{"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    420      0 --:--:-- --:--:-- --:--:--   421\n\r100  202k  100  202k    0     0   450k      0 --:--:-- --:--:-- --:--:--  450k\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 (20.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/rawLog.txt\nCompleted 3.4 KiB/3.4 KiB (30.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/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/BIOMD0000000386_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000386_url.sedml/autogen_plot_for_task1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 26%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 85.2 KiB/85.2 KiB (620.7 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/outputs/reports.h5\nCompleted 7.0 KiB/92.8 KiB (60.6 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/outputs/plots.zip\nCompleted 7.0 KiB/92.8 KiB (60.6 KiB/s) with 3 file(s) remaining\rCompleted 79.5 KiB/92.8 KiB (563.4 KiB/s) with 3 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/output.zip\nCompleted 79.5 KiB/92.8 KiB (563.4 KiB/s) with 2 file(s) remaining\rCompleted 90.2 KiB/92.8 KiB (563.6 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000386_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/outputs/BIOMD0000000386_url.sedml/autogen_plot_for_task1.pdf\nCompleted 90.2 KiB/92.8 KiB (563.6 KiB/s) with 1 file(s) remaining\rCompleted 92.8 KiB/92.8 KiB (523.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000386-biopax2.owl  \n  inflating: contents/BIOMD0000000386-biopax3.owl  \n  inflating: contents/BIOMD0000000386-matlab.m  \n  inflating: contents/BIOMD0000000386-octave.m  \n  inflating: contents/BIOMD0000000386.m  \n  inflating: contents/BIOMD0000000386.ode  \n  inflating: contents/BIOMD0000000386.pdf  \n  inflating: contents/BIOMD0000000386.png  \n  inflating: contents/BIOMD0000000386.svg  \n  inflating: contents/BIOMD0000000386_url.sedml  \n  inflating: contents/BIOMD0000000386_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 16.1 KiB/363.9 KiB (151.1 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000386-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/contents/BIOMD0000000386-biopax3.owl\nCompleted 16.1 KiB/363.9 KiB (151.1 KiB/s) with 14 file(s) remaining\rCompleted 23.1 KiB/363.9 KiB (165.5 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000386-octave.m to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/contents/BIOMD0000000386-octave.m\nCompleted 23.1 KiB/363.9 KiB (165.5 KiB/s) with 13 file(s) remaining\rCompleted 30.1 KiB/363.9 KiB (197.9 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000386-matlab.m to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/contents/BIOMD0000000386-matlab.m\nCompleted 30.1 KiB/363.9 KiB (197.9 KiB/s) with 12 file(s) remaining\rCompleted 34.1 KiB/363.9 KiB (212.6 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000386.ode to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/contents/BIOMD0000000386.ode\nCompleted 34.1 KiB/363.9 KiB (212.6 KiB/s) with 11 file(s) remaining\rCompleted 45.1 KiB/363.9 KiB (275.2 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000386-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/contents/BIOMD0000000386-biopax2.owl\nCompleted 45.1 KiB/363.9 KiB (275.2 KiB/s) with 10 file(s) remaining\rCompleted 56.9 KiB/363.9 KiB (329.1 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000386.svg to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/contents/BIOMD0000000386.svg\nCompleted 56.9 KiB/363.9 KiB (329.1 KiB/s) with 9 file(s) remaining\rCompleted 103.3 KiB/363.9 KiB (504.2 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000386_url.xml to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/contents/BIOMD0000000386_url.xml\nCompleted 103.3 KiB/363.9 KiB (504.2 KiB/s) with 8 file(s) remaining\rCompleted 278.8 KiB/363.9 KiB (1.3 MiB/s) with 8 file(s) remaining  \rupload: contents/BIOMD0000000386.pdf to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/contents/BIOMD0000000386.pdf\nCompleted 278.8 KiB/363.9 KiB (1.3 MiB/s) with 7 file(s) remaining\rCompleted 282.6 KiB/363.9 KiB (1.2 MiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/contents/metadata.rdf\nCompleted 282.6 KiB/363.9 KiB (1.2 MiB/s) with 6 file(s) remaining\rCompleted 317.1 KiB/363.9 KiB (1.3 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000386.png to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/contents/BIOMD0000000386.png\nCompleted 317.1 KiB/363.9 KiB (1.3 MiB/s) with 5 file(s) remaining\rCompleted 339.9 KiB/363.9 KiB (1.4 MiB/s) with 5 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/contents/curation_image.png\nCompleted 339.9 KiB/363.9 KiB (1.4 MiB/s) with 4 file(s) remaining\rCompleted 355.0 KiB/363.9 KiB (1.4 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000386_url.sedml to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/contents/BIOMD0000000386_url.sedml\nCompleted 355.0 KiB/363.9 KiB (1.4 MiB/s) with 3 file(s) remaining\rCompleted 355.2 KiB/363.9 KiB (1.4 MiB/s) with 3 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/contents/curation_notes.txt\nCompleted 355.2 KiB/363.9 KiB (1.4 MiB/s) with 2 file(s) remaining\rCompleted 356.9 KiB/363.9 KiB (1.3 MiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/contents/manifest.xml\nCompleted 356.9 KiB/363.9 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 363.9 KiB/363.9 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000386.m to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/contents/BIOMD0000000386.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (40.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b1b195afd5df175eb5a/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000386_url.sedml\ncreating dataset /BIOMD0000000386_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\ndataset created, uuid: d-3f0b97ad-09600898-adac-47f97f-3c39c3, chunk_size: (7, 1001)\ncreating dataset /BIOMD0000000386_url.sedml/autogen_report_for_task1, shape: (27, 1001), type: float64\ndataset created, uuid: d-3f0b97ad-09600898-2b98-c8c6d8-3c2bb2, chunk_size: (27, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000386_url.sedml\ncreating attribute uri in /BIOMD0000000386_url.sedml\ncreating attribute _type in /BIOMD0000000386_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000386_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000386_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000386_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000386_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000386_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000386_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000386_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000386_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000386_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000386_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000386_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000386_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000386_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000386_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000386_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000386_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000386_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000386_url.sedml\ncreate_links: /BIOMD0000000386_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000386_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000386_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\niterating over chunks for /BIOMD0000000386_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000386_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000386_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000386_url.sedml/autogen_report_for_task1, shape: (27, 1001), type: float64\niterating over chunks for /BIOMD0000000386_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 27, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000386_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b1b195afd5df175eb5a\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 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.\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 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":1.497771,"sedDocuments":[{"location":"BIOMD0000000386_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  BIOMD0000000386_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: BIOMD0000000386_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":1.073024,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.208256,"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":0.259668,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_RuBP","status":"SUCCEEDED"},{"id":"autogen_task1_PGA","status":"SUCCEEDED"},{"id":"autogen_task1_NADPH","status":"SUCCEEDED"},{"id":"autogen_task1_CO2","status":"SUCCEEDED"},{"id":"autogen_task1_O2","status":"SUCCEEDED"},{"id":"autogen_task1_NADP","status":"SUCCEEDED"},{"id":"autogen_task1_Rp","status":"SUCCEEDED"},{"id":"autogen_task1_Nt","status":"SUCCEEDED"},{"id":"autogen_task1_Rd","status":"SUCCEEDED"},{"id":"autogen_task1_J","status":"SUCCEEDED"},{"id":"autogen_task1_gm","status":"SUCCEEDED"},{"id":"autogen_task1_Gamma","status":"SUCCEEDED"},{"id":"autogen_task1_Vcmax","status":"SUCCEEDED"},{"id":"autogen_task1_Kc","status":"SUCCEEDED"},{"id":"autogen_task1_Ko","status":"SUCCEEDED"},{"id":"autogen_task1_phi","status":"SUCCEEDED"},{"id":"autogen_task1_TPU","status":"SUCCEEDED"},{"id":"autogen_task1_v_c","status":"SUCCEEDED"},{"id":"autogen_task1_Vj","status":"SUCCEEDED"},{"id":"autogen_task1_Vp","status":"SUCCEEDED"},{"id":"autogen_task1_Vc","status":"SUCCEEDED"},{"id":"autogen_task1_chloroplast","status":"SUCCEEDED"},{"id":"autogen_task1_PGA_prod_Vc","status":"SUCCEEDED"},{"id":"autogen_task1_PGA_prod_Vo","status":"SUCCEEDED"},{"id":"autogen_task1_PGA_cons","status":"SUCCEEDED"},{"id":"autogen_task1_NADPH_prod","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.467901,"curves":[{"id":"autogen_curve_task1_RuBP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PGA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADPH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CO2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_O2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADP","status":"SUCCEEDED"}]}]}]}