{"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  193k  100  193k    0     0   442k      0 --:--:-- --:--:-- --:--:--  442k\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 (19.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/rawLog.txt\nCompleted 3.3 KiB/3.3 KiB (44.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/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/BIOMD0000000384_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000384_url.sedml/autogen_plot_for_task1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 31%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 70.0 KiB/70.0 KiB (726.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/outputs/reports.h5\nCompleted 57.7 KiB/78.1 KiB (470.3 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/output.zip\nCompleted 57.7 KiB/78.1 KiB (470.3 KiB/s) with 3 file(s) remaining\rCompleted 68.4 KiB/78.1 KiB (545.6 KiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000384_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/outputs/BIOMD0000000384_url.sedml/autogen_plot_for_task1.pdf\nCompleted 68.4 KiB/78.1 KiB (545.6 KiB/s) with 2 file(s) remaining\rCompleted 75.5 KiB/78.1 KiB (490.5 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/outputs/plots.zip\nCompleted 75.5 KiB/78.1 KiB (490.5 KiB/s) with 1 file(s) remaining\rCompleted 78.1 KiB/78.1 KiB (477.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000384-biopax2.owl  \n  inflating: contents/BIOMD0000000384-biopax3.owl  \n  inflating: contents/BIOMD0000000384-matlab.m  \n  inflating: contents/BIOMD0000000384-octave.m  \n  inflating: contents/BIOMD0000000384.m  \n  inflating: contents/BIOMD0000000384.ode  \n  inflating: contents/BIOMD0000000384.pdf  \n  inflating: contents/BIOMD0000000384.png  \n  inflating: contents/BIOMD0000000384.svg  \n  inflating: contents/BIOMD0000000384_url.sedml  \n  inflating: contents/BIOMD0000000384_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 10.8 KiB/320.9 KiB (128.3 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000384-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/contents/BIOMD0000000384-biopax2.owl\nCompleted 10.8 KiB/320.9 KiB (128.3 KiB/s) with 14 file(s) remaining\rCompleted 21.1 KiB/320.9 KiB (162.4 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000384.svg to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/contents/BIOMD0000000384.svg\nCompleted 21.1 KiB/320.9 KiB (162.4 KiB/s) with 13 file(s) remaining\rCompleted 26.1 KiB/320.9 KiB (192.3 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000384-octave.m to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/contents/BIOMD0000000384-octave.m\nCompleted 26.1 KiB/320.9 KiB (192.3 KiB/s) with 12 file(s) remaining\rCompleted 31.2 KiB/320.9 KiB (204.4 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000384-matlab.m to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/contents/BIOMD0000000384-matlab.m\nCompleted 31.2 KiB/320.9 KiB (204.4 KiB/s) with 11 file(s) remaining\rCompleted 45.8 KiB/320.9 KiB (282.6 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000384_url.sedml to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/contents/BIOMD0000000384_url.sedml\nCompleted 45.8 KiB/320.9 KiB (282.6 KiB/s) with 10 file(s) remaining\rCompleted 75.5 KiB/320.9 KiB (434.8 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000384.png to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/contents/BIOMD0000000384.png\nCompleted 75.5 KiB/320.9 KiB (434.8 KiB/s) with 9 file(s) remaining\rCompleted 97.6 KiB/320.9 KiB (554.2 KiB/s) with 9 file(s) remaining\rCompleted 120.3 KiB/320.9 KiB (676.0 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000384_url.xml to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/contents/BIOMD0000000384_url.xml\nCompleted 120.3 KiB/320.9 KiB (676.0 KiB/s) with 8 file(s) remaining\rCompleted 123.9 KiB/320.9 KiB (686.4 KiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/contents/metadata.rdf\nCompleted 123.9 KiB/320.9 KiB (686.4 KiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/contents/curation_image.png\nCompleted 123.9 KiB/320.9 KiB (686.4 KiB/s) with 6 file(s) remaining\rCompleted 124.2 KiB/320.9 KiB (678.7 KiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/contents/curation_notes.txt\nCompleted 124.2 KiB/320.9 KiB (678.7 KiB/s) with 5 file(s) remaining\rCompleted 125.9 KiB/320.9 KiB (674.3 KiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/contents/manifest.xml\nCompleted 125.9 KiB/320.9 KiB (674.3 KiB/s) with 4 file(s) remaining\rCompleted 141.8 KiB/320.9 KiB (684.9 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000384-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/contents/BIOMD0000000384-biopax3.owl\nCompleted 141.8 KiB/320.9 KiB (684.9 KiB/s) with 3 file(s) remaining\rCompleted 312.6 KiB/320.9 KiB (1.4 MiB/s) with 3 file(s) remaining  \rupload: contents/BIOMD0000000384.pdf to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/contents/BIOMD0000000384.pdf\nCompleted 312.6 KiB/320.9 KiB (1.4 MiB/s) with 2 file(s) remaining\rCompleted 315.9 KiB/320.9 KiB (1.3 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000384.ode to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/contents/BIOMD0000000384.ode\nCompleted 315.9 KiB/320.9 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 320.9 KiB/320.9 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000384.m to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/contents/BIOMD0000000384.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (95.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b1a195afd5df175eb4f/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000384_url.sedml\ncreating dataset /BIOMD0000000384_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\ndataset created, uuid: d-1d215e7e-2416f8d8-f628-d47b4f-692574, chunk_size: (7, 1001)\ncreating dataset /BIOMD0000000384_url.sedml/autogen_report_for_task1, shape: (26, 1001), type: float64\ndataset created, uuid: d-1d215e7e-2416f8d8-5c45-7246f5-85b997, chunk_size: (26, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000384_url.sedml\ncreating attribute uri in /BIOMD0000000384_url.sedml\ncreating attribute _type in /BIOMD0000000384_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000384_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000384_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000384_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000384_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000384_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000384_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000384_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000384_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000384_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000384_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000384_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000384_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000384_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000384_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000384_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000384_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000384_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000384_url.sedml\ncreate_links: /BIOMD0000000384_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000384_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000384_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\niterating over chunks for /BIOMD0000000384_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000384_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000384_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000384_url.sedml/autogen_report_for_task1, shape: (26, 1001), type: float64\niterating over chunks for /BIOMD0000000384_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 26, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000384_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b1a195afd5df175eb4f\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 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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":19.22013,"sedDocuments":[{"location":"BIOMD0000000384_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  BIOMD0000000384_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 26 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 6 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000384_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":18.926906,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":18.122752,"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":0.25022,"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_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_Q","status":"SUCCEEDED"},{"id":"autogen_task1_J","status":"SUCCEEDED"},{"id":"autogen_task1_Gamma","status":"SUCCEEDED"},{"id":"autogen_task1_teta","status":"SUCCEEDED"},{"id":"autogen_task1_Vcmax","status":"SUCCEEDED"},{"id":"autogen_task1_Vomax","status":"SUCCEEDED"},{"id":"autogen_task1_Kc","status":"SUCCEEDED"},{"id":"autogen_task1_Ko","status":"SUCCEEDED"},{"id":"autogen_task1_Vj","status":"SUCCEEDED"},{"id":"autogen_task1_phi","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":0.430908,"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"}]}]}]}