{"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    439      0 --:--:-- --:--:-- --:--:--   438\r100   139  100   139    0     0    433      0 --:--:-- --:--:-- --:--:--   433\n\r100  189k  100  189k    0     0   436k      0 --:--:-- --:--:-- --:--:--  436k\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 (19.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/rawLog.txt\nCompleted 2.9 KiB/2.9 KiB (30.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 76%)\n  adding: outputs/BIOMD0000000072_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000072_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 14%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 151.1 KiB/151.1 KiB (1.7 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/outputs/reports.h5\nCompleted 139.6 KiB/159.9 KiB (1.2 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/output.zip\nCompleted 139.6 KiB/159.9 KiB (1.2 MiB/s) with 3 file(s) remaining\rCompleted 146.7 KiB/159.9 KiB (1.3 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/outputs/plots.zip\nCompleted 146.7 KiB/159.9 KiB (1.3 MiB/s) with 2 file(s) remaining\rCompleted 157.2 KiB/159.9 KiB (1.3 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000072_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/outputs/BIOMD0000000072_url.sedml/autogen_plot_for_task1.pdf\nCompleted 157.2 KiB/159.9 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 159.9 KiB/159.9 KiB (1003.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000072-biopax2.owl  \n  inflating: contents/BIOMD0000000072-biopax3.owl  \n  inflating: contents/BIOMD0000000072-matlab.m  \n  inflating: contents/BIOMD0000000072-octave.m  \n  inflating: contents/BIOMD0000000072.m  \n  inflating: contents/BIOMD0000000072.ode  \n  inflating: contents/BIOMD0000000072.pdf  \n  inflating: contents/BIOMD0000000072.png  \n  inflating: contents/BIOMD0000000072.sci  \n  inflating: contents/BIOMD0000000072.svg  \n  inflating: contents/BIOMD0000000072.vcml  \n  inflating: contents/BIOMD0000000072_url.sedml  \n  inflating: contents/BIOMD0000000072_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 18.0 KiB/357.6 KiB (241.6 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000072-biopax2.owl to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/contents/BIOMD0000000072-biopax2.owl\nCompleted 18.0 KiB/357.6 KiB (241.6 KiB/s) with 16 file(s) remaining\rCompleted 22.8 KiB/357.6 KiB (193.0 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000072-octave.m to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/contents/BIOMD0000000072-octave.m\nCompleted 22.8 KiB/357.6 KiB (193.0 KiB/s) with 15 file(s) remaining\rCompleted 27.6 KiB/357.6 KiB (218.5 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000072-matlab.m to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/contents/BIOMD0000000072-matlab.m\nCompleted 27.6 KiB/357.6 KiB (218.5 KiB/s) with 14 file(s) remaining\rCompleted 30.2 KiB/357.6 KiB (198.3 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000072.sci to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/contents/BIOMD0000000072.sci\nCompleted 30.2 KiB/357.6 KiB (198.3 KiB/s) with 13 file(s) remaining\rCompleted 75.4 KiB/357.6 KiB (487.7 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000072.png to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/contents/BIOMD0000000072.png\nCompleted 75.4 KiB/357.6 KiB (487.7 KiB/s) with 12 file(s) remaining\rCompleted 104.5 KiB/357.6 KiB (655.4 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000072.vcml to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/contents/BIOMD0000000072.vcml\nCompleted 104.5 KiB/357.6 KiB (655.4 KiB/s) with 11 file(s) remaining\rCompleted 121.4 KiB/357.6 KiB (733.1 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000072.svg to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/contents/BIOMD0000000072.svg\nCompleted 121.4 KiB/357.6 KiB (733.1 KiB/s) with 10 file(s) remaining\rCompleted 121.4 KiB/357.6 KiB (690.9 KiB/s) with 10 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/contents/curation_notes.txt\nCompleted 121.4 KiB/357.6 KiB (690.9 KiB/s) with 9 file(s) remaining\rCompleted 123.4 KiB/357.6 KiB (698.6 KiB/s) with 9 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/contents/manifest.xml\nCompleted 123.4 KiB/357.6 KiB (698.6 KiB/s) with 8 file(s) remaining\rCompleted 126.3 KiB/357.6 KiB (686.8 KiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/contents/metadata.rdf\nCompleted 126.3 KiB/357.6 KiB (686.8 KiB/s) with 7 file(s) remaining\rCompleted 136.3 KiB/357.6 KiB (703.6 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000072_url.sedml to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/contents/BIOMD0000000072_url.sedml\nCompleted 136.3 KiB/357.6 KiB (703.6 KiB/s) with 6 file(s) remaining\rCompleted 149.7 KiB/357.6 KiB (708.7 KiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/contents/curation_image.png\nCompleted 149.7 KiB/357.6 KiB (708.7 KiB/s) with 5 file(s) remaining\rCompleted 167.9 KiB/357.6 KiB (788.2 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000072_url.xml to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/contents/BIOMD0000000072_url.xml\nCompleted 167.9 KiB/357.6 KiB (788.2 KiB/s) with 4 file(s) remaining\rCompleted 172.7 KiB/357.6 KiB (764.0 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000072.m to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/contents/BIOMD0000000072.m\nCompleted 172.7 KiB/357.6 KiB (764.0 KiB/s) with 3 file(s) remaining\rCompleted 175.3 KiB/357.6 KiB (755.2 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000072.ode to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/contents/BIOMD0000000072.ode\nCompleted 175.3 KiB/357.6 KiB (755.2 KiB/s) with 2 file(s) remaining\rCompleted 199.9 KiB/357.6 KiB (828.7 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000072-biopax3.owl to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/contents/BIOMD0000000072-biopax3.owl\nCompleted 199.9 KiB/357.6 KiB (828.7 KiB/s) with 1 file(s) remaining\rCompleted 357.6 KiB/357.6 KiB (1.3 MiB/s) with 1 file(s) remaining  \rupload: contents/BIOMD0000000072.pdf to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/contents/BIOMD0000000072.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.2 KiB/9.2 KiB (137.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107e149c0d898ffdda6a4/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000072_url.sedml\ncreating dataset /BIOMD0000000072_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\ndataset created, uuid: d-ddfcff84-3ad87e80-7fd1-aeb274-81c4a2, chunk_size: (8, 1001)\ncreating dataset /BIOMD0000000072_url.sedml/autogen_report_for_task1, shape: (16, 1001), type: float64\ndataset created, uuid: d-ddfcff84-3ad87e80-0559-3792b6-c5384a, chunk_size: (16, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000072_url.sedml\ncreating attribute uri in /BIOMD0000000072_url.sedml\ncreating attribute _type in /BIOMD0000000072_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000072_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000072_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000072_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000072_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000072_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000072_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000072_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000072_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000072_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000072_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000072_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000072_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000072_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000072_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000072_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000072_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000072_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000072_url.sedml\ncreate_links: /BIOMD0000000072_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000072_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000072_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\niterating over chunks for /BIOMD0000000072_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 8, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000072_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000072_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000072_url.sedml/autogen_report_for_task1, shape: (16, 1001), type: float64\niterating over chunks for /BIOMD0000000072_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 16, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000072_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647107e149c0d898ffdda6a4\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 SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... 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.\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":1.282196,"sedDocuments":[{"location":"BIOMD0000000072_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  BIOMD0000000072_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 16 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 7 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000072_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":0.895314,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.138227,"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":0.172441,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_L","status":"SUCCEEDED"},{"id":"autogen_task1_R","status":"SUCCEEDED"},{"id":"autogen_task1_G","status":"SUCCEEDED"},{"id":"autogen_task1_Gbg","status":"SUCCEEDED"},{"id":"autogen_task1_Gd","status":"SUCCEEDED"},{"id":"autogen_task1_Ga","status":"SUCCEEDED"},{"id":"autogen_task1_RL","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_1","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_2","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_3","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_4","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_5","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_6","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.474659,"curves":[{"id":"autogen_curve_task1_L","status":"SUCCEEDED"},{"id":"autogen_curve_task1_R","status":"SUCCEEDED"},{"id":"autogen_curve_task1_G","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Gbg","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Gd","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ga","status":"SUCCEEDED"},{"id":"autogen_curve_task1_RL","status":"SUCCEEDED"}]}]}]}