{"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    436      0 --:--:-- --:--:-- --:--:--   437\n\r100 29949  100 29949    0     0  72581      0 --:--:-- --:--:-- --:--:-- 72581\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 (25.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b5e77b66696550611bc/rawLog.txt\nCompleted 3.2 KiB/3.2 KiB (41.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b5e77b66696550611bc/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/Bazjer2008.sedml/ (stored 0%)\n  adding: outputs/Bazjer2008.sedml/plot_1_task1.pdf (deflated 34%)\n  adding: outputs/reports.h5 (deflated 57%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 31.3 KiB/31.3 KiB (381.9 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b5e77b66696550611bc/outputs/reports.h5\nCompleted 21.8 KiB/39.5 KiB (294.0 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b5e77b66696550611bc/output.zip\nCompleted 21.8 KiB/39.5 KiB (294.0 KiB/s) with 3 file(s) remaining\rCompleted 31.0 KiB/39.5 KiB (299.3 KiB/s) with 3 file(s) remaining\rupload: outputs/Bazjer2008.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b5e77b66696550611bc/outputs/Bazjer2008.sedml/plot_1_task1.pdf\nCompleted 31.0 KiB/39.5 KiB (299.3 KiB/s) with 2 file(s) remaining\rCompleted 36.9 KiB/39.5 KiB (334.1 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b5e77b66696550611bc/outputs/plots.zip\nCompleted 36.9 KiB/39.5 KiB (334.1 KiB/s) with 1 file(s) remaining\rCompleted 39.5 KiB/39.5 KiB (348.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b5e77b66696550611bc/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Bazjer2008-biopax2.owl  \n  inflating: contents/Bazjer2008-biopax3.owl  \n  inflating: contents/Bazjer2008-matlab.m  \n  inflating: contents/Bazjer2008-octave.m  \n  inflating: contents/Bazjer2008.cps  \n  inflating: contents/Bazjer2008.ode  \n  inflating: contents/Bazjer2008.sedml  \n  inflating: contents/Bazjer2008.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 11.2 KiB/148.5 KiB (180.5 KiB/s) with 12 file(s) remaining\rupload: contents/Bazjer2008-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b5e77b66696550611bc/contents/Bazjer2008-biopax2.owl\nCompleted 11.2 KiB/148.5 KiB (180.5 KiB/s) with 11 file(s) remaining\rCompleted 15.8 KiB/148.5 KiB (144.3 KiB/s) with 11 file(s) remaining\rupload: contents/Bazjer2008-octave.m to s3://files.biosimulations.org/simulations/647a4b5e77b66696550611bc/contents/Bazjer2008-octave.m\nCompleted 15.8 KiB/148.5 KiB (144.3 KiB/s) with 10 file(s) remaining\rCompleted 20.5 KiB/148.5 KiB (164.4 KiB/s) with 10 file(s) remaining\rupload: contents/Bazjer2008-matlab.m to s3://files.biosimulations.org/simulations/647a4b5e77b66696550611bc/contents/Bazjer2008-matlab.m\nCompleted 20.5 KiB/148.5 KiB (164.4 KiB/s) with 9 file(s) remaining\rCompleted 73.6 KiB/148.5 KiB (571.7 KiB/s) with 9 file(s) remaining\rupload: contents/Bazjer2008.cps to s3://files.biosimulations.org/simulations/647a4b5e77b66696550611bc/contents/Bazjer2008.cps\nCompleted 73.6 KiB/148.5 KiB (571.7 KiB/s) with 8 file(s) remaining\rCompleted 83.2 KiB/148.5 KiB (601.4 KiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b5e77b66696550611bc/contents/curation_image.png\nCompleted 83.2 KiB/148.5 KiB (601.4 KiB/s) with 7 file(s) remaining\rCompleted 114.8 KiB/148.5 KiB (808.9 KiB/s) with 7 file(s) remaining\rupload: contents/Bazjer2008.xml to s3://files.biosimulations.org/simulations/647a4b5e77b66696550611bc/contents/Bazjer2008.xml\nCompleted 114.8 KiB/148.5 KiB (808.9 KiB/s) with 6 file(s) remaining\rCompleted 115.0 KiB/148.5 KiB (806.2 KiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b5e77b66696550611bc/contents/curation_notes.txt\nCompleted 115.0 KiB/148.5 KiB (806.2 KiB/s) with 5 file(s) remaining\rCompleted 116.3 KiB/148.5 KiB (732.4 KiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b5e77b66696550611bc/contents/manifest.xml\nCompleted 116.3 KiB/148.5 KiB (732.4 KiB/s) with 4 file(s) remaining\rCompleted 118.6 KiB/148.5 KiB (695.0 KiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b5e77b66696550611bc/contents/metadata.rdf\nCompleted 118.6 KiB/148.5 KiB (695.0 KiB/s) with 3 file(s) remaining\rCompleted 133.9 KiB/148.5 KiB (724.7 KiB/s) with 3 file(s) remaining\rupload: contents/Bazjer2008-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b5e77b66696550611bc/contents/Bazjer2008-biopax3.owl\nCompleted 133.9 KiB/148.5 KiB (724.7 KiB/s) with 2 file(s) remaining\rCompleted 145.6 KiB/148.5 KiB (748.8 KiB/s) with 2 file(s) remaining\rupload: contents/Bazjer2008.sedml to s3://files.biosimulations.org/simulations/647a4b5e77b66696550611bc/contents/Bazjer2008.sedml\nCompleted 145.6 KiB/148.5 KiB (748.8 KiB/s) with 1 file(s) remaining\rCompleted 148.5 KiB/148.5 KiB (746.3 KiB/s) with 1 file(s) remaining\rupload: contents/Bazjer2008.ode to s3://files.biosimulations.org/simulations/647a4b5e77b66696550611bc/contents/Bazjer2008.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.4 KiB/7.4 KiB (95.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b5e77b66696550611bc/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Bazjer2008.sedml\ncreating dataset /Bazjer2008.sedml/autogen_report_for_task1, shape: (19, 136), type: float64\ndataset created, uuid: d-3458afd7-973cbb6b-2360-60925c-3ec782, chunk_size: (19, 136)\ncreating dataset /Bazjer2008.sedml/plot_1_task1, shape: (2, 136), type: float64\ndataset created, uuid: d-3458afd7-973cbb6b-6f71-c9a1e8-086f02, chunk_size: (2, 136)\ncreating attribute combineArchiveLocation in /Bazjer2008.sedml\ncreating attribute uri in /Bazjer2008.sedml\ncreating attribute _type in /Bazjer2008.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Bazjer2008.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Bazjer2008.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Bazjer2008.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Bazjer2008.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Bazjer2008.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Bazjer2008.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Bazjer2008.sedml/autogen_report_for_task1\ncreating attribute uri in /Bazjer2008.sedml/autogen_report_for_task1\ncreating attribute _type in /Bazjer2008.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Bazjer2008.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Bazjer2008.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Bazjer2008.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Bazjer2008.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Bazjer2008.sedml/plot_1_task1\ncreating attribute sedmlId in /Bazjer2008.sedml/plot_1_task1\ncreating attribute sedmlName in /Bazjer2008.sedml/plot_1_task1\ncreating attribute uri in /Bazjer2008.sedml/plot_1_task1\ncreate_links: /\ngot link: Bazjer2008.sedml\ncreate_links: /Bazjer2008.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Bazjer2008.sedml/autogen_report_for_task1 to tgt: /Bazjer2008.sedml/autogen_report_for_task1, shape: (19, 136), type: float64\niterating over chunks for /Bazjer2008.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 19, 1), slice(0, 136, 1))\ndone with dataload for /Bazjer2008.sedml/autogen_report_for_task1\nwrite_dataset src: /Bazjer2008.sedml/plot_1_task1 to tgt: /Bazjer2008.sedml/plot_1_task1, shape: (2, 136), type: float64\niterating over chunks for /Bazjer2008.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 136, 1))\ndone with dataload for /Bazjer2008.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b5e77b66696550611bc\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 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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.249906,"sedDocuments":[{"location":"Bazjer2008.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  Bazjer2008.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 19 data sets\r\n    Plots (1):\r\n      plot_1_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: Bazjer2008.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":0.788611,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.222605,"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":0.36897,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.075608,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_y_Tumor_Cell","status":"SUCCEEDED"},{"id":"autogen_task1_v_Virus","status":"SUCCEEDED"},{"id":"autogen_task1_x_Infected_Cell","status":"SUCCEEDED"},{"id":"autogen_task1_r","status":"SUCCEEDED"},{"id":"autogen_task1_K","status":"SUCCEEDED"},{"id":"autogen_task1_epsilon","status":"SUCCEEDED"},{"id":"autogen_task1_kappa","status":"SUCCEEDED"},{"id":"autogen_task1_rho","status":"SUCCEEDED"},{"id":"autogen_task1_delta","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_omega","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_Growth","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_Cell_Infection","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_Cell_Fusion","status":"SUCCEEDED"},{"id":"autogen_task1_Infected_Cell_Death","status":"SUCCEEDED"},{"id":"autogen_task1_Virus_Production_Infected_Cell","status":"SUCCEEDED"},{"id":"autogen_task1_Virus_Elimination","status":"SUCCEEDED"}]}]}]}