{"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    433      0 --:--:-- --:--:-- --:--:--   434\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100  302k  100  302k    0     0   678k      0 --:--:-- --:--:-- --:--:-- 2628k\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 3 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 3\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 (3):\n    Succeeded: 3\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 1.6 KiB/1.6 KiB (25.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/rawLog.txt\nCompleted 4.2 KiB/4.2 KiB (67.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/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/MODEL1602280003.sedml/ (stored 0%)\n  adding: outputs/MODEL1602280003.sedml/plot_2_task1.pdf (deflated 30%)\n  adding: outputs/MODEL1602280003.sedml/plot_1_task1.pdf (deflated 33%)\n  adding: outputs/reports.h5 (deflated 19%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 193.1 KiB/193.1 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/outputs/reports.h5\nCompleted 176.9 KiB/220.7 KiB (2.0 MiB/s) with 5 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/output.zip\nCompleted 176.9 KiB/220.7 KiB (2.0 MiB/s) with 4 file(s) remaining\rCompleted 187.3 KiB/220.7 KiB (1.7 MiB/s) with 4 file(s) remaining\rupload: outputs/MODEL1602280003.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/outputs/MODEL1602280003.sedml/plot_1_task1.pdf\nCompleted 187.3 KiB/220.7 KiB (1.7 MiB/s) with 3 file(s) remaining\rCompleted 190.0 KiB/220.7 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/rawLog.txt\nCompleted 190.0 KiB/220.7 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 204.2 KiB/220.7 KiB (1.5 MiB/s) with 2 file(s) remaining\rupload: outputs/MODEL1602280003.sedml/plot_2_task1.pdf to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/outputs/MODEL1602280003.sedml/plot_2_task1.pdf\nCompleted 204.2 KiB/220.7 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 220.7 KiB/220.7 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000690-biopax2.owl  \n  inflating: contents/BIOMD0000000690-biopax3.owl  \n  inflating: contents/BIOMD0000000690-matlab.m  \n  inflating: contents/BIOMD0000000690-octave.m  \n  inflating: contents/BIOMD0000000690.m  \n  inflating: contents/BIOMD0000000690.ode  \n  inflating: contents/BIOMD0000000690.pdf  \n  inflating: contents/BIOMD0000000690.png  \n  inflating: contents/BIOMD0000000690.svg  \n  inflating: contents/BIOMD0000000690.vcml  \n  inflating: contents/BIOMD0000000690_url.xml  \n  inflating: contents/MODEL1602280003.cps  \n  inflating: contents/MODEL1602280003.sedml  \n  inflating: contents/curation_image.jpeg  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 44.1 KiB/672.6 KiB (561.6 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000690-biopax3.owl to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/contents/BIOMD0000000690-biopax3.owl\nCompleted 44.1 KiB/672.6 KiB (561.6 KiB/s) with 16 file(s) remaining\rCompleted 44.8 KiB/672.6 KiB (331.2 KiB/s) with 16 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/contents/curation_notes.txt\nCompleted 44.8 KiB/672.6 KiB (331.2 KiB/s) with 15 file(s) remaining\rCompleted 51.2 KiB/672.6 KiB (362.5 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000690-octave.m to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/contents/BIOMD0000000690-octave.m\nCompleted 51.2 KiB/672.6 KiB (362.5 KiB/s) with 14 file(s) remaining\rCompleted 57.6 KiB/672.6 KiB (399.4 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000690-matlab.m to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/contents/BIOMD0000000690-matlab.m\nCompleted 57.6 KiB/672.6 KiB (399.4 KiB/s) with 13 file(s) remaining\rCompleted 159.7 KiB/672.6 KiB (1.1 MiB/s) with 13 file(s) remaining \rupload: contents/BIOMD0000000690.vcml to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/contents/BIOMD0000000690.vcml\nCompleted 159.7 KiB/672.6 KiB (1.1 MiB/s) with 12 file(s) remaining\rCompleted 191.5 KiB/672.6 KiB (1.2 MiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000690-biopax2.owl to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/contents/BIOMD0000000690-biopax2.owl\nCompleted 191.5 KiB/672.6 KiB (1.2 MiB/s) with 11 file(s) remaining\rCompleted 216.2 KiB/672.6 KiB (1.3 MiB/s) with 11 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/contents/curation_image.jpeg\nCompleted 216.2 KiB/672.6 KiB (1.3 MiB/s) with 10 file(s) remaining\rCompleted 233.5 KiB/672.6 KiB (1.4 MiB/s) with 10 file(s) remaining\rupload: contents/MODEL1602280003.sedml to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/contents/MODEL1602280003.sedml\nCompleted 233.5 KiB/672.6 KiB (1.4 MiB/s) with 9 file(s) remaining\rCompleted 299.8 KiB/672.6 KiB (1.7 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000690_url.xml to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/contents/BIOMD0000000690_url.xml\nCompleted 299.8 KiB/672.6 KiB (1.7 MiB/s) with 8 file(s) remaining\rCompleted 323.5 KiB/672.6 KiB (1.7 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000690.svg to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/contents/BIOMD0000000690.svg\nCompleted 323.5 KiB/672.6 KiB (1.7 MiB/s) with 7 file(s) remaining\rCompleted 325.5 KiB/672.6 KiB (1.6 MiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/contents/manifest.xml\nCompleted 325.5 KiB/672.6 KiB (1.6 MiB/s) with 6 file(s) remaining\rCompleted 405.3 KiB/672.6 KiB (1.9 MiB/s) with 6 file(s) remaining\rupload: contents/MODEL1602280003.cps to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/contents/MODEL1602280003.cps\nCompleted 405.3 KiB/672.6 KiB (1.9 MiB/s) with 5 file(s) remaining\rCompleted 411.8 KiB/672.6 KiB (1.9 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000690.m to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/contents/BIOMD0000000690.m\nCompleted 411.8 KiB/672.6 KiB (1.9 MiB/s) with 4 file(s) remaining\rCompleted 497.3 KiB/672.6 KiB (2.2 MiB/s) with 4 file(s) remaining\rCompleted 663.0 KiB/672.6 KiB (2.8 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000690.png to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/contents/BIOMD0000000690.png\nCompleted 663.0 KiB/672.6 KiB (2.8 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000690.pdf to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/contents/BIOMD0000000690.pdf\nCompleted 663.0 KiB/672.6 KiB (2.8 MiB/s) with 2 file(s) remaining\rCompleted 667.5 KiB/672.6 KiB (2.8 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000690.ode to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/contents/BIOMD0000000690.ode\nCompleted 667.5 KiB/672.6 KiB (2.8 MiB/s) with 1 file(s) remaining\rCompleted 672.6 KiB/672.6 KiB (2.8 MiB/s) with 1 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/contents/metadata.rdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.5 KiB/9.5 KiB (155.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c4049c0d898ffdf2539/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /MODEL1602280003.sedml\ncreating dataset /MODEL1602280003.sedml/autogen_report_for_task1, shape: (29, 1001), type: float64\ndataset created, uuid: d-1c771ed2-b3dcbc20-0f0a-ff9484-75c5d8, chunk_size: (29, 1001)\ncreating dataset /MODEL1602280003.sedml/plot_1_task1, shape: (3, 1001), type: float64\ndataset created, uuid: d-1c771ed2-b3dcbc20-c982-5e7cae-e53178, chunk_size: (3, 1001)\ncreating dataset /MODEL1602280003.sedml/plot_2_task1, shape: (6, 1001), type: float64\ndataset created, uuid: d-1c771ed2-b3dcbc20-a07b-f3d8d6-d5ac55, chunk_size: (6, 1001)\ncreating attribute combineArchiveLocation in /MODEL1602280003.sedml\ncreating attribute uri in /MODEL1602280003.sedml\ncreating attribute _type in /MODEL1602280003.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /MODEL1602280003.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /MODEL1602280003.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /MODEL1602280003.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /MODEL1602280003.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /MODEL1602280003.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /MODEL1602280003.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /MODEL1602280003.sedml/autogen_report_for_task1\ncreating attribute uri in /MODEL1602280003.sedml/autogen_report_for_task1\ncreating attribute _type in /MODEL1602280003.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /MODEL1602280003.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /MODEL1602280003.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /MODEL1602280003.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /MODEL1602280003.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /MODEL1602280003.sedml/plot_1_task1\ncreating attribute sedmlId in /MODEL1602280003.sedml/plot_1_task1\ncreating attribute sedmlName in /MODEL1602280003.sedml/plot_1_task1\ncreating attribute uri in /MODEL1602280003.sedml/plot_1_task1\ncreating attribute _type in /MODEL1602280003.sedml/plot_2_task1\ncreating attribute sedmlDataSetDataTypes in /MODEL1602280003.sedml/plot_2_task1\ncreating attribute sedmlDataSetIds in /MODEL1602280003.sedml/plot_2_task1\ncreating attribute sedmlDataSetLabels in /MODEL1602280003.sedml/plot_2_task1\ncreating attribute sedmlDataSetNames in /MODEL1602280003.sedml/plot_2_task1\ncreating attribute sedmlDataSetShapes in /MODEL1602280003.sedml/plot_2_task1\ncreating attribute sedmlId in /MODEL1602280003.sedml/plot_2_task1\ncreating attribute sedmlName in /MODEL1602280003.sedml/plot_2_task1\ncreating attribute uri in /MODEL1602280003.sedml/plot_2_task1\ncreate_links: /\ngot link: MODEL1602280003.sedml\ncreate_links: /MODEL1602280003.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\ngot link: plot_2_task1\nwrite_dataset src: /MODEL1602280003.sedml/autogen_report_for_task1 to tgt: /MODEL1602280003.sedml/autogen_report_for_task1, shape: (29, 1001), type: float64\niterating over chunks for /MODEL1602280003.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 29, 1), slice(0, 1001, 1))\ndone with dataload for /MODEL1602280003.sedml/autogen_report_for_task1\nwrite_dataset src: /MODEL1602280003.sedml/plot_1_task1 to tgt: /MODEL1602280003.sedml/plot_1_task1, shape: (3, 1001), type: float64\niterating over chunks for /MODEL1602280003.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 1001, 1))\ndone with dataload for /MODEL1602280003.sedml/plot_1_task1\nwrite_dataset src: /MODEL1602280003.sedml/plot_2_task1 to tgt: /MODEL1602280003.sedml/plot_2_task1, shape: (6, 1001), type: float64\niterating over chunks for /MODEL1602280003.sedml/plot_2_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1001, 1))\ndone with dataload for /MODEL1602280003.sedml/plot_2_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711c4049c0d898ffdf2539\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 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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.718178,"sedDocuments":[{"location":"MODEL1602280003.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 2 plots:\r\n  MODEL1602280003.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 29 data sets\r\n    Plots (2):\r\n      plot_1_task1: 2 curves\r\n      plot_2_task1: 5 curves\r\n\r\nExecuting SED-ML file 1: MODEL1602280003.sedml ...\r\n  Found 1 tasks and 3 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_report_for_task1`\r\n      `plot_1_task1`\r\n      `plot_2_task1`\r\n  Executing task 1: `task1`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 3 outputs ...\r\n      Generating output 1: `plot_1_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `plot_2_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 3: `autogen_report_for_task1` ...","duration":1.248295,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.221503,"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":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.390549,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"}]},{"id":"plot_2_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.232174,"curves":[{"id":"p2_curve_1_task1","status":"SUCCEEDED"},{"id":"p2_curve_2_task1","status":"SUCCEEDED"},{"id":"p2_curve_3_task1","status":"SUCCEEDED"},{"id":"p2_curve_4_task1","status":"SUCCEEDED"},{"id":"p2_curve_5_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.235068,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_CH2_THF","status":"SUCCEEDED"},{"id":"autogen_task1_THF","status":"SUCCEEDED"},{"id":"autogen_task1_DHF","status":"SUCCEEDED"},{"id":"autogen_task1_H2_HMPt","status":"SUCCEEDED"},{"id":"autogen_task1_H2_HMPterinPP","status":"SUCCEEDED"},{"id":"autogen_task1_H2_Pteroate","status":"SUCCEEDED"},{"id":"autogen_task1_p_ABA","status":"SUCCEEDED"},{"id":"autogen_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_task1_AMP","status":"SUCCEEDED"},{"id":"autogen_task1_PPi","status":"SUCCEEDED"},{"id":"autogen_task1_L_Glutamate","status":"SUCCEEDED"},{"id":"autogen_task1_Phosphate","status":"SUCCEEDED"},{"id":"autogen_task1_ADP","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_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"}]}]}]}