{"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    427      0 --:--:-- --:--:-- --:--:--   426\n\r100  289k  100  289k    0     0   629k      0 --:--:-- --:--:-- --:--:--  629k\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 (24.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/rawLog.txt\nCompleted 4.1 KiB/4.1 KiB (60.8 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 79%)\n  adding: outputs/Proctor2017_model0.sedml/ (stored 0%)\n  adding: outputs/Proctor2017_model0.sedml/plot_1_task1.pdf (deflated 23%)\n  adding: outputs/reports.h5 (deflated 56%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 45.6 KiB/45.6 KiB (540.7 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/outputs/reports.h5\nCompleted 35.1 KiB/66.0 KiB (482.6 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/output.zip\nCompleted 35.1 KiB/66.0 KiB (482.6 KiB/s) with 3 file(s) remaining\rCompleted 47.3 KiB/66.0 KiB (421.3 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/outputs/plots.zip\nCompleted 47.3 KiB/66.0 KiB (421.3 KiB/s) with 2 file(s) remaining\rCompleted 63.4 KiB/66.0 KiB (551.3 KiB/s) with 2 file(s) remaining\rupload: outputs/Proctor2017_model0.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/outputs/Proctor2017_model0.sedml/plot_1_task1.pdf\nCompleted 63.4 KiB/66.0 KiB (551.3 KiB/s) with 1 file(s) remaining\rCompleted 66.0 KiB/66.0 KiB (559.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/MODEL1610100000-biopax2.owl  \n  inflating: contents/MODEL1610100000-biopax3.owl  \n  inflating: contents/MODEL1610100000-matlab.m  \n  inflating: contents/MODEL1610100000-octave.m  \n  inflating: contents/MODEL1610100000.m  \n  inflating: contents/MODEL1610100000.ode  \n  inflating: contents/MODEL1610100000.png  \n  inflating: contents/MODEL1610100000.svg  \n  inflating: contents/MODEL1610100000.vcml  \n  inflating: contents/MODEL1610100000_url.xml  \n  inflating: contents/Proctor2017_model0-biopax2.owl  \n  inflating: contents/Proctor2017_model0-biopax3.owl  \n  inflating: contents/Proctor2017_model0-matlab.m  \n  inflating: contents/Proctor2017_model0-octave.m  \n  inflating: contents/Proctor2017_model0.cps  \n  inflating: contents/Proctor2017_model0.ode  \n  inflating: contents/Proctor2017_model0.sedml  \n  inflating: contents/Proctor2017_model0.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 16.1 KiB/~268.3 KiB (233.0 KiB/s) with ~14 file(s) remaining (calculating...)\rupload: contents/MODEL1610100000-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/contents/MODEL1610100000-biopax2.owl\nCompleted 16.1 KiB/~268.3 KiB (233.0 KiB/s) with ~13 file(s) remaining (calculating...)\rCompleted 22.1 KiB/659.3 KiB (179.0 KiB/s) with 21 file(s) remaining                   \rupload: contents/MODEL1610100000-octave.m to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/contents/MODEL1610100000-octave.m\nCompleted 22.1 KiB/659.3 KiB (179.0 KiB/s) with 20 file(s) remaining\rCompleted 28.1 KiB/659.3 KiB (221.6 KiB/s) with 20 file(s) remaining\rupload: contents/MODEL1610100000-matlab.m to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/contents/MODEL1610100000-matlab.m\nCompleted 28.1 KiB/659.3 KiB (221.6 KiB/s) with 19 file(s) remaining\rCompleted 53.1 KiB/659.3 KiB (389.6 KiB/s) with 19 file(s) remaining\rupload: contents/MODEL1610100000.svg to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/contents/MODEL1610100000.svg\nCompleted 53.1 KiB/659.3 KiB (389.6 KiB/s) with 18 file(s) remaining\rCompleted 59.2 KiB/659.3 KiB (409.5 KiB/s) with 18 file(s) remaining\rupload: contents/MODEL1610100000.m to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/contents/MODEL1610100000.m\nCompleted 59.2 KiB/659.3 KiB (409.5 KiB/s) with 17 file(s) remaining\rCompleted 84.3 KiB/659.3 KiB (576.6 KiB/s) with 17 file(s) remaining\rupload: contents/MODEL1610100000.vcml to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/contents/MODEL1610100000.vcml\nCompleted 84.3 KiB/659.3 KiB (576.6 KiB/s) with 16 file(s) remaining\rCompleted 101.5 KiB/659.3 KiB (655.7 KiB/s) with 16 file(s) remaining\rupload: contents/MODEL1610100000_url.xml to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/contents/MODEL1610100000_url.xml\nCompleted 101.5 KiB/659.3 KiB (655.7 KiB/s) with 15 file(s) remaining\rCompleted 132.6 KiB/659.3 KiB (740.0 KiB/s) with 15 file(s) remaining\rupload: contents/Proctor2017_model0-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/contents/Proctor2017_model0-biopax3.owl\nCompleted 132.6 KiB/659.3 KiB (740.0 KiB/s) with 14 file(s) remaining\rCompleted 150.3 KiB/659.3 KiB (825.9 KiB/s) with 14 file(s) remaining\rupload: contents/Proctor2017_model0-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/contents/Proctor2017_model0-biopax2.owl\nCompleted 150.3 KiB/659.3 KiB (825.9 KiB/s) with 13 file(s) remaining\rCompleted 159.2 KiB/659.3 KiB (860.3 KiB/s) with 13 file(s) remaining\rupload: contents/Proctor2017_model0-matlab.m to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/contents/Proctor2017_model0-matlab.m\nCompleted 159.2 KiB/659.3 KiB (860.3 KiB/s) with 12 file(s) remaining\rCompleted 163.0 KiB/659.3 KiB (856.5 KiB/s) with 12 file(s) remaining\rupload: contents/MODEL1610100000.ode to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/contents/MODEL1610100000.ode\nCompleted 163.0 KiB/659.3 KiB (856.5 KiB/s) with 11 file(s) remaining\rCompleted 192.3 KiB/659.3 KiB (990.6 KiB/s) with 11 file(s) remaining\rupload: contents/MODEL1610100000-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/contents/MODEL1610100000-biopax3.owl\nCompleted 192.3 KiB/659.3 KiB (990.6 KiB/s) with 10 file(s) remaining\rCompleted 201.1 KiB/659.3 KiB (999.4 KiB/s) with 10 file(s) remaining\rupload: contents/Proctor2017_model0-octave.m to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/contents/Proctor2017_model0-octave.m\nCompleted 201.1 KiB/659.3 KiB (999.4 KiB/s) with 9 file(s) remaining\rCompleted 221.6 KiB/659.3 KiB (1.1 MiB/s) with 9 file(s) remaining  \rupload: contents/Proctor2017_model0.sedml to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/contents/Proctor2017_model0.sedml\nCompleted 221.6 KiB/659.3 KiB (1.1 MiB/s) with 8 file(s) remaining\rCompleted 228.2 KiB/659.3 KiB (1.1 MiB/s) with 8 file(s) remaining\rupload: contents/Proctor2017_model0.ode to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/contents/Proctor2017_model0.ode\nCompleted 228.2 KiB/659.3 KiB (1.1 MiB/s) with 7 file(s) remaining\rCompleted 295.4 KiB/659.3 KiB (1.4 MiB/s) with 7 file(s) remaining\rupload: contents/MODEL1610100000.png to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/contents/MODEL1610100000.png\nCompleted 295.4 KiB/659.3 KiB (1.4 MiB/s) with 6 file(s) remaining\rCompleted 543.5 KiB/659.3 KiB (2.3 MiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/contents/curation_image.png\nCompleted 543.5 KiB/659.3 KiB (2.3 MiB/s) with 5 file(s) remaining\rCompleted 548.6 KiB/659.3 KiB (2.1 MiB/s) with 5 file(s) remaining\rCompleted 551.2 KiB/659.3 KiB (2.1 MiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/contents/manifest.xml\nCompleted 551.2 KiB/659.3 KiB (2.1 MiB/s) with 4 file(s) remaining\rCompleted 584.0 KiB/659.3 KiB (2.2 MiB/s) with 4 file(s) remaining\rCompleted 584.1 KiB/659.3 KiB (2.2 MiB/s) with 4 file(s) remaining\rupload: contents/Proctor2017_model0.xml to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/contents/Proctor2017_model0.xml\nCompleted 584.1 KiB/659.3 KiB (2.2 MiB/s) with 3 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/contents/curation_notes.txt\nCompleted 584.1 KiB/659.3 KiB (2.2 MiB/s) with 2 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/contents/metadata.rdf\nCompleted 584.1 KiB/659.3 KiB (2.2 MiB/s) with 1 file(s) remaining\rCompleted 659.3 KiB/659.3 KiB (2.3 MiB/s) with 1 file(s) remaining\rupload: contents/Proctor2017_model0.cps to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/contents/Proctor2017_model0.cps\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 10.9 KiB/10.9 KiB (129.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b740fb37cdb9ae737a5/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Proctor2017_model0.sedml\ncreating dataset /Proctor2017_model0.sedml/autogen_report_for_task1, shape: (33, 101), type: float64\ndataset created, uuid: d-6c1dcd27-fdf5bcc1-2f32-ce3fd1-4b9f5f, chunk_size: (33, 101)\ncreating dataset /Proctor2017_model0.sedml/plot_1_task1, shape: (9, 101), type: float64\ndataset created, uuid: d-6c1dcd27-fdf5bcc1-626c-7463a9-b04fdf, chunk_size: (9, 101)\ncreating attribute combineArchiveLocation in /Proctor2017_model0.sedml\ncreating attribute uri in /Proctor2017_model0.sedml\ncreating attribute _type in /Proctor2017_model0.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Proctor2017_model0.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Proctor2017_model0.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Proctor2017_model0.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Proctor2017_model0.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Proctor2017_model0.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Proctor2017_model0.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Proctor2017_model0.sedml/autogen_report_for_task1\ncreating attribute uri in /Proctor2017_model0.sedml/autogen_report_for_task1\ncreating attribute _type in /Proctor2017_model0.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Proctor2017_model0.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Proctor2017_model0.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Proctor2017_model0.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Proctor2017_model0.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Proctor2017_model0.sedml/plot_1_task1\ncreating attribute sedmlId in /Proctor2017_model0.sedml/plot_1_task1\ncreating attribute sedmlName in /Proctor2017_model0.sedml/plot_1_task1\ncreating attribute uri in /Proctor2017_model0.sedml/plot_1_task1\ncreate_links: /\ngot link: Proctor2017_model0.sedml\ncreate_links: /Proctor2017_model0.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Proctor2017_model0.sedml/autogen_report_for_task1 to tgt: /Proctor2017_model0.sedml/autogen_report_for_task1, shape: (33, 101), type: float64\niterating over chunks for /Proctor2017_model0.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 33, 1), slice(0, 101, 1))\ndone with dataload for /Proctor2017_model0.sedml/autogen_report_for_task1\nwrite_dataset src: /Proctor2017_model0.sedml/plot_1_task1 to tgt: /Proctor2017_model0.sedml/plot_1_task1, shape: (9, 101), type: float64\niterating over chunks for /Proctor2017_model0.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 101, 1))\ndone with dataload for /Proctor2017_model0.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b740fb37cdb9ae737a5\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.\nProcess and upload the outputs of the simulation run ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... 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":1.166477,"sedDocuments":[{"location":"Proctor2017_model0.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_model0.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 33 data sets\r\n    Plots (1):\r\n      plot_1_task1: 8 curves\r\n\r\nExecuting SED-ML file 1: Proctor2017_model0.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":0.734366,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.137686,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"deterministic"},{"key":"methodCode","value":22},{"key":"parameters","value":{"Absolute Tolerance":1e-12,"Integrate Reduced Model":false,"Max Internal Steps":10000,"Relative Tolerance":0.000001}}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.375604,"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":"p1_curve_7_task1","status":"SUCCEEDED"},{"id":"p1_curve_8_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.079251,"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_miR_gene_TF2","status":"SUCCEEDED"},{"id":"autogen_task1_Signal","status":"SUCCEEDED"},{"id":"autogen_task1_TF1","status":"SUCCEEDED"},{"id":"autogen_task1_TF1_mRNA","status":"SUCCEEDED"},{"id":"autogen_task1_TF2","status":"SUCCEEDED"},{"id":"autogen_task1_Sink","status":"SUCCEEDED"},{"id":"autogen_task1_kbinTF1miRgene","status":"SUCCEEDED"},{"id":"autogen_task1_kbinTF2miRgene","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_krelTF2miRgene","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_gene_TF2_binding","status":"SUCCEEDED"},{"id":"autogen_task1_miR_gene_TF2_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"}]}]}]}