{"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    450      0 --:--:-- --:--:-- --:--:--   451\n\r100  236k  100  236k    0     0   545k      0 --:--:-- --:--:-- --:--:--  545k\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/6471079f9a62a8be53f744e1/rawLog.txt\nCompleted 3.6 KiB/3.6 KiB (54.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 79%)\n  adding: outputs/BIOMD0000000052_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000052_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 9%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/265.3 KiB (5.8 MiB/s) with 1 file(s) remaining\rCompleted 265.3 KiB/265.3 KiB (2.7 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/outputs/reports.h5\nCompleted 253.8 KiB/279.1 KiB (2.5 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/output.zip\nCompleted 253.8 KiB/279.1 KiB (2.5 MiB/s) with 3 file(s) remaining\rCompleted 262.9 KiB/279.1 KiB (2.3 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/outputs/plots.zip\nCompleted 262.9 KiB/279.1 KiB (2.3 MiB/s) with 2 file(s) remaining\rCompleted 276.4 KiB/279.1 KiB (2.3 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000052_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/outputs/BIOMD0000000052_url.sedml/autogen_plot_for_task1.pdf\nCompleted 276.4 KiB/279.1 KiB (2.3 MiB/s) with 1 file(s) remaining\rCompleted 279.1 KiB/279.1 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000052-biopax2.owl  \n  inflating: contents/BIOMD0000000052-biopax3.owl  \n  inflating: contents/BIOMD0000000052-matlab.m  \n  inflating: contents/BIOMD0000000052-octave.m  \n  inflating: contents/BIOMD0000000052.m  \n  inflating: contents/BIOMD0000000052.ode  \n  inflating: contents/BIOMD0000000052.pdf  \n  inflating: contents/BIOMD0000000052.png  \n  inflating: contents/BIOMD0000000052.sci  \n  inflating: contents/BIOMD0000000052.svg  \n  inflating: contents/BIOMD0000000052.vcml  \n  inflating: contents/BIOMD0000000052_url.sedml  \n  inflating: contents/BIOMD0000000052_url.xml  \n  inflating: contents/curation_image.jpeg  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 31.0 KiB/447.5 KiB (408.3 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000052-biopax3.owl to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/contents/BIOMD0000000052-biopax3.owl\nCompleted 31.0 KiB/447.5 KiB (408.3 KiB/s) with 16 file(s) remaining\rCompleted 36.5 KiB/447.5 KiB (311.2 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000052-matlab.m to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/contents/BIOMD0000000052-matlab.m\nCompleted 36.5 KiB/447.5 KiB (311.2 KiB/s) with 15 file(s) remaining\rCompleted 42.0 KiB/447.5 KiB (320.9 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000052-octave.m to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/contents/BIOMD0000000052-octave.m\nCompleted 42.0 KiB/447.5 KiB (320.9 KiB/s) with 14 file(s) remaining\rCompleted 61.8 KiB/447.5 KiB (466.9 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000052-biopax2.owl to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/contents/BIOMD0000000052-biopax2.owl\nCompleted 61.8 KiB/447.5 KiB (466.9 KiB/s) with 13 file(s) remaining\rCompleted 65.0 KiB/447.5 KiB (475.2 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000052.sci to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/contents/BIOMD0000000052.sci\nCompleted 65.0 KiB/447.5 KiB (475.2 KiB/s) with 12 file(s) remaining\rCompleted 92.3 KiB/447.5 KiB (646.0 KiB/s) with 12 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/contents/curation_image.jpeg\nCompleted 92.3 KiB/447.5 KiB (646.0 KiB/s) with 11 file(s) remaining\rCompleted 124.7 KiB/447.5 KiB (780.7 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000052.vcml to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/contents/BIOMD0000000052.vcml\nCompleted 124.7 KiB/447.5 KiB (780.7 KiB/s) with 10 file(s) remaining\rCompleted 146.6 KiB/447.5 KiB (866.2 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000052.svg to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/contents/BIOMD0000000052.svg\nCompleted 146.6 KiB/447.5 KiB (866.2 KiB/s) with 9 file(s) remaining\rCompleted 161.1 KiB/447.5 KiB (937.0 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000052_url.sedml to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/contents/BIOMD0000000052_url.sedml\nCompleted 161.1 KiB/447.5 KiB (937.0 KiB/s) with 8 file(s) remaining\rCompleted 163.1 KiB/447.5 KiB (928.6 KiB/s) with 8 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/contents/manifest.xml\nCompleted 163.1 KiB/447.5 KiB (928.6 KiB/s) with 7 file(s) remaining\rCompleted 163.2 KiB/447.5 KiB (857.8 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/contents/curation_notes.txt\nCompleted 163.2 KiB/447.5 KiB (857.8 KiB/s) with 6 file(s) remaining\rCompleted 168.2 KiB/447.5 KiB (871.3 KiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/contents/metadata.rdf\nCompleted 168.2 KiB/447.5 KiB (871.3 KiB/s) with 5 file(s) remaining\rCompleted 186.1 KiB/447.5 KiB (927.4 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000052_url.xml to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/contents/BIOMD0000000052_url.xml\nCompleted 186.1 KiB/447.5 KiB (927.4 KiB/s) with 4 file(s) remaining\rCompleted 191.6 KiB/447.5 KiB (935.5 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000052.m to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/contents/BIOMD0000000052.m\nCompleted 191.6 KiB/447.5 KiB (935.5 KiB/s) with 3 file(s) remaining\rCompleted 372.5 KiB/447.5 KiB (1.7 MiB/s) with 3 file(s) remaining  \rupload: contents/BIOMD0000000052.pdf to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/contents/BIOMD0000000052.pdf\nCompleted 372.5 KiB/447.5 KiB (1.7 MiB/s) with 2 file(s) remaining\rCompleted 375.8 KiB/447.5 KiB (1.7 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000052.ode to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/contents/BIOMD0000000052.ode\nCompleted 375.8 KiB/447.5 KiB (1.7 MiB/s) with 1 file(s) remaining\rCompleted 447.5 KiB/447.5 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000052.png to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/contents/BIOMD0000000052.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.2 KiB/9.2 KiB (135.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471079f9a62a8be53f744e1/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000052_url.sedml\ncreating dataset /BIOMD0000000052_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\ndataset created, uuid: d-e43b4f14-7cea737f-006d-b51b2f-69d697, chunk_size: (12, 1001)\ncreating dataset /BIOMD0000000052_url.sedml/autogen_report_for_task1, shape: (24, 1001), type: float64\ndataset created, uuid: d-e43b4f14-7cea737f-76b6-dfa5a7-b35f04, chunk_size: (24, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000052_url.sedml\ncreating attribute uri in /BIOMD0000000052_url.sedml\ncreating attribute _type in /BIOMD0000000052_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000052_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000052_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000052_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000052_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000052_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000052_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000052_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000052_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000052_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000052_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000052_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000052_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000052_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000052_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000052_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000052_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000052_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000052_url.sedml\ncreate_links: /BIOMD0000000052_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000052_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000052_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\niterating over chunks for /BIOMD0000000052_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 12, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000052_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000052_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000052_url.sedml/autogen_report_for_task1, shape: (24, 1001), type: float64\niterating over chunks for /BIOMD0000000052_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 24, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000052_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471079f9a62a8be53f744e1\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 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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":19.008139,"sedDocuments":[{"location":"BIOMD0000000052_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  BIOMD0000000052_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 24 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 11 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000052_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":18.693379,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":17.710448,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.279643,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Glu","status":"SUCCEEDED"},{"id":"autogen_task1_Fru","status":"SUCCEEDED"},{"id":"autogen_task1_Formic_acid","status":"SUCCEEDED"},{"id":"autogen_task1_Triose","status":"SUCCEEDED"},{"id":"autogen_task1_Acetic_acid","status":"SUCCEEDED"},{"id":"autogen_task1_Cn","status":"SUCCEEDED"},{"id":"autogen_task1_Amadori","status":"SUCCEEDED"},{"id":"autogen_task1_AMP","status":"SUCCEEDED"},{"id":"autogen_task1_C5","status":"SUCCEEDED"},{"id":"autogen_task1_lys_R","status":"SUCCEEDED"},{"id":"autogen_task1_Melanoidin","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1__J1","status":"SUCCEEDED"},{"id":"autogen_task1__J2","status":"SUCCEEDED"},{"id":"autogen_task1__J3","status":"SUCCEEDED"},{"id":"autogen_task1__J4","status":"SUCCEEDED"},{"id":"autogen_task1__J5","status":"SUCCEEDED"},{"id":"autogen_task1__J6","status":"SUCCEEDED"},{"id":"autogen_task1__J7","status":"SUCCEEDED"},{"id":"autogen_task1__J8","status":"SUCCEEDED"},{"id":"autogen_task1__J9","status":"SUCCEEDED"},{"id":"autogen_task1__J10","status":"SUCCEEDED"},{"id":"autogen_task1__J11","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.581415,"curves":[{"id":"autogen_curve_task1_Glu","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Fru","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Formic_acid","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Triose","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Acetic_acid","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Cn","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Amadori","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AMP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_C5","status":"SUCCEEDED"},{"id":"autogen_curve_task1_lys_R","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Melanoidin","status":"SUCCEEDED"}]}]}]}