{"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    413      0 --:--:-- --:--:-- --:--:--   413\n\r100  331k  100  331k    0     0   717k      0 --:--:-- --:--:-- --:--:--  717k\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 (24.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/rawLog.txt\nCompleted 4.2 KiB/4.2 KiB (59.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 82%)\n  adding: outputs/BIOMD0000000046_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000046_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 8%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/298.8 KiB (5.8 MiB/s) with 1 file(s) remaining\rCompleted 298.8 KiB/298.8 KiB (3.0 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/outputs/reports.h5\nCompleted 256.0 KiB/308.9 KiB (5.8 MiB/s) with 4 file(s) remaining\rCompleted 264.7 KiB/308.9 KiB (2.6 MiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/outputs/plots.zip\nCompleted 264.7 KiB/308.9 KiB (2.6 MiB/s) with 3 file(s) remaining\rCompleted 293.4 KiB/308.9 KiB (2.8 MiB/s) with 3 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/output.zip\nCompleted 293.4 KiB/308.9 KiB (2.8 MiB/s) with 2 file(s) remaining\rCompleted 306.2 KiB/308.9 KiB (2.7 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000046_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/outputs/BIOMD0000000046_url.sedml/autogen_plot_for_task1.pdf\nCompleted 306.2 KiB/308.9 KiB (2.7 MiB/s) with 1 file(s) remaining\rCompleted 308.9 KiB/308.9 KiB (2.5 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000046-biopax2.owl  \n  inflating: contents/BIOMD0000000046-biopax3.owl  \n  inflating: contents/BIOMD0000000046-matlab.m  \n  inflating: contents/BIOMD0000000046-octave.m  \n  inflating: contents/BIOMD0000000046.m  \n  inflating: contents/BIOMD0000000046.ode  \n  inflating: contents/BIOMD0000000046.pdf  \n  inflating: contents/BIOMD0000000046.png  \n  inflating: contents/BIOMD0000000046.sci  \n  inflating: contents/BIOMD0000000046.svg  \n  inflating: contents/BIOMD0000000046.vcml  \n  inflating: contents/BIOMD0000000046_url.sedml  \n  inflating: contents/BIOMD0000000046_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 50.5 KiB/645.4 KiB (636.4 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000046-biopax3.owl to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/contents/BIOMD0000000046-biopax3.owl\nCompleted 50.5 KiB/645.4 KiB (636.4 KiB/s) with 16 file(s) remaining\rCompleted 58.0 KiB/645.4 KiB (542.2 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000046-matlab.m to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/contents/BIOMD0000000046-matlab.m\nCompleted 58.0 KiB/645.4 KiB (542.2 KiB/s) with 15 file(s) remaining\rCompleted 63.2 KiB/645.4 KiB (477.6 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000046.sci to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/contents/BIOMD0000000046.sci\nCompleted 63.2 KiB/645.4 KiB (477.6 KiB/s) with 14 file(s) remaining\rCompleted 95.6 KiB/645.4 KiB (699.5 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000046-biopax2.owl to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/contents/BIOMD0000000046-biopax2.owl\nCompleted 95.6 KiB/645.4 KiB (699.5 KiB/s) with 13 file(s) remaining\rCompleted 95.7 KiB/645.4 KiB (691.0 KiB/s) with 13 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/contents/curation_notes.txt\nCompleted 95.7 KiB/645.4 KiB (691.0 KiB/s) with 12 file(s) remaining\rCompleted 130.9 KiB/645.4 KiB (913.5 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000046.svg to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/contents/BIOMD0000000046.svg\nCompleted 130.9 KiB/645.4 KiB (913.5 KiB/s) with 11 file(s) remaining\rCompleted 138.4 KiB/645.4 KiB (957.1 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000046-octave.m to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/contents/BIOMD0000000046-octave.m\nCompleted 138.4 KiB/645.4 KiB (957.1 KiB/s) with 10 file(s) remaining\rCompleted 140.4 KiB/645.4 KiB (897.2 KiB/s) with 10 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/contents/manifest.xml\nCompleted 140.4 KiB/645.4 KiB (897.2 KiB/s) with 9 file(s) remaining\rCompleted 186.5 KiB/645.4 KiB (1.1 MiB/s) with 9 file(s) remaining  \rupload: contents/BIOMD0000000046.vcml to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/contents/BIOMD0000000046.vcml\nCompleted 186.5 KiB/645.4 KiB (1.1 MiB/s) with 8 file(s) remaining\rCompleted 205.8 KiB/645.4 KiB (1.1 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000046_url.sedml to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/contents/BIOMD0000000046_url.sedml\nCompleted 205.8 KiB/645.4 KiB (1.1 MiB/s) with 7 file(s) remaining\rCompleted 210.5 KiB/645.4 KiB (1.0 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000046.ode to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/contents/BIOMD0000000046.ode\nCompleted 210.5 KiB/645.4 KiB (1.0 MiB/s) with 6 file(s) remaining\rCompleted 214.8 KiB/645.4 KiB (1.0 MiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/contents/metadata.rdf\nCompleted 214.8 KiB/645.4 KiB (1.0 MiB/s) with 5 file(s) remaining\rCompleted 222.2 KiB/645.4 KiB (1.1 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000046.m to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/contents/BIOMD0000000046.m\nCompleted 222.2 KiB/645.4 KiB (1.1 MiB/s) with 4 file(s) remaining\rCompleted 250.4 KiB/645.4 KiB (1.2 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000046_url.xml to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/contents/BIOMD0000000046_url.xml\nCompleted 250.4 KiB/645.4 KiB (1.2 MiB/s) with 3 file(s) remaining\rCompleted 267.5 KiB/645.4 KiB (1.2 MiB/s) with 3 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/contents/curation_image.png\nCompleted 267.5 KiB/645.4 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 436.1 KiB/645.4 KiB (1.9 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000046.png to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/contents/BIOMD0000000046.png\nCompleted 436.1 KiB/645.4 KiB (1.9 MiB/s) with 1 file(s) remaining\rCompleted 645.4 KiB/645.4 KiB (2.8 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000046.pdf to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/contents/BIOMD0000000046.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.3 KiB/9.3 KiB (130.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107850dcacb55678b42f5/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000046_url.sedml\ncreating dataset /BIOMD0000000046_url.sedml/autogen_plot_for_task1, shape: (17, 1001), type: float64\ndataset created, uuid: d-7594d122-a4068992-8d17-a59aba-61e57c, chunk_size: (17, 1001)\ncreating dataset /BIOMD0000000046_url.sedml/autogen_report_for_task1, shape: (33, 1001), type: float64\ndataset created, uuid: d-7594d122-a4068992-64e0-080a0a-bc0e32, chunk_size: (33, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000046_url.sedml\ncreating attribute uri in /BIOMD0000000046_url.sedml\ncreating attribute _type in /BIOMD0000000046_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000046_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000046_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000046_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000046_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000046_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000046_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000046_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000046_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000046_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000046_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000046_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000046_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000046_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000046_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000046_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000046_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000046_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000046_url.sedml\ncreate_links: /BIOMD0000000046_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000046_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000046_url.sedml/autogen_plot_for_task1, shape: (17, 1001), type: float64\niterating over chunks for /BIOMD0000000046_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 17, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000046_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000046_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000046_url.sedml/autogen_report_for_task1, shape: (33, 1001), type: float64\niterating over chunks for /BIOMD0000000046_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 33, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000046_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647107850dcacb55678b42f5\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.\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 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":1.646954,"sedDocuments":[{"location":"BIOMD0000000046_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  BIOMD0000000046_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 33 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 16 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000046_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":1.213252,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.164154,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"deterministic"},{"key":"methodCode","value":22},{"key":"parameters"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.294019,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_NADH","status":"SUCCEEDED"},{"id":"autogen_task1_O2","status":"SUCCEEDED"},{"id":"autogen_task1_H2O2","status":"SUCCEEDED"},{"id":"autogen_task1_per3","status":"SUCCEEDED"},{"id":"autogen_task1_coI","status":"SUCCEEDED"},{"id":"autogen_task1_ArH","status":"SUCCEEDED"},{"id":"autogen_task1_coII","status":"SUCCEEDED"},{"id":"autogen_task1_Ar","status":"SUCCEEDED"},{"id":"autogen_task1_NADrad","status":"SUCCEEDED"},{"id":"autogen_task1_super","status":"SUCCEEDED"},{"id":"autogen_task1_coIII","status":"SUCCEEDED"},{"id":"autogen_task1_per2","status":"SUCCEEDED"},{"id":"autogen_task1_NAD2","status":"SUCCEEDED"},{"id":"autogen_task1_NAD","status":"SUCCEEDED"},{"id":"autogen_task1_O2g","status":"SUCCEEDED"},{"id":"autogen_task1_NADHres","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_v1","status":"SUCCEEDED"},{"id":"autogen_task1_v2","status":"SUCCEEDED"},{"id":"autogen_task1_v3","status":"SUCCEEDED"},{"id":"autogen_task1_v4","status":"SUCCEEDED"},{"id":"autogen_task1_v5","status":"SUCCEEDED"},{"id":"autogen_task1_v6","status":"SUCCEEDED"},{"id":"autogen_task1_v7","status":"SUCCEEDED"},{"id":"autogen_task1_v8","status":"SUCCEEDED"},{"id":"autogen_task1_v9","status":"SUCCEEDED"},{"id":"autogen_task1_v10","status":"SUCCEEDED"},{"id":"autogen_task1_v11","status":"SUCCEEDED"},{"id":"autogen_task1_v12","status":"SUCCEEDED"},{"id":"autogen_task1_v131","status":"SUCCEEDED"},{"id":"autogen_task1_v132","status":"SUCCEEDED"},{"id":"autogen_task1_v14","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.614706,"curves":[{"id":"autogen_curve_task1_NADH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_O2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_H2O2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_per3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_coI","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ArH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_coII","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ar","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADrad","status":"SUCCEEDED"},{"id":"autogen_curve_task1_super","status":"SUCCEEDED"},{"id":"autogen_curve_task1_coIII","status":"SUCCEEDED"},{"id":"autogen_curve_task1_per2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NAD2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NAD","status":"SUCCEEDED"},{"id":"autogen_curve_task1_O2g","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADHres","status":"SUCCEEDED"}]}]}]}