{"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    427      0 --:--:-- --:--:-- --:--:--   427\n\r100  302k  100  302k    0     0   673k      0 --:--:-- --:--:-- --:--:--  673k\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 (25.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/rawLog.txt\nCompleted 3.9 KiB/3.9 KiB (54.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/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/MODEL1602280002.sedml/ (stored 0%)\n  adding: outputs/MODEL1602280002.sedml/plot_2_task1.pdf (deflated 31%)\n  adding: outputs/MODEL1602280002.sedml/plot_1_task1.pdf (deflated 35%)\n  adding: outputs/reports.h5 (deflated 19%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 195.5 KiB/195.5 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/outputs/reports.h5\nCompleted 177.5 KiB/218.6 KiB (1.9 MiB/s) with 5 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/output.zip\nCompleted 177.5 KiB/218.6 KiB (1.9 MiB/s) with 4 file(s) remaining\rCompleted 186.8 KiB/218.6 KiB (1.8 MiB/s) with 4 file(s) remaining\rupload: outputs/MODEL1602280002.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/outputs/MODEL1602280002.sedml/plot_1_task1.pdf\nCompleted 186.8 KiB/218.6 KiB (1.8 MiB/s) with 3 file(s) remaining\rCompleted 200.7 KiB/218.6 KiB (1.7 MiB/s) with 3 file(s) remaining\rupload: outputs/MODEL1602280002.sedml/plot_2_task1.pdf to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/outputs/MODEL1602280002.sedml/plot_2_task1.pdf\nCompleted 200.7 KiB/218.6 KiB (1.7 MiB/s) with 2 file(s) remaining\rCompleted 203.5 KiB/218.6 KiB (1.7 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/rawLog.txt\nCompleted 203.5 KiB/218.6 KiB (1.7 MiB/s) with 1 file(s) remaining\rCompleted 218.6 KiB/218.6 KiB (1.7 MiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000689-biopax2.owl  \n  inflating: contents/BIOMD0000000689-biopax3.owl  \n  inflating: contents/BIOMD0000000689-matlab.m  \n  inflating: contents/BIOMD0000000689-octave.m  \n  inflating: contents/BIOMD0000000689.m  \n  inflating: contents/BIOMD0000000689.ode  \n  inflating: contents/BIOMD0000000689.pdf  \n  inflating: contents/BIOMD0000000689.png  \n  inflating: contents/BIOMD0000000689.svg  \n  inflating: contents/BIOMD0000000689.vcml  \n  inflating: contents/BIOMD0000000689_url.xml  \n  inflating: contents/MODEL1602280002.cps  \n  inflating: contents/MODEL1602280002.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/671.1 KiB (532.6 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000689-biopax3.owl to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/contents/BIOMD0000000689-biopax3.owl\nCompleted 44.1 KiB/671.1 KiB (532.6 KiB/s) with 16 file(s) remaining\rCompleted 50.5 KiB/671.1 KiB (449.8 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000689-matlab.m to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/contents/BIOMD0000000689-matlab.m\nCompleted 50.5 KiB/671.1 KiB (449.8 KiB/s) with 15 file(s) remaining\rCompleted 56.8 KiB/671.1 KiB (466.3 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000689-octave.m to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/contents/BIOMD0000000689-octave.m\nCompleted 56.8 KiB/671.1 KiB (466.3 KiB/s) with 14 file(s) remaining\rCompleted 80.6 KiB/671.1 KiB (603.6 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000689.svg to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/contents/BIOMD0000000689.svg\nCompleted 80.6 KiB/671.1 KiB (603.6 KiB/s) with 13 file(s) remaining\rCompleted 81.1 KiB/671.1 KiB (590.5 KiB/s) with 13 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/contents/curation_notes.txt\nCompleted 81.1 KiB/671.1 KiB (590.5 KiB/s) with 12 file(s) remaining\rCompleted 112.9 KiB/671.1 KiB (804.1 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000689-biopax2.owl to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/contents/BIOMD0000000689-biopax2.owl\nCompleted 112.9 KiB/671.1 KiB (804.1 KiB/s) with 11 file(s) remaining\rCompleted 214.9 KiB/671.1 KiB (1.5 MiB/s) with 11 file(s) remaining  \rupload: contents/BIOMD0000000689.vcml to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/contents/BIOMD0000000689.vcml\nCompleted 214.9 KiB/671.1 KiB (1.5 MiB/s) with 10 file(s) remaining\rCompleted 293.7 KiB/671.1 KiB (1.8 MiB/s) with 10 file(s) remaining\rupload: contents/MODEL1602280002.cps to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/contents/MODEL1602280002.cps\nCompleted 293.7 KiB/671.1 KiB (1.8 MiB/s) with 9 file(s) remaining\rCompleted 311.0 KiB/671.1 KiB (1.9 MiB/s) with 9 file(s) remaining\rupload: contents/MODEL1602280002.sedml to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/contents/MODEL1602280002.sedml\nCompleted 311.0 KiB/671.1 KiB (1.9 MiB/s) with 8 file(s) remaining\rCompleted 377.3 KiB/671.1 KiB (2.2 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000689_url.xml to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/contents/BIOMD0000000689_url.xml\nCompleted 377.3 KiB/671.1 KiB (2.2 MiB/s) with 7 file(s) remaining\rCompleted 402.0 KiB/671.1 KiB (2.4 MiB/s) with 7 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/contents/curation_image.jpeg\nCompleted 402.0 KiB/671.1 KiB (2.4 MiB/s) with 6 file(s) remaining\rCompleted 404.0 KiB/671.1 KiB (2.3 MiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/contents/manifest.xml\nCompleted 404.0 KiB/671.1 KiB (2.3 MiB/s) with 5 file(s) remaining\rCompleted 409.1 KiB/671.1 KiB (2.0 MiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/contents/metadata.rdf\nCompleted 409.1 KiB/671.1 KiB (2.0 MiB/s) with 4 file(s) remaining\rCompleted 415.5 KiB/671.1 KiB (1.9 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000689.m to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/contents/BIOMD0000000689.m\nCompleted 415.5 KiB/671.1 KiB (1.9 MiB/s) with 3 file(s) remaining\rCompleted 581.1 KiB/671.1 KiB (2.7 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000689.pdf to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/contents/BIOMD0000000689.pdf\nCompleted 581.1 KiB/671.1 KiB (2.7 MiB/s) with 2 file(s) remaining\rCompleted 666.6 KiB/671.1 KiB (2.8 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000689.png to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/contents/BIOMD0000000689.png\nCompleted 666.6 KiB/671.1 KiB (2.8 MiB/s) with 1 file(s) remaining\rCompleted 671.1 KiB/671.1 KiB (2.5 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000689.ode to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/contents/BIOMD0000000689.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.5 KiB/9.5 KiB (157.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c3e0dcacb55678cc422/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /MODEL1602280002.sedml\ncreating dataset /MODEL1602280002.sedml/autogen_report_for_task1, shape: (29, 1001), type: float64\ndataset created, uuid: d-5bb867f0-29c3beab-b985-8ce55a-3c1ba6, chunk_size: (29, 1001)\ncreating dataset /MODEL1602280002.sedml/plot_1_task1, shape: (3, 1001), type: float64\ndataset created, uuid: d-5bb867f0-29c3beab-17a2-c0342c-4dacab, chunk_size: (3, 1001)\ncreating dataset /MODEL1602280002.sedml/plot_2_task1, shape: (6, 1001), type: float64\ndataset created, uuid: d-5bb867f0-29c3beab-490a-9d6c0d-2cfb92, chunk_size: (6, 1001)\ncreating attribute combineArchiveLocation in /MODEL1602280002.sedml\ncreating attribute uri in /MODEL1602280002.sedml\ncreating attribute _type in /MODEL1602280002.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /MODEL1602280002.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /MODEL1602280002.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /MODEL1602280002.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /MODEL1602280002.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /MODEL1602280002.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /MODEL1602280002.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /MODEL1602280002.sedml/autogen_report_for_task1\ncreating attribute uri in /MODEL1602280002.sedml/autogen_report_for_task1\ncreating attribute _type in /MODEL1602280002.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /MODEL1602280002.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /MODEL1602280002.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /MODEL1602280002.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /MODEL1602280002.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /MODEL1602280002.sedml/plot_1_task1\ncreating attribute sedmlId in /MODEL1602280002.sedml/plot_1_task1\ncreating attribute sedmlName in /MODEL1602280002.sedml/plot_1_task1\ncreating attribute uri in /MODEL1602280002.sedml/plot_1_task1\ncreating attribute _type in /MODEL1602280002.sedml/plot_2_task1\ncreating attribute sedmlDataSetDataTypes in /MODEL1602280002.sedml/plot_2_task1\ncreating attribute sedmlDataSetIds in /MODEL1602280002.sedml/plot_2_task1\ncreating attribute sedmlDataSetLabels in /MODEL1602280002.sedml/plot_2_task1\ncreating attribute sedmlDataSetNames in /MODEL1602280002.sedml/plot_2_task1\ncreating attribute sedmlDataSetShapes in /MODEL1602280002.sedml/plot_2_task1\ncreating attribute sedmlId in /MODEL1602280002.sedml/plot_2_task1\ncreating attribute sedmlName in /MODEL1602280002.sedml/plot_2_task1\ncreating attribute uri in /MODEL1602280002.sedml/plot_2_task1\ncreate_links: /\ngot link: MODEL1602280002.sedml\ncreate_links: /MODEL1602280002.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\ngot link: plot_2_task1\nwrite_dataset src: /MODEL1602280002.sedml/autogen_report_for_task1 to tgt: /MODEL1602280002.sedml/autogen_report_for_task1, shape: (29, 1001), type: float64\niterating over chunks for /MODEL1602280002.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 29, 1), slice(0, 1001, 1))\ndone with dataload for /MODEL1602280002.sedml/autogen_report_for_task1\nwrite_dataset src: /MODEL1602280002.sedml/plot_1_task1 to tgt: /MODEL1602280002.sedml/plot_1_task1, shape: (3, 1001), type: float64\niterating over chunks for /MODEL1602280002.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 1001, 1))\ndone with dataload for /MODEL1602280002.sedml/plot_1_task1\nwrite_dataset src: /MODEL1602280002.sedml/plot_2_task1 to tgt: /MODEL1602280002.sedml/plot_2_task1, shape: (6, 1001), type: float64\niterating over chunks for /MODEL1602280002.sedml/plot_2_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1001, 1))\ndone with dataload for /MODEL1602280002.sedml/plot_2_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711c3e0dcacb55678cc422\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":1.529887,"sedDocuments":[{"location":"MODEL1602280002.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  MODEL1602280002.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: MODEL1602280002.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":1.117512,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.135622,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"deterministic"},{"key":"methodCode","value":22},{"key":"parameters","value":{"Absolute Tolerance":1e-12,"Integrate Reduced Model":false,"Max Internal Steps":10000,"Relative Tolerance":0.000001}}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.312302,"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":0.240617,"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":0.259611,"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"}]}]}]}