{"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    455      0 --:--:-- --:--:-- --:--:--   457\n\r100  381k  100  381k    0     0   872k      0 --:--:-- --:--:-- --:--:--  872k\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 (9.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/rawLog.txt\nCompleted 3.3 KiB/3.3 KiB (48.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/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/BIOMD0000000253_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000253_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 13%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 162.0 KiB/162.0 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/outputs/reports.h5\nCompleted 150.4 KiB/171.9 KiB (1.5 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/output.zip\nCompleted 150.4 KiB/171.9 KiB (1.5 MiB/s) with 3 file(s) remaining\rCompleted 158.0 KiB/171.9 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/outputs/plots.zip\nCompleted 158.0 KiB/171.9 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 160.7 KiB/171.9 KiB (1.3 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/rawLog.txt\nCompleted 160.7 KiB/171.9 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 171.9 KiB/171.9 KiB (884.9 KiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000253_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/outputs/BIOMD0000000253_url.sedml/autogen_plot_for_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000253-biopax2.owl  \n  inflating: contents/BIOMD0000000253-biopax3.owl  \n  inflating: contents/BIOMD0000000253-matlab.m  \n  inflating: contents/BIOMD0000000253-octave.m  \n  inflating: contents/BIOMD0000000253.m  \n  inflating: contents/BIOMD0000000253.ode  \n  inflating: contents/BIOMD0000000253.pdf  \n  inflating: contents/BIOMD0000000253.png  \n  inflating: contents/BIOMD0000000253.svg  \n  inflating: contents/BIOMD0000000253.vcml  \n  inflating: contents/BIOMD0000000253_manual.png  \n  inflating: contents/BIOMD0000000253_manual.svg  \n  inflating: contents/BIOMD0000000253_url.sedml  \n  inflating: contents/BIOMD0000000253_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 24.4 KiB/636.4 KiB (324.5 KiB/s) with 18 file(s) remaining\rupload: contents/BIOMD0000000253-biopax3.owl to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/contents/BIOMD0000000253-biopax3.owl\nCompleted 24.4 KiB/636.4 KiB (324.5 KiB/s) with 17 file(s) remaining\rCompleted 30.5 KiB/636.4 KiB (290.1 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000253-matlab.m to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/contents/BIOMD0000000253-matlab.m\nCompleted 30.5 KiB/636.4 KiB (290.1 KiB/s) with 16 file(s) remaining\rCompleted 36.6 KiB/636.4 KiB (297.6 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000253-octave.m to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/contents/BIOMD0000000253-octave.m\nCompleted 36.6 KiB/636.4 KiB (297.6 KiB/s) with 15 file(s) remaining\rCompleted 56.1 KiB/636.4 KiB (420.4 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000253-biopax2.owl to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/contents/BIOMD0000000253-biopax2.owl\nCompleted 56.1 KiB/636.4 KiB (420.4 KiB/s) with 14 file(s) remaining\rCompleted 81.8 KiB/636.4 KiB (603.7 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000253_url.xml to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/contents/BIOMD0000000253_url.xml\nCompleted 81.8 KiB/636.4 KiB (603.7 KiB/s) with 13 file(s) remaining\rCompleted 112.5 KiB/636.4 KiB (715.3 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000253.vcml to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/contents/BIOMD0000000253.vcml\nCompleted 112.5 KiB/636.4 KiB (715.3 KiB/s) with 12 file(s) remaining\rCompleted 112.7 KiB/636.4 KiB (685.3 KiB/s) with 12 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/contents/curation_notes.txt\nCompleted 112.7 KiB/636.4 KiB (685.3 KiB/s) with 11 file(s) remaining\rCompleted 150.5 KiB/636.4 KiB (901.1 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000253.svg to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/contents/BIOMD0000000253.svg\nCompleted 150.5 KiB/636.4 KiB (901.1 KiB/s) with 10 file(s) remaining\rCompleted 188.3 KiB/636.4 KiB (1.1 MiB/s) with 10 file(s) remaining  \rupload: contents/BIOMD0000000253_manual.svg to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/contents/BIOMD0000000253_manual.svg\nCompleted 188.3 KiB/636.4 KiB (1.1 MiB/s) with 9 file(s) remaining\rCompleted 203.3 KiB/636.4 KiB (1.1 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000253_url.sedml to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/contents/BIOMD0000000253_url.sedml\nCompleted 203.3 KiB/636.4 KiB (1.1 MiB/s) with 8 file(s) remaining\rCompleted 205.4 KiB/636.4 KiB (1.1 MiB/s) with 8 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/contents/manifest.xml\nCompleted 205.4 KiB/636.4 KiB (1.1 MiB/s) with 7 file(s) remaining\rCompleted 232.8 KiB/636.4 KiB (1.2 MiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/contents/curation_image.png\nCompleted 232.8 KiB/636.4 KiB (1.2 MiB/s) with 6 file(s) remaining\rCompleted 343.4 KiB/636.4 KiB (1.7 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000253_manual.png to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/contents/BIOMD0000000253_manual.png\nCompleted 343.4 KiB/636.4 KiB (1.7 MiB/s) with 5 file(s) remaining\rCompleted 511.9 KiB/636.4 KiB (2.3 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000253.pdf to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/contents/BIOMD0000000253.pdf\nCompleted 511.9 KiB/636.4 KiB (2.3 MiB/s) with 4 file(s) remaining\rCompleted 515.7 KiB/636.4 KiB (2.3 MiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/contents/metadata.rdf\nCompleted 515.7 KiB/636.4 KiB (2.3 MiB/s) with 3 file(s) remaining\rCompleted 519.6 KiB/636.4 KiB (2.3 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000253.ode to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/contents/BIOMD0000000253.ode\nCompleted 519.6 KiB/636.4 KiB (2.3 MiB/s) with 2 file(s) remaining\rCompleted 525.8 KiB/636.4 KiB (2.2 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000253.m to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/contents/BIOMD0000000253.m\nCompleted 525.8 KiB/636.4 KiB (2.2 MiB/s) with 1 file(s) remaining\rCompleted 636.4 KiB/636.4 KiB (2.6 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000253.png to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/contents/BIOMD0000000253.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.5 KiB/9.5 KiB (159.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a400dcacb55678b91b8/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000253_url.sedml\ncreating dataset /BIOMD0000000253_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\ndataset created, uuid: d-d546270b-7a884589-ee0b-dba477-65f0e1, chunk_size: (7, 1001)\ncreating dataset /BIOMD0000000253_url.sedml/autogen_report_for_task1, shape: (27, 1001), type: float64\ndataset created, uuid: d-d546270b-7a884589-abb2-d203fe-11df55, chunk_size: (27, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000253_url.sedml\ncreating attribute uri in /BIOMD0000000253_url.sedml\ncreating attribute _type in /BIOMD0000000253_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000253_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000253_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000253_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000253_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000253_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000253_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000253_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000253_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000253_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000253_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000253_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000253_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000253_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000253_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000253_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000253_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000253_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000253_url.sedml\ncreate_links: /BIOMD0000000253_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000253_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000253_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\niterating over chunks for /BIOMD0000000253_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000253_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000253_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000253_url.sedml/autogen_report_for_task1, shape: (27, 1001), type: float64\niterating over chunks for /BIOMD0000000253_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 27, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000253_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710a400dcacb55678b91b8\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 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.357549,"sedDocuments":[{"location":"BIOMD0000000253_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  BIOMD0000000253_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 27 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 6 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000253_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":0.921853,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.144385,"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":0.237331,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_HMP","status":"SUCCEEDED"},{"id":"autogen_task1_Fru16P2","status":"SUCCEEDED"},{"id":"autogen_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_task1_Glc","status":"SUCCEEDED"},{"id":"autogen_task1_Tre6P","status":"SUCCEEDED"},{"id":"autogen_task1_ADP","status":"SUCCEEDED"},{"id":"autogen_task1_lambda1","status":"SUCCEEDED"},{"id":"autogen_task1_lambda2","status":"SUCCEEDED"},{"id":"autogen_task1_lambda3","status":"SUCCEEDED"},{"id":"autogen_task1_R","status":"SUCCEEDED"},{"id":"autogen_task1_T","status":"SUCCEEDED"},{"id":"autogen_task1_L","status":"SUCCEEDED"},{"id":"autogen_task1_KRHMP","status":"SUCCEEDED"},{"id":"autogen_task1_gR","status":"SUCCEEDED"},{"id":"autogen_task1_c1","status":"SUCCEEDED"},{"id":"autogen_task1_L0","status":"SUCCEEDED"},{"id":"autogen_task1_KRATP","status":"SUCCEEDED"},{"id":"autogen_task1_gT","status":"SUCCEEDED"},{"id":"autogen_task1_c2","status":"SUCCEEDED"},{"id":"autogen_task1_KiATP","status":"SUCCEEDED"},{"id":"autogen_task1_ci","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_HK","status":"SUCCEEDED"},{"id":"autogen_task1_PFK","status":"SUCCEEDED"},{"id":"autogen_task1_lower","status":"SUCCEEDED"},{"id":"autogen_task1_ATPase","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.390124,"curves":[{"id":"autogen_curve_task1_HMP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Fru16P2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Glc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Tre6P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ADP","status":"SUCCEEDED"}]}]}]}