{"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    447      0 --:--:-- --:--:-- --:--:--   448\n\r100  442k  100  442k    0     0  1026k      0 --:--:-- --:--:-- --:--:-- 1026k\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 (17.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/rawLog.txt\nCompleted 3.4 KiB/3.4 KiB (50.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 78%)\n  adding: outputs/BIOMD0000000624_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000624_url.sedml/autogen_plot_for_task1.pdf (deflated 34%)\n  adding: outputs/reports.h5 (deflated 15%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 139.7 KiB/139.7 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/outputs/reports.h5\nCompleted 128.2 KiB/149.4 KiB (1.6 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/output.zip\nCompleted 128.2 KiB/149.4 KiB (1.6 MiB/s) with 3 file(s) remaining\rCompleted 135.5 KiB/149.4 KiB (1.1 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/outputs/plots.zip\nCompleted 135.5 KiB/149.4 KiB (1.1 MiB/s) with 2 file(s) remaining\rCompleted 146.8 KiB/149.4 KiB (1.0 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000624_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/outputs/BIOMD0000000624_url.sedml/autogen_plot_for_task1.pdf\nCompleted 146.8 KiB/149.4 KiB (1.0 MiB/s) with 1 file(s) remaining\rCompleted 149.4 KiB/149.4 KiB (1006.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000624-biopax2.owl  \n  inflating: contents/BIOMD0000000624-biopax3.owl  \n  inflating: contents/BIOMD0000000624-matlab.m  \n  inflating: contents/BIOMD0000000624-octave.m  \n  inflating: contents/BIOMD0000000624.m  \n  inflating: contents/BIOMD0000000624.ode  \n  inflating: contents/BIOMD0000000624.pdf  \n  inflating: contents/BIOMD0000000624.png  \n  inflating: contents/BIOMD0000000624.svg  \n  inflating: contents/BIOMD0000000624_APAP_metabolism.png  \n  inflating: contents/BIOMD0000000624_url.sedml  \n  inflating: contents/BIOMD0000000624_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 19.6 KiB/595.5 KiB (195.7 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000624-biopax3.owl to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/contents/BIOMD0000000624-biopax3.owl\nCompleted 19.6 KiB/595.5 KiB (195.7 KiB/s) with 15 file(s) remaining\rCompleted 275.6 KiB/595.5 KiB (2.2 MiB/s) with 15 file(s) remaining \rCompleted 290.5 KiB/595.5 KiB (2.2 MiB/s) with 15 file(s) remaining \rupload: contents/BIOMD0000000624-biopax2.owl to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/contents/BIOMD0000000624-biopax2.owl\nCompleted 290.5 KiB/595.5 KiB (2.2 MiB/s) with 14 file(s) remaining\rCompleted 295.2 KiB/595.5 KiB (2.2 MiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000624-matlab.m to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/contents/BIOMD0000000624-matlab.m\nCompleted 295.2 KiB/595.5 KiB (2.2 MiB/s) with 13 file(s) remaining\rCompleted 304.9 KiB/595.5 KiB (2.1 MiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000624.svg to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/contents/BIOMD0000000624.svg\nCompleted 304.9 KiB/595.5 KiB (2.1 MiB/s) with 12 file(s) remaining\rCompleted 309.6 KiB/595.5 KiB (2.0 MiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000624-octave.m to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/contents/BIOMD0000000624-octave.m\nCompleted 309.6 KiB/595.5 KiB (2.0 MiB/s) with 11 file(s) remaining\rCompleted 311.4 KiB/595.5 KiB (1.9 MiB/s) with 11 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/contents/manifest.xml\nCompleted 311.4 KiB/595.5 KiB (1.9 MiB/s) with 10 file(s) remaining\rCompleted 316.4 KiB/595.5 KiB (1.7 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000624_APAP_metabolism.png to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/contents/BIOMD0000000624_APAP_metabolism.png\nCompleted 316.4 KiB/595.5 KiB (1.7 MiB/s) with 9 file(s) remaining\rCompleted 348.3 KiB/595.5 KiB (1.8 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000624_url.xml to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/contents/BIOMD0000000624_url.xml\nCompleted 348.3 KiB/595.5 KiB (1.8 MiB/s) with 8 file(s) remaining\rCompleted 369.5 KiB/595.5 KiB (1.9 MiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/contents/curation_image.png\nCompleted 369.5 KiB/595.5 KiB (1.9 MiB/s) with 7 file(s) remaining\rCompleted 369.6 KiB/595.5 KiB (1.9 MiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/contents/curation_notes.txt\nCompleted 369.6 KiB/595.5 KiB (1.9 MiB/s) with 6 file(s) remaining\rCompleted 383.6 KiB/595.5 KiB (1.9 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000624_url.sedml to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/contents/BIOMD0000000624_url.sedml\nCompleted 383.6 KiB/595.5 KiB (1.9 MiB/s) with 5 file(s) remaining\rCompleted 410.1 KiB/595.5 KiB (2.0 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000624.png to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/contents/BIOMD0000000624.png\nCompleted 410.1 KiB/595.5 KiB (2.0 MiB/s) with 4 file(s) remaining\rCompleted 582.6 KiB/595.5 KiB (2.7 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000624.pdf to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/contents/BIOMD0000000624.pdf\nCompleted 582.6 KiB/595.5 KiB (2.7 MiB/s) with 3 file(s) remaining\rCompleted 588.0 KiB/595.5 KiB (2.7 MiB/s) with 3 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/contents/metadata.rdf\nCompleted 588.0 KiB/595.5 KiB (2.7 MiB/s) with 2 file(s) remaining\rCompleted 590.8 KiB/595.5 KiB (2.6 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000624.ode to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/contents/BIOMD0000000624.ode\nCompleted 590.8 KiB/595.5 KiB (2.6 MiB/s) with 1 file(s) remaining\rCompleted 595.5 KiB/595.5 KiB (2.5 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000624.m to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/contents/BIOMD0000000624.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (130.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711b5a49c0d898ffdf0c07/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000624_url.sedml\ncreating dataset /BIOMD0000000624_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\ndataset created, uuid: d-9104973b-db00607f-598d-898fe0-05fa71, chunk_size: (8, 1001)\ncreating dataset /BIOMD0000000624_url.sedml/autogen_report_for_task1, shape: (23, 1001), type: float64\ndataset created, uuid: d-9104973b-db00607f-f6c2-39f5cb-03eb0e, chunk_size: (23, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000624_url.sedml\ncreating attribute uri in /BIOMD0000000624_url.sedml\ncreating attribute _type in /BIOMD0000000624_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000624_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000624_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000624_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000624_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000624_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000624_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000624_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000624_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000624_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000624_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000624_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000624_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000624_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000624_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000624_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000624_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000624_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000624_url.sedml\ncreate_links: /BIOMD0000000624_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000624_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000624_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\niterating over chunks for /BIOMD0000000624_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 8, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000624_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000624_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000624_url.sedml/autogen_report_for_task1, shape: (23, 1001), type: float64\niterating over chunks for /BIOMD0000000624_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 23, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000624_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711b5a49c0d898ffdf0c07\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 SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file 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 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":18.326459,"sedDocuments":[{"location":"BIOMD0000000624_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  BIOMD0000000624_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 23 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 7 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000624_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":18.013635,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":17.330479,"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":0.222311,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_X1","status":"SUCCEEDED"},{"id":"autogen_task1_APAP","status":"SUCCEEDED"},{"id":"autogen_task1_NAPQI","status":"SUCCEEDED"},{"id":"autogen_task1_GSH","status":"SUCCEEDED"},{"id":"autogen_task1_NAPQIGSH","status":"SUCCEEDED"},{"id":"autogen_task1_APAPconj_Glu","status":"SUCCEEDED"},{"id":"autogen_task1_APAPconj_Sul","status":"SUCCEEDED"},{"id":"autogen_task1_Vmax_2E1_APAP","status":"SUCCEEDED"},{"id":"autogen_task1_Km_2E1_APAP","status":"SUCCEEDED"},{"id":"autogen_task1_kNapqiGsh","status":"SUCCEEDED"},{"id":"autogen_task1_kGsh","status":"SUCCEEDED"},{"id":"autogen_task1_GSHmax","status":"SUCCEEDED"},{"id":"autogen_task1_Vmax_PhaseIIEnzGlu_APAP","status":"SUCCEEDED"},{"id":"autogen_task1_Km_PhaseIIEnzGlu_APAP","status":"SUCCEEDED"},{"id":"autogen_task1_Vmax_PhaseIIEnzSul_APAP","status":"SUCCEEDED"},{"id":"autogen_task1_Km_PhaseIIEnzSul_APAP","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_J0","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_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.319808,"curves":[{"id":"autogen_curve_task1_X1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_APAP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NAPQI","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GSH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NAPQIGSH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_APAPconj_Glu","status":"SUCCEEDED"},{"id":"autogen_curve_task1_APAPconj_Sul","status":"SUCCEEDED"}]}]}]}