{"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    430      0 --:--:-- --:--:-- --:--:--   430\n\r100 61730  100 61730    0     0   142k      0 --:--:-- --:--:-- --:--:--  142k\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 (16.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c8049c0d898ffdf2d6d/rawLog.txt\nCompleted 3.8 KiB/3.8 KiB (59.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711c8049c0d898ffdf2d6d/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/ (stored 0%)\n  adding: outputs/Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_plot_for_task1.pdf (deflated 33%)\n  adding: outputs/log.yml (deflated 79%)\n  adding: outputs/reports.h5 (deflated 17%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 166.6 KiB/166.6 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711c8049c0d898ffdf2d6d/outputs/reports.h5\nCompleted 146.6 KiB/164.4 KiB (1.7 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711c8049c0d898ffdf2d6d/output.zip\nCompleted 146.6 KiB/164.4 KiB (1.7 MiB/s) with 3 file(s) remaining\rCompleted 155.7 KiB/164.4 KiB (1.4 MiB/s) with 3 file(s) remaining\rupload: outputs/Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64711c8049c0d898ffdf2d6d/outputs/Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_plot_for_task1.pdf\nCompleted 155.7 KiB/164.4 KiB (1.4 MiB/s) with 2 file(s) remaining\rCompleted 161.7 KiB/164.4 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711c8049c0d898ffdf2d6d/outputs/plots.zip\nCompleted 161.7 KiB/164.4 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 164.4 KiB/164.4 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c8049c0d898ffdf2d6d/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth-biopax2.owl  \n  inflating: contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth-biopax3.owl  \n  inflating: contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth-matlab.m  \n  inflating: contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth-octave.m  \n  inflating: contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth.cps  \n  inflating: contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth.ode  \n  inflating: contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml  \n  inflating: contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 19.9 KiB/225.6 KiB (286.5 KiB/s) with 12 file(s) remaining\rupload: contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth-biopax3.owl to s3://files.biosimulations.org/simulations/64711c8049c0d898ffdf2d6d/contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth-biopax3.owl\nCompleted 19.9 KiB/225.6 KiB (286.5 KiB/s) with 11 file(s) remaining\rCompleted 25.7 KiB/225.6 KiB (230.0 KiB/s) with 11 file(s) remaining\rupload: contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth-matlab.m to s3://files.biosimulations.org/simulations/64711c8049c0d898ffdf2d6d/contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth-matlab.m\nCompleted 25.7 KiB/225.6 KiB (230.0 KiB/s) with 10 file(s) remaining\rCompleted 39.0 KiB/225.6 KiB (339.4 KiB/s) with 10 file(s) remaining\rupload: contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth-biopax2.owl to s3://files.biosimulations.org/simulations/64711c8049c0d898ffdf2d6d/contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth-biopax2.owl\nCompleted 39.0 KiB/225.6 KiB (339.4 KiB/s) with 9 file(s) remaining\rCompleted 56.9 KiB/225.6 KiB (430.8 KiB/s) with 9 file(s) remaining\rupload: contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml to s3://files.biosimulations.org/simulations/64711c8049c0d898ffdf2d6d/contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml\nCompleted 56.9 KiB/225.6 KiB (430.8 KiB/s) with 8 file(s) remaining\rCompleted 62.7 KiB/225.6 KiB (431.8 KiB/s) with 8 file(s) remaining\rupload: contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth-octave.m to s3://files.biosimulations.org/simulations/64711c8049c0d898ffdf2d6d/contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth-octave.m\nCompleted 62.7 KiB/225.6 KiB (431.8 KiB/s) with 7 file(s) remaining\rCompleted 63.2 KiB/225.6 KiB (428.8 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711c8049c0d898ffdf2d6d/contents/curation_notes.txt\nCompleted 63.2 KiB/225.6 KiB (428.8 KiB/s) with 6 file(s) remaining\rCompleted 102.6 KiB/225.6 KiB (627.4 KiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64711c8049c0d898ffdf2d6d/contents/curation_image.png\nCompleted 102.6 KiB/225.6 KiB (627.4 KiB/s) with 5 file(s) remaining\rCompleted 104.3 KiB/225.6 KiB (623.7 KiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711c8049c0d898ffdf2d6d/contents/manifest.xml\nCompleted 104.3 KiB/225.6 KiB (623.7 KiB/s) with 4 file(s) remaining\rCompleted 105.5 KiB/225.6 KiB (596.6 KiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711c8049c0d898ffdf2d6d/contents/metadata.rdf\nCompleted 105.5 KiB/225.6 KiB (596.6 KiB/s) with 3 file(s) remaining\rCompleted 109.5 KiB/225.6 KiB (587.9 KiB/s) with 3 file(s) remaining\rupload: contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth.ode to s3://files.biosimulations.org/simulations/64711c8049c0d898ffdf2d6d/contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth.ode\nCompleted 109.5 KiB/225.6 KiB (587.9 KiB/s) with 2 file(s) remaining\rCompleted 179.3 KiB/225.6 KiB (942.8 KiB/s) with 2 file(s) remaining\rupload: contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth.cps to s3://files.biosimulations.org/simulations/64711c8049c0d898ffdf2d6d/contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth.cps\nCompleted 179.3 KiB/225.6 KiB (942.8 KiB/s) with 1 file(s) remaining\rCompleted 225.6 KiB/225.6 KiB (1.1 MiB/s) with 1 file(s) remaining  \rupload: contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth.xml to s3://files.biosimulations.org/simulations/64711c8049c0d898ffdf2d6d/contents/Liu2017 - Dynamics of Avian Influenza with Logistic Growth.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.7 KiB/8.7 KiB (99.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c8049c0d898ffdf2d6d/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml\ncreating dataset /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\ndataset created, uuid: d-f2ae2d0c-70cd2267-087b-31eafd-c482aa, chunk_size: (6, 1001)\ncreating dataset /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_report_for_task1, shape: (31, 1001), type: float64\ndataset created, uuid: d-f2ae2d0c-70cd2267-5086-6ed1df-9a85a4, chunk_size: (31, 1001)\ncreating attribute combineArchiveLocation in /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml\ncreating attribute uri in /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml\ncreating attribute _type in /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_plot_for_task1\ncreating attribute uri in /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_plot_for_task1\ncreating attribute _type in /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_report_for_task1\ncreating attribute uri in /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml\ncreate_links: /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_plot_for_task1 to tgt: /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\niterating over chunks for /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1001, 1))\ndone with dataload for /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_plot_for_task1\nwrite_dataset src: /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_report_for_task1 to tgt: /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_report_for_task1, shape: (31, 1001), type: float64\niterating over chunks for /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 31, 1), slice(0, 1001, 1))\ndone with dataload for /Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711c8049c0d898ffdf2d6d\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 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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.44045,"sedDocuments":[{"location":"Liu2017 - Dynamics of Avian Influenza with Logistic Growth.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  Liu2017 - Dynamics of Avian Influenza with Logistic Growth.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 31 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 5 curves\r\n\r\nExecuting SED-ML file 1: Liu2017 - Dynamics of Avian Influenza with Logistic Growth.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":1.036781,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.146323,"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":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.312532,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_S_a","status":"SUCCEEDED"},{"id":"autogen_task1_I_a","status":"SUCCEEDED"},{"id":"autogen_task1_S_h","status":"SUCCEEDED"},{"id":"autogen_task1_I_h","status":"SUCCEEDED"},{"id":"autogen_task1_R_h","status":"SUCCEEDED"},{"id":"autogen_task1_r_a","status":"SUCCEEDED"},{"id":"autogen_task1_K_a","status":"SUCCEEDED"},{"id":"autogen_task1_beta_a","status":"SUCCEEDED"},{"id":"autogen_task1_mu_a","status":"SUCCEEDED"},{"id":"autogen_task1_delta_a","status":"SUCCEEDED"},{"id":"autogen_task1_pi_h","status":"SUCCEEDED"},{"id":"autogen_task1_beta_h","status":"SUCCEEDED"},{"id":"autogen_task1_mu_h","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_delta_h","status":"SUCCEEDED"},{"id":"autogen_task1_M_a","status":"SUCCEEDED"},{"id":"autogen_task1_m_a","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_Avian_population","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_1","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_2","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_3","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_4","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_5","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_6","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_7","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_8","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_9","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_10","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_11","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.44213,"curves":[{"id":"autogen_curve_task1_S_a","status":"SUCCEEDED"},{"id":"autogen_curve_task1_I_a","status":"SUCCEEDED"},{"id":"autogen_curve_task1_S_h","status":"SUCCEEDED"},{"id":"autogen_curve_task1_I_h","status":"SUCCEEDED"},{"id":"autogen_curve_task1_R_h","status":"SUCCEEDED"}]}]}]}