{"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    471      0 --:--:-- --:--:-- --:--:--   472\n\r100  149k  100  149k    0     0   368k      0 --:--:-- --:--:-- --:--:--  368k\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 (17.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/rawLog.txt\nCompleted 2.0 KiB/2.0 KiB (29.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 70%)\n  adding: outputs/BIOMD0000000425_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000425_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 34%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 63.5 KiB/63.5 KiB (810.0 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/outputs/reports.h5\nCompleted 53.1 KiB/76.4 KiB (661.4 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/output.zip\nCompleted 53.1 KiB/76.4 KiB (661.4 KiB/s) with 3 file(s) remaining\rCompleted 65.4 KiB/76.4 KiB (586.4 KiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000425_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/outputs/BIOMD0000000425_url.sedml/autogen_plot_for_task1.pdf\nCompleted 65.4 KiB/76.4 KiB (586.4 KiB/s) with 2 file(s) remaining\rCompleted 73.8 KiB/76.4 KiB (640.9 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/outputs/plots.zip\nCompleted 73.8 KiB/76.4 KiB (640.9 KiB/s) with 1 file(s) remaining\rCompleted 76.4 KiB/76.4 KiB (648.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000425-biopax2.owl  \n  inflating: contents/BIOMD0000000425-biopax3.owl  \n  inflating: contents/BIOMD0000000425-matlab.m  \n  inflating: contents/BIOMD0000000425-octave.m  \n  inflating: contents/BIOMD0000000425.m  \n  inflating: contents/BIOMD0000000425.ode  \n  inflating: contents/BIOMD0000000425.pdf  \n  inflating: contents/BIOMD0000000425.sci  \n  inflating: contents/BIOMD0000000425.svg  \n  inflating: contents/BIOMD0000000425.vcml  \n  inflating: contents/BIOMD0000000425_url.sedml  \n  inflating: contents/BIOMD0000000425_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 7.2 KiB/244.7 KiB (119.6 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000425-biopax2.owl to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/contents/BIOMD0000000425-biopax2.owl\nCompleted 7.2 KiB/244.7 KiB (119.6 KiB/s) with 15 file(s) remaining\rCompleted 10.5 KiB/244.7 KiB (94.6 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000425.m to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/contents/BIOMD0000000425.m\nCompleted 10.5 KiB/244.7 KiB (94.6 KiB/s) with 14 file(s) remaining\rCompleted 13.7 KiB/244.7 KiB (118.1 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000425-matlab.m to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/contents/BIOMD0000000425-matlab.m\nCompleted 13.7 KiB/244.7 KiB (118.1 KiB/s) with 13 file(s) remaining\rCompleted 15.6 KiB/244.7 KiB (132.1 KiB/s) with 13 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/contents/manifest.xml\nCompleted 15.6 KiB/244.7 KiB (132.1 KiB/s) with 12 file(s) remaining\rCompleted 25.2 KiB/244.7 KiB (205.0 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000425-biopax3.owl to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/contents/BIOMD0000000425-biopax3.owl\nCompleted 25.2 KiB/244.7 KiB (205.0 KiB/s) with 11 file(s) remaining\rCompleted 26.3 KiB/244.7 KiB (211.4 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000425.sci to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/contents/BIOMD0000000425.sci\nCompleted 26.3 KiB/244.7 KiB (211.4 KiB/s) with 10 file(s) remaining\rCompleted 31.2 KiB/244.7 KiB (233.7 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000425_url.sedml to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/contents/BIOMD0000000425_url.sedml\nCompleted 31.2 KiB/244.7 KiB (233.7 KiB/s) with 9 file(s) remaining\rCompleted 48.5 KiB/244.7 KiB (336.0 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000425.vcml to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/contents/BIOMD0000000425.vcml\nCompleted 48.5 KiB/244.7 KiB (336.0 KiB/s) with 8 file(s) remaining\rCompleted 60.9 KiB/244.7 KiB (396.1 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000425_url.xml to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/contents/BIOMD0000000425_url.xml\nCompleted 60.9 KiB/244.7 KiB (396.1 KiB/s) with 7 file(s) remaining\rCompleted 84.3 KiB/244.7 KiB (542.7 KiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/contents/curation_image.png\nCompleted 84.3 KiB/244.7 KiB (542.7 KiB/s) with 6 file(s) remaining\rCompleted 87.6 KiB/244.7 KiB (483.2 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000425-octave.m to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/contents/BIOMD0000000425-octave.m\nCompleted 87.6 KiB/244.7 KiB (483.2 KiB/s) with 5 file(s) remaining\rCompleted 89.0 KiB/244.7 KiB (483.4 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000425.ode to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/contents/BIOMD0000000425.ode\nCompleted 89.0 KiB/244.7 KiB (483.4 KiB/s) with 4 file(s) remaining\rCompleted 98.3 KiB/244.7 KiB (525.7 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000425.svg to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/contents/BIOMD0000000425.svg\nCompleted 98.3 KiB/244.7 KiB (525.7 KiB/s) with 3 file(s) remaining\rCompleted 98.5 KiB/244.7 KiB (504.9 KiB/s) with 3 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/contents/curation_notes.txt\nCompleted 98.5 KiB/244.7 KiB (504.9 KiB/s) with 2 file(s) remaining\rCompleted 103.2 KiB/244.7 KiB (476.8 KiB/s) with 2 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/contents/metadata.rdf\nCompleted 103.2 KiB/244.7 KiB (476.8 KiB/s) with 1 file(s) remaining\rCompleted 244.7 KiB/244.7 KiB (1.1 MiB/s) with 1 file(s) remaining  \rupload: contents/BIOMD0000000425.pdf to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/contents/BIOMD0000000425.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.8 KiB/8.8 KiB (123.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710c7c9a62a8be53f7e135/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000425_url.sedml\ncreating dataset /BIOMD0000000425_url.sedml/autogen_plot_for_task1, shape: (2, 1001), type: float64\ndataset created, uuid: d-2c96013f-2616365f-1920-6dbf59-673c30, chunk_size: (2, 1001)\ncreating dataset /BIOMD0000000425_url.sedml/autogen_report_for_task1, shape: (7, 1001), type: float64\ndataset created, uuid: d-2c96013f-2616365f-88fc-0147a9-f78cd9, chunk_size: (7, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000425_url.sedml\ncreating attribute uri in /BIOMD0000000425_url.sedml\ncreating attribute _type in /BIOMD0000000425_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000425_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000425_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000425_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000425_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000425_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000425_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000425_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000425_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000425_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000425_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000425_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000425_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000425_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000425_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000425_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000425_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000425_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000425_url.sedml\ncreate_links: /BIOMD0000000425_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000425_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000425_url.sedml/autogen_plot_for_task1, shape: (2, 1001), type: float64\niterating over chunks for /BIOMD0000000425_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000425_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000425_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000425_url.sedml/autogen_report_for_task1, shape: (7, 1001), type: float64\niterating over chunks for /BIOMD0000000425_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000425_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710c7c9a62a8be53f7e135\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.\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.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file 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":0.924276,"sedDocuments":[{"location":"BIOMD0000000425_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  BIOMD0000000425_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 7 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000425_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":0.607188,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.090549,"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":0.09602,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_c","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_1","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_3","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_2","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_4","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.328346,"curves":[{"id":"autogen_curve_task1_c","status":"SUCCEEDED"}]}]}]}