{"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    450      0 --:--:-- --:--:-- --:--:--   449\n\r100  230k  100  230k    0     0   532k      0 --:--:-- --:--:-- --:--:--  532k\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 (26.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/rawLog.txt\nCompleted 4.0 KiB/4.0 KiB (51.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 78%)\n  adding: outputs/Proctor2017_model1.sedml/ (stored 0%)\n  adding: outputs/Proctor2017_model1.sedml/plot_1_task1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 74%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 35.0 KiB/35.0 KiB (481.0 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/outputs/reports.h5\nCompleted 20.1 KiB/43.6 KiB (263.6 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/output.zip\nCompleted 20.1 KiB/43.6 KiB (263.6 KiB/s) with 3 file(s) remaining\rCompleted 28.4 KiB/43.6 KiB (277.4 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/outputs/plots.zip\nCompleted 28.4 KiB/43.6 KiB (277.4 KiB/s) with 2 file(s) remaining\rCompleted 41.0 KiB/43.6 KiB (391.1 KiB/s) with 2 file(s) remaining\rupload: outputs/Proctor2017_model1.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/outputs/Proctor2017_model1.sedml/plot_1_task1.pdf\nCompleted 41.0 KiB/43.6 KiB (391.1 KiB/s) with 1 file(s) remaining\rCompleted 43.6 KiB/43.6 KiB (392.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/MODEL1610100001-biopax2.owl  \n  inflating: contents/MODEL1610100001-biopax3.owl  \n  inflating: contents/MODEL1610100001-matlab.m  \n  inflating: contents/MODEL1610100001-octave.m  \n  inflating: contents/MODEL1610100001.m  \n  inflating: contents/MODEL1610100001.ode  \n  inflating: contents/MODEL1610100001.png  \n  inflating: contents/MODEL1610100001.svg  \n  inflating: contents/MODEL1610100001.vcml  \n  inflating: contents/MODEL1610100001_url.xml  \n  inflating: contents/Proctor2017_model1-biopax2.owl  \n  inflating: contents/Proctor2017_model1-biopax3.owl  \n  inflating: contents/Proctor2017_model1-matlab.m  \n  inflating: contents/Proctor2017_model1-octave.m  \n  inflating: contents/Proctor2017_model1.cps  \n  inflating: contents/Proctor2017_model1.ode  \n  inflating: contents/Proctor2017_model1.sedml  \n  inflating: contents/Proctor2017_model1.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 24.0 KiB/549.5 KiB (297.4 KiB/s) with 22 file(s) remaining\rupload: contents/MODEL1610100001-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/contents/MODEL1610100001-biopax3.owl\nCompleted 24.0 KiB/549.5 KiB (297.4 KiB/s) with 21 file(s) remaining\rCompleted 29.1 KiB/549.5 KiB (254.1 KiB/s) with 21 file(s) remaining\rupload: contents/MODEL1610100001-matlab.m to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/contents/MODEL1610100001-matlab.m\nCompleted 29.1 KiB/549.5 KiB (254.1 KiB/s) with 20 file(s) remaining\rCompleted 42.6 KiB/549.5 KiB (323.0 KiB/s) with 20 file(s) remaining\rupload: contents/MODEL1610100001-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/contents/MODEL1610100001-biopax2.owl\nCompleted 42.6 KiB/549.5 KiB (323.0 KiB/s) with 19 file(s) remaining\rCompleted 47.8 KiB/549.5 KiB (352.0 KiB/s) with 19 file(s) remaining\rupload: contents/MODEL1610100001-octave.m to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/contents/MODEL1610100001-octave.m\nCompleted 47.8 KiB/549.5 KiB (352.0 KiB/s) with 18 file(s) remaining\rCompleted 55.0 KiB/549.5 KiB (401.0 KiB/s) with 18 file(s) remaining\rupload: contents/Proctor2017_model1-octave.m to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/contents/Proctor2017_model1-octave.m\nCompleted 55.0 KiB/549.5 KiB (401.0 KiB/s) with 17 file(s) remaining\rCompleted 60.1 KiB/549.5 KiB (359.5 KiB/s) with 17 file(s) remaining\rupload: contents/Proctor2017_model1.ode to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/contents/Proctor2017_model1.ode\nCompleted 60.1 KiB/549.5 KiB (359.5 KiB/s) with 16 file(s) remaining\rCompleted 74.8 KiB/549.5 KiB (440.0 KiB/s) with 16 file(s) remaining\rupload: contents/MODEL1610100001_url.xml to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/contents/MODEL1610100001_url.xml\nCompleted 74.8 KiB/549.5 KiB (440.0 KiB/s) with 15 file(s) remaining\rCompleted 92.2 KiB/549.5 KiB (531.7 KiB/s) with 15 file(s) remaining\rupload: contents/MODEL1610100001.vcml to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/contents/MODEL1610100001.vcml\nCompleted 92.2 KiB/549.5 KiB (531.7 KiB/s) with 14 file(s) remaining\rCompleted 107.3 KiB/549.5 KiB (607.2 KiB/s) with 14 file(s) remaining\rupload: contents/Proctor2017_model1-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/contents/Proctor2017_model1-biopax2.owl\nCompleted 107.3 KiB/549.5 KiB (607.2 KiB/s) with 13 file(s) remaining\rCompleted 124.2 KiB/549.5 KiB (656.1 KiB/s) with 13 file(s) remaining\rupload: contents/Proctor2017_model1.sedml to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/contents/Proctor2017_model1.sedml\nCompleted 124.2 KiB/549.5 KiB (656.1 KiB/s) with 12 file(s) remaining\rCompleted 131.4 KiB/549.5 KiB (680.8 KiB/s) with 12 file(s) remaining\rupload: contents/Proctor2017_model1-matlab.m to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/contents/Proctor2017_model1-matlab.m\nCompleted 131.4 KiB/549.5 KiB (680.8 KiB/s) with 11 file(s) remaining\rCompleted 160.0 KiB/549.5 KiB (766.6 KiB/s) with 11 file(s) remaining\rupload: contents/Proctor2017_model1.xml to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/contents/Proctor2017_model1.xml\nCompleted 160.0 KiB/549.5 KiB (766.6 KiB/s) with 10 file(s) remaining\rCompleted 225.6 KiB/549.5 KiB (1.0 MiB/s) with 10 file(s) remaining  \rupload: contents/Proctor2017_model1.cps to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/contents/Proctor2017_model1.cps\nCompleted 225.6 KiB/549.5 KiB (1.0 MiB/s) with 9 file(s) remaining\rCompleted 251.3 KiB/549.5 KiB (1.1 MiB/s) with 9 file(s) remaining\rupload: contents/Proctor2017_model1-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/contents/Proctor2017_model1-biopax3.owl\nCompleted 251.3 KiB/549.5 KiB (1.1 MiB/s) with 8 file(s) remaining\rCompleted 457.6 KiB/549.5 KiB (2.0 MiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/contents/curation_image.png\nCompleted 457.6 KiB/549.5 KiB (2.0 MiB/s) with 7 file(s) remaining\rCompleted 462.7 KiB/549.5 KiB (1.9 MiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/contents/metadata.rdf\nCompleted 462.7 KiB/549.5 KiB (1.9 MiB/s) with 6 file(s) remaining\rCompleted 462.9 KiB/549.5 KiB (1.8 MiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/contents/curation_notes.txt\nCompleted 462.9 KiB/549.5 KiB (1.8 MiB/s) with 5 file(s) remaining\rCompleted 465.5 KiB/549.5 KiB (1.8 MiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/contents/manifest.xml\nCompleted 465.5 KiB/549.5 KiB (1.8 MiB/s) with 4 file(s) remaining\rCompleted 485.9 KiB/549.5 KiB (1.9 MiB/s) with 4 file(s) remaining\rupload: contents/MODEL1610100001.svg to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/contents/MODEL1610100001.svg\nCompleted 485.9 KiB/549.5 KiB (1.9 MiB/s) with 3 file(s) remaining\rCompleted 541.2 KiB/549.5 KiB (2.1 MiB/s) with 3 file(s) remaining\rupload: contents/MODEL1610100001.png to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/contents/MODEL1610100001.png\nCompleted 541.2 KiB/549.5 KiB (2.1 MiB/s) with 2 file(s) remaining\rCompleted 546.4 KiB/549.5 KiB (2.1 MiB/s) with 2 file(s) remaining\rupload: contents/MODEL1610100001.m to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/contents/MODEL1610100001.m\nCompleted 546.4 KiB/549.5 KiB (2.1 MiB/s) with 1 file(s) remaining\rCompleted 549.5 KiB/549.5 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: contents/MODEL1610100001.ode to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/contents/MODEL1610100001.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 10.8 KiB/10.8 KiB (161.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b75195afd5df175f1f1/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Proctor2017_model1.sedml\ncreating dataset /Proctor2017_model1.sedml/autogen_report_for_task1, shape: (27, 101), type: float64\ndataset created, uuid: d-3debb8f9-0ce0ae4b-a75b-0462e2-24317e, chunk_size: (27, 101)\ncreating dataset /Proctor2017_model1.sedml/plot_1_task1, shape: (7, 101), type: float64\ndataset created, uuid: d-3debb8f9-0ce0ae4b-1827-b62707-df1141, chunk_size: (7, 101)\ncreating attribute combineArchiveLocation in /Proctor2017_model1.sedml\ncreating attribute uri in /Proctor2017_model1.sedml\ncreating attribute _type in /Proctor2017_model1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Proctor2017_model1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Proctor2017_model1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Proctor2017_model1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Proctor2017_model1.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Proctor2017_model1.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Proctor2017_model1.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Proctor2017_model1.sedml/autogen_report_for_task1\ncreating attribute uri in /Proctor2017_model1.sedml/autogen_report_for_task1\ncreating attribute _type in /Proctor2017_model1.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Proctor2017_model1.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Proctor2017_model1.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Proctor2017_model1.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Proctor2017_model1.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Proctor2017_model1.sedml/plot_1_task1\ncreating attribute sedmlId in /Proctor2017_model1.sedml/plot_1_task1\ncreating attribute sedmlName in /Proctor2017_model1.sedml/plot_1_task1\ncreating attribute uri in /Proctor2017_model1.sedml/plot_1_task1\ncreate_links: /\ngot link: Proctor2017_model1.sedml\ncreate_links: /Proctor2017_model1.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Proctor2017_model1.sedml/autogen_report_for_task1 to tgt: /Proctor2017_model1.sedml/autogen_report_for_task1, shape: (27, 101), type: float64\niterating over chunks for /Proctor2017_model1.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 27, 1), slice(0, 101, 1))\ndone with dataload for /Proctor2017_model1.sedml/autogen_report_for_task1\nwrite_dataset src: /Proctor2017_model1.sedml/plot_1_task1 to tgt: /Proctor2017_model1.sedml/plot_1_task1, shape: (7, 101), type: float64\niterating over chunks for /Proctor2017_model1.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 101, 1))\ndone with dataload for /Proctor2017_model1.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b75195afd5df175f1f1\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 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.\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 metadata in the COMBINE archive ... succeeded.\nPost the metadata 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":1.322454,"sedDocuments":[{"location":"Proctor2017_model1.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_model1.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 27 data sets\r\n    Plots (1):\r\n      plot_1_task1: 6 curves\r\n\r\nExecuting SED-ML file 1: Proctor2017_model1.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":0.854142,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.237213,"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":0.400726,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"},{"id":"p1_curve_4_task1","status":"SUCCEEDED"},{"id":"p1_curve_5_task1","status":"SUCCEEDED"},{"id":"p1_curve_6_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.073835,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_miR","status":"SUCCEEDED"},{"id":"autogen_task1_miR_gene","status":"SUCCEEDED"},{"id":"autogen_task1_miR_gene_TF1","status":"SUCCEEDED"},{"id":"autogen_task1_Signal","status":"SUCCEEDED"},{"id":"autogen_task1_TF1","status":"SUCCEEDED"},{"id":"autogen_task1_TF1_mRNA","status":"SUCCEEDED"},{"id":"autogen_task1_Sink","status":"SUCCEEDED"},{"id":"autogen_task1_kbinTF1miRgene","status":"SUCCEEDED"},{"id":"autogen_task1_kdegMiR","status":"SUCCEEDED"},{"id":"autogen_task1_kdegTF1","status":"SUCCEEDED"},{"id":"autogen_task1_kdegTF1mRNA","status":"SUCCEEDED"},{"id":"autogen_task1_kdegTF1mRNAbyMiR","status":"SUCCEEDED"},{"id":"autogen_task1_krelTF1miRgene","status":"SUCCEEDED"},{"id":"autogen_task1_ksynMiR","status":"SUCCEEDED"},{"id":"autogen_task1_ksynTF1","status":"SUCCEEDED"},{"id":"autogen_task1_ksynTF1mRNA","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_miR_gene_TF1_binding","status":"SUCCEEDED"},{"id":"autogen_task1_miR_gene_TF1_release","status":"SUCCEEDED"},{"id":"autogen_task1_miR_synthesis","status":"SUCCEEDED"},{"id":"autogen_task1_miR_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_TF1_transcription","status":"SUCCEEDED"},{"id":"autogen_task1_TF1_mRNA_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_TF1_mRNA_degradation_via_miR","status":"SUCCEEDED"},{"id":"autogen_task1_TF1_translation","status":"SUCCEEDED"},{"id":"autogen_task1_TF1_degradation","status":"SUCCEEDED"}]}]}]}