{"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    418      0 --:--:-- --:--:-- --:--:--   418\n\r100  427k  100  427k    0     0   912k      0 --:--:-- --:--:-- --:--:--  912k\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 (23.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/rawLog.txt\nCompleted 4.7 KiB/4.7 KiB (65.5 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 80%)\n  adding: outputs/BIOMD0000000639_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000639_url.sedml/autogen_plot_for_task1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 15%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 172.8 KiB/172.8 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/outputs/reports.h5\nCompleted 159.6 KiB/186.0 KiB (1.5 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/output.zip\nCompleted 159.6 KiB/186.0 KiB (1.5 MiB/s) with 3 file(s) remaining\rCompleted 162.3 KiB/186.0 KiB (1.4 MiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/rawLog.txt\nCompleted 162.3 KiB/186.0 KiB (1.4 MiB/s) with 2 file(s) remaining\rCompleted 171.7 KiB/186.0 KiB (1.5 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/outputs/plots.zip\nCompleted 171.7 KiB/186.0 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 186.0 KiB/186.0 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000639_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/outputs/BIOMD0000000639_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/BIOMD0000000639-biopax2.owl  \n  inflating: contents/BIOMD0000000639-biopax3.owl  \n  inflating: contents/BIOMD0000000639-matlab.m  \n  inflating: contents/BIOMD0000000639-octave.m  \n  inflating: contents/BIOMD0000000639.m  \n  inflating: contents/BIOMD0000000639.ode  \n  inflating: contents/BIOMD0000000639.png  \n  inflating: contents/BIOMD0000000639.svg  \n  inflating: contents/BIOMD0000000639.vcml  \n  inflating: contents/BIOMD0000000639_url.sedml  \n  inflating: contents/BIOMD0000000639_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 29.5 KiB/669.1 KiB (389.9 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000639-biopax3.owl to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/contents/BIOMD0000000639-biopax3.owl\nCompleted 29.5 KiB/669.1 KiB (389.9 KiB/s) with 14 file(s) remaining\rCompleted 35.7 KiB/669.1 KiB (331.2 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000639-matlab.m to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/contents/BIOMD0000000639-matlab.m\nCompleted 35.7 KiB/669.1 KiB (331.2 KiB/s) with 13 file(s) remaining\rCompleted 52.9 KiB/669.1 KiB (393.7 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000639-biopax2.owl to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/contents/BIOMD0000000639-biopax2.owl\nCompleted 52.9 KiB/669.1 KiB (393.7 KiB/s) with 12 file(s) remaining\rCompleted 54.6 KiB/669.1 KiB (385.6 KiB/s) with 12 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/contents/manifest.xml\nCompleted 54.6 KiB/669.1 KiB (385.6 KiB/s) with 11 file(s) remaining\rCompleted 310.6 KiB/669.1 KiB (2.1 MiB/s) with 11 file(s) remaining \rCompleted 377.6 KiB/669.1 KiB (2.5 MiB/s) with 11 file(s) remaining \rupload: contents/BIOMD0000000639.vcml to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/contents/BIOMD0000000639.vcml\nCompleted 377.6 KiB/669.1 KiB (2.5 MiB/s) with 10 file(s) remaining\rCompleted 418.2 KiB/669.1 KiB (2.6 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000639_url.xml to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/contents/BIOMD0000000639_url.xml\nCompleted 418.2 KiB/669.1 KiB (2.6 MiB/s) with 9 file(s) remaining\rCompleted 436.6 KiB/669.1 KiB (2.5 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000639_url.sedml to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/contents/BIOMD0000000639_url.sedml\nCompleted 436.6 KiB/669.1 KiB (2.5 MiB/s) with 8 file(s) remaining\rCompleted 442.8 KiB/669.1 KiB (2.3 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000639-octave.m to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/contents/BIOMD0000000639-octave.m\nCompleted 442.8 KiB/669.1 KiB (2.3 MiB/s) with 7 file(s) remaining\rCompleted 532.2 KiB/669.1 KiB (2.8 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000639.png to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/contents/BIOMD0000000639.png\nCompleted 532.2 KiB/669.1 KiB (2.8 MiB/s) with 6 file(s) remaining\rCompleted 537.6 KiB/669.1 KiB (2.8 MiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/contents/metadata.rdf\nCompleted 537.6 KiB/669.1 KiB (2.8 MiB/s) with 5 file(s) remaining\rCompleted 561.1 KiB/669.1 KiB (2.8 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000639.svg to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/contents/BIOMD0000000639.svg\nCompleted 561.1 KiB/669.1 KiB (2.8 MiB/s) with 4 file(s) remaining\rCompleted 565.4 KiB/669.1 KiB (2.7 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000639.ode to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/contents/BIOMD0000000639.ode\nCompleted 565.4 KiB/669.1 KiB (2.7 MiB/s) with 3 file(s) remaining\rCompleted 662.5 KiB/669.1 KiB (3.1 MiB/s) with 3 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/contents/curation_image.jpeg\nCompleted 662.5 KiB/669.1 KiB (3.1 MiB/s) with 2 file(s) remaining\rCompleted 662.9 KiB/669.1 KiB (2.7 MiB/s) with 2 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/contents/curation_notes.txt\nCompleted 662.9 KiB/669.1 KiB (2.7 MiB/s) with 1 file(s) remaining\rCompleted 669.1 KiB/669.1 KiB (2.6 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000639.m to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/contents/BIOMD0000000639.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (124.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711b960dcacb55678cb363/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000639_url.sedml\ncreating dataset /BIOMD0000000639_url.sedml/autogen_plot_for_task1, shape: (18, 1001), type: float64\ndataset created, uuid: d-993fdf52-08b76d35-30f0-9095b0-006a01, chunk_size: (18, 1001)\ncreating dataset /BIOMD0000000639_url.sedml/autogen_report_for_task1, shape: (29, 1001), type: float64\ndataset created, uuid: d-993fdf52-08b76d35-21ef-a6718b-6f0839, chunk_size: (29, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000639_url.sedml\ncreating attribute uri in /BIOMD0000000639_url.sedml\ncreating attribute _type in /BIOMD0000000639_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000639_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000639_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000639_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000639_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000639_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000639_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000639_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000639_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000639_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000639_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000639_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000639_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000639_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000639_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000639_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000639_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000639_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000639_url.sedml\ncreate_links: /BIOMD0000000639_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000639_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000639_url.sedml/autogen_plot_for_task1, shape: (18, 1001), type: float64\niterating over chunks for /BIOMD0000000639_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 18, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000639_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000639_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000639_url.sedml/autogen_report_for_task1, shape: (29, 1001), type: float64\niterating over chunks for /BIOMD0000000639_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 29, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000639_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711b960dcacb55678cb363\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 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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.832317,"sedDocuments":[{"location":"BIOMD0000000639_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  BIOMD0000000639_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 29 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 17 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000639_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":1.337854,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.231785,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"simulate"},{"key":"solver","value":"cvode"},{"key":"relative_tolerance","value":0.000001},{"key":"absolute_tolerance","value":1e-12},{"key":"stiff","value":true},{"key":"maximum_bdf_order","value":5},{"key":"maximum_adams_order","value":12},{"key":"maximum_num_steps","value":20000},{"key":"maximum_time_step","value":0},{"key":"minimum_time_step","value":0},{"key":"initial_time_step","value":0},{"key":"multiple_steps","value":false},{"key":"variable_step_size","value":false},{"key":"max_output_rows","value":100000}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.241784,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_H2_HMPt","status":"SUCCEEDED"},{"id":"autogen_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_task1_H2_HMPterinPP","status":"SUCCEEDED"},{"id":"autogen_task1_AMP","status":"SUCCEEDED"},{"id":"autogen_task1_p_ABA","status":"SUCCEEDED"},{"id":"autogen_task1_PPi","status":"SUCCEEDED"},{"id":"autogen_task1_H2_Pteroate","status":"SUCCEEDED"},{"id":"autogen_task1_L_Glutamate","status":"SUCCEEDED"},{"id":"autogen_task1_Phosphate","status":"SUCCEEDED"},{"id":"autogen_task1_ADP","status":"SUCCEEDED"},{"id":"autogen_task1_DHF","status":"SUCCEEDED"},{"id":"autogen_task1_L_serine","status":"SUCCEEDED"},{"id":"autogen_task1_Glycine","status":"SUCCEEDED"},{"id":"autogen_task1_NADP","status":"SUCCEEDED"},{"id":"autogen_task1_NADPH","status":"SUCCEEDED"},{"id":"autogen_task1_THF","status":"SUCCEEDED"},{"id":"autogen_task1_CH2_THF","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_FolK","status":"SUCCEEDED"},{"id":"autogen_task1_FolP","status":"SUCCEEDED"},{"id":"autogen_task1_FolC","status":"SUCCEEDED"},{"id":"autogen_task1_GlyA","status":"SUCCEEDED"},{"id":"autogen_task1_FolA","status":"SUCCEEDED"},{"id":"autogen_task1_PanB","status":"SUCCEEDED"},{"id":"autogen_task1_p_ABA_production","status":"SUCCEEDED"},{"id":"autogen_task1_H2_HMPt_production","status":"SUCCEEDED"},{"id":"autogen_task1_THF_drain","status":"SUCCEEDED"},{"id":"autogen_task1_CH2_THF_drain","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.713649,"curves":[{"id":"autogen_curve_task1_H2_HMPt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_H2_HMPterinPP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AMP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_p_ABA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PPi","status":"SUCCEEDED"},{"id":"autogen_curve_task1_H2_Pteroate","status":"SUCCEEDED"},{"id":"autogen_curve_task1_L_Glutamate","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Phosphate","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ADP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DHF","status":"SUCCEEDED"},{"id":"autogen_curve_task1_L_serine","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Glycine","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADPH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_THF","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CH2_THF","status":"SUCCEEDED"}]}]}]}