{"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    462      0 --:--:-- --:--:-- --:--:--   461\n\r100  307k  100  307k    0     0   733k      0 --:--:-- --:--:-- --:--:--  733k\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 (18.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/rawLog.txt\nCompleted 4.6 KiB/4.6 KiB (64.8 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 83%)\n  adding: outputs/BIOMD0000000380_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000380_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 20%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 130.7 KiB/130.7 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/outputs/reports.h5\nCompleted 115.4 KiB/137.2 KiB (1.4 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/output.zip\nCompleted 115.4 KiB/137.2 KiB (1.4 MiB/s) with 3 file(s) remaining\rCompleted 123.1 KiB/137.2 KiB (1.0 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/outputs/plots.zip\nCompleted 123.1 KiB/137.2 KiB (1.0 MiB/s) with 2 file(s) remaining\rCompleted 134.5 KiB/137.2 KiB (1.0 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000380_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/outputs/BIOMD0000000380_url.sedml/autogen_plot_for_task1.pdf\nCompleted 134.5 KiB/137.2 KiB (1.0 MiB/s) with 1 file(s) remaining\rCompleted 137.2 KiB/137.2 KiB (969.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000380-biopax2.owl  \n  inflating: contents/BIOMD0000000380-biopax3.owl  \n  inflating: contents/BIOMD0000000380-matlab.m  \n  inflating: contents/BIOMD0000000380-octave.m  \n  inflating: contents/BIOMD0000000380.m  \n  inflating: contents/BIOMD0000000380.pdf  \n  inflating: contents/BIOMD0000000380.png  \n  inflating: contents/BIOMD0000000380.svg  \n  inflating: contents/BIOMD0000000380.vcml  \n  inflating: contents/BIOMD0000000380_url.sedml  \n  inflating: contents/BIOMD0000000380_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 34.6 KiB/605.0 KiB (419.3 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000380-biopax3.owl to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/contents/BIOMD0000000380-biopax3.owl\nCompleted 34.6 KiB/605.0 KiB (419.3 KiB/s) with 14 file(s) remaining\rCompleted 46.0 KiB/605.0 KiB (350.0 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000380-octave.m to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/contents/BIOMD0000000380-octave.m\nCompleted 46.0 KiB/605.0 KiB (350.0 KiB/s) with 13 file(s) remaining\rCompleted 57.4 KiB/605.0 KiB (429.6 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000380-matlab.m to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/contents/BIOMD0000000380-matlab.m\nCompleted 57.4 KiB/605.0 KiB (429.6 KiB/s) with 12 file(s) remaining\rCompleted 60.7 KiB/605.0 KiB (420.2 KiB/s) with 12 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/contents/metadata.rdf\nCompleted 60.7 KiB/605.0 KiB (420.2 KiB/s) with 11 file(s) remaining\rCompleted 83.5 KiB/605.0 KiB (553.3 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000380_url.sedml to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/contents/BIOMD0000000380_url.sedml\nCompleted 83.5 KiB/605.0 KiB (553.3 KiB/s) with 10 file(s) remaining\rCompleted 140.2 KiB/605.0 KiB (902.7 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000380.vcml to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/contents/BIOMD0000000380.vcml\nCompleted 140.2 KiB/605.0 KiB (902.7 KiB/s) with 9 file(s) remaining\rCompleted 191.0 KiB/605.0 KiB (1.2 MiB/s) with 9 file(s) remaining  \rupload: contents/BIOMD0000000380_url.xml to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/contents/BIOMD0000000380_url.xml\nCompleted 191.0 KiB/605.0 KiB (1.2 MiB/s) with 8 file(s) remaining\rCompleted 214.4 KiB/605.0 KiB (1.3 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000380-biopax2.owl to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/contents/BIOMD0000000380-biopax2.owl\nCompleted 214.4 KiB/605.0 KiB (1.3 MiB/s) with 7 file(s) remaining\rCompleted 235.8 KiB/605.0 KiB (1.2 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000380.svg to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/contents/BIOMD0000000380.svg\nCompleted 235.8 KiB/605.0 KiB (1.2 MiB/s) with 6 file(s) remaining\rCompleted 237.6 KiB/605.0 KiB (1.2 MiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/contents/manifest.xml\nCompleted 237.6 KiB/605.0 KiB (1.2 MiB/s) with 5 file(s) remaining\rCompleted 248.9 KiB/605.0 KiB (1.2 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000380.m to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/contents/BIOMD0000000380.m\nCompleted 248.9 KiB/605.0 KiB (1.2 MiB/s) with 4 file(s) remaining\rCompleted 294.4 KiB/605.0 KiB (1.4 MiB/s) with 4 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/contents/curation_image.png\nCompleted 294.4 KiB/605.0 KiB (1.4 MiB/s) with 3 file(s) remaining\rCompleted 294.8 KiB/605.0 KiB (1.3 MiB/s) with 3 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/contents/curation_notes.txt\nCompleted 294.8 KiB/605.0 KiB (1.3 MiB/s) with 2 file(s) remaining\rCompleted 405.4 KiB/605.0 KiB (1.8 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000380.png to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/contents/BIOMD0000000380.png\nCompleted 405.4 KiB/605.0 KiB (1.8 MiB/s) with 1 file(s) remaining\rCompleted 605.0 KiB/605.0 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000380.pdf to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/contents/BIOMD0000000380.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (140.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710be49a62a8be53f7c8c3/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000380_url.sedml\ncreating dataset /BIOMD0000000380_url.sedml/autogen_plot_for_task1, shape: (17, 1001), type: float64\ndataset created, uuid: d-3bbb6e18-2219fe11-dcc6-a2186e-dbc5ac, chunk_size: (17, 1001)\ncreating dataset /BIOMD0000000380_url.sedml/autogen_report_for_task1, shape: (40, 1001), type: float64\ndataset created, uuid: d-3bbb6e18-2219fe11-c52e-6ee6aa-5aa1e4, chunk_size: (40, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000380_url.sedml\ncreating attribute uri in /BIOMD0000000380_url.sedml\ncreating attribute _type in /BIOMD0000000380_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000380_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000380_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000380_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000380_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000380_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000380_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000380_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000380_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000380_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000380_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000380_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000380_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000380_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000380_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000380_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000380_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000380_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000380_url.sedml\ncreate_links: /BIOMD0000000380_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000380_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000380_url.sedml/autogen_plot_for_task1, shape: (17, 1001), type: float64\niterating over chunks for /BIOMD0000000380_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 17, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000380_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000380_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000380_url.sedml/autogen_report_for_task1, shape: (40, 1001), type: float64\niterating over chunks for /BIOMD0000000380_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 40, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000380_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710be49a62a8be53f7c8c3\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 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.\nProcess and upload the outputs of the simulation run ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.539052,"sedDocuments":[{"location":"BIOMD0000000380_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  BIOMD0000000380_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 40 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 16 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000380_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":1.13625,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.178188,"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":0.276153,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_glc","status":"SUCCEEDED"},{"id":"autogen_task1_g1p","status":"SUCCEEDED"},{"id":"autogen_task1_g6p","status":"SUCCEEDED"},{"id":"autogen_task1_trh","status":"SUCCEEDED"},{"id":"autogen_task1_t6p","status":"SUCCEEDED"},{"id":"autogen_task1_udg","status":"SUCCEEDED"},{"id":"autogen_task1_adp","status":"SUCCEEDED"},{"id":"autogen_task1_atp","status":"SUCCEEDED"},{"id":"autogen_task1_ppi","status":"SUCCEEDED"},{"id":"autogen_task1_f6p","status":"SUCCEEDED"},{"id":"autogen_task1_h","status":"SUCCEEDED"},{"id":"autogen_task1_pho","status":"SUCCEEDED"},{"id":"autogen_task1_udp","status":"SUCCEEDED"},{"id":"autogen_task1_utp","status":"SUCCEEDED"},{"id":"autogen_task1_h2o","status":"SUCCEEDED"},{"id":"autogen_task1_glx","status":"SUCCEEDED"},{"id":"autogen_task1_heat","status":"SUCCEEDED"},{"id":"autogen_task1_glc_0","status":"SUCCEEDED"},{"id":"autogen_task1_glc_change","status":"SUCCEEDED"},{"id":"autogen_task1_g1p_0","status":"SUCCEEDED"},{"id":"autogen_task1_g1p_change","status":"SUCCEEDED"},{"id":"autogen_task1_g6p_0","status":"SUCCEEDED"},{"id":"autogen_task1_g6p_change","status":"SUCCEEDED"},{"id":"autogen_task1_trh_0","status":"SUCCEEDED"},{"id":"autogen_task1_trh_change","status":"SUCCEEDED"},{"id":"autogen_task1_t6p_0","status":"SUCCEEDED"},{"id":"autogen_task1_t6p_change","status":"SUCCEEDED"},{"id":"autogen_task1_udg_0","status":"SUCCEEDED"},{"id":"autogen_task1_udg_change","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_medium","status":"SUCCEEDED"},{"id":"autogen_task1_pgi","status":"SUCCEEDED"},{"id":"autogen_task1_hxt","status":"SUCCEEDED"},{"id":"autogen_task1_hxk","status":"SUCCEEDED"},{"id":"autogen_task1_pgm","status":"SUCCEEDED"},{"id":"autogen_task1_tpp","status":"SUCCEEDED"},{"id":"autogen_task1_tps","status":"SUCCEEDED"},{"id":"autogen_task1_nth","status":"SUCCEEDED"},{"id":"autogen_task1_ugp","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.501078,"curves":[{"id":"autogen_curve_task1_glc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_g1p","status":"SUCCEEDED"},{"id":"autogen_curve_task1_g6p","status":"SUCCEEDED"},{"id":"autogen_curve_task1_trh","status":"SUCCEEDED"},{"id":"autogen_curve_task1_t6p","status":"SUCCEEDED"},{"id":"autogen_curve_task1_udg","status":"SUCCEEDED"},{"id":"autogen_curve_task1_adp","status":"SUCCEEDED"},{"id":"autogen_curve_task1_atp","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ppi","status":"SUCCEEDED"},{"id":"autogen_curve_task1_f6p","status":"SUCCEEDED"},{"id":"autogen_curve_task1_h","status":"SUCCEEDED"},{"id":"autogen_curve_task1_pho","status":"SUCCEEDED"},{"id":"autogen_curve_task1_udp","status":"SUCCEEDED"},{"id":"autogen_curve_task1_utp","status":"SUCCEEDED"},{"id":"autogen_curve_task1_h2o","status":"SUCCEEDED"},{"id":"autogen_curve_task1_glx","status":"SUCCEEDED"}]}]}]}