{"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    432      0 --:--:-- --:--:-- --:--:--   433\n\r100  243k  100  243k    0     0   517k      0 --:--:-- --:--:-- --:--:--  517k\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 (25.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/rawLog.txt\nCompleted 5.3 KiB/5.3 KiB (78.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 83%)\n  adding: outputs/BIOMD0000000108_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000108_url.sedml/autogen_plot_for_task1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 16%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 180.6 KiB/180.6 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/outputs/reports.h5\nCompleted 161.3 KiB/180.6 KiB (1.9 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/output.zip\nCompleted 161.3 KiB/180.6 KiB (1.9 MiB/s) with 3 file(s) remaining\rCompleted 167.9 KiB/180.6 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/outputs/plots.zip\nCompleted 167.9 KiB/180.6 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 178.0 KiB/180.6 KiB (1.6 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000108_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/outputs/BIOMD0000000108_url.sedml/autogen_plot_for_task1.pdf\nCompleted 178.0 KiB/180.6 KiB (1.6 MiB/s) with 1 file(s) remaining\rCompleted 180.6 KiB/180.6 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000108-biopax2.owl  \n  inflating: contents/BIOMD0000000108-biopax3.owl  \n  inflating: contents/BIOMD0000000108-matlab.m  \n  inflating: contents/BIOMD0000000108-octave.m  \n  inflating: contents/BIOMD0000000108.m  \n  inflating: contents/BIOMD0000000108.ode  \n  inflating: contents/BIOMD0000000108.pdf  \n  inflating: contents/BIOMD0000000108.png  \n  inflating: contents/BIOMD0000000108.sci  \n  inflating: contents/BIOMD0000000108.svg  \n  inflating: contents/BIOMD0000000108.vcml  \n  inflating: contents/BIOMD0000000108_url.sedml  \n  inflating: contents/BIOMD0000000108_url.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 26.1 KiB/513.9 KiB (388.9 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000108-biopax2.owl to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/contents/BIOMD0000000108-biopax2.owl\nCompleted 26.1 KiB/513.9 KiB (388.9 KiB/s) with 16 file(s) remaining\rCompleted 33.4 KiB/513.9 KiB (289.0 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000108-octave.m to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/contents/BIOMD0000000108-octave.m\nCompleted 33.4 KiB/513.9 KiB (289.0 KiB/s) with 15 file(s) remaining\rCompleted 40.7 KiB/513.9 KiB (332.8 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000108-matlab.m to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/contents/BIOMD0000000108-matlab.m\nCompleted 40.7 KiB/513.9 KiB (332.8 KiB/s) with 14 file(s) remaining\rCompleted 43.8 KiB/513.9 KiB (348.4 KiB/s) with 14 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/contents/curation_image.png\nCompleted 43.8 KiB/513.9 KiB (348.4 KiB/s) with 13 file(s) remaining\rCompleted 48.0 KiB/513.9 KiB (351.9 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000108.sci to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/contents/BIOMD0000000108.sci\nCompleted 48.0 KiB/513.9 KiB (351.9 KiB/s) with 12 file(s) remaining\rCompleted 127.6 KiB/513.9 KiB (868.9 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000108.png to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/contents/BIOMD0000000108.png\nCompleted 127.6 KiB/513.9 KiB (868.9 KiB/s) with 11 file(s) remaining\rCompleted 160.5 KiB/513.9 KiB (1.0 MiB/s) with 11 file(s) remaining  \rupload: contents/BIOMD0000000108.svg to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/contents/BIOMD0000000108.svg\nCompleted 160.5 KiB/513.9 KiB (1.0 MiB/s) with 10 file(s) remaining\rCompleted 162.4 KiB/513.9 KiB (955.6 KiB/s) with 10 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/contents/manifest.xml\nCompleted 162.4 KiB/513.9 KiB (955.6 KiB/s) with 9 file(s) remaining\rCompleted 188.7 KiB/513.9 KiB (1.0 MiB/s) with 9 file(s) remaining  \rupload: contents/BIOMD0000000108_url.sedml to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/contents/BIOMD0000000108_url.sedml\nCompleted 188.7 KiB/513.9 KiB (1.0 MiB/s) with 8 file(s) remaining\rCompleted 192.2 KiB/513.9 KiB (1019.4 KiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/contents/metadata.rdf\nCompleted 192.2 KiB/513.9 KiB (1019.4 KiB/s) with 7 file(s) remaining\rCompleted 219.6 KiB/513.9 KiB (1.1 MiB/s) with 7 file(s) remaining   \rCompleted 419.5 KiB/513.9 KiB (2.1 MiB/s) with 7 file(s) remaining   \rupload: contents/BIOMD0000000108.pdf to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/contents/BIOMD0000000108.pdf\nCompleted 419.5 KiB/513.9 KiB (2.1 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000108_url.xml to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/contents/BIOMD0000000108_url.xml\nCompleted 419.5 KiB/513.9 KiB (2.1 MiB/s) with 5 file(s) remaining\rCompleted 419.8 KiB/513.9 KiB (2.0 MiB/s) with 5 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/contents/curation_notes.txt\nCompleted 419.8 KiB/513.9 KiB (2.0 MiB/s) with 4 file(s) remaining\rCompleted 424.8 KiB/513.9 KiB (2.0 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000108.ode to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/contents/BIOMD0000000108.ode\nCompleted 424.8 KiB/513.9 KiB (2.0 MiB/s) with 3 file(s) remaining\rCompleted 432.1 KiB/513.9 KiB (2.0 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000108.m to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/contents/BIOMD0000000108.m\nCompleted 432.1 KiB/513.9 KiB (2.0 MiB/s) with 2 file(s) remaining\rCompleted 474.0 KiB/513.9 KiB (2.1 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000108.vcml to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/contents/BIOMD0000000108.vcml\nCompleted 474.0 KiB/513.9 KiB (2.1 MiB/s) with 1 file(s) remaining\rCompleted 513.9 KiB/513.9 KiB (2.2 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000108-biopax3.owl to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/contents/BIOMD0000000108-biopax3.owl\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.1 KiB/9.1 KiB (143.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471085d49c0d898ffddb4ac/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000108_url.sedml\ncreating dataset /BIOMD0000000108_url.sedml/autogen_plot_for_task1, shape: (10, 1001), type: float64\ndataset created, uuid: d-2da4ab3e-b62c857c-78f7-4e6dda-8ec634, chunk_size: (10, 1001)\ncreating dataset /BIOMD0000000108_url.sedml/autogen_report_for_task1, shape: (46, 1001), type: float64\ndataset created, uuid: d-2da4ab3e-b62c857c-f1f5-8bc47e-bbdc2c, chunk_size: (46, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000108_url.sedml\ncreating attribute uri in /BIOMD0000000108_url.sedml\ncreating attribute _type in /BIOMD0000000108_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000108_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000108_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000108_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000108_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000108_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000108_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000108_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000108_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000108_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000108_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000108_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000108_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000108_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000108_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000108_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000108_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000108_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000108_url.sedml\ncreate_links: /BIOMD0000000108_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000108_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000108_url.sedml/autogen_plot_for_task1, shape: (10, 1001), type: float64\niterating over chunks for /BIOMD0000000108_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 10, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000108_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000108_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000108_url.sedml/autogen_report_for_task1, shape: (46, 1001), type: float64\niterating over chunks for /BIOMD0000000108_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 46, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000108_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471085d49c0d898ffddb4ac\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 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.\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":1.803265,"sedDocuments":[{"location":"BIOMD0000000108_url.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  BIOMD0000000108_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 46 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 9 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000108_url.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":1.307991,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.240251,"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":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.354882,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_species_0000001","status":"SUCCEEDED"},{"id":"autogen_task1_species_0000002","status":"SUCCEEDED"},{"id":"autogen_task1_species_0000006","status":"SUCCEEDED"},{"id":"autogen_task1_species_0000007","status":"SUCCEEDED"},{"id":"autogen_task1_species_0000008","status":"SUCCEEDED"},{"id":"autogen_task1_species_0000009","status":"SUCCEEDED"},{"id":"autogen_task1_species_0000011","status":"SUCCEEDED"},{"id":"autogen_task1_species_0000016","status":"SUCCEEDED"},{"id":"autogen_task1_species_0000017","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_k4","status":"SUCCEEDED"},{"id":"autogen_task1_k5","status":"SUCCEEDED"},{"id":"autogen_task1_k6","status":"SUCCEEDED"},{"id":"autogen_task1_k7","status":"SUCCEEDED"},{"id":"autogen_task1_k9","status":"SUCCEEDED"},{"id":"autogen_task1_k10","status":"SUCCEEDED"},{"id":"autogen_task1_k11","status":"SUCCEEDED"},{"id":"autogen_task1_k12","status":"SUCCEEDED"},{"id":"autogen_task1_k13a","status":"SUCCEEDED"},{"id":"autogen_task1_k13b","status":"SUCCEEDED"},{"id":"autogen_task1_k17","status":"SUCCEEDED"},{"id":"autogen_task1_k18","status":"SUCCEEDED"},{"id":"autogen_task1_k19","status":"SUCCEEDED"},{"id":"autogen_task1_HO2star","status":"SUCCEEDED"},{"id":"autogen_task1_Cu_I_ZnSOD","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_0000001","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000001","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0","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_task1_reaction_12","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_13","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_14","status":"SUCCEEDED"},{"id":"autogen_task1_fast","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.551284,"curves":[{"id":"autogen_curve_task1_species_0000001","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_0000002","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_0000006","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_0000007","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_0000008","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_0000009","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_0000011","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_0000016","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_0000017","status":"SUCCEEDED"}]}]}]}