{"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    455      0 --:--:-- --:--:-- --:--:--   455\n\r100 79395  100 79395    0     0   181k      0 --:--:-- --:--:-- --:--:--  181k\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 (20.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/rawLog.txt\nCompleted 4.0 KiB/4.0 KiB (36.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/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/reports.h5 (deflated 65%)\n  adding: outputs/Schwarz2018.sedml/ (stored 0%)\n  adding: outputs/Schwarz2018.sedml/plot_1_task1.pdf (deflated 31%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 40.2 KiB/40.2 KiB (416.2 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/outputs/reports.h5\nCompleted 23.6 KiB/43.7 KiB (262.3 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/output.zip\nCompleted 23.6 KiB/43.7 KiB (262.3 KiB/s) with 3 file(s) remaining\rCompleted 26.2 KiB/43.7 KiB (200.1 KiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/rawLog.txt\nCompleted 26.2 KiB/43.7 KiB (200.1 KiB/s) with 2 file(s) remaining\rCompleted 33.2 KiB/43.7 KiB (251.5 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/outputs/plots.zip\nCompleted 33.2 KiB/43.7 KiB (251.5 KiB/s) with 1 file(s) remaining\rCompleted 43.7 KiB/43.7 KiB (289.7 KiB/s) with 1 file(s) remaining\rupload: outputs/Schwarz2018.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/outputs/Schwarz2018.sedml/plot_1_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Schwarz2018-biopax2.owl  \n  inflating: contents/Schwarz2018-biopax3.owl  \n  inflating: contents/Schwarz2018-matlab.m  \n  inflating: contents/Schwarz2018.cps  \n  inflating: contents/Schwarz2018.ode  \n  inflating: contents/Schwarz2018.sedml  \n  inflating: contents/Schwarz2018.xml  \n  inflating: contents/Schwarz2018_orignal-biopax2.owl  \n  inflating: contents/Schwarz2018_orignal-biopax3.owl  \n  inflating: contents/Schwarz2018_orignal-matlab.m  \n  inflating: contents/Schwarz2018_orignal.ode  \n  inflating: contents/Schwarz2018_orignal.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 12.7 KiB/441.0 KiB (180.4 KiB/s) with 16 file(s) remaining\rupload: contents/Schwarz2018-biopax2.owl to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/contents/Schwarz2018-biopax2.owl\nCompleted 12.7 KiB/441.0 KiB (180.4 KiB/s) with 15 file(s) remaining\rCompleted 24.0 KiB/441.0 KiB (182.4 KiB/s) with 15 file(s) remaining\rupload: contents/Schwarz2018_orignal-biopax2.owl to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/contents/Schwarz2018_orignal-biopax2.owl\nCompleted 24.0 KiB/441.0 KiB (182.4 KiB/s) with 14 file(s) remaining\rCompleted 143.5 KiB/441.0 KiB (1.0 MiB/s) with 14 file(s) remaining \rupload: contents/Schwarz2018.cps to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/contents/Schwarz2018.cps\nCompleted 143.5 KiB/441.0 KiB (1.0 MiB/s) with 13 file(s) remaining\rCompleted 151.1 KiB/441.0 KiB (996.1 KiB/s) with 13 file(s) remaining\rupload: contents/Schwarz2018-matlab.m to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/contents/Schwarz2018-matlab.m\nCompleted 151.1 KiB/441.0 KiB (996.1 KiB/s) with 12 file(s) remaining\rCompleted 151.5 KiB/441.0 KiB (964.5 KiB/s) with 12 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/contents/curation_notes.txt\nCompleted 151.5 KiB/441.0 KiB (964.5 KiB/s) with 11 file(s) remaining\rCompleted 158.3 KiB/441.0 KiB (978.1 KiB/s) with 11 file(s) remaining\rupload: contents/Schwarz2018_orignal.ode to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/contents/Schwarz2018_orignal.ode\nCompleted 158.3 KiB/441.0 KiB (978.1 KiB/s) with 10 file(s) remaining\rCompleted 166.6 KiB/441.0 KiB (976.7 KiB/s) with 10 file(s) remaining\rupload: contents/Schwarz2018_orignal-matlab.m to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/contents/Schwarz2018_orignal-matlab.m\nCompleted 166.6 KiB/441.0 KiB (976.7 KiB/s) with 9 file(s) remaining\rCompleted 181.8 KiB/441.0 KiB (1.0 MiB/s) with 9 file(s) remaining  \rupload: contents/Schwarz2018_orignal-biopax3.owl to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/contents/Schwarz2018_orignal-biopax3.owl\nCompleted 181.8 KiB/441.0 KiB (1.0 MiB/s) with 8 file(s) remaining\rCompleted 275.3 KiB/441.0 KiB (1.5 MiB/s) with 8 file(s) remaining\rupload: contents/Schwarz2018_orignal.xml to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/contents/Schwarz2018_orignal.xml\nCompleted 275.3 KiB/441.0 KiB (1.5 MiB/s) with 7 file(s) remaining\rCompleted 317.7 KiB/441.0 KiB (1.5 MiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/contents/curation_image.png\nCompleted 317.7 KiB/441.0 KiB (1.5 MiB/s) with 6 file(s) remaining\rCompleted 392.0 KiB/441.0 KiB (1.8 MiB/s) with 6 file(s) remaining\rupload: contents/Schwarz2018.xml to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/contents/Schwarz2018.xml\nCompleted 392.0 KiB/441.0 KiB (1.8 MiB/s) with 5 file(s) remaining\rCompleted 393.8 KiB/441.0 KiB (1.7 MiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/contents/manifest.xml\nCompleted 393.8 KiB/441.0 KiB (1.7 MiB/s) with 4 file(s) remaining\rCompleted 399.6 KiB/441.0 KiB (1.7 MiB/s) with 4 file(s) remaining\rupload: contents/Schwarz2018.ode to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/contents/Schwarz2018.ode\nCompleted 399.6 KiB/441.0 KiB (1.7 MiB/s) with 3 file(s) remaining\rCompleted 402.1 KiB/441.0 KiB (1.6 MiB/s) with 3 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/contents/metadata.rdf\nCompleted 402.1 KiB/441.0 KiB (1.6 MiB/s) with 2 file(s) remaining\rCompleted 418.8 KiB/441.0 KiB (1.6 MiB/s) with 2 file(s) remaining\rupload: contents/Schwarz2018-biopax3.owl to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/contents/Schwarz2018-biopax3.owl\nCompleted 418.8 KiB/441.0 KiB (1.6 MiB/s) with 1 file(s) remaining\rCompleted 441.0 KiB/441.0 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: contents/Schwarz2018.sedml to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/contents/Schwarz2018.sedml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.7 KiB/8.7 KiB (114.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a61930fb37cdb9ae76e81/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Schwarz2018.sedml\ncreating dataset /Schwarz2018.sedml/autogen_report_for_task1, shape: (42, 101), type: float64\ndataset created, uuid: d-6a9e3d5e-6166d6fc-58ad-80a6b5-4f16b4, chunk_size: (42, 101)\ncreating dataset /Schwarz2018.sedml/plot_1_task1, shape: (3, 101), type: float64\ndataset created, uuid: d-6a9e3d5e-6166d6fc-8923-17c27e-c16a15, chunk_size: (3, 101)\ncreating attribute combineArchiveLocation in /Schwarz2018.sedml\ncreating attribute uri in /Schwarz2018.sedml\ncreating attribute _type in /Schwarz2018.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Schwarz2018.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Schwarz2018.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Schwarz2018.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Schwarz2018.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Schwarz2018.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Schwarz2018.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Schwarz2018.sedml/autogen_report_for_task1\ncreating attribute uri in /Schwarz2018.sedml/autogen_report_for_task1\ncreating attribute _type in /Schwarz2018.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Schwarz2018.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Schwarz2018.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Schwarz2018.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Schwarz2018.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Schwarz2018.sedml/plot_1_task1\ncreating attribute sedmlId in /Schwarz2018.sedml/plot_1_task1\ncreating attribute sedmlName in /Schwarz2018.sedml/plot_1_task1\ncreating attribute uri in /Schwarz2018.sedml/plot_1_task1\ncreate_links: /\ngot link: Schwarz2018.sedml\ncreate_links: /Schwarz2018.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Schwarz2018.sedml/autogen_report_for_task1 to tgt: /Schwarz2018.sedml/autogen_report_for_task1, shape: (42, 101), type: float64\niterating over chunks for /Schwarz2018.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 42, 1), slice(0, 101, 1))\ndone with dataload for /Schwarz2018.sedml/autogen_report_for_task1\nwrite_dataset src: /Schwarz2018.sedml/plot_1_task1 to tgt: /Schwarz2018.sedml/plot_1_task1, shape: (3, 101), type: float64\niterating over chunks for /Schwarz2018.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 101, 1))\ndone with dataload for /Schwarz2018.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a61930fb37cdb9ae76e81\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 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 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 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":1.245323,"sedDocuments":[{"location":"Schwarz2018.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  Schwarz2018.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 42 data sets\r\n    Plots (1):\r\n      plot_1_task1: 2 curves\r\n\r\nExecuting SED-ML file 1: Schwarz2018.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":0.791855,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.175586,"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":100000,"Relative Tolerance":0.000001}}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.359258,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.090463,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_CycE","status":"SUCCEEDED"},{"id":"autogen_task1_serum","status":"SUCCEEDED"},{"id":"autogen_task1_Myc","status":"SUCCEEDED"},{"id":"autogen_task1_E2F","status":"SUCCEEDED"},{"id":"autogen_task1_CycD","status":"SUCCEEDED"},{"id":"autogen_task1_Rb","status":"SUCCEEDED"},{"id":"autogen_task1_Phosphorylated_Rb","status":"SUCCEEDED"},{"id":"autogen_task1_Rb_E2F_complex","status":"SUCCEEDED"},{"id":"autogen_task1_kE","status":"SUCCEEDED"},{"id":"autogen_task1_kM","status":"SUCCEEDED"},{"id":"autogen_task1_kCD","status":"SUCCEEDED"},{"id":"autogen_task1_kCDS","status":"SUCCEEDED"},{"id":"autogen_task1_kR","status":"SUCCEEDED"},{"id":"autogen_task1_kRE","status":"SUCCEEDED"},{"id":"autogen_task1_kb","status":"SUCCEEDED"},{"id":"autogen_task1_KS","status":"SUCCEEDED"},{"id":"autogen_task1_kCE","status":"SUCCEEDED"},{"id":"autogen_task1_dM","status":"SUCCEEDED"},{"id":"autogen_task1_dE","status":"SUCCEEDED"},{"id":"autogen_task1_dCD","status":"SUCCEEDED"},{"id":"autogen_task1_dCE","status":"SUCCEEDED"},{"id":"autogen_task1_dR","status":"SUCCEEDED"},{"id":"autogen_task1_dRP","status":"SUCCEEDED"},{"id":"autogen_task1_dRE","status":"SUCCEEDED"},{"id":"autogen_task1_kP1","status":"SUCCEEDED"},{"id":"autogen_task1_kP2","status":"SUCCEEDED"},{"id":"autogen_task1_kDP","status":"SUCCEEDED"},{"id":"autogen_task1_KM","status":"SUCCEEDED"},{"id":"autogen_task1_KE","status":"SUCCEEDED"},{"id":"autogen_task1_KCD","status":"SUCCEEDED"},{"id":"autogen_task1_KCE","status":"SUCCEEDED"},{"id":"autogen_task1_KRP","status":"SUCCEEDED"},{"id":"autogen_task1_kpfb","status":"SUCCEEDED"},{"id":"autogen_task1_Cell","status":"SUCCEEDED"},{"id":"autogen_task1_For_Myc","status":"SUCCEEDED"},{"id":"autogen_task1_For_E2F","status":"SUCCEEDED"},{"id":"autogen_task1_For_CycD","status":"SUCCEEDED"},{"id":"autogen_task1_for_CycE","status":"SUCCEEDED"},{"id":"autogen_task1_For_Rb","status":"SUCCEEDED"},{"id":"autogen_task1_for_Phosphorylated_Rb","status":"SUCCEEDED"},{"id":"autogen_task1_for_Rb_E2F_complex","status":"SUCCEEDED"}]}]}]}