{"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    422      0 --:--:-- --:--:-- --:--:--   422\n\r100  424k  100  424k    0     0   921k      0 --:--:-- --:--:-- --:--:--  921k\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 (22.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/rawLog.txt\nCompleted 5.5 KiB/5.5 KiB (55.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 84%)\n  adding: outputs/BIOMD0000000172_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000172_url.sedml/autogen_plot_for_task1.pdf (deflated 28%)\n  adding: outputs/reports.h5 (deflated 14%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 217.8 KiB/217.8 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/outputs/reports.h5\nCompleted 202.8 KiB/236.7 KiB (2.0 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/output.zip\nCompleted 202.8 KiB/236.7 KiB (2.0 MiB/s) with 3 file(s) remaining\rCompleted 215.7 KiB/236.7 KiB (1.8 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/outputs/plots.zip\nCompleted 215.7 KiB/236.7 KiB (1.8 MiB/s) with 2 file(s) remaining\rCompleted 234.0 KiB/236.7 KiB (2.0 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000172_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/outputs/BIOMD0000000172_url.sedml/autogen_plot_for_task1.pdf\nCompleted 234.0 KiB/236.7 KiB (2.0 MiB/s) with 1 file(s) remaining\rCompleted 236.7 KiB/236.7 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000172-biopax2.owl  \n  inflating: contents/BIOMD0000000172-biopax3.owl  \n  inflating: contents/BIOMD0000000172-matlab.m  \n  inflating: contents/BIOMD0000000172-octave.m  \n  inflating: contents/BIOMD0000000172.m  \n  inflating: contents/BIOMD0000000172.ode  \n  inflating: contents/BIOMD0000000172.pdf  \n  inflating: contents/BIOMD0000000172.png  \n  inflating: contents/BIOMD0000000172.sci  \n  inflating: contents/BIOMD0000000172.svg  \n  inflating: contents/BIOMD0000000172_url.sedml  \n  inflating: contents/BIOMD0000000172_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 87.5 KiB/892.4 KiB (1.1 MiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000172-biopax3.owl to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/contents/BIOMD0000000172-biopax3.owl\nCompleted 87.5 KiB/892.4 KiB (1.1 MiB/s) with 15 file(s) remaining\rCompleted 107.3 KiB/892.4 KiB (905.4 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000172-matlab.m to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/contents/BIOMD0000000172-matlab.m\nCompleted 107.3 KiB/892.4 KiB (905.4 KiB/s) with 14 file(s) remaining\rCompleted 127.1 KiB/892.4 KiB (989.6 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000172-octave.m to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/contents/BIOMD0000000172-octave.m\nCompleted 127.1 KiB/892.4 KiB (989.6 KiB/s) with 13 file(s) remaining\rCompleted 127.3 KiB/892.4 KiB (913.7 KiB/s) with 13 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/contents/curation_notes.txt\nCompleted 127.3 KiB/892.4 KiB (913.7 KiB/s) with 12 file(s) remaining\rCompleted 190.6 KiB/892.4 KiB (1.3 MiB/s) with 12 file(s) remaining  \rupload: contents/BIOMD0000000172-biopax2.owl to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/contents/BIOMD0000000172-biopax2.owl\nCompleted 190.6 KiB/892.4 KiB (1.3 MiB/s) with 11 file(s) remaining\rCompleted 213.1 KiB/892.4 KiB (1.3 MiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000172.sci to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/contents/BIOMD0000000172.sci\nCompleted 213.1 KiB/892.4 KiB (1.3 MiB/s) with 10 file(s) remaining\rCompleted 258.0 KiB/892.4 KiB (1.4 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000172.svg to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/contents/BIOMD0000000172.svg\nCompleted 258.0 KiB/892.4 KiB (1.4 MiB/s) with 9 file(s) remaining\rCompleted 285.7 KiB/892.4 KiB (1.6 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000172_url.sedml to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/contents/BIOMD0000000172_url.sedml\nCompleted 285.7 KiB/892.4 KiB (1.6 MiB/s) with 8 file(s) remaining\rCompleted 289.2 KiB/892.4 KiB (1.5 MiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/contents/metadata.rdf\nCompleted 289.2 KiB/892.4 KiB (1.5 MiB/s) with 7 file(s) remaining\rCompleted 369.2 KiB/892.4 KiB (1.9 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000172_url.xml to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/contents/BIOMD0000000172_url.xml\nCompleted 369.2 KiB/892.4 KiB (1.9 MiB/s) with 6 file(s) remaining\rCompleted 625.2 KiB/892.4 KiB (3.0 MiB/s) with 6 file(s) remaining\rCompleted 632.1 KiB/892.4 KiB (3.0 MiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/contents/curation_image.png\nCompleted 632.1 KiB/892.4 KiB (3.0 MiB/s) with 5 file(s) remaining\rCompleted 633.9 KiB/892.4 KiB (3.0 MiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/contents/manifest.xml\nCompleted 633.9 KiB/892.4 KiB (3.0 MiB/s) with 4 file(s) remaining\rCompleted 653.7 KiB/892.4 KiB (3.0 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000172.m to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/contents/BIOMD0000000172.m\nCompleted 653.7 KiB/892.4 KiB (3.0 MiB/s) with 3 file(s) remaining\rCompleted 877.1 KiB/892.4 KiB (3.8 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000172.png to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/contents/BIOMD0000000172.png\nCompleted 877.1 KiB/892.4 KiB (3.8 MiB/s) with 2 file(s) remaining\rCompleted 891.0 KiB/892.4 KiB (3.8 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000172.ode to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/contents/BIOMD0000000172.ode\nCompleted 891.0 KiB/892.4 KiB (3.8 MiB/s) with 1 file(s) remaining\rCompleted 892.4 KiB/892.4 KiB (3.4 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000172.pdf to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/contents/BIOMD0000000172.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (136.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109299a62a8be53f7764b/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000172_url.sedml\ncreating dataset /BIOMD0000000172_url.sedml/autogen_plot_for_task1, shape: (26, 1001), type: float64\ndataset created, uuid: d-1418a7fd-ed8dd204-85d6-cd11ea-12ff3d, chunk_size: (26, 1001)\ncreating dataset /BIOMD0000000172_url.sedml/autogen_report_for_task1, shape: (47, 1001), type: float64\ndataset created, uuid: d-1418a7fd-ed8dd204-b560-99db7a-96fb56, chunk_size: (47, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000172_url.sedml\ncreating attribute uri in /BIOMD0000000172_url.sedml\ncreating attribute _type in /BIOMD0000000172_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000172_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000172_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000172_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000172_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000172_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000172_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000172_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000172_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000172_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000172_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000172_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000172_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000172_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000172_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000172_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000172_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000172_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000172_url.sedml\ncreate_links: /BIOMD0000000172_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000172_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000172_url.sedml/autogen_plot_for_task1, shape: (26, 1001), type: float64\niterating over chunks for /BIOMD0000000172_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 26, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000172_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000172_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000172_url.sedml/autogen_report_for_task1, shape: (47, 1001), type: float64\niterating over chunks for /BIOMD0000000172_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 47, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000172_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647109299a62a8be53f7764b\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 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 and upload the outputs of the simulation run ... 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":2.269293,"sedDocuments":[{"location":"BIOMD0000000172_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  BIOMD0000000172_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 47 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 25 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000172_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":1.740135,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.297317,"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":0.409898,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_GLCo","status":"SUCCEEDED"},{"id":"autogen_task1_GLCi","status":"SUCCEEDED"},{"id":"autogen_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_task1_G6P","status":"SUCCEEDED"},{"id":"autogen_task1_ADP","status":"SUCCEEDED"},{"id":"autogen_task1_F6P","status":"SUCCEEDED"},{"id":"autogen_task1_F16bP","status":"SUCCEEDED"},{"id":"autogen_task1_AMP","status":"SUCCEEDED"},{"id":"autogen_task1_F26bP","status":"SUCCEEDED"},{"id":"autogen_task1_DHAP","status":"SUCCEEDED"},{"id":"autogen_task1_GAP","status":"SUCCEEDED"},{"id":"autogen_task1_NAD","status":"SUCCEEDED"},{"id":"autogen_task1_BPG","status":"SUCCEEDED"},{"id":"autogen_task1_NADH","status":"SUCCEEDED"},{"id":"autogen_task1_P3G","status":"SUCCEEDED"},{"id":"autogen_task1_P2G","status":"SUCCEEDED"},{"id":"autogen_task1_PEP","status":"SUCCEEDED"},{"id":"autogen_task1_PYR","status":"SUCCEEDED"},{"id":"autogen_task1_AcAld","status":"SUCCEEDED"},{"id":"autogen_task1_CO2","status":"SUCCEEDED"},{"id":"autogen_task1_EtOH","status":"SUCCEEDED"},{"id":"autogen_task1_Glycerol","status":"SUCCEEDED"},{"id":"autogen_task1_Glycogen","status":"SUCCEEDED"},{"id":"autogen_task1_Trehalose","status":"SUCCEEDED"},{"id":"autogen_task1_Succinate","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_ext","status":"SUCCEEDED"},{"id":"autogen_task1_HXT","status":"SUCCEEDED"},{"id":"autogen_task1_HK","status":"SUCCEEDED"},{"id":"autogen_task1_PGI","status":"SUCCEEDED"},{"id":"autogen_task1_PFK","status":"SUCCEEDED"},{"id":"autogen_task1_ALD","status":"SUCCEEDED"},{"id":"autogen_task1_TPI","status":"SUCCEEDED"},{"id":"autogen_task1_GAPDH","status":"SUCCEEDED"},{"id":"autogen_task1_PGK","status":"SUCCEEDED"},{"id":"autogen_task1_PGM","status":"SUCCEEDED"},{"id":"autogen_task1_ENO","status":"SUCCEEDED"},{"id":"autogen_task1_PYK","status":"SUCCEEDED"},{"id":"autogen_task1_PDC","status":"SUCCEEDED"},{"id":"autogen_task1_ADH","status":"SUCCEEDED"},{"id":"autogen_task1_ATPase","status":"SUCCEEDED"},{"id":"autogen_task1_AK","status":"SUCCEEDED"},{"id":"autogen_task1_G3PDH","status":"SUCCEEDED"},{"id":"autogen_task1_Glycogen_Branch","status":"SUCCEEDED"},{"id":"autogen_task1_Trehalose_Branch","status":"SUCCEEDED"},{"id":"autogen_task1_Succinate_Branch","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.838119,"curves":[{"id":"autogen_curve_task1_GLCo","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GLCi","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_G6P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ADP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_F6P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_F16bP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AMP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_F26bP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DHAP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GAP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NAD","status":"SUCCEEDED"},{"id":"autogen_curve_task1_BPG","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_P3G","status":"SUCCEEDED"},{"id":"autogen_curve_task1_P2G","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PEP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PYR","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AcAld","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CO2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_EtOH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Glycerol","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Glycogen","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Trehalose","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Succinate","status":"SUCCEEDED"}]}]}]}