344.5 KiB/s) with 17 file(s) remaining\rupload: contents/MODEL1610100004.vcml to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/contents/MODEL1610100004.vcml\nCompleted 50.1 KiB/476.2 KiB (344.5 KiB/s) with 16 file(s) remaining\rCompleted 102.4 KiB/476.2 KiB (613.0 KiB/s) with 16 file(s) remaining\rupload: contents/Proctor2017_model4.cps to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/contents/Proctor2017_model4.cps\nCompleted 102.4 KiB/476.2 KiB (613.0 KiB/s) with 15 file(s) remaining\rCompleted 113.3 KiB/476.2 KiB (617.2 KiB/s) with 15 file(s) remaining\rupload: contents/MODEL1610100004_url.xml to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/contents/MODEL1610100004_url.xml\nCompleted 113.3 KiB/476.2 KiB (617.2 KiB/s) with 14 file(s) remaining\rCompleted 124.1 KiB/476.2 KiB (661.5 KiB/s) with 14 file(s) remaining\rupload: contents/proctor2017_model4-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/contents/proctor2017_model4-biopax2.owl\nCompleted 124.1 KiB/476.2 KiB (661.5 KiB/s) with 13 file(s) remaining\rCompleted 141.2 KiB/476.2 KiB (737.6 KiB/s) with 13 file(s) remaining\rupload: contents/proctor2017_model4-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/contents/proctor2017_model4-biopax3.owl\nCompleted 141.2 KiB/476.2 KiB (737.6 KiB/s) with 12 file(s) remaining\rCompleted 146.7 KiB/476.2 KiB (754.5 KiB/s) with 12 file(s) remaining\rupload: contents/proctor2017_model4-octave.m to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/contents/proctor2017_model4-octave.m\nCompleted 146.7 KiB/476.2 KiB (754.5 KiB/s) with 11 file(s) remaining\rCompleted 152.2 KiB/476.2 KiB (760.7 KiB/s) with 11 file(s) remaining\rupload: contents/proctor2017_model4-matlab.m to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/contents/proctor2017_model4-matlab.m\nCompleted 152.2 KiB/476.2 KiB (760.7 KiB/s) with 10 file(s) remaining\rCompleted 152.4 KiB/476.2 KiB (751.6 KiB/s) with 10 file(s) remaining\rCompleted 156.0 KiB/476.2 KiB (764.5 KiB/s) with 10 file(s) remaining\rupload: contents/proctor2017_model4.ode to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/contents/proctor2017_model4.ode\nCompleted 156.0 KiB/476.2 KiB (764.5 KiB/s) with 9 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/contents/curation_notes.txt\nCompleted 156.0 KiB/476.2 KiB (764.5 KiB/s) with 8 file(s) remaining\rCompleted 161.1 KiB/476.2 KiB (756.3 KiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/contents/metadata.rdf\nCompleted 161.1 KiB/476.2 KiB (756.3 KiB/s) with 7 file(s) remaining\rCompleted 396.9 KiB/476.2 KiB (1.7 MiB/s) with 7 file(s) remaining  \rCompleted 407.7 KiB/476.2 KiB (1.8 MiB/s) with 7 file(s) remaining  \rupload: contents/proctor2017_model4.sedml to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/contents/proctor2017_model4.sedml\nCompleted 407.7 KiB/476.2 KiB (1.8 MiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/contents/curation_image.png\nCompleted 407.7 KiB/476.2 KiB (1.8 MiB/s) with 5 file(s) remaining\rCompleted 409.8 KiB/476.2 KiB (1.5 MiB/s) with 5 file(s) remaining\rCompleted 413.7 KiB/476.2 KiB (1.5 MiB/s) with 5 file(s) remaining\rupload: contents/MODEL1610100004.m to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/contents/MODEL1610100004.m\nCompleted 413.7 KiB/476.2 KiB (1.5 MiB/s) with 4 file(s) remaining\rupload: contents/MODEL1610100004.ode to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/contents/MODEL1610100004.ode\nCompleted 413.7 KiB/476.2 KiB (1.5 MiB/s) with 3 file(s) remaining\rCompleted 425.8 KiB/476.2 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: contents/MODEL1610100004.svg to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/contents/MODEL1610100004.svg\nCompleted 425.8 KiB/476.2 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 449.9 KiB/476.2 KiB (1.6 MiB/s) with 2 file(s) remaining\rupload: contents/MODEL1610100004.png to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/contents/MODEL1610100004.png\nCompleted 449.9 KiB/476.2 KiB (1.6 MiB/s) with 1 file(s) remaining\rCompleted 476.2 KiB/476.2 KiB (1.7 MiB/s) with 1 file(s) remaining\rupload: contents/proctor2017_model4.xml to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/contents/proctor2017_model4.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 10.8 KiB/10.8 KiB (173.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b73195afd5df175f1da/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /proctor2017_model4.sedml\ncreating dataset /proctor2017_model4.sedml/autogen_report_for_task1, shape: (16, 1001), type: float64\ndataset created, uuid: d-3b1d98e7-e9951302-943f-f9717d-037e52, chunk_size: (16, 1001)\ncreating dataset /proctor2017_model4.sedml/plot_1_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-3b1d98e7-e9951302-2494-29da8d-cf69b8, chunk_size: (4, 1001)\ncreating attribute combineArchiveLocation in /proctor2017_model4.sedml\ncreating attribute uri in /proctor2017_model4.sedml\ncreating attribute _type in /proctor2017_model4.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /proctor2017_model4.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /proctor2017_model4.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /proctor2017_model4.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /proctor2017_model4.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /proctor2017_model4.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /proctor2017_model4.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /proctor2017_model4.sedml/autogen_report_for_task1\ncreating attribute uri in /proctor2017_model4.sedml/autogen_report_for_task1\ncreating attribute _type in /proctor2017_model4.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /proctor2017_model4.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /proctor2017_model4.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /proctor2017_model4.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /proctor2017_model4.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /proctor2017_model4.sedml/plot_1_task1\ncreating attribute sedmlId in /proctor2017_model4.sedml/plot_1_task1\ncreating attribute sedmlName in /proctor2017_model4.sedml/plot_1_task1\ncreating attribute uri in /proctor2017_model4.sedml/plot_1_task1\ncreate_links: /\ngot link: proctor2017_model4.sedml\ncreate_links: /proctor2017_model4.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /proctor2017_model4.sedml/autogen_report_for_task1 to tgt: /proctor2017_model4.sedml/autogen_report_for_task1, shape: (16, 1001), type: float64\niterating over chunks for /proctor2017_model4.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 16, 1), slice(0, 1001, 1))\ndone with dataload for /proctor2017_model4.sedml/autogen_report_for_task1\nwrite_dataset src: /proctor2017_model4.sedml/plot_1_task1 to tgt: /proctor2017_model4.sedml/plot_1_task1, shape: (4, 1001), type: float64\niterating over chunks for /proctor2017_model4.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /proctor2017_model4.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b73195afd5df175f1da\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":1.35598,"sedDocuments":[{"location":"proctor2017_model4.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  proctor2017_model4.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 16 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: proctor2017_model4.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_report_for_task1`\r\n      `plot_1_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: `plot_1_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_report_for_task1` ...","duration":0.913368,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.215185,"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":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.426729,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.159987,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_miR","status":"SUCCEEDED"},{"id":"autogen_task1_TF1","status":"SUCCEEDED"},{"id":"autogen_task1_TF1target_mRNA","status":"SUCCEEDED"},{"id":"autogen_task1_Sink","status":"SUCCEEDED"},{"id":"autogen_task1_kdegMiR","status":"SUCCEEDED"},{"id":"autogen_task1_kdegTF1targetmRNA","status":"SUCCEEDED"},{"id":"autogen_task1_kdegTF1targetmRNAbyMiR","status":"SUCCEEDED"},{"id":"autogen_task1_ksynTF1targetmRNA","status":"SUCCEEDED"},{"id":"autogen_task1_ksynMiR","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_miR_synthesis","status":"SUCCEEDED"},{"id":"autogen_task1_miR_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_TF1target_transcription","status":"SUCCEEDED"},{"id":"autogen_task1_TF1target_mRNA_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_TF1target_mRNA_degradation_via_MiR","status":"SUCCEEDED"}]}]}]}