{"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    406      0 --:--:-- --:--:-- --:--:--   406\n\r100  212k  100  212k    0     0   441k      0 --:--:-- --:--:-- --:--:--  441k\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 (24.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/rawLog.txt\nCompleted 3.1 KiB/3.1 KiB (43.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/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/munz2000.sedml/ (stored 0%)\n  adding: outputs/munz2000.sedml/plot_1_task1.pdf (deflated 29%)\n  adding: outputs/reports.h5 (deflated 75%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 26.5 KiB/26.5 KiB (232.0 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/outputs/reports.h5\nCompleted 17.9 KiB/41.6 KiB (246.2 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/output.zip\nCompleted 17.9 KiB/41.6 KiB (246.2 KiB/s) with 3 file(s) remaining\rCompleted 26.5 KiB/41.6 KiB (255.3 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/outputs/plots.zip\nCompleted 26.5 KiB/41.6 KiB (255.3 KiB/s) with 2 file(s) remaining\rCompleted 39.0 KiB/41.6 KiB (329.4 KiB/s) with 2 file(s) remaining\rupload: outputs/munz2000.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/outputs/munz2000.sedml/plot_1_task1.pdf\nCompleted 39.0 KiB/41.6 KiB (329.4 KiB/s) with 1 file(s) remaining\rCompleted 41.6 KiB/41.6 KiB (320.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/MODEL1008060001-biopax2.owl  \n  inflating: contents/MODEL1008060001-biopax3.owl  \n  inflating: contents/MODEL1008060001-matlab.m  \n  inflating: contents/MODEL1008060001-octave.m  \n  inflating: contents/MODEL1008060001.m  \n  inflating: contents/MODEL1008060001.ode  \n  inflating: contents/MODEL1008060001.pdf  \n  inflating: contents/MODEL1008060001.png  \n  inflating: contents/MODEL1008060001.svg  \n  inflating: contents/MODEL1008060001.vcml  \n  inflating: contents/MODEL1008060001_url.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/munz2000-biopax2.owl  \n  inflating: contents/munz2000-biopax3.owl  \n  inflating: contents/munz2000-matlab.m  \n  inflating: contents/munz2000-octave.m  \n  inflating: contents/munz2000.cps   \n  inflating: contents/munz2000.ode   \n  inflating: contents/munz2000.sedml  \n  inflating: contents/munz2000.xml   \n  inflating: contents/manifest.xml   \nCompleted 16.4 KiB/~312.9 KiB (204.6 KiB/s) with ~14 file(s) remaining (calculating...)\rupload: contents/MODEL1008060001-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/MODEL1008060001-biopax3.owl\nCompleted 16.4 KiB/~312.9 KiB (204.6 KiB/s) with ~13 file(s) remaining (calculating...)\rCompleted 20.4 KiB/449.8 KiB (174.4 KiB/s) with 22 file(s) remaining                   \rupload: contents/MODEL1008060001-matlab.m to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/MODEL1008060001-matlab.m\nCompleted 20.4 KiB/449.8 KiB (174.4 KiB/s) with 21 file(s) remaining\rCompleted 30.6 KiB/449.8 KiB (242.2 KiB/s) with 21 file(s) remaining\rupload: contents/MODEL1008060001-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/MODEL1008060001-biopax2.owl\nCompleted 30.6 KiB/449.8 KiB (242.2 KiB/s) with 20 file(s) remaining\rCompleted 34.6 KiB/449.8 KiB (262.5 KiB/s) with 20 file(s) remaining\rupload: contents/MODEL1008060001-octave.m to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/MODEL1008060001-octave.m\nCompleted 34.6 KiB/449.8 KiB (262.5 KiB/s) with 19 file(s) remaining\rCompleted 37.2 KiB/449.8 KiB (271.8 KiB/s) with 19 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/manifest.xml\nCompleted 37.2 KiB/449.8 KiB (271.8 KiB/s) with 18 file(s) remaining\rCompleted 53.3 KiB/449.8 KiB (345.2 KiB/s) with 18 file(s) remaining\rupload: contents/MODEL1008060001.svg to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/MODEL1008060001.svg\nCompleted 53.3 KiB/449.8 KiB (345.2 KiB/s) with 17 file(s) remaining\rCompleted 71.8 KiB/449.8 KiB (434.6 KiB/s) with 17 file(s) remaining\rupload: contents/MODEL1008060001.vcml to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/MODEL1008060001.vcml\nCompleted 71.8 KiB/449.8 KiB (434.6 KiB/s) with 16 file(s) remaining\rCompleted 81.3 KiB/449.8 KiB (454.1 KiB/s) with 16 file(s) remaining\rupload: contents/munz2000-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/munz2000-biopax2.owl\nCompleted 81.3 KiB/449.8 KiB (454.1 KiB/s) with 15 file(s) remaining\rCompleted 93.4 KiB/449.8 KiB (511.3 KiB/s) with 15 file(s) remaining\rupload: contents/MODEL1008060001_url.xml to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/MODEL1008060001_url.xml\nCompleted 93.4 KiB/449.8 KiB (511.3 KiB/s) with 14 file(s) remaining\rCompleted 106.3 KiB/449.8 KiB (570.8 KiB/s) with 14 file(s) remaining\rupload: contents/munz2000-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/munz2000-biopax3.owl\nCompleted 106.3 KiB/449.8 KiB (570.8 KiB/s) with 13 file(s) remaining\rCompleted 132.2 KiB/449.8 KiB (698.7 KiB/s) with 13 file(s) remaining\rCompleted 136.9 KiB/449.8 KiB (702.4 KiB/s) with 13 file(s) remaining\rupload: contents/munz2000-octave.m to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/munz2000-octave.m\nCompleted 136.9 KiB/449.8 KiB (702.4 KiB/s) with 12 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/curation_image.png\nCompleted 136.9 KiB/449.8 KiB (702.4 KiB/s) with 11 file(s) remaining\rCompleted 137.0 KiB/449.8 KiB (673.0 KiB/s) with 11 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/curation_notes.txt\nCompleted 137.0 KiB/449.8 KiB (673.0 KiB/s) with 10 file(s) remaining\rCompleted 140.5 KiB/449.8 KiB (677.2 KiB/s) with 10 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/metadata.rdf\nCompleted 140.5 KiB/449.8 KiB (677.2 KiB/s) with 9 file(s) remaining\rCompleted 145.2 KiB/449.8 KiB (656.1 KiB/s) with 9 file(s) remaining\rupload: contents/munz2000-matlab.m to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/munz2000-matlab.m\nCompleted 145.2 KiB/449.8 KiB (656.1 KiB/s) with 8 file(s) remaining\rCompleted 199.7 KiB/449.8 KiB (895.6 KiB/s) with 8 file(s) remaining\rupload: contents/munz2000.cps to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/munz2000.cps\nCompleted 199.7 KiB/449.8 KiB (895.6 KiB/s) with 7 file(s) remaining\rCompleted 202.8 KiB/449.8 KiB (904.1 KiB/s) with 7 file(s) remaining\rupload: contents/munz2000.ode to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/munz2000.ode\nCompleted 202.8 KiB/449.8 KiB (904.1 KiB/s) with 6 file(s) remaining\rCompleted 213.3 KiB/449.8 KiB (833.4 KiB/s) with 6 file(s) remaining\rupload: contents/munz2000.sedml to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/munz2000.sedml\nCompleted 213.3 KiB/449.8 KiB (833.4 KiB/s) with 5 file(s) remaining\rCompleted 255.3 KiB/449.8 KiB (982.6 KiB/s) with 5 file(s) remaining\rCompleted 288.8 KiB/449.8 KiB (1.1 MiB/s) with 5 file(s) remaining  \rupload: contents/MODEL1008060001.png to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/MODEL1008060001.png\nCompleted 288.8 KiB/449.8 KiB (1.1 MiB/s) with 4 file(s) remaining\rupload: contents/munz2000.xml to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/munz2000.xml\nCompleted 288.8 KiB/449.8 KiB (1.1 MiB/s) with 3 file(s) remaining\rCompleted 290.9 KiB/449.8 KiB (1.1 MiB/s) with 3 file(s) remaining\rCompleted 294.2 KiB/449.8 KiB (1.1 MiB/s) with 3 file(s) remaining\rupload: contents/MODEL1008060001.m to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/MODEL1008060001.m\nCompleted 294.2 KiB/449.8 KiB (1.1 MiB/s) with 2 file(s) remaining\rupload: contents/MODEL1008060001.ode to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/MODEL1008060001.ode\nCompleted 294.2 KiB/449.8 KiB (1.1 MiB/s) with 1 file(s) remaining\rCompleted 449.8 KiB/449.8 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: contents/MODEL1008060001.pdf to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/contents/MODEL1008060001.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 10.9 KiB/10.9 KiB (174.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b77195afd5df175f205/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /munz2000.sedml\ncreating dataset /munz2000.sedml/autogen_report_for_task1, shape: (16, 51), type: float64\ndataset created, uuid: d-640e9ace-024d6f37-7213-ef99e7-9e73ef, chunk_size: (16, 51)\ncreating dataset /munz2000.sedml/plot_1_task1, shape: (4, 51), type: float64\ndataset created, uuid: d-640e9ace-024d6f37-0ca5-5bc2ed-5ff343, chunk_size: (4, 51)\ncreating attribute combineArchiveLocation in /munz2000.sedml\ncreating attribute uri in /munz2000.sedml\ncreating attribute _type in /munz2000.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /munz2000.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /munz2000.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /munz2000.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /munz2000.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /munz2000.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /munz2000.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /munz2000.sedml/autogen_report_for_task1\ncreating attribute uri in /munz2000.sedml/autogen_report_for_task1\ncreating attribute _type in /munz2000.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /munz2000.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /munz2000.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /munz2000.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /munz2000.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /munz2000.sedml/plot_1_task1\ncreating attribute sedmlId in /munz2000.sedml/plot_1_task1\ncreating attribute sedmlName in /munz2000.sedml/plot_1_task1\ncreating attribute uri in /munz2000.sedml/plot_1_task1\ncreate_links: /\ngot link: munz2000.sedml\ncreate_links: /munz2000.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /munz2000.sedml/autogen_report_for_task1 to tgt: /munz2000.sedml/autogen_report_for_task1, shape: (16, 51), type: float64\niterating over chunks for /munz2000.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 16, 1), slice(0, 51, 1))\ndone with dataload for /munz2000.sedml/autogen_report_for_task1\nwrite_dataset src: /munz2000.sedml/plot_1_task1 to tgt: /munz2000.sedml/plot_1_task1, shape: (4, 51), type: float64\niterating over chunks for /munz2000.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 51, 1))\ndone with dataload for /munz2000.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b77195afd5df175f205\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 and upload the outputs of the simulation run ... 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.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.262328,"sedDocuments":[{"location":"munz2000.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  munz2000.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 16 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: munz2000.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":0.780942,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.221273,"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":0.380062,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.061439,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Susceptible","status":"SUCCEEDED"},{"id":"autogen_task1_Zombie","status":"SUCCEEDED"},{"id":"autogen_task1_Removal","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_delta","status":"SUCCEEDED"},{"id":"autogen_task1_zeta","status":"SUCCEEDED"},{"id":"autogen_task1_p","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_Birth","status":"SUCCEEDED"},{"id":"autogen_task1_Zombification","status":"SUCCEEDED"},{"id":"autogen_task1_Susceptible_to_Zombie_or_death","status":"SUCCEEDED"},{"id":"autogen_task1_Removal_of_zombie_or_susceptible","status":"SUCCEEDED"},{"id":"autogen_task1_Resurrection_to_Zombie","status":"SUCCEEDED"},{"id":"autogen_task1_Death_from_Zombie","status":"SUCCEEDED"}]}]}]}